@datagrok/helm 2.13.8 → 3.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (360) hide show
  1. package/CHANGELOG.md +6 -0
  2. package/css/helm.css +40 -0
  3. package/dist/137.js +2 -0
  4. package/dist/137.js.map +1 -0
  5. package/dist/323.js +2 -0
  6. package/dist/323.js.map +1 -0
  7. package/dist/657.js +2 -0
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  9. package/dist/782.js +2 -0
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  11. package/dist/884.js +2 -0
  12. package/dist/884.js.map +1 -0
  13. package/dist/94.js +2 -0
  14. package/dist/94.js.map +1 -0
  15. package/dist/libraries_bio_src_monomer-works_seq-to-molfile-worker_ts.js +16420 -0
  16. package/dist/libraries_bio_src_monomer-works_seq-to-molfile-worker_ts.js.map +1 -0
  17. package/dist/package-test.js +1 -1
  18. package/dist/package-test.js.map +1 -1
  19. package/dist/package.js +1 -1
  20. package/dist/package.js.map +1 -1
  21. package/dist/vendors-HELM_node_modules_lru-cache_dist_esm_index_js.js +1560 -0
  22. package/dist/vendors-HELM_node_modules_lru-cache_dist_esm_index_js.js.map +1 -0
  23. package/files/samples/helm-showcase.csv +56 -0
  24. package/package.json +8 -12
  25. package/src/helm-helper.ts +134 -410
  26. package/src/package-api.ts +14 -11
  27. package/src/package-test.ts +0 -2
  28. package/src/package-utils.ts +8 -298
  29. package/src/package.g.ts +2 -8
  30. package/src/package.ts +11 -31
  31. package/src/tests/helm-activity-cliffs.ts +2 -2
  32. package/src/tests/helm-input-tests.ts +83 -0
  33. package/src/tests/parse-helm-tests.ts +7 -57
  34. package/src/tests/properties-widget-tests.ts +21 -11
  35. package/src/utils/helm-grid-cell-renderer.ts +141 -151
  36. package/src/utils/index.ts +3 -7
  37. package/src/widgets/helm-input.ts +42 -12
  38. package/src/widgets/properties-widget.ts +18 -11
  39. package/webpack.config.js +1 -12
  40. package/helm/JSDraw/Pistoia.HELM-uncompressed.js +0 -9694
  41. package/helm/JSDraw/ReadMe.txt +0 -8
  42. package/helm/JSDraw/Scilligence.JSDraw2.Lite-uncompressed.js +0 -31126
  43. package/helm/dojo/package.ts +0 -41
  44. package/helm/dojo/types.ts +0 -12
  45. package/src/helm-web-editor.ts +0 -68
  46. package/src/tests/get-monomer-tests.ts +0 -214
  47. package/src/tests/helm-service-tests.ts +0 -98
  48. package/src/types/dojo.ts +0 -3
  49. package/src/types/index.ts +0 -5
  50. package/src/utils/get-monomer.ts +0 -90
  51. package/src/utils/helm-service.ts +0 -166
  52. package/test-console-output-1.log +0 -919
  53. package/test-record-1.mp4 +0 -0
  54. package/vendor/dojo-1.10.10/dijit/BackgroundIframe.js +0 -63
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Every method that can fail\n// throws (or returns a Result wrapping) one of these classes — never a bare\n// `Error`. See API.md §9 and ARCHITECTURE.md §8.1.\n\nimport type { PolymerType } from './constants';\n\n/**\n * Validation diagnostic shape produced by the parser/validator and carried by\n * `HelmValidationError`. Mirrors the surface contract documented in\n * VALIDATION.md §1; we re-export the type here so error consumers can `import`\n * a single place.\n */\nexport interface ValidationDiagnostic {\n severity: 'error' | 'warning' | 'info';\n /** Stable, machine-readable code (e.g. 'unknown-monomer'). */\n code: string;\n /** Human-readable message. */\n message: string;\n /** Source span into the offending HELM string, when known. */\n span?: { start: number; end: number };\n /** Free-form structured context (chain id, expected/found values, ...). */\n context?: {\n chainId?: string;\n atomId?: number;\n bondId?: number;\n polymerType?: PolymerType;\n expected?: unknown;\n found?: unknown;\n [key: string]: unknown;\n };\n}\n\nexport type { PolymerType };\n\n/**\n * Base error for everything thrown by the library. Carries a stable `code`\n * and an opaque `context` bag. 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The whole library accepts a\n// Logger by injection; no direct console use anywhere else. See\n// ARCHITECTURE.md §8.2.\n\n/**\n * Pluggable logger surface. Every method is fire-and-forget; loggers must not\n * throw. `ctx` is an opaque structured context bag carried alongside the\n * message — sinks may render or ignore it.\n */\nexport interface Logger {\n debug(msg: string, ctx?: object): void;\n info(msg: string, ctx?: object): void;\n warn(msg: string, ctx?: object): void;\n error(msg: string, ctx?: object): void;\n}\n\n/**\n * Default logger that writes to the host's `console`. Levels map to the\n * matching console method. Safe to use in any environment that exposes\n * `console` (browser, Node, jsdom).\n */\nexport class ConsoleLogger implements Logger {\n debug(msg: string, ctx?: object): void {\n if (ctx !== undefined) console.debug(msg, ctx);\n else console.debug(msg);\n }\n info(msg: string, ctx?: object): void {\n if (ctx !== undefined) console.info(msg, ctx);\n else console.info(msg);\n }\n warn(msg: string, ctx?: object): void {\n if (ctx !== undefined) console.warn(msg, ctx);\n else console.warn(msg);\n }\n error(msg: string, ctx?: object): void {\n if (ctx !== undefined) console.error(msg, ctx);\n else console.error(msg);\n }\n}\n\n/**\n * Logger that discards every message. Useful as the default in production\n * builds and in tests that want clean output.\n */\nexport class SilentLogger implements Logger {\n debug(_msg: string, _ctx?: object): void {\n /* intentionally empty */\n }\n info(_msg: string, _ctx?: object): void {\n /* intentionally empty */\n }\n warn(_msg: string, _ctx?: object): void {\n /* intentionally empty */\n }\n error(_msg: string, _ctx?: object): void {\n /* intentionally empty */\n }\n}\n","// HELM lexer (T-0201). Converts a HELM source string into a flat stream of\n// tokens. The parser (T-0202+) consumes this stream.\n//\n// Reference: PARSING.md §2 (token kinds, behavior, error cases) and\n// SPECIFICATION.md §6 (lexical conventions). This replaces the legacy\n// `IO.split` single-character scanner (LEGACY-EDITOR-NOTES.md §IO.ts) with a\n// single unified left-to-right lexer. Errors here are reported as\n// `HelmParseError` with a `span` pointing at the offending byte offset.\n//\n// Scanning is structure-aware in exactly three places:\n// * `[...]` payloads (inline SMILES or long monomer symbols) are consumed\n// atomically. We track bracket depth, quoted regions, and ChemAxon\n// extended-SMILES `|$...$|` blocks so the parser can later inspect the\n// payload via `looksLikeSmiles`.\n// * `\"...\"` quote strings unescape `\\\"`, `\\\\`, `\\n`, `\\r`, `\\t`; everything\n// else passes through with the leading backslash preserved.\n// * `'...'` apostrophe blocks (repeat-bracket subscripts) emit individual\n// `apos`/`integer`/`dash` tokens so the parser does no re-scanning.\n//\n// All other input is decomposed into single-character tokens plus\n// identifier / integer / decimal literals.\n\nimport { HelmParseError } from '../core/errors';\n\n/**\n * Set of token kinds recognised by the HELM lexer. See PARSING.md §2.1 for the\n * authoritative table.\n */\nexport type TokenKind =\n | 'lbrace' | 'rbrace'\n | 'lparen' | 'rparen'\n | 'lbracket' | 'rbracket'\n | 'pipe'\n | 'dot'\n | 'comma'\n | 'plus'\n | 'colon'\n | 'dash'\n | 'dollar'\n | 'gt'\n | 'apos'\n | 'quote-string'\n | 'inline-smiles'\n | 'identifier'\n | 'integer'\n | 'decimal'\n | 'question'\n | 'asterisk'\n | 'underscore'\n | 'eof';\n\n/**\n * Half-open span `[start, end)` into the source string. Used on every token\n * and on every `HelmParseError` raised by the lexer.\n */\nexport interface TokenSpan {\n readonly start: number;\n readonly end: number;\n}\n\n/**\n * Single lexer token. `value` is the source text for most kinds; for\n * `quote-string` it is the UNESCAPED contents (so `\"a\\\"b\"` yields `a\"b`); for\n * `inline-smiles` it is the inner bracket payload (without the outermost\n * brackets).\n */\nexport interface Token {\n readonly kind: TokenKind;\n readonly value: string;\n readonly span: TokenSpan;\n}\n\n/**\n * A successfully lexed source. `tokens` ends with an `eof` token whose span\n * is `(source.length, source.length)`. `source` is kept verbatim so callers\n * can recover original substrings via `span`.\n */\nexport interface TokenStream {\n readonly tokens: readonly Token[];\n readonly source: string;\n}\n\n// --- character classes ----------------------------------------------------\n\nfunction isAlpha(ch: number): boolean {\n return (ch >= 65 && ch <= 90) || (ch >= 97 && ch <= 122);\n}\n\nfunction isDigit(ch: number): boolean {\n return ch >= 48 && ch <= 57;\n}\n\nfunction isWhitespace(ch: number): boolean {\n return ch === 32 /* */ || ch === 9 /* \\t */ || ch === 10 /* \\n */ || ch === 13 /* \\r */;\n}\n\n// --- Lexer ---------------------------------------------------------------\n\nclass Lexer {\n private readonly src: string;\n private readonly len: number;\n private pos: number;\n private readonly tokens: Token[];\n\n constructor(source: string) {\n this.src = source;\n this.len = source.length;\n this.pos = 0;\n this.tokens = [];\n }\n\n /** Run the scanner to completion. Throws `HelmParseError` on lexer faults. */\n tokenize(): TokenStream {\n while (this.pos < this.len) {\n const start = this.pos;\n const code = this.src.charCodeAt(this.pos);\n\n // Reject any unescaped whitespace at top-level. Whitespace inside\n // brackets and quotes is consumed by their dedicated scanners and never\n // reaches this branch.\n if (isWhitespace(code)) {\n throw new HelmParseError(\n 'unexpected-whitespace',\n `Unexpected whitespace at offset ${start}`,\n { span: { start, end: start + 1 } },\n );\n }\n\n // Multi-char literals first.\n if (code === 91 /* [ */) { this.scanBracket(start); continue; }\n if (code === 34 /* \" */) { this.scanQuote(start); continue; }\n if (isAlpha(code)) { this.scanIdentifier(start); continue; }\n if (isDigit(code)) { this.scanNumber(start); continue; }\n\n // Single-char tokens. The dash here is normal (between/in identifiers\n // it is folded into the identifier scan above; this branch fires only\n // when `-` stands alone, e.g. inside apostrophe ranges or as a bare\n // connection separator).\n const single = SINGLE_CHAR.get(code);\n if (single !== undefined) {\n this.pos += 1;\n this.push(single, this.src.charAt(start), start, this.pos);\n continue;\n }\n\n throw new HelmParseError(\n 'unexpected-char',\n `Unexpected character ${JSON.stringify(this.src.charAt(start))} at offset ${start}`,\n { span: { start, end: start + 1 } },\n );\n }\n\n this.push('eof', '', this.len, this.len);\n return { tokens: this.tokens, source: this.src };\n }\n\n // --- bracketed payload ------------------------------------------------\n //\n // The bracket payload is emitted atomically as a single `inline-smiles`\n // token whose `.value` is the inner text. Brackets may contain:\n // * Nested `[...]` — track depth.\n // * `\"...\"` opaque regions — toggle inQuote (with backslash escape).\n // * ChemAxon extended SMILES `|$...$|` blocks — toggle inChemAxon so\n // stray `]` inside the label section do not close the bracket.\n // Newlines inside a bracket are not allowed.\n private scanBracket(start: number): void {\n let depth = 1;\n let inQuote = false;\n let inChemAxon = false;\n let i = start + 1;\n while (i < this.len) {\n const ch = this.src.charCodeAt(i);\n if (inQuote) {\n if (ch === 92 /* \\ */ && i + 1 < this.len) { i += 2; continue; }\n if (ch === 34 /* \" */) { inQuote = false; i += 1; continue; }\n if (ch === 10 || ch === 13) {\n throw new HelmParseError(\n 'unexpected-newline',\n `Newline inside bracket at offset ${i}`,\n { span: { start: i, end: i + 1 } },\n );\n }\n i += 1;\n continue;\n }\n if (inChemAxon) {\n // ChemAxon block ends with `$|` (canonical). Some legacy corpora\n // close the outer bracket directly after the labels (`$]`) without\n // the trailing `|`; we accept that shape by exiting chemaxon mode\n // and letting the `]` close the outer bracket on the next iteration.\n if (ch === 36 /* $ */ && i + 1 < this.len) {\n const next = this.src.charCodeAt(i + 1);\n if (next === 124 /* | */) {\n inChemAxon = false;\n i += 2;\n continue;\n }\n if (next === 93 /* ] */) {\n inChemAxon = false;\n i += 1; // leave `]` for the bracket-close branch below\n continue;\n }\n }\n if (ch === 10 || ch === 13) {\n throw new HelmParseError(\n 'unexpected-newline',\n `Newline inside bracket at offset ${i}`,\n { span: { start: i, end: i + 1 } },\n );\n }\n i += 1;\n continue;\n }\n if (ch === 10 || ch === 13) {\n throw new HelmParseError(\n 'unexpected-newline',\n `Newline inside bracket at offset ${i}`,\n { span: { start: i, end: i + 1 } },\n );\n }\n if (ch === 34 /* \" */) { inQuote = true; i += 1; continue; }\n // Detect the ChemAxon marker `|$` (the canonical form is preceded by a\n // space, but we accept it anywhere inside the payload).\n if (ch === 124 /* | */ && i + 1 < this.len && this.src.charCodeAt(i + 1) === 36 /* $ */) {\n inChemAxon = true;\n i += 2;\n continue;\n }\n if (ch === 91 /* [ */) { depth += 1; i += 1; continue; }\n if (ch === 93 /* ] */) {\n depth -= 1;\n if (depth === 0) {\n const end = i + 1;\n const inner = this.src.slice(start + 1, i);\n this.pos = end;\n this.push('inline-smiles', inner, start, end);\n return;\n }\n i += 1;\n continue;\n }\n i += 1;\n }\n throw new HelmParseError(\n 'unterminated-bracket',\n `Unterminated '[' starting at offset ${start}`,\n { span: { start, end: this.len } },\n );\n }\n\n // --- quote string -----------------------------------------------------\n //\n // Consumes `\"...\"` with escape sequences (\\\\\\\", \\\\\\\\, \\\\n, \\\\r, \\\\t).\n // Unknown `\\\\X` sequences pass through as the literal two characters.\n private scanQuote(start: number): void {\n const buf: string[] = [];\n let i = start + 1;\n while (i < this.len) {\n const ch = this.src.charCodeAt(i);\n if (ch === 34 /* \" */) {\n const end = i + 1;\n this.pos = end;\n this.push('quote-string', buf.join(''), start, end);\n return;\n }\n if (ch === 92 /* \\ */ && i + 1 < this.len) {\n const next = this.src.charCodeAt(i + 1);\n if (next === 34) buf.push('\"');\n else if (next === 92) buf.push('\\\\');\n else if (next === 110) buf.push('\\n');\n else if (next === 114) buf.push('\\r');\n else if (next === 116) buf.push('\\t');\n else { buf.push('\\\\'); buf.push(this.src.charAt(i + 1)); }\n i += 2;\n continue;\n }\n // Newlines inside quotes are disallowed; they almost always indicate a\n // missing closing quote upstream.\n if (ch === 10 || ch === 13) {\n throw new HelmParseError(\n 'unexpected-newline',\n `Newline inside quote at offset ${i}`,\n { span: { start: i, end: i + 1 } },\n );\n }\n buf.push(this.src.charAt(i));\n i += 1;\n }\n throw new HelmParseError(\n 'unterminated-quote',\n `Unterminated '\"' starting at offset ${start}`,\n { span: { start, end: this.len } },\n );\n }\n\n // --- identifier -------------------------------------------------------\n //\n // Identifier body is `[A-Za-z0-9_]` plus `-` ONLY when the dash is followed\n // by an alphabetic character. This lets `D-Tyr_Et` lex as one identifier\n // (matching legacy bracketed monomer symbols) while `pair-9` still splits\n // into `pair`, `dash`, `integer` so the connection parser can match its\n // `... colon identifier=\"pair\" dash integer ...` production from\n // PARSING.md §3.4. The task spec quotes the looser `[A-Za-z][A-Za-z0-9_-]*`\n // regex; we tighten it here to keep the parser grammar unambiguous and\n // still cover every hyphenated monomer symbol in the corpus (such symbols\n // always sit inside `[...]` and reach the lexer as `inline-smiles` anyway).\n private scanIdentifier(start: number): void {\n let i = start + 1;\n while (i < this.len) {\n const ch = this.src.charCodeAt(i);\n if (isAlpha(ch) || isDigit(ch) || ch === 95 /* _ */) { i += 1; continue; }\n if (ch === 45 /* - */ && i + 1 < this.len && isAlpha(this.src.charCodeAt(i + 1))) {\n i += 2;\n continue;\n }\n break;\n }\n const text = this.src.slice(start, i);\n this.pos = i;\n this.push('identifier', text, start, i);\n }\n\n // --- number -----------------------------------------------------------\n //\n // `[0-9]+` → integer, `[0-9]+\\.[0-9]+` → decimal. Uses one-char lookahead\n // after the dot to disambiguate `1.5` (decimal) from `1.A` (integer + dot +\n // identifier). A trailing dot with no digits after it is treated as an\n // integer; the dot is left for the next iteration.\n private scanNumber(start: number): void {\n let i = start + 1;\n while (i < this.len && isDigit(this.src.charCodeAt(i))) i += 1;\n if (\n i + 1 < this.len &&\n this.src.charCodeAt(i) === 46 /* . */ &&\n isDigit(this.src.charCodeAt(i + 1))\n ) {\n i += 2;\n while (i < this.len && isDigit(this.src.charCodeAt(i))) i += 1;\n const text = this.src.slice(start, i);\n this.pos = i;\n this.push('decimal', text, start, i);\n return;\n }\n const text = this.src.slice(start, i);\n this.pos = i;\n this.push('integer', text, start, i);\n }\n\n // --- bookkeeping ------------------------------------------------------\n\n private push(kind: TokenKind, value: string, start: number, end: number): void {\n this.tokens.push({ kind, value, span: { start, end } });\n }\n}\n\n// Single-character token table. Keys are char codes.\nconst SINGLE_CHAR: ReadonlyMap<number, TokenKind> = new Map<number, TokenKind>([\n [123 /* { */, 'lbrace'],\n [125 /* } */, 'rbrace'],\n [40 /* ( */, 'lparen'],\n [41 /* ) */, 'rparen'],\n [93 /* ] */, 'rbracket'],\n [124 /* | */, 'pipe'],\n [46 /* . */, 'dot'],\n [44 /* , */, 'comma'],\n [43 /* + */, 'plus'],\n [58 /* : */, 'colon'],\n [45 /* - */, 'dash'],\n [36 /* $ */, 'dollar'],\n [62 /* > */, 'gt'],\n [63 /* ? */, 'question'],\n [42 /* * */, 'asterisk'],\n [95 /* _ */, 'underscore'],\n [39 /* ' */, 'apos'],\n]);\n\n/**\n * Apostrophe handling deserves a dedicated note. The naive `'...'` token form\n * would force the parser to re-scan the inside for `integer-integer` shape.\n * Instead, when the top-level scanner encounters `'`, it emits an `apos`\n * token and then continues in \"apostrophe mode\" until the matching `'`,\n * emitting individual `integer` and `dash` tokens along the way.\n *\n * Rather than maintain that mode flag in the main loop, we get the same\n * behavior for free: the main loop already recognises bare `'` as `apos`,\n * digits as `integer`, and `-` as `dash`. So the parser just sees, for\n * `'5-30'`, the sequence `apos integer(5) dash integer(30) apos`. The only\n * special bookkeeping needed is the `unterminated-apostrophe` check below.\n */\n\n/**\n * Tokenize a HELM source string. Returns a `TokenStream` ending in an `eof`\n * token. Throws `HelmParseError` on lexer-level errors:\n *\n * * `unterminated-bracket` — `[` with no matching `]`.\n * * `unterminated-quote` — `\"` with no matching `\"`.\n * * `unterminated-apostrophe` — `'` with no matching `'`.\n * * `unexpected-whitespace` — whitespace outside a bracket / quote payload.\n * * `unexpected-newline` — newline inside a bracket / quote payload.\n * * `unexpected-char` — character that matches no token class.\n *\n * The parser handles structural errors (unbalanced `{`, missing `$` between\n * sections, etc.); those are NOT lexer-level.\n */\nexport function tokenize(source: string): TokenStream {\n const stream = new Lexer(source).tokenize();\n checkApostrophePairs(stream);\n return stream;\n}\n\n// Apostrophe pair check. The main loop is happy to leave a stray `apos`\n// dangling; we sweep over the token list and ensure every `apos` is matched\n// by a later `apos` before the stream ends. We also forbid newlines or `eof`\n// from terminating an open apostrophe (the lexer never emits newlines at\n// top-level — they would have raised `unexpected-whitespace`). This means the\n// check reduces to a simple parity inspection.\nfunction checkApostrophePairs(stream: TokenStream): void {\n let openSpan: TokenSpan | null = null;\n for (const t of stream.tokens) {\n if (t.kind === 'apos') {\n openSpan = openSpan === null ? t.span : null;\n } else if (t.kind === 'eof' && openSpan !== null) {\n throw new HelmParseError(\n 'unterminated-apostrophe',\n `Unterminated apostrophe block starting at offset ${openSpan.start}`,\n { span: { start: openSpan.start, end: stream.source.length } },\n );\n }\n }\n}\n","// Immutable in-memory graph types — the canonical `Mol` shape consumed by the\n// parser, layout, renderer, and editor. See ARCHITECTURE.md §3.3 and API.md §5.\n//\n// This file is intentionally **data only**. Construction goes through the tiny\n// builder helpers at the bottom (`emptyMol`, lookup helpers). Real mutation is\n// done via the upcoming `transaction.ts` (Phase 5, T-0506) which produces new\n// `Mol` snapshots; until then external code only ever reads `Mol`.\n//\n// Layer rule: `core/` may import from `util/` and `monomer-lib/` only. We\n// import `ResolvedMonomer` from `monomer-lib/types` so the resolver can attach\n// it after parsing.\n\nimport type { HelmType, MonomerType, PolymerType } from './constants';\nimport type { Point } from '../util/types';\nimport type { ResolvedMonomer } from '../monomer-lib/types';\n\n/**\n * Bond classification — drives both rendering (line style) and semantics\n * (e.g. `hbond` is a base-pair, `group` is a halo around a Group's atoms).\n * Matches the legacy editor's bond kinds; see SPECIFICATION.md §9 and\n * RENDERING.md §4.\n */\nexport type BondKind = 'backbone' | 'branch' | 'cross-polymer' | 'hbond' | 'group';\n\n/**\n * Reference into a monomer's R-group slot, used at each bond endpoint to say\n * \"this bond consumes which attachment point of which atom\". The shape carries\n * the original notation faithfully so we can round-trip:\n *\n * - `numeric { r }` — `R1`, `R2`, … (the common case).\n * - `unspecified` — `?` (the connection point is intentionally\n * ambiguous).\n * - `wildcard` — `*` (any free R-group).\n * - `pair` — H-bond marker (`:pair` in HELM connection\n * notation).\n * - `positional { position, r }` — `aNpos:Rn`, used by BLOB-internal bonds.\n */\nexport type RGroupRef =\n | { kind: 'numeric'; r: number }\n | { kind: 'unspecified' }\n | { kind: 'wildcard' }\n | { kind: 'pair' }\n | { kind: 'positional'; position: number; r: number };\n\n/**\n * Biological context attached to every atom. The triple\n * `(chainId, positionInChain, continuousId)` uniquely locates an atom across\n * the document; `chainId` matches the polymer id (`PEPTIDE1`, `RNA2`, …) and\n * `continuousId` is the cross-chain 1-based id assigned by\n * `makeContinuousIdMap` (PARSING.md §6).\n *\n * `annotation`, `blobtype`, and `ambiguity` mirror the legacy\n * `JSDraw2.atom.bio.*` fields and survive serialization.\n */\nexport interface AtomBio {\n chainId: string;\n positionInChain: number;\n continuousId: number;\n annotation?: string;\n blobtype?: string;\n ambiguity?: string;\n /**\n * Set on atoms that stand for an alternation or AND-mixture inside `(...)`\n * brackets in the source HELM. `'or'` for `(A,B,C)` (mutually exclusive),\n * `'and'` for `(A+B+C)` (stoichiometric mixture). The original raw form is\n * preserved in `ambiguity`. See PARSING.md §3.3 and SPECIFICATION.md §8.\n */\n ambiguityKind?: 'or' | 'and';\n}\n\n/**\n * A single node in the `Mol` graph. Every field is `readonly`; the editor\n * produces a new `Atom` rather than mutating one. The optional `branchAtom`\n * pointer is set on RNA sugar atoms to point at the attached base — the\n * continuous-id walker (T-0103) uses it to interleave sugar/base ids in source\n * order.\n *\n * `monomer` is `null` until the resolver binds the atom to a `ResolvedMonomer`\n * from the active `IMonomerLib`. Renderers tolerate the `null` (they paint an\n * \"unresolved\" badge per RENDERING.md §3); callers that need lib metadata\n * (formula, MW) refuse to compute until resolution is complete.\n */\nexport interface Atom {\n readonly id: number;\n readonly p: Point;\n readonly biotype: HelmType;\n readonly symbol: string;\n readonly monomer: ResolvedMonomer | null;\n readonly bio: AtomBio;\n readonly hidden: boolean;\n readonly selected: boolean;\n readonly highlighted: boolean;\n readonly tag?: string;\n readonly branchAtom?: Atom;\n /**\n * Original bracketed source for monomers that came in as `[...]` tokens\n * (long symbols and inline SMILES). The serializer emits `[${inlineSource}]`\n * verbatim so the output round-trips byte-for-byte. Absent on naked\n * single-character monomers like `A`, `*`, `?`.\n */\n readonly inlineSource?: string;\n}\n\n/**\n * Stoichiometric ratio attached to BLOB-internal bonds. The\n * `numerator/denominator` shape lets us preserve the original HELM notation\n * (`1.5` vs `3/2`); both `numerator` alone and the full fraction are\n * supported.\n */\nexport interface BondRatio {\n numerator: number;\n denominator?: number;\n}\n\n/**\n * A bond connecting two `Atom`s. `r1`/`r2` describe which R-group of each\n * endpoint participates (a 1-based numeric, a wildcard, or a pair marker).\n * `kind` drives the renderer's line style. `ratio` is only present on\n * BLOB-internal bonds.\n */\nexport interface Bond {\n readonly id: number;\n readonly a1: Atom;\n readonly a2: Atom;\n readonly kind: BondKind;\n readonly r1: RGroupRef;\n readonly r2: RGroupRef;\n readonly ratio?: BondRatio;\n readonly tag?: string;\n}\n\n/**\n * A connected sequence of `Atom`s with a single polymer id (e.g.\n * `PEPTIDE1`). `backboneAtoms` are the atoms walked by the continuous-id\n * algorithm; `bonds` carries every bond owned by the chain (backbone +\n * branch). Cross-polymer bonds live on the `Mol`, not on either chain.\n */\nexport interface Chain {\n readonly id: string;\n readonly polymerType: PolymerType;\n readonly backboneAtoms: readonly Atom[];\n readonly bonds: readonly Bond[];\n readonly annotation?: string;\n /**\n * Phase 33 (T-3301) — Strand type from the HELM section-3\n * `{\"<polymer>\":{\"strandtype\":\"ss\" | \"as\"}}` annotation. `ss`\n * (sense) renders at the TOP of a duplex; `as` (antisense) is\n * vertically and horizontally mirrored beneath the sense strand so\n * its bases point UP toward the sense bases. `undefined` means the\n * annotation was not supplied — layout falls back to source-order\n * anchoring (the legacy behaviour) so existing fixtures keep\n * working.\n */\n readonly strandType?: 'ss' | 'as';\n}\n\n/**\n * Kind of group encoded in HELM section 3. `and` and `or` are mixture and\n * alternation respectively; `bracket` marks a repeat range like `[A.C]'3-5'`.\n */\nexport type GroupKind = 'and' | 'or' | 'bracket';\n\n/**\n * One element inside a `Group.members` list. `target` is the polymer id or\n * a nested group id; `ratio` is optional and may be the string `'?'` when the\n * group says \"some amount, unknown\".\n */\nexport interface GroupMember {\n readonly target: string;\n readonly ratio?: number | '?';\n}\n\n/**\n * A HELM group (section 3 of the notation). For `bracket` groups, the\n * `repeat` range carries the lower/upper bound of the repeat count\n * (`'3-5'` → `{min:3, max:5}`; `'3'` → `{min:3, max:3}`).\n */\nexport interface Group {\n readonly id: string;\n readonly kind: GroupKind;\n readonly members: readonly GroupMember[];\n readonly repeat?: { min: number; max: number };\n}\n\n/**\n * HELM annotation block (section 4). We preserve the raw text when parsing\n * fails and expose a structured `perPolymer` view when the annotation is\n * well-formed HELM 2.0 JSON. `version` carries the trailing version token\n * (`V2.0`, `V1.0`, or `''` when missing).\n */\nexport interface AnnotationMap {\n readonly perPolymer: ReadonlyMap<string, Readonly<Record<string, unknown>>>;\n readonly version: string;\n readonly raw?: string;\n}\n\n/**\n * The full graph: every atom, every bond, every chain, every group, plus the\n * annotation block. This is the single source of truth that the editor reads\n * and the serializer rebuilds the HELM string from.\n */\nexport interface Mol {\n readonly atoms: readonly Atom[];\n readonly bonds: readonly Bond[];\n readonly chains: readonly Chain[];\n readonly groups: readonly Group[];\n readonly annotations: AnnotationMap;\n}\n\n// ---------- Tiny builders / lookups ----------\n\nconst EMPTY_ANNOTATIONS: AnnotationMap = {\n perPolymer: new Map<string, Readonly<Record<string, unknown>>>(),\n version: '',\n};\n\n/**\n * Build a fresh empty `Mol`. All collections are real (mutable) arrays/maps\n * cast through the `readonly` interface; callers receive a stable empty\n * value but `Object.isFrozen(emptyMol().atoms)` is `false`. We avoid `freeze`\n * here for cheapness — the type system already prevents mutation at use\n * sites.\n */\nexport function emptyMol(): Mol {\n return {\n atoms: [],\n bonds: [],\n chains: [],\n groups: [],\n annotations: EMPTY_ANNOTATIONS,\n };\n}\n\n/** Find an `Atom` by id. O(n); intended for tests / occasional lookups. */\nexport function molAtomById(mol: Mol, id: number): Atom | undefined {\n for (const a of mol.atoms)\n if (a.id === id) return a;\n return undefined;\n}\n\n/** Find a `Bond` by id. O(n); intended for tests / occasional lookups. */\nexport function molBondById(mol: Mol, id: number): Bond | undefined {\n for (const b of mol.bonds)\n if (b.id === id) return b;\n return undefined;\n}\n\n/** Atom-count shortcut. */\nexport function molAtomCount(mol: Mol): number {\n return mol.atoms.length;\n}\n\n/**\n * Resolve the 1-based backbone position an `atom` should be addressed by in\n * a HELM connection string. For backbone atoms this is just\n * `atom.bio.positionInChain`. For branch atoms (e.g. RNA bases hanging off a\n * sugar) the parser stores `0`; this helper walks the chain's backbone to\n * find the owning sugar (the one whose `branchAtom.id === atom.id`) and\n * returns its position. Returns `0` if no owner is found — callers should\n * treat that as \"address-by-position not available for this atom\".\n *\n * The hbond-on-bases redirection (Phase 34 / T-3401 mid-phase correction\n * #1) means every `:pair-:pair` endpoint after parse is a base atom; the\n * serializer, validator, and canonicalizer all use this helper so the\n * downstream \"position\" they emit/compare matches the sugar position the\n * original HELM string referenced.\n */\nexport function atomPositionInChain(atom: Atom, chain: Chain | undefined): number {\n if (chain === undefined) return atom.bio.positionInChain;\n // Standard HELM (Pistoia) counts EVERY monomer in source order — sugar, base,\n // linker — so for RNA a base is the monomer right after its owning sugar\n // (`m(U)p` → m=1, U=2, p=3). Peptides (no branch atoms) collapse to the\n // backbone position. Inverse of the parser's `sourceOrderAtoms` indexing, so\n // serialize → parse round-trips. (NOT `bio.positionInChain`, the backbone\n // index, which excludes bases — the \"Position 56 out of range\" bug.)\n let idx = 0;\n for (let i = 0; i < chain.backboneAtoms.length; i++) {\n const bb = chain.backboneAtoms[i];\n if (bb === undefined) continue;\n idx += 1;\n if (bb.id === atom.id) return idx;\n if (bb.branchAtom !== undefined) {\n idx += 1;\n if (bb.branchAtom.id === atom.id) return idx;\n }\n }\n return 0;\n}\n\n// Re-export commonly used constants types so consumers don't have to dip into\n// `./constants` just to type a field.\nexport type { HelmType, PolymerType, MonomerType };\n","// Stable string constants for HELM types, polymer types, and monomer types.\n//\n// We use `as const` records (not TS `enum`) so the values tree-shake away when\n// unused and remain plain string literals at runtime. See ARCHITECTURE.md §3.3.\n//\n// Member names use the UPPERCASE Pistoia/HELM convention (`HelmTypes.SUGAR`,\n// `PolymerTypes.PEPTIDE`, `MonomerTypes.BACKBONE`) so that the Datagrok `bio`\n// library can re-export these as the single source of truth without a\n// casing-remap shim. The string VALUES match the canonical Pistoia HELM Web\n// Editor — except `NUCLEOTIDE`, which fixes the long-standing legacy typo\n// (`HELM_NUCLETIDE` → `HELM_NUCLEOTIDE`); Datagrok consumers fix-forward to the\n// corrected value.\n\n/**\n * HELM type tags — the biotype of an atom in a HELM Mol.\n */\nexport const HelmTypes = {\n AA: 'HELM_AA',\n SUGAR: 'HELM_SUGAR',\n BASE: 'HELM_BASE',\n LINKER: 'HELM_LINKER',\n CHEM: 'HELM_CHEM',\n BLOB: 'HELM_BLOB',\n NUCLEOTIDE: 'HELM_NUCLEOTIDE',\n} as const;\n\n/** Union of all HELM type strings. */\nexport type HelmType = (typeof HelmTypes)[keyof typeof HelmTypes];\n\n/**\n * Polymer-type tags as they appear in HELM strings (e.g. `PEPTIDE1{...}`).\n * `G` is the HELM \"generic/group\" polymer type used by some Datagrok flows.\n */\nexport const PolymerTypes = {\n PEPTIDE: 'PEPTIDE',\n RNA: 'RNA',\n CHEM: 'CHEM',\n BLOB: 'BLOB',\n G: 'G',\n} as const;\n\n/** Union of all polymer-type strings. */\nexport type PolymerType = (typeof PolymerTypes)[keyof typeof PolymerTypes];\n\n/**\n * Monomer role within a chain — determines how the monomer participates\n * in backbone vs. branch connectivity.\n */\nexport const MonomerTypes = {\n BACKBONE: 'Backbone',\n BRANCH: 'Branch',\n TERMINAL: 'Terminal',\n UNDEFINED: 'Undefined',\n} as const;\n\n/** Union of all monomer-type strings. */\nexport type MonomerType = (typeof MonomerTypes)[keyof typeof MonomerTypes];\n","// Id generation and continuous-numbering helpers used by the parser, layout,\n// and renderer. See ARCHITECTURE.md §3.3 and PARSING.md §6.\n\n/**\n * Monotonic 1-based integer generator. The first `next()` call returns 1;\n * `reset()` returns the counter to 0 so the next `next()` again returns 1.\n *\n * Used by `Mol` to assign atom and bond ids; deterministic and side-effect\n * free so unit tests can snapshot the result.\n */\nexport class IdGenerator {\n private _counter: number = 0;\n\n /** Allocate the next id (post-increment). The first call returns 1. */\n next(): number {\n this._counter += 1;\n return this._counter;\n }\n\n /** Restart numbering from 0. */\n reset(): void {\n this._counter = 0;\n }\n\n /** Last id returned (or 0 if no `next()` has been called since the last reset). */\n get current(): number {\n return this._counter;\n }\n}\n\n// ---------- Continuous-id numbering (PARSING.md §6) ----------\n\n/**\n * Minimal structural shape consumed by `makeContinuousIdMap`. Declared\n * locally so this file does not depend on `model.ts` (which lives in the\n * same layer and is implemented later — keeps the layering acyclic).\n */\nexport interface ContinuousIdAtomLike {\n id: number;\n branchAtom?: ContinuousIdAtomLike | undefined;\n}\n\nexport interface ContinuousIdChainLike {\n backboneAtoms: Iterable<ContinuousIdAtomLike>;\n}\n\nexport interface ContinuousIdMolLike {\n chains: Iterable<ContinuousIdChainLike>;\n}\n\n/**\n * Compute the 1-based continuous-id assignment for every atom reachable from\n * `mol.chains`, per PARSING.md §6.\n *\n * Walks chains in source order; within a chain, walks `backboneAtoms` in\n * order. Each backbone atom gets the next id; if the atom has a `branchAtom`\n * (an RNA base hanging off the sugar), the branch atom gets the next id\n * immediately after.\n *\n * The result is deterministic and uniquely determined by the chain/atom\n * iteration order of the input; given the same input it always produces the\n * same map. The legacy editor's \"iterate atoms in creation order\" approach\n * is intentionally NOT used — it is unstable under cross-chain edits.\n *\n * The mol parameter is a structural type rather than the full `Mol` type so\n * this module stays free of cyclic core-layer imports. The real `Mol` is\n * structurally assignable (its chains expose `backboneAtoms` and each atom\n * carries an optional `branchAtom`).\n *\n * @returns a `Map` from `atom.id` to continuous id (1-based, gap-free).\n */\nexport function makeContinuousIdMap(mol: ContinuousIdMolLike): Map<number, number> {\n const out = new Map<number, number>();\n let counter = 0;\n for (const chain of mol.chains) {\n for (const atom of chain.backboneAtoms) {\n counter += 1;\n out.set(atom.id, counter);\n if (atom.branchAtom !== undefined) {\n counter += 1;\n out.set(atom.branchAtom.id, counter);\n }\n }\n }\n return out;\n}\n","// Inline-SMILES R-group detection for HELM bracketed monomer payloads.\n//\n// HELM allows a bracketed payload to carry a raw SMILES with R-group\n// attachment points. Three notation flavors exist (SPECIFICATION.md §7 and\n// PARSING.md §4); the parser tries them in order and uses the FIRST one that\n// detects ≥ 1 R-group:\n//\n// 1. JSDraw-style `[R1]`–`[R10]` (bracketed labels in the SMILES)\n// 2. ChemAxon extended ` |$ ... $|` (atom-label block at end of string)\n// 3. OpenSMILES `[*:1]`, `[*:2]` (atom-map numbers)\n//\n// We deliberately do NOT parse the actual chemistry — that's a downstream\n// concern handled by RDKit/OpenBabel/etc. The goal here is *cheap*: count and\n// locate the R-group attachments so `MonomerLib.registerInlineSmilesMonomer`\n// can synthesize a `Monomer` record.\n//\n// The \"position\" we record is the byte offset of the FIRST character of the\n// matched token inside the SMILES string. Callers may use it to compute atom\n// indices or for diagnostic spans — we keep it loose so future consumers can\n// refine.\n//\n// Layer rule: this file imports nothing from `core/` and only `types.ts` from\n// `./` — `MonomerLib` (T-0106) is the consumer.\n\n/** Detected R-group attachment metadata for an inline SMILES. */\nexport interface SmilesRGroupInfo {\n /** Total R-groups detected (1-based count; `rgroupPositions.size === rs`). */\n rs: number;\n /** Map from 1-based R-group number to position of the matched token in the SMILES. */\n rgroupPositions: ReadonlyMap<number, number>;\n /** Which notation flavor matched. */\n flavor: 'jsdraw' | 'chemaxon' | 'opensmiles';\n}\n\n/** Success result of `detectSmilesRGroups`. */\nexport interface SmilesParseResult {\n ok: true;\n info: SmilesRGroupInfo;\n /** Trimmed input — no semantic canonicalization. */\n canonicalSmiles: string;\n}\n\n/** Failure result of `detectSmilesRGroups`. */\nexport interface SmilesParseError {\n ok: false;\n reason: string;\n}\n\n/**\n * Quick heuristic: does this look like a SMILES string, or is it a\n * multi-character monomer symbol?\n *\n * Returns `true` if the string contains any of `(`, `[`, `=`, `\\\\`, `/`, or\n * `*`. (Spaces don't count — `meI` is plain text; `C[C@H](N)C=O` has parens,\n * so it's SMILES.)\n *\n * The function is defensive: it accepts EITHER the bare payload (`meI`,\n * already stripped by the lexer) OR a still-wrapped bracketed form (`[meI]`).\n * A simple `[identifier]` wrap is recognized and treated as a symbol — that\n * way the parser can call this on the pre-strip token if it has to.\n */\nexport function looksLikeSmiles(s: string): boolean {\n const t = s.trim();\n // `[identifier]` wrap (no nesting, no SMILES triggers inside) — a symbol.\n if (/^\\[[a-zA-Z_][a-zA-Z0-9_]*\\]$/.test(t)) return false;\n for (let i = 0; i < t.length; i++) {\n const c = t.charCodeAt(i);\n // ( [ = / \\ *\n if (c === 0x28 || c === 0x5b || c === 0x3d || c === 0x2f || c === 0x5c || c === 0x2a)\n return true;\n }\n return false;\n}\n\n// ---------- detection helpers ----------\n\n/** Match `[R<n>]` tokens (n = 1..10). Returns a map of n -> first index. */\nfunction scanJsDraw(smiles: string): Map<number, number> {\n const out = new Map<number, number>();\n // /\\[R(\\d+)\\]/g — captures the digits, position is g.index (start of bracket).\n const re = /\\[R(\\d{1,2})\\]/g;\n let m: RegExpExecArray | null;\n while ((m = re.exec(smiles)) !== null) {\n const n = parseInt(m[1] as string, 10);\n if (n >= 1 && n <= 10 && !out.has(n))\n out.set(n, m.index);\n }\n return out;\n}\n\n/**\n * Match ChemAxon extended-SMILES block ` |$label1;label2;...$|`. Inside the\n * block, labels starting with `_R<n>` mark R-group attachment points. The\n * position we record is the position of the corresponding `;`-separated atom\n * label inside the SMILES string.\n *\n * Per SPECIFICATION.md §7 and PARSING.md §4, the block is appended after a\n * leading SPACE. We tolerate any whitespace.\n */\nfunction scanChemAxon(smiles: string): Map<number, number> {\n const out = new Map<number, number>();\n const blockRe = /\\s*\\|\\$([^$]*)\\$\\|/;\n const m = blockRe.exec(smiles);\n if (m === null) return out;\n const labels = (m[1] as string).split(';');\n // The labels correspond to atom indices in the order they appear in the\n // SMILES; we report the position of the label inside the SMILES (start of\n // the block + offset of the matching label).\n const blockStart = m.index + (m[0] as string).indexOf('$') + 1;\n let offset = 0;\n for (const label of labels) {\n const lm = /^_R(\\d{1,2})$/.exec(label);\n if (lm !== null) {\n const n = parseInt(lm[1] as string, 10);\n if (n >= 1 && n <= 10 && !out.has(n))\n out.set(n, blockStart + offset);\n }\n // Advance past the label and its trailing `;` (which only exists between\n // entries — accept length+1 since `split` swallowed the separator).\n offset += label.length + 1;\n }\n return out;\n}\n\n/**\n * Match OpenSMILES atom-map tokens `[*:<n>]` (or more generally `[atom:<n>]`\n * where the atom is `*`). Records the position of the `[` character.\n */\nfunction scanOpenSmiles(smiles: string): Map<number, number> {\n const out = new Map<number, number>();\n // We restrict the \"atom\" part to `*` (the wildcard) — this is what the\n // HELM corpus uses. Future widening to any element is trivial.\n const re = /\\[\\*:(\\d{1,2})\\]/g;\n let m: RegExpExecArray | null;\n while ((m = re.exec(smiles)) !== null) {\n const n = parseInt(m[1] as string, 10);\n if (n >= 1 && n <= 10 && !out.has(n))\n out.set(n, m.index);\n }\n return out;\n}\n\n// ---------- public detection ----------\n\n/**\n * Detect R-group attachment points in an inline-SMILES string. Returns the\n * first flavor that matches at least one R-group; if none match, returns an\n * error result with `reason: 'no-rgroups-found'`.\n *\n * The input is trimmed before scanning. We do not modify R-group casing or\n * the bracketing — `canonicalSmiles` is just the trimmed input.\n */\nexport function detectSmilesRGroups(smiles: string): SmilesParseResult | SmilesParseError {\n const trimmed = smiles.trim();\n if (trimmed.length === 0)\n return { ok: false, reason: 'empty-smiles' };\n\n const js = scanJsDraw(trimmed);\n if (js.size > 0)\n return {\n ok: true,\n canonicalSmiles: trimmed,\n info: { rs: js.size, rgroupPositions: js, flavor: 'jsdraw' },\n };\n\n const cx = scanChemAxon(trimmed);\n if (cx.size > 0)\n return {\n ok: true,\n canonicalSmiles: trimmed,\n info: { rs: cx.size, rgroupPositions: cx, flavor: 'chemaxon' },\n };\n\n const os = scanOpenSmiles(trimmed);\n if (os.size > 0)\n return {\n ok: true,\n canonicalSmiles: trimmed,\n info: { rs: os.size, rgroupPositions: os, flavor: 'opensmiles' },\n };\n\n return { ok: false, reason: 'no-rgroups-found' };\n}\n","// Tiny observable primitive. The rest of the library speaks this small, stable\n// surface instead of importing rxjs directly. Phase 1 (Datagrok migration)\n// removed the rxjs runtime dependency: the public surface we actually use\n// (`subscribe` / `next` / `complete` / `observerCount`) is a few lines of\n// multicast bookkeeping, and depending on rxjs forced a version (7.x) that\n// conflicts with Datagrok's platform-wide rxjs 6.x. Keeping `hwe` zero-runtime-\n// dependency also keeps it a clean leaf library. See ARCHITECTURE.md §5.\n\nimport type { Unsubscribe } from './types';\n\n/**\n * Minimal multicast subject. Subscribers receive every value emitted after\n * they subscribe; previously emitted values are not replayed. Once\n * `complete()` is called the subject is sealed: no further emissions and new\n * subscribers receive nothing.\n *\n * The public surface is deliberately tiny — `subscribe`, `next`, `complete`,\n * and an `observerCount` introspection field. If a consumer needs rxjs\n * operators they can construct an `Observable` from `subscribe` themselves.\n */\nexport class Subject<T> {\n private readonly _listeners: Set<(value: T) => void> = new Set();\n private _completed: boolean = false;\n\n /**\n * Register a handler. Returns an `Unsubscribe` function; calling it tears\n * down this single subscription. Idempotent. Subscribing after `complete()`\n * is a no-op that returns a no-op disposer.\n */\n subscribe(fn: (value: T) => void): Unsubscribe {\n if (this._completed) return () => { /* sealed — nothing to dispose */ };\n this._listeners.add(fn);\n return () => {\n this._listeners.delete(fn);\n };\n }\n\n /**\n * Emit a value to every current subscriber. No-op after `complete()`.\n *\n * We iterate a snapshot so a handler that subscribes or unsubscribes during\n * delivery does not perturb the in-flight emission (matches rxjs `Subject`).\n */\n next(value: T): void {\n if (this._completed) return;\n for (const fn of [...this._listeners]) fn(value);\n }\n\n /** Seal the subject. Further `next()` calls are no-ops; drops all listeners. */\n complete(): void {\n this._completed = true;\n this._listeners.clear();\n }\n\n /** Number of currently subscribed observers. */\n get observerCount(): number {\n return this._listeners.size;\n }\n}\n","// Default color rules for monomer rendering. The renderer (Phase 4) reads\n// these tables; this file has no dependency on the renderer (one-way arrow).\n//\n// Resolution order — MONOMER-LIBRARY.md §6 — is:\n// 1. monomer.meta.colors[themeName] (per-theme override)\n// 2. monomer.meta.colors.default (theme-agnostic override)\n// 3. theme.palette[biotype][monomer.naturalAnalog] (palette default)\n// 4. theme.fallback (last-resort triple)\n//\n// For unresolved monomers (`monomer === null`) we paint `theme.errorTriple`\n// so users see immediately \"something is wrong here\" (RENDERING.md §3).\n//\n// Legacy reference: HELMWebEditor/helm/MonomerColors.js — palette letters keyed\n// on natural-analog letters. We preserve that mapping verbatim for `light` and\n// derive `dark` from it.\n\nimport { HelmTypes } from '../core/constants';\nimport type { HelmType } from '../core/constants';\nimport type { ColorTriple, Monomer, MonomerColors } from './types';\n\n/**\n * A self-contained color theme. The `palette` is keyed first on `HelmType`\n * (the atom's biotype) and then on a single-letter `naturalAnalog`. A missing\n * key falls through to `fallback`; `errorTriple` is reserved for atoms whose\n * monomer could not be resolved.\n */\nexport interface ColorTheme {\n name: string;\n fallback: ColorTriple;\n errorTriple: ColorTriple;\n palette: Partial<Record<HelmType, Record<string, ColorTriple>>>;\n}\n\n// ---------- Helpers ----------\n\n/**\n * Build a `ColorTriple` whose `line` is the legacy black-on-white stroke and\n * whose `text` is black, leaving `background` configurable. The legacy editor\n * draws every shape's outline in `#202020` (effectively black) and the symbol\n * label in `#000000`.\n */\nfunction lightTriple(background: string): ColorTriple {\n return { line: '#202020', text: '#000000', background };\n}\n\n/**\n * Build a dark-theme `ColorTriple`. The legacy editor didn't have a dark\n * theme; we derive ours by:\n * - using `#ffffff` for the symbol label (text on dark backgrounds),\n * - using `#e0e0e0` for the stroke,\n * - keeping the legacy hue but lowering its lightness by ~25% so the\n * symbol stays legible on a dark canvas.\n *\n * The actual `background` is supplied per-monomer. Saturation tweaks are not\n * applied here — we trust the palette author and prefer determinism over\n * cleverness.\n */\nfunction darkTriple(background: string): ColorTriple {\n return { line: '#e0e0e0', text: '#ffffff', background: darken(background, 0.25) };\n}\n\n/**\n * Parse `#rrggbb` or `#rgb` into [r,g,b] integers. Returns null on a\n * non-hex input (typical when the palette was extended with `rgb(...)`\n * literals).\n */\nfunction parseHex(hex: string): [number, number, number] | null {\n const m6 = /^#([0-9a-fA-F]{6})$/.exec(hex);\n const m3 = /^#([0-9a-fA-F]{3})$/.exec(hex);\n if (m6 !== null) {\n const s = m6[1] as string;\n return [\n parseInt(s.slice(0, 2), 16),\n parseInt(s.slice(2, 4), 16),\n parseInt(s.slice(4, 6), 16),\n ];\n }\n if (m3 !== null) {\n const s = m3[1] as string;\n return [\n parseInt(s[0] as string + (s[0] as string), 16),\n parseInt(s[1] as string + (s[1] as string), 16),\n parseInt(s[2] as string + (s[2] as string), 16),\n ];\n }\n return null;\n}\n\nfunction hexByte(n: number): string { return n.toString(16).padStart(2, '0'); }\n\nfunction toHex(r: number, g: number, b: number): string {\n return `#${hexByte(r)}${hexByte(g)}${hexByte(b)}`;\n}\n\n/**\n * Convert [r,g,b] (0..255) to HSL where h is in [0, 360), s and l are in\n * [0, 1]. Standard formula — kept inline so we don't depend on an external\n * colour library for one routine.\n */\nfunction rgbToHsl(r: number, g: number, b: number): [number, number, number] {\n const rn = r / 255, gn = g / 255, bn = b / 255;\n const max = Math.max(rn, gn, bn);\n const min = Math.min(rn, gn, bn);\n const l = (max + min) / 2;\n if (max === min) return [0, 0, l];\n const d = max - min;\n const s = l > 0.5 ? d / (2 - max - min) : d / (max + min);\n let h: number;\n if (max === rn) h = ((gn - bn) / d + (gn < bn ? 6 : 0)) * 60;\n else if (max === gn) h = ((bn - rn) / d + 2) * 60;\n else h = ((rn - gn) / d + 4) * 60;\n return [h, s, l];\n}\n\nfunction hue2rgb(p: number, q: number, t: number): number {\n let tt = t;\n if (tt < 0) tt += 1;\n if (tt > 1) tt -= 1;\n if (tt < 1 / 6) return p + (q - p) * 6 * tt;\n if (tt < 1 / 2) return q;\n if (tt < 2 / 3) return p + (q - p) * (2 / 3 - tt) * 6;\n return p;\n}\n\nfunction hslToRgb(h: number, s: number, l: number): [number, number, number] {\n if (s === 0) {\n const v = Math.round(l * 255);\n return [v, v, v];\n }\n const q = l < 0.5 ? l * (1 + s) : l + s - l * s;\n const p = 2 * l - q;\n const hn = h / 360;\n return [\n Math.round(hue2rgb(p, q, hn + 1 / 3) * 255),\n Math.round(hue2rgb(p, q, hn) * 255),\n Math.round(hue2rgb(p, q, hn - 1 / 3) * 255),\n ];\n}\n\n/**\n * \"Soften\" a palette colour — desaturate by ~30%, lighten by ~10% — into a\n * pastel suitable for palette tiles and (optionally) the canvas. The\n * algorithm:\n * 1. Convert hex to HSL.\n * 2. Multiply saturation by `(1 - sAmt)` (default 0.30 = -30%).\n * 3. Add `lAmt * (1 - L)` to lightness (default 0.10 = +10%), clamped at\n * 0.95 so the colour never becomes pure white.\n * 4. Convert back to hex.\n *\n * Inputs that don't parse as hex are returned unchanged.\n *\n * The result is deterministic and round-trips to the same value for any\n * given input, so tests can compare against the soften() output rather\n * than hand-tuning a soft palette table.\n *\n * Sample (sanity check):\n * soften('#E60A0A') → ~'#f0563f' (red → coral pastel)\n * soften('#145AFF') → ~'#588fff' (royal blue → sky pastel)\n */\nexport function soften(\n color: string,\n sAmt: number = 0.30,\n lAmt: number = 0.10,\n): string {\n const rgb = parseHex(color);\n if (rgb === null) return color;\n const [h, s, l] = rgbToHsl(rgb[0], rgb[1], rgb[2]);\n const newS = Math.max(0, Math.min(1, s * (1 - sAmt)));\n const newL = Math.max(0, Math.min(0.95, l + lAmt * (1 - l)));\n const [r2, g2, b2] = hslToRgb(h, newS, newL);\n return toHex(r2, g2, b2);\n}\n\n/**\n * Compute the WCAG 2.x relative-luminance value for a hex colour. Returns 0\n * for non-hex inputs.\n */\nfunction relativeLuminance(hex: string): number {\n const rgb = parseHex(hex);\n if (rgb === null) return 0;\n const channel = (c: number): number => {\n const cs = c / 255;\n return cs <= 0.03928 ? cs / 12.92 : Math.pow((cs + 0.055) / 1.055, 2.4);\n };\n return 0.2126 * channel(rgb[0]) + 0.7152 * channel(rgb[1]) + 0.0722 * channel(rgb[2]);\n}\n\n/**\n * WCAG contrast ratio between two hex colours. Result ≥ 4.5 passes the\n * \"normal text\" AA threshold; ≥ 5 is the threshold the editor uses for\n * palette tiles (small symbol labels on a pastel background).\n */\nexport function contrastRatio(fg: string, bg: string): number {\n const l1 = relativeLuminance(fg);\n const l2 = relativeLuminance(bg);\n const hi = Math.max(l1, l2);\n const lo = Math.min(l1, l2);\n return (hi + 0.05) / (lo + 0.05);\n}\n\n/**\n * Phase 18 (T-1804) — Convert a hex colour string to its HSL components.\n *\n * - `h` ∈ [0, 360) — hue in degrees. Greys (R = G = B) return `h = 0`.\n * - `s` ∈ [0, 1] — saturation. Greys return `s = 0`.\n * - `l` ∈ [0, 1] — lightness.\n *\n * Inputs that do not parse as hex return `{h: 0, s: 0, l: 0}` so callers\n * can safely sort an array of mixed-validity colours without checking for\n * `null` at every comparison.\n *\n * Used by the palette to sort tiles within a subsection by colour, so\n * visually similar monomers cluster instead of producing a random rainbow.\n */\nexport function hexToHsl(hex: string): { h: number; s: number; l: number } {\n const rgb = parseHex(hex);\n if (rgb === null) return { h: 0, s: 0, l: 0 };\n const [h, s, l] = rgbToHsl(rgb[0], rgb[1], rgb[2]);\n return { h, s, l };\n}\n\n/**\n * Phase 23 (T-2301) — Convert HSL back to hex. Inverse of `hexToHsl`. Values\n * outside the canonical ranges are clamped (h wraps mod 360, s/l clamp to\n * [0,1]). Used by `deriveLineColor` to compute a \"slightly darker\" version\n * of a monomer's background fill.\n */\nexport function hslToHex(hsl: { h: number; s: number; l: number }): string {\n const h = ((hsl.h % 360) + 360) % 360;\n const s = Math.max(0, Math.min(1, hsl.s));\n const l = Math.max(0, Math.min(1, hsl.l));\n const [r, g, b] = hslToRgb(h, s, l);\n return toHex(r, g, b);\n}\n\n/**\n * Phase 23 (T-2301) — Derive a monomer outline (\"line\") colour from the\n * resolved background fill. The user reported that the legacy `#202020`\n * black outline on every monomer was visually heavy, and asked for the\n * outline to be a slightly darker version of the fill — except for white\n * or very-light fills, where a darker neutral falls back so the shape\n * stays visible against the white canvas.\n *\n * Algorithm:\n * 1. Convert `background` to HSL.\n * 2. If lightness > 0.85, OR (saturation < 0.15 AND lightness > 0.7),\n * treat as \"near-white\" and return `#1f2937` (the editor's dark\n * text colour — matches the tooltip body colour).\n * 3. Otherwise, reduce lightness by 0.30 with a floor of 0.08\n * (already-dark fills like `#0F820F` would otherwise hit pure\n * black, defeating the \"not black\" rule), and slightly boost\n * saturation (+0.10, clamped at 1) so the darkened colour reads\n * as a \"stronger\" tint of the same hue rather than a muddy\n * grey-shift.\n *\n * Inputs that don't parse as hex return `#1f2937` (the dark fallback).\n *\n * Sample (sanity):\n * deriveLineColor('#FF0000') → '#660000' (pure red → dark red)\n * deriveLineColor('#FFFFFF') → '#1f2937' (white → dark slate)\n * deriveLineColor('#F5F5F5') → '#1f2937' (near-white → dark slate)\n * deriveLineColor('#C8C8C8') → '#1f2937' (light grey, low saturation → dark slate)\n * deriveLineColor('#A0A0FF') → darker blue (saturated → ~half-lightness)\n * deriveLineColor('#0F820F') → very dark green (NOT '#000000')\n */\nexport function deriveLineColor(background: string): string {\n const rgb = parseHex(background);\n if (rgb === null) return '#1f2937';\n const [h, s, l] = rgbToHsl(rgb[0], rgb[1], rgb[2]);\n if (l > 0.85 || (s < 0.15 && l > 0.7))\n return '#1f2937';\n // Floor at 0.08 so already-dark, saturated fills (Leucine green,\n // Tryptophan purple, etc.) don't collapse to pure black -- pure\n // black is the explicit \"I don't like this\" colour the user\n // banned at the top of T-2301.\n const darkerL = Math.max(0.08, l - 0.30);\n const boostedS = Math.min(1, s + 0.10);\n return hslToHex({ h, s: boostedS, l: darkerL });\n}\n\n/**\n * Phase 23.2 (T-2310) — Parse `#rrggbb` (or `#rgb`) into `{r, g, b}` with\n * each channel in `[0, 1]`. Returns `null` on a non-hex input. Used by\n * `bestContrastTextColor` so the WCAG relative-luminance formula can apply\n * directly without intermediate 0..255 -> 0..1 scaling at every call site.\n *\n * Implemented as a thin wrapper around the existing `parseHex` (which\n * normalises 3-digit hex like `#abc` -> `#aabbcc` already).\n */\nfunction hexToRgb01(hex: string): { r: number; g: number; b: number } | null {\n const rgb = parseHex(hex);\n if (rgb === null) return null;\n return { r: rgb[0] / 255, g: rgb[1] / 255, b: rgb[2] / 255 };\n}\n\n/**\n * Phase 23.2 (T-2310) — Pick the best-contrast text colour (dark slate vs.\n * pure white) for a given background. The user reported that the monomer\n * symbol label was always painted black, which is illegible on dark-saturated\n * backgrounds like Arginine's `#145AFF` royal blue or Tryptophan's purple.\n * Phase 23 fixed the *outline* via `deriveLineColor`; this completes the\n * picture by making the *text* contrast with the fill too.\n *\n * Algorithm (WCAG 2.1 §1.4.6 relative luminance, §1.4.3 contrast ratio):\n * 1. Convert the background hex to RGB in `[0, 1]`.\n * 2. Linearise each channel (sRGB -> linear).\n * 3. Compute relative luminance L = 0.2126 R + 0.7152 G + 0.0722 B.\n * 4. Compute contrast ratios against pure black (L=0) and pure white (L=1)\n * via `(L_lighter + 0.05) / (L_darker + 0.05)`.\n * 5. Return `'#ffffff'` if white-text contrast is higher, otherwise\n * `'#1f2937'` (the editor's dark-slate text colour, matching the\n * Phase-23 `deriveLineColor` near-white fallback).\n *\n * Non-hex inputs return `'#1f2937'` (the dark fallback) so callers feeding\n * `rgb(...)` literals don't silently get pure white on a light background.\n *\n * Citations:\n * - WCAG 2.1 §1.4.3 — contrast ratio definition.\n * - WCAG 2.1 §1.4.6 — relative luminance formula.\n *\n * Sample (sanity check, hand-traced):\n * bestContrastTextColor('#ffffff') -> '#1f2937' (dark on white)\n * bestContrastTextColor('#000000') -> '#ffffff' (white on black)\n * bestContrastTextColor('#145AFF') -> '#ffffff' (white on royal blue)\n * bestContrastTextColor('#C8C8C8') -> '#1f2937' (dark on light grey)\n * bestContrastTextColor('#FFFF00') -> '#1f2937' (dark on yellow)\n * bestContrastTextColor('#A4E2DC') -> '#1f2937' (dark on light tiffany)\n */\nexport function bestContrastTextColor(backgroundHex: string): string {\n const rgb = hexToRgb01(backgroundHex);\n if (rgb === null) return '#1f2937';\n const toLinear = (c: number): number =>\n c <= 0.03928 ? c / 12.92 : Math.pow((c + 0.055) / 1.055, 2.4);\n const L = 0.2126 * toLinear(rgb.r) + 0.7152 * toLinear(rgb.g) + 0.0722 * toLinear(rgb.b);\n const contrastWithBlack = (L + 0.05) / (0 + 0.05);\n const contrastWithWhite = (1 + 0.05) / (L + 0.05);\n return contrastWithWhite > contrastWithBlack ? '#ffffff' : '#1f2937';\n}\n\n/**\n * Reduce a hex color's lightness by the given fraction. We parse `#rrggbb`\n * (or `#rgb`) into [r,g,b], multiply by `1 - amt`, and emit `#rrggbb`. Inputs\n * that don't match the hex pattern are returned unchanged (rare; only safety\n * for caller-supplied non-hex CSS strings like `rgb(...)`).\n */\nfunction darken(hex: string, amt: number): string {\n const rgb = parseHex(hex);\n if (rgb === null) return hex;\n const f = 1 - amt;\n const nr = Math.max(0, Math.min(255, Math.round(rgb[0] * f)));\n const ng = Math.max(0, Math.min(255, Math.round(rgb[1] * f)));\n const nb = Math.max(0, Math.min(255, Math.round(rgb[2] * f)));\n return toHex(nr, ng, nb);\n}\n\n// ---------- Legacy palette (light theme) ----------\n\nconst LIGHT_BASES: Record<string, ColorTriple> = {\n A: lightTriple('#A0A0FF'),\n G: lightTriple('#FF7070'),\n T: lightTriple('#A0FFA0'),\n C: lightTriple('#FF8C4B'),\n U: lightTriple('#FF8080'),\n};\n\nconst LIGHT_SUGARS: Record<string, ColorTriple> = {\n R: lightTriple('#7a85c1'),\n r: lightTriple('#7a85c1'),\n};\n\nconst LIGHT_LINKERS: Record<string, ColorTriple> = {\n P: lightTriple('#9aa5e1'),\n p: lightTriple('#9aa5e1'),\n};\n\nconst LIGHT_AAS: Record<string, ColorTriple> = {\n A: lightTriple('#C8C8C8'),\n R: lightTriple('#145AFF'),\n N: lightTriple('#00DCDC'),\n D: lightTriple('#E60A0A'),\n C: lightTriple('#E6E600'),\n E: lightTriple('#00DCDC'),\n Q: lightTriple('#E60A0A'),\n G: lightTriple('#EBEBEB'),\n H: lightTriple('#8282D2'),\n I: lightTriple('#0F820F'),\n L: lightTriple('#0F820F'),\n K: lightTriple('#145AFF'),\n M: lightTriple('#E6E600'),\n F: lightTriple('#3232AA'),\n P: lightTriple('#DC9682'),\n S: lightTriple('#FA9600'),\n T: lightTriple('#FA9600'),\n W: lightTriple('#B45AB4'),\n Y: lightTriple('#3232AA'),\n V: lightTriple('#0F820F'),\n};\n\nconst LIGHT_CHEMS: Record<string, ColorTriple> = {\n R: lightTriple('#eeeeee'),\n};\n\nconst LIGHT_BLOBS: Record<string, ColorTriple> = {\n B: lightTriple('#999999'),\n G: lightTriple('#e2e2e2'),\n};\n\nconst LIGHT_NUCLEOTIDES: Record<string, ColorTriple> = {\n // Pseudo-biotype used for the gap base-pair marker; mirror the linker palette.\n P: lightTriple('#9aa5e1'),\n};\n\n/** Built-in light theme — matches the legacy `MonomerColors.js` palette. */\nexport const lightPalette: ColorTheme = {\n name: 'light',\n fallback: { line: '#202020', text: '#000000', background: '#eeeeee' },\n errorTriple: { line: '#cc0000', text: '#000000', background: '#FFFF00' },\n palette: {\n [HelmTypes.BASE]: LIGHT_BASES,\n [HelmTypes.SUGAR]: LIGHT_SUGARS,\n [HelmTypes.LINKER]: LIGHT_LINKERS,\n [HelmTypes.AA]: LIGHT_AAS,\n [HelmTypes.CHEM]: LIGHT_CHEMS,\n [HelmTypes.BLOB]: LIGHT_BLOBS,\n [HelmTypes.NUCLEOTIDE]: LIGHT_NUCLEOTIDES,\n },\n};\n\n// ---------- Dark theme derivation ----------\n\nfunction darkenMap(src: Record<string, ColorTriple>): Record<string, ColorTriple> {\n const out: Record<string, ColorTriple> = {};\n for (const [k, v] of Object.entries(src))\n out[k] = darkTriple(v.background);\n return out;\n}\n\n/** Dark theme — derived from `lightPalette` by lightening text & darkening fills. */\nexport const darkPalette: ColorTheme = {\n name: 'dark',\n fallback: { line: '#e0e0e0', text: '#ffffff', background: darken('#eeeeee', 0.5) },\n errorTriple: { line: '#ff5050', text: '#ffffff', background: darken('#FFFF00', 0.4) },\n palette: {\n [HelmTypes.BASE]: darkenMap(LIGHT_BASES),\n [HelmTypes.SUGAR]: darkenMap(LIGHT_SUGARS),\n [HelmTypes.LINKER]: darkenMap(LIGHT_LINKERS),\n [HelmTypes.AA]: darkenMap(LIGHT_AAS),\n [HelmTypes.CHEM]: darkenMap(LIGHT_CHEMS),\n [HelmTypes.BLOB]: darkenMap(LIGHT_BLOBS),\n [HelmTypes.NUCLEOTIDE]: darkenMap(LIGHT_NUCLEOTIDES),\n },\n};\n\n// ---------- Public resolution function ----------\n\n/**\n * Resolve the final `MonomerColors` triple for the given (monomer, biotype)\n * pair under the given theme. Follows the order in MONOMER-LIBRARY.md §6.\n *\n * - `monomer === null` paints `theme.errorTriple` (the \"missing monomer\"\n * cue).\n * - `monomer.meta.colors[themeName]` wins over `default`.\n * - `monomer.meta.colors.default` wins over the palette.\n * - Palette lookup is keyed on `biotype` first, then `monomer.naturalAnalog`\n * (case-sensitive — matches the legacy table).\n * - Final fallback is `theme.fallback`.\n *\n * Phase 23 (T-2301) — Outline colour policy. The user reported that the\n * legacy `#202020` black outline on every monomer was visually heavy and\n * asked for the outline to be a slightly darker version of the monomer's\n * fill, falling back to a dark neutral when the fill is white-ish. We\n * implement that by post-processing the resolved triple: the `line`\n * field is ALWAYS replaced by `deriveLineColor(background)`. Palette-\n * supplied `line` fields (the legacy `#202020` defaults) are overridden,\n * and Phase 23.3 (T-2311) extended this to per-monomer `meta.colors.*.line`\n * overrides too — the HELMCoreLibrary ships every monomer with an\n * explicit `meta.colors.default.line: \"#202020\"`, which is the same\n * legacy near-black value Phase 23 was meant to abolish. Respecting it\n * would re-introduce the exact \"outline is still black\" complaint the\n * user filed on 2026-05-18. We treat outline as a derived presentational\n * property, NOT user data; the background and text fields from\n * `meta.colors` are still respected (only the line is derived).\n *\n * Phase 23.2 (T-2310) — Text colour policy. The user reported a similar\n * complaint about the symbol label: the legacy palette always painted\n * the text `#000000` (pure black), which is illegible on dark-saturated\n * backgrounds like Arginine's `#145AFF` royal blue. We mirror the Phase 23\n * outline approach: unless the monomer's `meta.colors` explicitly supplied\n * a `text` field, the `text` is replaced by\n * `bestContrastTextColor(background)` (WCAG 2.1 relative-luminance pick\n * between `'#1f2937'` dark-slate and `'#ffffff'` pure white). The\n * missing-monomer error path keeps its `errorTriple.text` so the\n * \"something is wrong here\" cue stays intact. Unlike the outline path,\n * an explicit `meta.colors.*.text` is still respected — text is treated\n * as content the library author may deliberately want (e.g. a custom\n * branded glyph colour), while outline is treated as a derived chrome\n * property the renderer owns.\n *\n * The returned `MonomerColors` is always fully populated (no undefined\n * fields).\n */\nexport function resolveMonomerColors(\n monomer: Monomer | null,\n biotype: HelmType,\n theme: ColorTheme = lightPalette,\n): MonomerColors {\n if (monomer === null)\n return { ...theme.errorTriple };\n\n const metaColors = monomer.meta?.colors;\n if (metaColors !== undefined) {\n // `themeName === 'light' | 'dark' | custom` — only `light` and `dark`\n // get auto-resolved from the meta block; any other theme name still\n // checks `default` first.\n //\n // Phase 23.3 (T-2311) — the resolved `line` is ALWAYS derived from\n // the background. The HELMCoreLibrary ships every monomer with\n // `meta.colors.default.line: \"#202020\"` (the same legacy near-black\n // value Phase 23 set out to abolish from the palette branch). The\n // earlier Phase-23 code respected explicit meta `line` fields,\n // which re-introduced exactly the \"outline is still black\"\n // complaint the user filed on 2026-05-18 for the ~30% of monomers\n // that carry colour metadata. Treat outline as derived chrome,\n // NOT user data; the background and text fields stay sourced from\n // the meta block.\n const themed =\n theme.name === 'light' ? metaColors.light :\n theme.name === 'dark' ? metaColors.dark :\n undefined;\n if (themed !== undefined)\n return { ...themed, line: deriveLineColor(themed.background) };\n if (metaColors.default !== undefined)\n return { ...metaColors.default, line: deriveLineColor(metaColors.default.background) };\n }\n\n const na = monomer.naturalAnalog;\n if (na !== undefined && na !== '') {\n const perType = theme.palette[biotype];\n if (perType !== undefined) {\n const hit = perType[na];\n if (hit !== undefined)\n // Phase 23 (T-2301): palette `line` is the legacy `#202020`\n // default. The user wants the outline derived from the\n // background; override.\n // Phase 23.2 (T-2310): palette `text` is the legacy `#000000`\n // (or `#ffffff` for dark theme). The user wants the text to\n // contrast with the resolved background; override via WCAG\n // relative-luminance pick.\n return {\n ...hit,\n line: deriveLineColor(hit.background),\n text: bestContrastTextColor(hit.background),\n };\n }\n }\n\n return {\n ...theme.fallback,\n line: deriveLineColor(theme.fallback.background),\n text: bestContrastTextColor(theme.fallback.background),\n };\n}\n","// Case-insensitive resolution of the R-group cap-group SMILES field.\n//\n// HELM monomer JSON appears in the wild with two casings for the same field:\n// `capGroupSMILES` (the Pistoia HELMmonomerSchema spelling) and `capGroupSmiles`\n// (the spelling Datagrok's `bio` library uses). Rather than force either side to\n// rename — which would ripple across the whole platform — we resolve both to the\n// same value on ingestion and normalize to our canonical `capGroupSMILES` field.\n// See MONOMER-LIBRARY.md §1.\n\nimport type { Monomer } from './types';\n\n/**\n * Read an R-group's cap-group SMILES regardless of key casing. Returns the\n * string value of whichever `capgroupsmiles`-cased key is present, or\n * `undefined` when none is.\n *\n * @param rg An R-group-like object (raw JSON or a typed `RGroupSpec`).\n * @returns The cap-group SMILES string, or `undefined` when absent / non-string.\n */\nexport function readCapGroupSMILES(rg: Record<string, unknown>): string | undefined {\n for (const key in rg) {\n if (Object.prototype.hasOwnProperty.call(rg, key) && key.toLowerCase() === 'capgroupsmiles') {\n const v = rg[key];\n if (typeof v === 'string') return v;\n }\n }\n return undefined;\n}\n\n/**\n * Return `monomer` with every R-group's cap-group SMILES normalized onto the\n * canonical `capGroupSMILES` field (reading any-cased input). Pure: returns a\n * shallow copy only when at least one R-group needed normalizing, so the\n * common case (already-canonical input, e.g. hwe's own libraries) is a no-op.\n *\n * @param monomer The monomer to normalize.\n * @returns The same monomer, or a normalized copy when a re-cased field was found.\n */\nexport function normalizeCapGroupSMILES(monomer: Monomer): Monomer {\n let changed = false;\n const rgroups = monomer.rgroups.map((rg) => {\n const resolved = readCapGroupSMILES(rg as unknown as Record<string, unknown>);\n if (resolved !== undefined && rg.capGroupSMILES !== resolved) {\n changed = true;\n return { ...rg, capGroupSMILES: resolved };\n }\n return rg;\n });\n return changed ? { ...monomer, rgroups } : monomer;\n}\n","// Hand-rolled validator for the monomer-library JSON schema. Zero runtime\n// dependencies: walks the tree imperatively and reports every error with a\n// JSON-Pointer-ish path. The schema document is in `./schema.json` and is\n// loaded purely by JSON parsers; this file is the executable equivalent.\n//\n// We deliberately do not pull in ajv: keeps the bundle small and avoids the\n// \"ajv requires Node polyfills\" surprise for browser consumers.\n\nimport type { Monomer, MonomerLibSchema, RGroupSpec } from './types';\nimport { readCapGroupSMILES } from './rgroup-fields';\n\n/** A single schema violation, with a JSON-path-ish locator (`$.0.rgroups[0].label`). */\nexport interface SchemaError {\n /** Path into the original input, starting at `$`. */\n path: string;\n /** Human-readable error message. */\n message: string;\n}\n\nexport type ValidateResult =\n | { ok: true; data: MonomerLibSchema }\n | { ok: false; errors: SchemaError[] };\n\nconst POLYMER_TYPES = new Set(['PEPTIDE', 'RNA', 'CHEM', 'BLOB']);\nconst MONOMER_TYPES = new Set(['Backbone', 'Branch', 'Terminal', 'Undefined']);\nconst RLABEL_RE = /^R[1-9][0-9]*$/;\n\n/**\n * Validate `input` against the monomer-library JSON schema. Returns\n * `{ ok: true, data }` when every entry is a valid `Monomer`, or\n * `{ ok: false, errors }` with one entry per violation. Validation does\n * NOT mutate the input; on success the returned `data` reference is the\n * same object (already correctly typed).\n *\n * Path format mirrors typical JSON-pointer output but uses `$` for the\n * root and dot/bracket access for properties/indices, e.g.\n * `$.0.rgroups[0].label`. Easier to grep than RFC-6901.\n */\nexport function validateMonomerLibSchema(input: unknown): ValidateResult {\n const errors: SchemaError[] = [];\n\n if (!Array.isArray(input)) {\n return {\n ok: false,\n errors: [{ path: '$', message: `Expected a JSON array of monomers, got ${describeType(input)}` }],\n };\n }\n\n for (let i = 0; i < input.length; i++) {\n validateMonomer(input[i], `$.${i}`, errors);\n }\n\n if (errors.length > 0) return { ok: false, errors };\n return { ok: true, data: input as MonomerLibSchema };\n}\n\nfunction validateMonomer(value: unknown, path: string, errors: SchemaError[]): void {\n if (!isPlainObject(value)) {\n errors.push({ path, message: `Expected an object, got ${describeType(value)}` });\n return;\n }\n\n // Required string fields.\n requireString(value, 'symbol', path, errors, { minLength: 1 });\n requireString(value, 'molfile', path, errors);\n\n // polymerType\n const pt = value.polymerType;\n if (pt === undefined) {\n errors.push({ path: `${path}.polymerType`, message: 'Required property missing' });\n } else if (typeof pt !== 'string') {\n errors.push({\n path: `${path}.polymerType`,\n message: `Expected string, got ${describeType(pt)}`,\n });\n } else if (!POLYMER_TYPES.has(pt)) {\n errors.push({\n path: `${path}.polymerType`,\n message: `Expected one of PEPTIDE|RNA|CHEM|BLOB, got '${pt}'`,\n });\n }\n\n // monomerType\n const mt = value.monomerType;\n if (mt === undefined) {\n errors.push({ path: `${path}.monomerType`, message: 'Required property missing' });\n } else if (typeof mt !== 'string') {\n errors.push({\n path: `${path}.monomerType`,\n message: `Expected string, got ${describeType(mt)}`,\n });\n } else if (!MONOMER_TYPES.has(mt)) {\n errors.push({\n path: `${path}.monomerType`,\n message: `Expected one of Backbone|Branch|Terminal|Undefined, got '${mt}'`,\n });\n }\n\n // rgroups\n const rg = value.rgroups;\n if (rg === undefined) {\n errors.push({ path: `${path}.rgroups`, message: 'Required property missing' });\n } else if (!Array.isArray(rg)) {\n errors.push({\n path: `${path}.rgroups`,\n message: `Expected array, got ${describeType(rg)}`,\n });\n } else {\n const seen = new Set<string>();\n for (let i = 0; i < rg.length; i++)\n validateRGroup(rg[i], `${path}.rgroups[${i}]`, errors, seen);\n }\n\n // Optional strings.\n optionalString(value, 'name', path, errors);\n optionalString(value, 'smiles', path, errors);\n optionalString(value, 'naturalAnalog', path, errors);\n optionalString(value, 'author', path, errors);\n\n // createDate is string | null | undefined.\n if ('createDate' in value && value.createDate !== undefined && value.createDate !== null) {\n if (typeof value.createDate !== 'string') {\n errors.push({\n path: `${path}.createDate`,\n message: `Expected string or null, got ${describeType(value.createDate)}`,\n });\n }\n }\n\n // id is integer | string | undefined.\n if ('id' in value && value.id !== undefined) {\n const id = value.id;\n const ok =\n typeof id === 'string' || (typeof id === 'number' && Number.isInteger(id));\n if (!ok) {\n errors.push({\n path: `${path}.id`,\n message: `Expected integer or string, got ${describeType(id)}`,\n });\n }\n }\n\n // meta (optional object); validate colors substructure when present.\n if ('meta' in value && value.meta !== undefined) {\n const meta = value.meta;\n if (!isPlainObject(meta)) {\n errors.push({ path: `${path}.meta`, message: `Expected object, got ${describeType(meta)}` });\n } else if (meta.colors !== undefined) {\n validateColorsBlock(meta.colors, `${path}.meta.colors`, errors);\n }\n }\n}\n\nfunction validateRGroup(\n value: unknown,\n path: string,\n errors: SchemaError[],\n seenLabels: Set<string>,\n): void {\n if (!isPlainObject(value)) {\n errors.push({ path, message: `Expected an object, got ${describeType(value)}` });\n return;\n }\n // label: required, pattern.\n const label = value.label;\n if (label === undefined) {\n errors.push({ path: `${path}.label`, message: 'Required property missing' });\n } else if (typeof label !== 'string') {\n errors.push({ path: `${path}.label`, message: `Expected string, got ${describeType(label)}` });\n } else if (!RLABEL_RE.test(label)) {\n errors.push({\n path: `${path}.label`,\n message: `Expected pattern /^R[1-9][0-9]*$/, got '${label}'`,\n });\n } else if (seenLabels.has(label)) {\n errors.push({ path: `${path}.label`, message: `Duplicate R-group label '${label}'` });\n } else {\n seenLabels.add(label);\n }\n\n requireString(value, 'capGroupName', path, errors);\n // capGroupSMILES — accept either the Pistoia (`capGroupSMILES`) or Datagrok\n // (`capGroupSmiles`) casing; both resolve to the same value (case-insensitive).\n if (readCapGroupSMILES(value) === undefined) {\n const present = Object.keys(value).some((k) => k.toLowerCase() === 'capgroupsmiles');\n errors.push({\n path: `${path}.capGroupSMILES`,\n message: present ? 'Expected string' : 'Required property missing',\n });\n }\n optionalString(value, 'alternateId', path, errors);\n\n // Optional id.\n if ('id' in value && value.id !== undefined) {\n if (typeof value.id !== 'number' || !Number.isInteger(value.id)) {\n errors.push({\n path: `${path}.id`,\n message: `Expected integer, got ${describeType(value.id)}`,\n });\n }\n }\n}\n\nfunction validateColorsBlock(value: unknown, path: string, errors: SchemaError[]): void {\n if (!isPlainObject(value)) {\n errors.push({ path, message: `Expected object, got ${describeType(value)}` });\n return;\n }\n for (const key of ['default', 'light', 'dark'] as const) {\n if (value[key] !== undefined) validateColorTriple(value[key], `${path}.${key}`, errors);\n }\n}\n\nfunction validateColorTriple(value: unknown, path: string, errors: SchemaError[]): void {\n if (!isPlainObject(value)) {\n errors.push({ path, message: `Expected object, got ${describeType(value)}` });\n return;\n }\n for (const key of ['line', 'text', 'background'] as const) {\n if (value[key] === undefined) {\n errors.push({ path: `${path}.${key}`, message: 'Required property missing' });\n } else if (typeof value[key] !== 'string') {\n errors.push({\n path: `${path}.${key}`,\n message: `Expected string, got ${describeType(value[key])}`,\n });\n }\n }\n}\n\n// ---------- helpers ----------\n\nfunction requireString(\n obj: Record<string, unknown>,\n key: string,\n parent: string,\n errors: SchemaError[],\n opts?: { minLength?: number },\n): void {\n const v = obj[key];\n const childPath = `${parent}.${key}`;\n if (v === undefined) {\n errors.push({ path: childPath, message: 'Required property missing' });\n return;\n }\n if (typeof v !== 'string') {\n errors.push({ path: childPath, message: `Expected string, got ${describeType(v)}` });\n return;\n }\n if (opts?.minLength !== undefined && v.length < opts.minLength) {\n errors.push({\n path: childPath,\n message: `Expected string of length >= ${opts.minLength}, got ${v.length}`,\n });\n }\n}\n\nfunction optionalString(\n obj: Record<string, unknown>,\n key: string,\n parent: string,\n errors: SchemaError[],\n): void {\n const v = obj[key];\n if (v === undefined) return;\n if (typeof v !== 'string') {\n errors.push({\n path: `${parent}.${key}`,\n message: `Expected string, got ${describeType(v)}`,\n });\n }\n}\n\nfunction isPlainObject(v: unknown): v is Record<string, unknown> {\n return typeof v === 'object' && v !== null && !Array.isArray(v);\n}\n\nfunction describeType(v: unknown): string {\n if (v === null) return 'null';\n if (Array.isArray(v)) return 'array';\n return typeof v;\n}\n\n// Re-export so consumers have one place to import related types from.\nexport type { Monomer, MonomerLibSchema, RGroupSpec };\n","// Concrete `MonomerLib` class — implements `IMonomerLib`. Indexes monomers by\n// `(polymerType, symbol)` for O(1) lookup, mirrors the index by HELM biotype,\n// and pre-computes `ResolvedMonomer` data attached out-of-band so the public\n// `Monomer` type stays clean. See API.md §5 and MONOMER-LIBRARY.md §3.\n//\n// Layering: this file is monomer-lib only — no core/io/render/etc. imports\n// beyond `HelmTypes` (a constant) and the typed error class (`HwError`).\n//\n// Pistoia HELM Web Editor parity references:\n// - `helm2Type` — Monomers.ts:518 (legacy)\n// - case sensitivity — `kCaseSensitive = true` in `packages/Helm/src/utils/package-utils.ts:255`\n// - inline SMILES `#N` — Monomers.ts:548\n\nimport { HelmTypes, PolymerTypes } from '../core/constants';\nimport type { HelmType, PolymerType } from '../core/constants';\nimport { HwError } from '../core/errors';\nimport { Subject } from '../util/observable';\nimport { resolveMonomerColors, lightPalette, darkPalette } from './color-rules';\nimport type { ColorTheme } from './color-rules';\nimport { detectSmilesRGroups } from './smiles-monomer';\nimport type {\n IMonomerLib,\n Monomer,\n MonomerColors,\n MonomerLibChangeEvent,\n MonomerLibSchema,\n MonomerMeta,\n RGroupSpec,\n ResolvedMonomer,\n} from './types';\nimport {\n validateMonomerLibSchema,\n type SchemaError,\n} from './validate-schema';\nimport { normalizeCapGroupSMILES } from './rgroup-fields';\n\n/** Optional diagnostics sink for `fromJSON` — used to surface skipped entries. */\nexport interface MonomerLibLoadDiagnostics {\n /** Errors reported by the schema validator for skipped entries. */\n skipped: { index: number; errors: SchemaError[] }[];\n}\n\nconst RLABEL_RE = /^R([1-9][0-9]*)$/;\n\n// ---------- biotype mapping (`helm2Type`) ----------\n\n/**\n * Compute the HELM biotype for a monomer record. Mirrors `helm2Type` from\n * the legacy editor (Monomers.ts:518) — the only HELM-specific business\n * rule that lives in the library layer.\n *\n * Rules:\n * - `PEPTIDE` → `HELM_AA`\n * - `CHEM` → `HELM_CHEM`\n * - `BLOB` → `HELM_BLOB`\n * - `RNA` Branch → `HELM_BASE`\n * - `RNA` Backbone + naturalAnalog in {'P','p'} → `HELM_LINKER`\n * - `RNA` Backbone otherwise → `HELM_SUGAR`\n * - anything else → `null` (caller can fall back to a default)\n */\nexport function helm2Type(monomer: Monomer): HelmType | null {\n switch (monomer.polymerType) {\n case PolymerTypes.PEPTIDE:\n return HelmTypes.AA;\n case PolymerTypes.CHEM:\n return HelmTypes.CHEM;\n case PolymerTypes.BLOB:\n return HelmTypes.BLOB;\n case PolymerTypes.RNA: {\n if (monomer.monomerType === 'Branch') return HelmTypes.BASE;\n if (monomer.monomerType === 'Backbone') {\n const na = monomer.naturalAnalog;\n if (na === 'P' || na === 'p') return HelmTypes.LINKER;\n return HelmTypes.SUGAR;\n }\n return null;\n }\n default:\n return null;\n }\n}\n\n// ---------- resolved-monomer construction ----------\n\nfunction buildResolved(m: Monomer): ResolvedMonomer {\n const rgroupMap = new Map<number, RGroupSpec>();\n for (const rg of m.rgroups) {\n const match = RLABEL_RE.exec(rg.label);\n if (match !== null)\n rgroupMap.set(parseInt(match[1] as string, 10), rg);\n }\n return Object.assign({}, m, {\n rs: m.rgroups.length,\n rgroupMap: rgroupMap as ReadonlyMap<number, RGroupSpec>,\n });\n}\n\n// ---------- the class ----------\n\n/**\n * In-process monomer library. Loads JSON in the Pistoia shape, indexes by\n * polymer type / biotype / natural analog, and provides reactive mutations\n * via `onChanged`.\n *\n * Lookups are **case-sensitive** to match `kCaseSensitive = true` in the\n * Datagrok Helm package. `version` starts at `0` and is bumped on every\n * mutation; consumers cache derived values keyed on `${source}@${version}`.\n *\n * The class implements `IMonomerLib`; the `getTooltipDom` method is omitted\n * (it's optional in the interface — DOM construction lives in the editor\n * layer).\n */\nexport class MonomerLib implements IMonomerLib {\n readonly source: string;\n readonly onChanged: Subject<MonomerLibChangeEvent>;\n\n private _version: number = 0;\n private readonly _byPolymerSymbol: Map<PolymerType, Map<string, Monomer>> = new Map();\n private readonly _byBiotypeSymbol: Map<HelmType, Map<string, Monomer>> = new Map();\n private readonly _byNaturalAnalog: Map<PolymerType, Map<string, Monomer[]>> = new Map();\n private readonly _resolved: WeakMap<Monomer, ResolvedMonomer> = new WeakMap();\n private _inlineSmilesCounter: number = 0;\n\n /**\n * Private — use `MonomerLib.fromJSON`, `fromText`, `fromUrl`, or `empty`\n * to construct. Direct construction would force every caller to learn the\n * indexing rules.\n */\n private constructor(source: string) {\n this.source = source;\n this.onChanged = new Subject<MonomerLibChangeEvent>();\n }\n\n // ---------- factories ----------\n\n /** Construct an empty library. */\n static empty(source: string = 'empty'): MonomerLib {\n return new MonomerLib(source);\n }\n\n /**\n * Construct from an already-parsed schema array. Invalid entries are\n * SKIPPED (with a console warning, not thrown) so a corrupt library\n * doesn't poison every editor on the page. If you want strict validation,\n * call `validateMonomerLibSchema` first.\n *\n * @param schema the array of `Monomer` records.\n * @param source identity string used in cache keys (default `'inline'`).\n * @param diagnostics optional sink for the skipped-entry report.\n */\n static fromJSON(\n schema: MonomerLibSchema,\n source: string = 'inline',\n diagnostics?: MonomerLibLoadDiagnostics,\n ): MonomerLib {\n const lib = new MonomerLib(source);\n for (let i = 0; i < schema.length; i++) {\n const entry = schema[i] as Monomer;\n const validation = validateMonomerLibSchema([entry]);\n if (!validation.ok) {\n if (diagnostics !== undefined)\n diagnostics.skipped.push({ index: i, errors: validation.errors });\n else\n console.warn(`MonomerLib.fromJSON: skipping invalid entry at index ${i}`, validation.errors);\n continue;\n }\n lib._addNoFire(entry);\n }\n return lib;\n }\n\n /**\n * Parse JSON text and construct. Validation failures throw `HwError`\n * (`'invalid-monomer-lib'`) because at this stage we have no idea what\n * shape was attempted.\n */\n static fromText(jsonText: string, source: string = 'inline'): MonomerLib {\n let parsed: unknown;\n try {\n parsed = JSON.parse(jsonText);\n } catch (e) {\n const msg = e instanceof Error ? e.message : String(e);\n throw new HwError('invalid-monomer-lib', `MonomerLib.fromText: JSON.parse failed — ${msg}`);\n }\n const validation = validateMonomerLibSchema(parsed);\n if (!validation.ok) {\n throw new HwError(\n 'invalid-monomer-lib',\n `MonomerLib.fromText: schema validation failed (${validation.errors.length} errors)`,\n { errors: validation.errors },\n );\n }\n return MonomerLib.fromJSON(validation.data, source);\n }\n\n /**\n * Load a library over the network. `fetchImpl` defaults to `globalThis.fetch`;\n * in Node 16 (no built-in fetch) the caller must supply one or the function\n * throws.\n */\n static async fromUrl(url: string, fetchImpl?: typeof fetch): Promise<MonomerLib> {\n const f = fetchImpl ?? (globalThis as { fetch?: typeof fetch }).fetch;\n if (f === undefined)\n throw new HwError(\n 'fetch-unavailable',\n 'MonomerLib.fromUrl: no fetch implementation available — pass `fetchImpl` or run in a fetch-capable environment.',\n { url },\n );\n const res = await f(url);\n if (!res.ok)\n throw new HwError(\n 'monomer-lib-fetch-failed',\n `MonomerLib.fromUrl: HTTP ${res.status} fetching ${url}`,\n { url, status: res.status },\n );\n const text = await res.text();\n return MonomerLib.fromText(text, url);\n }\n\n /**\n * Merge any number of libraries into a new `MonomerLib`. Later arguments\n * win on `(polymerType, symbol)` collisions, matching the convention in\n * MONOMER-LIBRARY.md §3.\n */\n static merge(...libs: IMonomerLib[]): MonomerLib {\n const source = libs.map((l) => l.source).join('+') || 'empty';\n const merged = new MonomerLib(source);\n for (const lib of libs) {\n for (const polymerType of lib.getPolymerTypes()) {\n for (const sym of lib.getMonomerSymbolsByType(polymerType)) {\n const m = lib.getMonomer(polymerType, sym);\n if (m !== null) merged._addNoFire(m);\n }\n }\n }\n return merged;\n }\n\n // ---------- identity ----------\n\n get isEmpty(): boolean {\n for (const inner of this._byPolymerSymbol.values())\n if (inner.size > 0) return false;\n return true;\n }\n\n get version(): number {\n return this._version;\n }\n\n // ---------- reads ----------\n\n getMonomer(polymerType: PolymerType, symbol: string): Monomer | null {\n const inner = this._byPolymerSymbol.get(polymerType);\n if (inner === undefined) return null;\n return inner.get(symbol) ?? null;\n }\n\n getMonomerSet(biotype: HelmType): Map<string, Monomer> {\n const inner = this._byBiotypeSymbol.get(biotype);\n // We return a copy so callers can't mutate our index.\n return inner === undefined ? new Map() : new Map(inner);\n }\n\n getMonomerSymbolsByType(polymerType: PolymerType): string[] {\n const inner = this._byPolymerSymbol.get(polymerType);\n return inner === undefined ? [] : Array.from(inner.keys());\n }\n\n getByNaturalAnalog(polymerType: PolymerType, na: string): Monomer[] {\n const outer = this._byNaturalAnalog.get(polymerType);\n if (outer === undefined) return [];\n const arr = outer.get(na);\n return arr === undefined ? [] : arr.slice();\n }\n\n getPolymerTypes(): PolymerType[] {\n const out: PolymerType[] = [];\n for (const [pt, inner] of this._byPolymerSymbol.entries())\n if (inner.size > 0) out.push(pt);\n return out;\n }\n\n /**\n * Resolve the monomer's color triple. `themeName` is `'light'` (default),\n * `'dark'`, or a custom theme name. Unknown theme names fall back to the\n * light palette so colors are always produced.\n */\n getColors(monomer: Monomer | null, themeName?: string): MonomerColors {\n const theme = pickTheme(themeName);\n const biotype = monomer === null\n ? HelmTypes.AA // unused by resolveMonomerColors when monomer===null\n : helm2Type(monomer) ?? HelmTypes.AA;\n return resolveMonomerColors(monomer, biotype, theme);\n }\n\n /** Lookup the precomputed `ResolvedMonomer` for a `Monomer` from this lib. */\n getResolved(monomer: Monomer): ResolvedMonomer | undefined {\n return this._resolved.get(monomer);\n }\n\n // ---------- mutations ----------\n\n /** Register or replace a monomer. Fires `onChanged({ type: 'add'|'update' })`. */\n addMonomer(monomer: Monomer): void {\n const validation = validateMonomerLibSchema([monomer]);\n if (!validation.ok)\n throw new HwError(\n 'invalid-monomer',\n `MonomerLib.addMonomer: schema validation failed`,\n { errors: validation.errors },\n );\n const existed = this._addNoFire(monomer);\n this._bumpVersion();\n this.onChanged.next({\n type: existed ? 'update' : 'add',\n affectedSymbols: [monomer.symbol],\n });\n }\n\n /** Bulk add. Fires a single `onChanged` after all entries are inserted. */\n addMonomers(monomers: Iterable<Monomer>): void {\n const affected: string[] = [];\n let anyExisted = false;\n for (const m of monomers) {\n const existed = this._addNoFire(m);\n if (existed) anyExisted = true;\n affected.push(m.symbol);\n }\n if (affected.length === 0) return;\n this._bumpVersion();\n this.onChanged.next({\n type: anyExisted ? 'update' : 'add',\n affectedSymbols: affected,\n });\n }\n\n /** Remove by identity. Returns true iff a record was removed. */\n removeMonomer(polymerType: PolymerType, symbol: string): boolean {\n const inner = this._byPolymerSymbol.get(polymerType);\n if (inner === undefined) return false;\n const existing = inner.get(symbol);\n if (existing === undefined) return false;\n\n inner.delete(symbol);\n\n const biotype = helm2Type(existing);\n if (biotype !== null) {\n const byBio = this._byBiotypeSymbol.get(biotype);\n if (byBio !== undefined) byBio.delete(symbol);\n }\n\n const na = existing.naturalAnalog;\n if (na !== undefined && na !== '') {\n const naOuter = this._byNaturalAnalog.get(polymerType);\n const arr = naOuter?.get(na);\n if (arr !== undefined) {\n const idx = arr.indexOf(existing);\n if (idx >= 0) arr.splice(idx, 1);\n }\n }\n\n this._bumpVersion();\n this.onChanged.next({ type: 'remove', affectedSymbols: [symbol] });\n return true;\n }\n\n /**\n * Update the `meta.colors` block of an existing monomer. We replace the\n * matched record with a new one whose `meta.colors` is merged with\n * `colors`. Fires `onChanged({ type: 'update' })`.\n */\n setMonomerColors(\n polymerType: PolymerType,\n symbol: string,\n colors: Partial<NonNullable<MonomerMeta['colors']>>,\n ): void {\n const existing = this.getMonomer(polymerType, symbol);\n if (existing === null)\n throw new HwError(\n 'monomer-not-found',\n `MonomerLib.setMonomerColors: ${polymerType}/${symbol} not found`,\n { polymerType, symbol },\n );\n\n const prevMeta: MonomerMeta = existing.meta ?? {};\n const prevColors = prevMeta.colors ?? {};\n const nextMeta: MonomerMeta = Object.assign({}, prevMeta, {\n colors: Object.assign({}, prevColors, colors),\n });\n const updated: Monomer = Object.assign({}, existing, { meta: nextMeta });\n\n this._addNoFire(updated);\n this._bumpVersion();\n this.onChanged.next({ type: 'update', affectedSymbols: [symbol] });\n }\n\n /**\n * Instance-level merge (per `IMonomerLib`): copy every monomer from\n * `other` into this lib; later wins. Fires `onChanged({ type: 'reload' })`\n * because it can touch many records at once.\n */\n merge(other: IMonomerLib): void {\n for (const polymerType of other.getPolymerTypes()) {\n for (const sym of other.getMonomerSymbolsByType(polymerType)) {\n const m = other.getMonomer(polymerType, sym);\n if (m !== null) this._addNoFire(m);\n }\n }\n this._bumpVersion();\n this.onChanged.next({ type: 'reload' });\n }\n\n /**\n * Register an inline-SMILES monomer synthesized from a HELM bracketed\n * payload. Returns the new `Monomer` record so the parser can attach it to\n * the atom that triggered the registration.\n *\n * The synthesized symbol is `#1`, `#2`, … unique within THIS lib. The\n * caller can supply a `symbolHint` (typically the original raw SMILES) for\n * provenance — we ignore it for ID purposes but may surface it via\n * `meta.smilesHint`.\n */\n registerInlineSmilesMonomer(\n polymerType: PolymerType,\n smiles: string,\n options?: { symbolHint?: string },\n ): Monomer {\n const detection = detectSmilesRGroups(smiles);\n if (!detection.ok)\n throw new HwError(\n 'inline-smiles-without-r-groups',\n `MonomerLib.registerInlineSmilesMonomer: ${detection.reason}`,\n { smiles },\n );\n\n this._inlineSmilesCounter += 1;\n const symbol = `#${this._inlineSmilesCounter}`;\n const rgroups: RGroupSpec[] = [];\n // We emit `R1..Rn` in numeric order so the rgroupMap is sensible.\n const numbers = Array.from(detection.info.rgroupPositions.keys()).sort((a, b) => a - b);\n for (const n of numbers) {\n rgroups.push({\n label: `R${n}` as `R${number}`,\n capGroupName: 'H',\n capGroupSMILES: '',\n });\n }\n\n const meta: MonomerMeta | undefined =\n options?.symbolHint !== undefined ? { smilesHint: options.symbolHint } : undefined;\n\n const monomer: Monomer = {\n symbol,\n polymerType,\n monomerType: 'Undefined',\n molfile: '',\n smiles: detection.canonicalSmiles,\n rgroups,\n ...(meta !== undefined ? { meta } : {}),\n };\n\n this._addNoFire(monomer);\n this._bumpVersion();\n this.onChanged.next({ type: 'add', affectedSymbols: [symbol] });\n return monomer;\n }\n\n // ---------- schema ----------\n\n /**\n * Snapshot the library in the on-disk array shape. Order matches insertion\n * order: the per-polymer `Map` insertion order is the canonical iteration\n * order. Duplicates across polymers are preserved verbatim.\n */\n toJSON(): MonomerLibSchema {\n const out: Monomer[] = [];\n for (const inner of this._byPolymerSymbol.values())\n for (const m of inner.values())\n out.push(m);\n return out;\n }\n\n // ---------- internals ----------\n\n /**\n * Insert (or replace) a monomer in every index. Does NOT fire `onChanged`\n * or bump version — caller is responsible. Returns `true` if a previous\n * record was replaced.\n */\n private _addNoFire(monomer: Monomer): boolean {\n // Normalize any-cased capGroupSMILES (e.g. Datagrok's `capGroupSmiles`)\n // onto the canonical field so every stored monomer reads consistently.\n monomer = normalizeCapGroupSMILES(monomer);\n const pt = monomer.polymerType;\n let byPoly = this._byPolymerSymbol.get(pt);\n if (byPoly === undefined) {\n byPoly = new Map();\n this._byPolymerSymbol.set(pt, byPoly);\n }\n const prev = byPoly.get(monomer.symbol);\n byPoly.set(monomer.symbol, monomer);\n\n // Remove the previous record from secondary indices.\n if (prev !== undefined) {\n const prevBio = helm2Type(prev);\n if (prevBio !== null) {\n const byBio = this._byBiotypeSymbol.get(prevBio);\n if (byBio !== undefined) byBio.delete(prev.symbol);\n }\n const prevNa = prev.naturalAnalog;\n if (prevNa !== undefined && prevNa !== '') {\n const byNa = this._byNaturalAnalog.get(pt)?.get(prevNa);\n if (byNa !== undefined) {\n const idx = byNa.indexOf(prev);\n if (idx >= 0) byNa.splice(idx, 1);\n }\n }\n this._resolved.delete(prev);\n }\n\n // Insert in the biotype mirror.\n const bio = helm2Type(monomer);\n if (bio !== null) {\n let byBio = this._byBiotypeSymbol.get(bio);\n if (byBio === undefined) {\n byBio = new Map();\n this._byBiotypeSymbol.set(bio, byBio);\n }\n byBio.set(monomer.symbol, monomer);\n }\n\n // Insert in the natural-analog mirror.\n const na = monomer.naturalAnalog;\n if (na !== undefined && na !== '') {\n let naOuter = this._byNaturalAnalog.get(pt);\n if (naOuter === undefined) {\n naOuter = new Map();\n this._byNaturalAnalog.set(pt, naOuter);\n }\n let arr = naOuter.get(na);\n if (arr === undefined) {\n arr = [];\n naOuter.set(na, arr);\n }\n arr.push(monomer);\n }\n\n this._resolved.set(monomer, buildResolved(monomer));\n return prev !== undefined;\n }\n\n private _bumpVersion(): void {\n this._version += 1;\n }\n}\n\n// ---------- helpers ----------\n\nfunction pickTheme(themeName: string | undefined): ColorTheme {\n if (themeName === 'dark') return darkPalette;\n // 'light', undefined, or any custom name → use lightPalette as the\n // anchor; resolveMonomerColors still honors meta.colors[customName] iff\n // we feed it a theme whose `name` matches. To keep things deterministic\n // here we hand out the canonical lightPalette unless 'dark' is requested.\n return lightPalette;\n}\n","// T-0209 — Monomer resolver. Takes the parser's \"raw\" `Mol` (where every\n// `atom.monomer` is `null`) and binds each atom to a `Monomer` from the\n// supplied `IMonomerLib`. The output is a NEW `Mol` (the input is immutable)\n// with `atom.monomer` set on every atom plus `atom.biotype` refined to match\n// the library's `helm2Type` classification of the resolved record.\n//\n// Algorithm — MONOMER-LIBRARY.md §4:\n// 1. Look up `(polymerType, symbol)` in the lib (case-sensitive).\n// 2. Otherwise: synthesize an \"ambiguous\" placeholder for `?`/`*`/`_`/`X`/`N`\n// or `(...)` alternation symbols, emit info `ambiguous-monomer`.\n// 3. Otherwise: if the symbol looks like SMILES, register an inline-SMILES\n// monomer in the lib and use that.\n// 4. Otherwise (opt-in): legacy case fallback for RNA (`R -> r`, `P -> p`),\n// info `case-mismatch`.\n// 5. Otherwise: synthesize a \"missing\" placeholder, warning `unresolved-\n// monomer`.\n//\n// Layering: this file imports from `core/` and `monomer-lib/` only — strictly\n// downstream of both. No DOM, no console, no `eval`.\n\nimport type { HelmType, PolymerType } from '../core/constants';\nimport type { Atom, Bond, Chain, Mol } from '../core/model';\nimport type { ValidationDiagnostic } from '../core/errors';\nimport { helm2Type } from '../monomer-lib/library';\nimport { looksLikeSmiles } from '../monomer-lib/smiles-monomer';\nimport type {\n IMonomerLib,\n Monomer,\n ResolvedMonomer,\n RGroupSpec,\n} from '../monomer-lib/types';\n\n// --------------------------------------------------------------------------\n// Public surface\n// --------------------------------------------------------------------------\n\n/**\n * Resolver options. `mode` exists for symmetry with the parser but does not\n * change behavior today (we always emit diagnostics; strict callers re-throw\n * the first error via `HelmValidationError`). `legacyCaseFallback` enables\n * the historical RNA fallback (`R` -> `r`, `P` -> `p`) — disabled by default\n * because Datagrok's corpus uses case-distinct symbols (`dV` vs `dv`).\n */\nexport interface ResolveOptions {\n readonly mode?: 'strict' | 'lenient';\n readonly legacyCaseFallback?: boolean;\n}\n\n/**\n * Result returned by `resolveMonomers`. `mol` is the new graph with every\n * `atom.monomer` populated; `diagnostics` is the list of info/warning entries\n * emitted during resolution (the resolver does not surface error severity —\n * unresolved monomers are warnings in lenient mode, leaving recovery to the\n * caller).\n */\nexport interface ResolveResult {\n readonly mol: Mol;\n readonly diagnostics: readonly ValidationDiagnostic[];\n}\n\n/**\n * Bind every atom in `mol` to a `Monomer` from `lib`. The input `mol` is not\n * modified; a new `Mol` is returned with refreshed `atom.monomer` and refined\n * `atom.biotype` fields.\n *\n * Reconstruction is performed via a `Map<oldAtomId, newAtom>` followed by a\n * walk of bonds/chains/groups to rewrite references onto the new atoms.\n *\n * @param mol the raw `Mol` from the parser (atoms have `monomer === null`).\n * @param lib the active `IMonomerLib`. Concrete `MonomerLib` instances\n * gain inline-SMILES registration via duck-typed probing.\n * @param options optional `ResolveOptions`.\n */\nexport function resolveMonomers(mol: Mol, lib: IMonomerLib, options?: ResolveOptions): ResolveResult {\n const ctx = new ResolveCtx(mol, lib, options ?? {});\n return ctx.run();\n}\n\n// --------------------------------------------------------------------------\n// Implementation\n// --------------------------------------------------------------------------\n\nconst AMBIGUITY_SYMBOLS = new Set<string>(['?', '*', '_', 'X', 'N']);\nconst RLABEL_RE = /^R([1-9][0-9]*)$/;\n\ninterface InlineSmilesCapableLib extends IMonomerLib {\n registerInlineSmilesMonomer(\n polymerType: PolymerType,\n smiles: string,\n options?: { symbolHint?: string },\n ): Monomer;\n}\n\nfunction hasRegisterInlineSmiles(lib: IMonomerLib): lib is InlineSmilesCapableLib {\n return typeof (lib as Partial<InlineSmilesCapableLib>).registerInlineSmilesMonomer === 'function';\n}\n\nclass ResolveCtx {\n private readonly mol: Mol;\n private readonly lib: IMonomerLib;\n private readonly options: ResolveOptions;\n private readonly diagnostics: ValidationDiagnostic[] = [];\n private readonly oldToNew: Map<number, Atom> = new Map();\n /** Per-(polymerType, symbol) cache of synthesised placeholders. */\n private readonly placeholderCache: Map<string, Monomer> = new Map();\n\n constructor(mol: Mol, lib: IMonomerLib, options: ResolveOptions) {\n this.mol = mol;\n this.lib = lib;\n this.options = options;\n }\n\n run(): ResolveResult {\n // 1. Determine polymer-type per chain so we can look up each atom by\n // `(polymerType, symbol)`.\n const chainPolymerType = new Map<string, PolymerType>();\n for (const c of this.mol.chains) chainPolymerType.set(c.id, c.polymerType);\n\n // 2. First pass: materialise every atom with a fresh `monomer` field and\n // refined biotype. We defer `branchAtom` patching to a second pass so\n // the references point at the new atoms.\n for (const a of this.mol.atoms) {\n const pt = chainPolymerType.get(a.bio.chainId) ?? null;\n const next = this.resolveAtom(a, pt);\n this.oldToNew.set(a.id, next);\n }\n for (const a of this.mol.atoms) {\n const newAtom = this.oldToNew.get(a.id);\n if (newAtom === undefined || a.branchAtom === undefined) continue;\n const linkedBranch = this.oldToNew.get(a.branchAtom.id);\n if (linkedBranch === undefined) continue;\n // We have to break the readonly contract here once to set the\n // back-reference; the alternative is to allocate every atom twice.\n (newAtom as { branchAtom?: Atom }).branchAtom = linkedBranch;\n }\n\n // 3. Rebuild bonds with new atom references.\n const newBonds: Bond[] = [];\n for (const b of this.mol.bonds) {\n const a1 = this.oldToNew.get(b.a1.id);\n const a2 = this.oldToNew.get(b.a2.id);\n if (a1 === undefined || a2 === undefined) continue;\n newBonds.push({ ...b, a1, a2 });\n }\n\n // 4. Rebuild chains. Each chain's `backboneAtoms` and `bonds` must point at\n // the new atom/bond instances.\n const newBondsById = new Map<number, Bond>();\n for (const b of newBonds) newBondsById.set(b.id, b);\n const newChains: Chain[] = [];\n for (const c of this.mol.chains) {\n const backbone: Atom[] = [];\n for (const a of c.backboneAtoms) {\n const na = this.oldToNew.get(a.id);\n if (na !== undefined) backbone.push(na);\n }\n const bonds: Bond[] = [];\n for (const b of c.bonds) {\n const nb = newBondsById.get(b.id);\n if (nb !== undefined) bonds.push(nb);\n }\n newChains.push({\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: backbone as readonly Atom[],\n bonds: bonds as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n // Phase 33 (T-3301) — Preserve `strandType` through monomer\n // resolution. Without this the field would be silently\n // dropped here and at `layoutMol` (which also rebuilds chains\n // via a shallow merge); downstream consumers reading\n // `chain.strandType` would always see `undefined`.\n ...(c.strandType !== undefined ? { strandType: c.strandType } : {}),\n });\n }\n\n // Groups are atom-id-keyed via `member.target = String(atomId)` for\n // brackets; for connection groups the targets are chain ids. Either way,\n // groups themselves do not hold direct atom references, so we copy them\n // unchanged.\n const newAtoms: Atom[] = this.mol.atoms.map((a) => this.oldToNew.get(a.id) as Atom);\n\n const newMol: Mol = {\n atoms: newAtoms as readonly Atom[],\n bonds: newBonds as readonly Bond[],\n chains: newChains as readonly Chain[],\n groups: this.mol.groups,\n annotations: this.mol.annotations,\n };\n return { mol: newMol, diagnostics: this.diagnostics };\n }\n\n /**\n * Resolve one atom. Returns a new `Atom` with `monomer` set and the biotype\n * refined to match the resolved record. The original atom is never\n * mutated.\n */\n private resolveAtom(atom: Atom, polymerType: PolymerType | null): Atom {\n let resolved: ResolvedMonomer | null = null;\n let nextBiotype = atom.biotype;\n\n if (polymerType !== null) {\n const direct = this.lib.getMonomer(polymerType, atom.symbol);\n if (direct !== null) {\n resolved = this.toResolved(direct);\n nextBiotype = helm2Type(direct) ?? atom.biotype;\n } else if (this.isAmbiguitySymbol(atom)) {\n resolved = this.synthesizeAmbiguity(polymerType, atom);\n this.emit('info', 'ambiguous-monomer',\n `Ambiguous monomer '${atom.symbol}' on chain '${atom.bio.chainId}'`,\n atom,\n );\n } else if (looksLikeSmiles(atom.symbol)) {\n resolved = this.registerInlineSmilesFallback(polymerType, atom);\n } else if (\n this.options.legacyCaseFallback === true &&\n polymerType === 'RNA'\n ) {\n const flipped = this.findCaseInsensitiveMatch(polymerType, atom.symbol);\n if (flipped !== null) {\n resolved = this.toResolved(flipped);\n nextBiotype = helm2Type(flipped) ?? atom.biotype;\n this.emit('info', 'case-mismatch',\n `Symbol '${atom.symbol}' matched library entry '${flipped.symbol}' only after case fold`,\n atom,\n );\n }\n }\n\n if (resolved === null) {\n resolved = this.synthesizeMissing(polymerType, atom);\n this.emit('warning', 'unresolved-monomer',\n `Monomer '${atom.symbol}' not found in library for ${polymerType}`,\n atom,\n );\n }\n }\n\n return {\n ...atom,\n monomer: resolved,\n biotype: nextBiotype,\n };\n }\n\n // -- placeholder factories ----------------------------------------------\n\n private toResolved(m: Monomer): ResolvedMonomer {\n // Try the concrete lib's cached `getResolved` first (MonomerLib).\n const cached = (this.lib as { getResolved?: (m: Monomer) => ResolvedMonomer | undefined }).getResolved?.(m);\n if (cached !== undefined) return cached;\n // Fallback: build one inline (matches MonomerLib.buildResolved).\n const rgroupMap = new Map<number, RGroupSpec>();\n for (const rg of m.rgroups) {\n const mm = RLABEL_RE.exec(rg.label);\n if (mm !== null) rgroupMap.set(parseInt(mm[1] as string, 10), rg);\n }\n return Object.assign({}, m, {\n rs: m.rgroups.length,\n rgroupMap: rgroupMap as ReadonlyMap<number, RGroupSpec>,\n });\n }\n\n private isAmbiguitySymbol(atom: Atom): boolean {\n if (AMBIGUITY_SYMBOLS.has(atom.symbol)) return true;\n if (atom.bio.ambiguity !== undefined) return true;\n return false;\n }\n\n private synthesizeAmbiguity(polymerType: PolymerType, atom: Atom): ResolvedMonomer {\n const cacheKey = `ambig:${polymerType}:${atom.symbol}`;\n let m = this.placeholderCache.get(cacheKey);\n if (m === undefined) {\n m = {\n symbol: atom.symbol,\n polymerType,\n monomerType: 'Undefined',\n molfile: '',\n rgroups: [\n { label: 'R1', capGroupName: 'H', capGroupSMILES: '' },\n { label: 'R2', capGroupName: 'H', capGroupSMILES: '' },\n ],\n meta: { ambiguous: true },\n };\n this.placeholderCache.set(cacheKey, m);\n }\n return this.toResolved(m);\n }\n\n private synthesizeMissing(polymerType: PolymerType, atom: Atom): ResolvedMonomer {\n const cacheKey = `missing:${polymerType}:${atom.symbol}`;\n let m = this.placeholderCache.get(cacheKey);\n if (m === undefined) {\n m = {\n symbol: atom.symbol,\n polymerType,\n monomerType: 'Undefined',\n molfile: '',\n rgroups: [\n { label: 'R1', capGroupName: 'H', capGroupSMILES: '' },\n { label: 'R2', capGroupName: 'H', capGroupSMILES: '' },\n ],\n meta: { missing: true },\n };\n this.placeholderCache.set(cacheKey, m);\n }\n return this.toResolved(m);\n }\n\n private registerInlineSmilesFallback(polymerType: PolymerType, atom: Atom): ResolvedMonomer {\n if (hasRegisterInlineSmiles(this.lib)) {\n try {\n const registered = this.lib.registerInlineSmilesMonomer(polymerType, atom.symbol);\n return this.toResolved(registered);\n } catch {\n this.emit('warning', 'inline-smiles-without-r-groups',\n `Inline SMILES '${truncate(atom.symbol, 40)}' has no detectable R-groups`,\n atom,\n );\n }\n } else {\n this.emit('warning', 'inline-smiles-without-r-groups',\n `Inline SMILES seen but lib has no registerInlineSmilesMonomer`,\n atom,\n );\n }\n return this.synthesizeMissing(polymerType, atom);\n }\n\n private findCaseInsensitiveMatch(polymerType: PolymerType, symbol: string): Monomer | null {\n const lower = symbol.toLowerCase();\n for (const candidate of this.lib.getMonomerSymbolsByType(polymerType)) {\n if (candidate.toLowerCase() === lower && candidate !== symbol) {\n const m = this.lib.getMonomer(polymerType, candidate);\n if (m !== null) return m;\n }\n }\n return null;\n }\n\n // -- diagnostics --------------------------------------------------------\n\n private emit(severity: ValidationDiagnostic['severity'], code: string, message: string, atom: Atom): void {\n const ctx: Record<string, unknown> = { chainId: atom.bio.chainId, atomId: atom.id, symbol: atom.symbol };\n this.diagnostics.push({ severity, code, message, context: ctx });\n }\n}\n\nfunction truncate(s: string, max: number): string {\n return s.length <= max ? s : s.slice(0, max - 1) + '…';\n}\n\n// Re-export `HelmType` so consumers of the resolver can type their callsites\n// without dipping into `../core/constants`.\nexport type { HelmType };\n","// HELM parser (T-0202..T-0208). Consumes a `TokenStream` produced by the\n// lexer and produces a `Mol` plus `ValidationDiagnostic[]`. The resolver\n// (Wave C, T-0209) is responsible for binding atoms to library monomers;\n// here every emitted atom has `monomer: null` and its `biotype` is derived\n// purely from syntactic context (PEPTIDE -> AA, RNA sugar -> SUGAR, etc.).\n//\n// References:\n// - PARSING.md §3 (parser)\n// - SPECIFICATION.md §§1-10 (grammar)\n// - VALIDATION.md §§2.1, 2.2, 2.5, 2.7, 2.8 (diagnostic codes emitted here)\n// - API.md §4 (`ParseResult`)\n//\n// The parser is recursive descent with non-throwing error recovery in\n// lenient mode (errors become diagnostics; the cursor advances past the\n// offending token and we keep going to surface the maximum information\n// about a malformed string). In strict mode, the first error diagnostic is\n// re-thrown as `HelmParseError`.\n//\n// Layering: this file imports from `core/`, `monomer-lib/`, `util/`, and\n// `./lexer`. No DOM, no console, no eval.\n\nimport type { Atom, AtomBio, Bond, BondKind, BondRatio, Chain, Group, GroupKind, GroupMember, Mol, RGroupRef } from '../core/model';\nimport { type AnnotationMap, emptyMol } from '../core/model';\nimport { HelmTypes, type HelmType, PolymerTypes, type PolymerType } from '../core/constants';\nimport { HelmParseError, type ValidationDiagnostic } from '../core/errors';\nimport { IdGenerator } from '../core/ids';\nimport type { IMonomerLib } from '../monomer-lib/types';\nimport { looksLikeSmiles } from '../monomer-lib/smiles-monomer';\nimport { tokenize, type Token, type TokenKind, type TokenSpan, type TokenStream } from './lexer';\nimport { resolveMonomers as _resolveMonomers } from './resolver';\n\n// --------------------------------------------------------------------------\n// Public API\n// --------------------------------------------------------------------------\n\n/**\n * Parsing options. `mode: 'strict'` re-throws the first error-severity\n * diagnostic as a `HelmParseError`; `'lenient'` (default) returns a\n * best-effort `Mol` plus the full diagnostic list.\n *\n * `resolveMonomers` controls the post-parse resolver pass that binds every\n * atom's `symbol` to a `Monomer` from the supplied library. When a `lib` is\n * passed AND `resolveMonomers !== false`, the resolver runs automatically and\n * its diagnostics are appended to the parser's diagnostic list. Set it to\n * `false` to keep `atom.monomer === null` (the resolver runs on demand later).\n *\n * `legacyCaseFallback` is forwarded to the resolver; default `false`. See\n * MONOMER-LIBRARY.md §4.\n */\nexport interface ParseOptions {\n readonly mode?: 'strict' | 'lenient';\n readonly resolveMonomers?: boolean;\n readonly legacyCaseFallback?: boolean;\n}\n\n/**\n * Parse result returned by both entry points. `diagnostics` is always\n * defined (may be empty); `mol` is always defined (may be empty in lenient\n * mode when parsing fails very early).\n */\nexport interface ParseResult {\n readonly mol: Mol;\n readonly diagnostics: readonly ValidationDiagnostic[];\n}\n\n/**\n * Parse a HELM source string. Runs the lexer first, then the parser. Lexer\n * errors become diagnostics in lenient mode (and the function returns an\n * empty `Mol`), or are re-thrown in strict mode.\n */\nexport function parseHelm(\n source: string,\n lib: IMonomerLib | null,\n options?: ParseOptions,\n): ParseResult {\n const mode = options?.mode ?? 'lenient';\n let stream: TokenStream;\n try {\n stream = tokenize(source);\n } catch (e) {\n if (e instanceof HelmParseError) {\n if (mode === 'strict') throw e;\n const diag: ValidationDiagnostic = {\n severity: 'error',\n code: e.code,\n message: e.message,\n ...(e.span !== undefined ? { span: { start: e.span.start, end: e.span.end } } : {}),\n };\n return { mol: emptyMol(), diagnostics: [diag] };\n }\n throw e;\n }\n return parseTokens(stream, lib, options);\n}\n\n/**\n * Parse an already-lexed token stream. Useful for testing and for callers\n * that lex once and parse multiple times against different libraries.\n *\n * If `lib` is non-null and `options.resolveMonomers !== false`, the resolver\n * runs after the parser succeeds; its `diagnostics` are appended to the\n * parser's list and its `mol` (with `atom.monomer` populated) is returned.\n */\nexport function parseTokens(\n stream: TokenStream,\n lib: IMonomerLib | null,\n options?: ParseOptions,\n): ParseResult {\n const parser = new Parser(stream, lib, options?.mode ?? 'lenient');\n const parsed = parser.parseDocument();\n if (lib === null || options?.resolveMonomers === false) return parsed;\n const resolved = _resolveMonomers(parsed.mol, lib, {\n mode: options?.mode ?? 'lenient',\n ...(options?.legacyCaseFallback === true ? { legacyCaseFallback: true } : {}),\n });\n return {\n mol: resolved.mol,\n diagnostics: [...parsed.diagnostics, ...resolved.diagnostics],\n };\n}\n\n// --------------------------------------------------------------------------\n// Internal builder types (mutable; cast to readonly Mol structures on finalize)\n// --------------------------------------------------------------------------\n\ninterface AtomBuilder {\n id: number;\n p: { x: number; y: number };\n biotype: HelmType;\n symbol: string;\n monomer: null;\n bio: AtomBio;\n hidden: boolean;\n selected: boolean;\n highlighted: boolean;\n tag?: string;\n branchAtom?: AtomBuilder;\n inlineSource?: string;\n}\n\ninterface BondBuilder {\n id: number;\n a1: AtomBuilder;\n a2: AtomBuilder;\n kind: BondKind;\n r1: RGroupRef;\n r2: RGroupRef;\n ratio?: BondRatio;\n tag?: string;\n}\n\ninterface ChainBuilder {\n id: string;\n polymerType: PolymerType;\n // The raw token used so we keep a stable display name (e.g. `DNA1` even\n // though we coerce its polymerType to RNA for the model).\n rawTypeName: string;\n rawNumber: number;\n backboneAtoms: AtomBuilder[];\n /** Every atom belonging to this chain, including bases (R3 branches). */\n allAtoms: AtomBuilder[];\n bonds: BondBuilder[];\n annotation?: string;\n span: TokenSpan;\n}\n\ninterface PendingBond {\n chain1: string;\n pos1: PositionRef;\n r1: RGroupRef;\n chain2: string;\n pos2: PositionRef;\n r2: RGroupRef;\n kind: BondKind;\n tag?: string;\n ratio?: BondRatio;\n span: TokenSpan;\n}\n\n/**\n * Position reference inside a connection. `integer` is the 1-based\n * monomer position; `question` is the wildcard `?`; `symbol` is a\n * single-character monomer symbol (e.g. `C` meaning \"first cysteine\").\n * The legacy editor accepts the symbol form for chain-level ambiguity;\n * we accept it and emit an info diagnostic.\n */\ntype PositionRef =\n | { kind: 'index'; value: number }\n | { kind: 'any' }\n | { kind: 'symbol'; value: string };\n\ninterface GroupBuilder {\n id: string;\n kind: GroupKind;\n members: GroupMember[];\n repeat?: { min: number; max: number };\n}\n\n// --------------------------------------------------------------------------\n// Token cursor — forward-only cursor over a TokenStream\n// --------------------------------------------------------------------------\n\n// T-0901 PROFILING NOTES (Phase 9): the parser drives every input through a\n// `TokenCursor` whose `peek()`, `at()`, and `optional()` are the hottest\n// frames in the cold-parse bench. The original `at(...kinds)` used a rest\n// parameter, so every call site allocated a fresh `kinds` array — observed\n// ~2× allocations vs. the actual token count on the peptide-100 cold path.\n//\n// The class below splits `at(...)` into:\n// - `at(kind)` (single arg, the overwhelmingly common case),\n// - `at2(kind1, kind2)` / `at3(kind1, kind2, kind3)` for the multi-kind sites.\n// Every call site is rewritten to use the appropriate variant — no rest-args\n// remain. `peek()` is also rewritten to skip the always-false negative-index\n// branch (the parser never peeks backward) and to elide the `as Token` cast\n// at the boundary (the lexer guarantees the token table is non-empty and\n// terminated by `eof`, so the lookup never returns undefined in practice).\nclass TokenCursor {\n private readonly tokens: readonly Token[];\n private readonly len: number;\n private readonly eof: Token;\n private idx: number;\n\n constructor(stream: TokenStream) {\n this.tokens = stream.tokens;\n this.len = stream.tokens.length;\n // `tokenize()` always emits an `eof` sentinel last; hoist it so out-of-\n // range peeks return the same cached reference without re-reading the\n // tokens array tail.\n this.eof = stream.tokens[stream.tokens.length - 1] as Token;\n this.idx = 0;\n }\n\n /** Returns the token at offset `n` from the current cursor (`0` = current). */\n peek(offset: number = 0): Token {\n const target = this.idx + offset;\n if (target >= this.len) return this.eof;\n return this.tokens[target] as Token;\n }\n\n /** Advance past one token unconditionally. */\n advance(): Token {\n const t = this.idx < this.len ? this.tokens[this.idx] as Token : this.eof;\n if (t.kind !== 'eof') this.idx += 1;\n return t;\n }\n\n /** Consume one token if it matches `kind`, else return null. */\n optional(kind: TokenKind): Token | null {\n const t = this.idx < this.len ? this.tokens[this.idx] as Token : this.eof;\n if (t.kind === kind) {\n if (t.kind !== 'eof') this.idx += 1;\n return t;\n }\n return null;\n }\n\n /** True iff the current token has the given kind. */\n at(kind: TokenKind): boolean {\n const t = this.idx < this.len ? this.tokens[this.idx] as Token : this.eof;\n return t.kind === kind;\n }\n\n /** Two-kind variant of `at` — avoids rest-arg allocation. */\n at2(k1: TokenKind, k2: TokenKind): boolean {\n const t = this.idx < this.len ? this.tokens[this.idx] as Token : this.eof;\n const k = t.kind;\n return k === k1 || k === k2;\n }\n\n /** Three-kind variant of `at` — avoids rest-arg allocation. */\n at3(k1: TokenKind, k2: TokenKind, k3: TokenKind): boolean {\n const t = this.idx < this.len ? this.tokens[this.idx] as Token : this.eof;\n const k = t.kind;\n return k === k1 || k === k2 || k === k3;\n }\n\n /** The half-open span of the current token. */\n currentSpan(): TokenSpan {\n const t = this.idx < this.len ? this.tokens[this.idx] as Token : this.eof;\n return t.span;\n }\n\n /** Cursor index. Used to detect lack-of-progress in error-recovery loops. */\n position(): number {\n return this.idx;\n }\n\n /** Reset cursor to a previously captured index. */\n setPosition(p: number): void {\n this.idx = p;\n }\n\n /** True at the eof token. */\n isAtEnd(): boolean {\n const t = this.idx < this.len ? this.tokens[this.idx] as Token : this.eof;\n return t.kind === 'eof';\n }\n}\n\n// --------------------------------------------------------------------------\n// Polymer-id classification\n// --------------------------------------------------------------------------\n\nconst POLYMER_ID_RE = /^(PEPTIDE|RNA|DNA|CHEM|BLOB|G)([0-9]+)$/;\n\ninterface PolymerIdParts {\n rawTypeName: string;\n polymerType: PolymerType;\n number: number;\n isDnaShim: boolean;\n isGroup: boolean;\n}\n\nfunction classifyPolymerId(raw: string): PolymerIdParts | null {\n const m = POLYMER_ID_RE.exec(raw);\n if (m === null) return null;\n const head = m[1] as string;\n const num = parseInt(m[2] as string, 10);\n switch (head) {\n case 'PEPTIDE': return { rawTypeName: 'PEPTIDE', polymerType: PolymerTypes.PEPTIDE, number: num, isDnaShim: false, isGroup: false };\n case 'RNA': return { rawTypeName: 'RNA', polymerType: PolymerTypes.RNA, number: num, isDnaShim: false, isGroup: false };\n case 'DNA': return { rawTypeName: 'DNA', polymerType: PolymerTypes.RNA, number: num, isDnaShim: true, isGroup: false };\n case 'CHEM': return { rawTypeName: 'CHEM', polymerType: PolymerTypes.CHEM, number: num, isDnaShim: false, isGroup: false };\n case 'BLOB': return { rawTypeName: 'BLOB', polymerType: PolymerTypes.BLOB, number: num, isDnaShim: false, isGroup: false };\n case 'G': return { rawTypeName: 'G', polymerType: PolymerTypes.PEPTIDE, number: num, isDnaShim: false, isGroup: true };\n default: return null;\n }\n}\n\n// --------------------------------------------------------------------------\n// Parser class\n// --------------------------------------------------------------------------\n\nclass Parser {\n private readonly cursor: TokenCursor;\n private readonly source: string;\n private readonly lib: IMonomerLib | null;\n private readonly mode: 'strict' | 'lenient';\n private readonly diagnostics: ValidationDiagnostic[] = [];\n private readonly chains: ChainBuilder[] = [];\n private readonly chainById: Map<string, ChainBuilder> = new Map();\n private readonly pendingBonds: PendingBond[] = [];\n private readonly groups: GroupBuilder[] = [];\n private readonly atomIds: IdGenerator = new IdGenerator();\n private readonly bondIds: IdGenerator = new IdGenerator();\n private annotations: AnnotationMap;\n\n constructor(stream: TokenStream, lib: IMonomerLib | null, mode: 'strict' | 'lenient') {\n this.cursor = new TokenCursor(stream);\n this.source = stream.source;\n this.lib = lib;\n this.mode = mode;\n this.annotations = { perPolymer: new Map(), version: '' };\n }\n\n // ---- Top-level dispatch ------------------------------------------------\n\n parseDocument(): ParseResult {\n if (this.cursor.isAtEnd()) {\n // Empty source -> empty mol with a single warning.\n this.emit('warning', 'empty-helm', 'Empty HELM string');\n return { mol: emptyMol(), diagnostics: this.diagnostics };\n }\n\n this.parseSimplePolymers();\n this.expectDollarSeparator(1);\n this.parseConnections();\n this.expectDollarSeparator(2);\n this.parseGroupsSection();\n this.expectDollarSeparator(3);\n this.parseAnnotationsSection();\n\n // Optional `$V2.0` trailer.\n if (this.cursor.at('dollar')) {\n this.cursor.advance();\n this.parseVersionTrailer();\n }\n\n // Any remaining tokens are extras.\n if (!this.cursor.isAtEnd()) {\n this.emit('warning', 'extra-section-separator',\n `Unexpected trailing tokens after HELM document`,\n this.cursor.currentSpan(),\n );\n // Consume the rest to avoid hanging the test runner.\n while (!this.cursor.isAtEnd()) this.cursor.advance();\n }\n\n return { mol: this.finalize(), diagnostics: this.diagnostics };\n }\n\n /**\n * Expect a `$` separator between top-level sections. `ordinal` is the\n * 1-based section boundary (1 between sections 1-2 etc.). We emit\n * `missing-section-separator` when absent (lenient: continue, strict:\n * throw).\n */\n private expectDollarSeparator(ordinal: number): void {\n if (this.cursor.at('dollar')) {\n this.cursor.advance();\n return;\n }\n this.emit('error', 'missing-section-separator',\n `Expected '$' separator before section ${ordinal + 1}`,\n this.cursor.currentSpan(),\n );\n }\n\n // ---- Section 1: simple polymers ---------------------------------------\n\n private parseSimplePolymers(): void {\n if (this.cursor.at('dollar') || this.cursor.isAtEnd()) return;\n this.parsePolymer();\n while (this.cursor.at('pipe')) {\n this.cursor.advance();\n if (this.cursor.at('dollar') || this.cursor.isAtEnd()) {\n this.emit('warning', 'empty-polymer-body',\n `Empty polymer after '|'`, this.cursor.currentSpan());\n return;\n }\n this.parsePolymer();\n }\n }\n\n /** Parse one `<polymer-id>{<body>}` plus optional annotation. */\n private parsePolymer(): void {\n const startSpan = this.cursor.currentSpan();\n const idTok = this.cursor.optional('identifier');\n if (idTok === null) {\n this.emit('error', 'unexpected-token',\n `Expected polymer id, got '${this.cursor.peek().value}'`,\n this.cursor.currentSpan(),\n );\n // Skip until next pipe / dollar so we don't loop forever.\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n const parts = classifyPolymerId(idTok.value);\n if (parts === null) {\n this.emit('error', 'unknown-polymer-type',\n `Unknown polymer type '${idTok.value}'`,\n idTok.span,\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n\n // Detect duplicate ids and emit warning, but still register the polymer\n // (last writer wins on the lookup map for connection resolution).\n if (this.chainById.has(idTok.value)) {\n this.emit('warning', 'duplicate-polymer-id',\n `Duplicate polymer id '${idTok.value}'`,\n idTok.span,\n );\n }\n\n if (this.cursor.optional('lbrace') === null) {\n this.emit('error', 'unexpected-token',\n `Expected '{' after polymer id '${idTok.value}'`,\n this.cursor.currentSpan(),\n );\n return;\n }\n\n const chain: ChainBuilder = {\n id: idTok.value,\n polymerType: parts.polymerType,\n rawTypeName: parts.rawTypeName,\n rawNumber: parts.number,\n backboneAtoms: [],\n allAtoms: [],\n bonds: [],\n span: { start: startSpan.start, end: startSpan.end },\n };\n this.chains.push(chain);\n this.chainById.set(chain.id, chain);\n\n // Empty body is allowed (`PEPTIDE1{}`) but we warn on it.\n if (this.cursor.at('rbrace')) {\n this.emit('warning', 'empty-polymer-body',\n `Empty body for polymer '${chain.id}'`,\n this.cursor.currentSpan(),\n );\n } else {\n // Dispatch by polymer-type.\n if (parts.isGroup) {\n this.parseGroupBody(chain);\n } else {\n switch (parts.polymerType) {\n case PolymerTypes.PEPTIDE:\n this.parsePeptideBody(chain);\n break;\n case PolymerTypes.RNA:\n this.parseRnaBody(chain, parts.isDnaShim);\n if (parts.isDnaShim)\n this.emit('info', 'dna-emitted-as-rna',\n `DNA polymer '${chain.id}' will be emitted as RNA on canonicalize`,\n idTok.span,\n );\n break;\n case PolymerTypes.CHEM:\n this.parseChemBody(chain);\n break;\n case PolymerTypes.BLOB:\n this.parseBlobBody(chain);\n break;\n default:\n // Unreachable — classifyPolymerId returns one of the above.\n break;\n }\n }\n }\n\n if (this.cursor.optional('rbrace') === null) {\n this.emit('error', 'unterminated-brace',\n `Expected '}' to close polymer '${chain.id}'`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n\n // Optional polymer-level annotation.\n const ann = this.cursor.optional('quote-string');\n if (ann !== null) chain.annotation = ann.value;\n }\n\n // ---- Peptide body parsing (T-0203) ------------------------------------\n\n private parsePeptideBody(chain: ChainBuilder): void {\n this.parsePeptideItem(chain);\n while (this.cursor.at('dot')) {\n this.cursor.advance();\n if (this.cursor.at('rbrace') || this.cursor.at('gt')) break;\n this.parsePeptideItem(chain);\n }\n if (this.cursor.at('gt')) {\n const span = this.cursor.currentSpan();\n this.cursor.advance();\n this.emit('warning', 'peptide-cyclic-without-closure',\n `Peptide '${chain.id}' marked cyclic with '>' — no explicit closure connection emitted`,\n span,\n );\n }\n }\n\n /**\n * Parse one peptide item: a single amino acid, a bracketed alternation,\n * optionally followed by a repeat bracket and/or an annotation. Builds\n * the corresponding atom, links it to the previous atom via R2->R1 if\n * applicable.\n */\n private parsePeptideItem(chain: ChainBuilder): void {\n if (this.cursor.at('lparen')) {\n this.parsePeptideAlternation(chain);\n } else {\n const atom = this.parsePeptideAtom(chain);\n this.maybeRepeatBracket(chain, [atom]);\n }\n // Maybe attach annotation to the most recently emitted atom on the\n // chain. We do this *after* repeat bracket parsing so repeat doesn't\n // swallow the annotation.\n this.maybeAttachAnnotation(chain);\n }\n\n private parsePeptideAtom(chain: ChainBuilder): AtomBuilder {\n const consumed = this.consumeMonomerSymbol(false);\n const { symbol, annotation, ambiguity, ambiguityKind, isInlineSmiles, rawPayload, inlineSource, span } = consumed;\n const atom = this.makeAtom(chain, HelmTypes.AA, symbol);\n if (annotation !== undefined) atom.tag = annotation;\n if (ambiguity !== undefined) atom.bio.ambiguity = ambiguity;\n if (ambiguityKind !== undefined) atom.bio.ambiguityKind = ambiguityKind;\n if (inlineSource !== undefined) atom.inlineSource = inlineSource;\n if (isInlineSmiles) this.registerInlineSmiles(rawPayload, span, PolymerTypes.PEPTIDE);\n this.addToChain(chain, atom, /*isBackbone*/ true);\n // R2 -> R1 backbone bond from the previous backbone atom.\n const prev = chain.backboneAtoms[chain.backboneAtoms.length - 2];\n if (prev !== undefined) this.addBond(chain, prev, atom, 'backbone', { kind: 'numeric', r: 2 }, { kind: 'numeric', r: 1 });\n return atom;\n }\n\n private parsePeptideAlternation(chain: ChainBuilder): void {\n const startSpan = this.cursor.currentSpan();\n this.cursor.advance(); // consume '('\n // Two flavors of parenthesised content:\n // - dot-separated sub-sequence: (A.C.D)'3' -> expand inline, wrap in\n // a bracket group for the repeat range.\n // - alternation / mixture: (A,G,C) / (A+B+C) -> emit ONE atom with\n // `bio.ambiguity` and `bio.ambiguityKind` set.\n if (this.peptideContentIsSubsequence()) {\n const startIdx = chain.backboneAtoms.length;\n // Parse like a regular peptide body until we hit `)`.\n this.parsePeptideItem(chain);\n while (this.cursor.at('dot')) {\n this.cursor.advance();\n if (this.cursor.at('rparen') || this.cursor.isAtEnd()) break;\n this.parsePeptideItem(chain);\n }\n if (this.cursor.optional('rparen') === null) {\n this.emit('error', 'unterminated-paren',\n `Expected ')' to close repeat sub-sequence`,\n this.cursor.currentSpan(),\n );\n }\n const atoms = chain.backboneAtoms.slice(startIdx);\n this.maybeRepeatBracket(chain, atoms);\n this.maybeAttachAnnotation(chain);\n return;\n }\n\n const candidates: { symbol: string; ratio?: number | '?' }[] = [];\n let separator: 'or' | 'and' | null = null;\n while (!this.cursor.at('rparen') && !this.cursor.isAtEnd()) {\n const item = this.parseAlternationCandidate(PolymerTypes.PEPTIDE);\n candidates.push(item);\n if (this.cursor.at('comma')) {\n if (separator === 'and')\n this.emit('warning', 'mixed-separator-in-alternation',\n `Mixed ',' and '+' separators in alternation`,\n this.cursor.currentSpan(),\n );\n separator = 'or';\n this.cursor.advance();\n } else if (this.cursor.at('plus')) {\n if (separator === 'or')\n this.emit('warning', 'mixed-separator-in-alternation',\n `Mixed ',' and '+' separators in alternation`,\n this.cursor.currentSpan(),\n );\n separator = 'and';\n this.cursor.advance();\n } else {\n break;\n }\n }\n if (this.cursor.optional('rparen') === null) {\n this.emit('error', 'unterminated-paren',\n `Expected ')' to close alternation`,\n this.cursor.currentSpan(),\n );\n }\n // Build the synthetic atom.\n const sep = separator === 'and' ? '+' : ',';\n const raw = `(${candidates.map((c) => c.symbol + (c.ratio !== undefined ? `:${String(c.ratio)}` : '')).join(sep)})`;\n const atom = this.makeAtom(chain, HelmTypes.AA, '?');\n atom.bio.ambiguity = raw;\n atom.bio.ambiguityKind = separator === 'and' ? 'and' : 'or';\n this.addToChain(chain, atom, /*isBackbone*/ true);\n const prev = chain.backboneAtoms[chain.backboneAtoms.length - 2];\n if (prev !== undefined) this.addBond(chain, prev, atom, 'backbone', { kind: 'numeric', r: 2 }, { kind: 'numeric', r: 1 });\n\n // Validate negative AND ratios.\n if (separator === 'and') {\n for (const c of candidates) {\n if (typeof c.ratio === 'number' && c.ratio < 0)\n this.emit('error', 'ratio-and-negative',\n `Negative ratio ${c.ratio} in AND mixture`,\n startSpan,\n );\n }\n }\n\n this.maybeRepeatBracket(chain, [atom]);\n this.maybeAttachAnnotation(chain);\n }\n\n /**\n * Peek ahead to decide whether `(...)` is a peptide sub-sequence (uses\n * `.` separators) or a flat alternation/mixture (`,` or `+`).\n */\n private peptideContentIsSubsequence(): boolean {\n let depth = 1;\n let i = 0;\n while (true) {\n const t = this.cursor.peek(i);\n if (t.kind === 'eof') return false;\n if (t.kind === 'lparen') { depth += 1; i += 1; continue; }\n if (t.kind === 'rparen') {\n depth -= 1;\n // No alternation-only token at depth 1 was seen — treat as a\n // single-item sub-sequence. This makes `(A)'n'` round-trip cleanly:\n // it parses as one atom A with a repeat bracket, rather than as a\n // degenerate alternation-of-1 (which would emit `((A))` on\n // re-serialize via `bio.ambiguity = '(A)'`).\n if (depth === 0) return true;\n i += 1;\n continue;\n }\n if (depth === 1) {\n if (t.kind === 'dot') return true;\n // A `:`/`,`/`+` at depth 1 means the body is an alternation/ratio.\n if (t.kind === 'comma' || t.kind === 'plus' || t.kind === 'colon') return false;\n }\n i += 1;\n if (i > 1024) return false;\n }\n }\n\n private parseAlternationCandidate(polymerType: PolymerType): { symbol: string; ratio?: number | '?' } {\n const { symbol, isInlineSmiles, rawPayload, span } = this.consumeMonomerSymbol(true);\n if (isInlineSmiles) this.registerInlineSmiles(rawPayload, span, polymerType);\n let ratio: number | '?' | undefined;\n if (this.cursor.optional('colon') !== null) {\n const t = this.cursor.peek();\n if (t.kind === 'integer' || t.kind === 'decimal') {\n this.cursor.advance();\n ratio = parseFloat(t.value);\n } else if (t.kind === 'question') {\n this.cursor.advance();\n ratio = '?';\n } else {\n this.emit('error', 'unexpected-token',\n `Expected ratio after ':' in alternation`,\n t.span,\n );\n }\n }\n return ratio === undefined ? { symbol } : { symbol, ratio };\n }\n\n // ---- RNA / DNA body parsing (T-0204) ----------------------------------\n\n private parseRnaBody(chain: ChainBuilder, isDna: boolean): void {\n this.parseRnaItem(chain, isDna);\n while (this.cursor.at('dot')) {\n this.cursor.advance();\n if (this.cursor.at('rbrace') || this.cursor.at('dollar') || this.cursor.isAtEnd()) break;\n this.parseRnaItem(chain, isDna);\n }\n }\n\n private parseRnaItem(chain: ChainBuilder, isDna: boolean): void {\n if (this.cursor.at('lparen')) {\n this.parseRnaAlternation(chain, isDna);\n return;\n }\n // Standalone `*` -> pseudo-nucleotide.\n if (this.cursor.at('asterisk')) {\n const span = this.cursor.currentSpan();\n this.cursor.advance();\n const atom = this.makeAtom(chain, HelmTypes.NUCLEOTIDE, '*');\n this.addToChain(chain, atom, /*isBackbone*/ true);\n // R2->R1 backbone bond if not the first item.\n const prev = chain.backboneAtoms[chain.backboneAtoms.length - 2];\n if (prev !== undefined) this.addBond(chain, prev, atom, 'backbone', { kind: 'numeric', r: 2 }, { kind: 'numeric', r: 1 });\n this.maybeRepeatBracket(chain, [atom]);\n this.maybeAttachAnnotation(chain);\n void span;\n return;\n }\n\n // sugar ( '(' base ')' )? linker?\n const sugar = this.parseRnaSugar(chain, isDna);\n // Annotation between sugar and base: `R\"mut\"(U)P`.\n this.maybeAttachAnnotation(chain);\n\n let base: AtomBuilder | undefined;\n if (this.cursor.at('lparen')) {\n this.cursor.advance();\n if (!this.cursor.at('rparen')) {\n base = this.parseRnaBaseSymbol(chain);\n // Annotation on the base.\n this.maybeAttachAnnotationTo(base);\n }\n if (this.cursor.optional('rparen') === null) {\n this.emit('error', 'unterminated-paren',\n `Expected ')' after RNA base`, this.cursor.currentSpan());\n }\n if (base !== undefined) {\n // R3 (sugar) -> R1 (base) branch bond.\n this.addBond(chain, sugar, base, 'branch', { kind: 'numeric', r: 3 }, { kind: 'numeric', r: 1 });\n sugar.branchAtom = base;\n }\n }\n\n let linker: AtomBuilder | undefined;\n if (this.canStartRnaLinker()) {\n linker = this.parseRnaLinker(chain);\n // Annotation on linker.\n this.maybeAttachAnnotationTo(linker);\n }\n\n // R2 (sugar) -> R1 (linker) backbone bond.\n if (linker !== undefined)\n this.addBond(chain, sugar, linker, 'backbone', { kind: 'numeric', r: 2 }, { kind: 'numeric', r: 1 });\n\n // Backbone-bond from the previous backbone atom to this sugar.\n const idxOfSugar = chain.backboneAtoms.indexOf(sugar);\n if (idxOfSugar > 0) {\n const prev = chain.backboneAtoms[idxOfSugar - 1] as AtomBuilder;\n // If the previous backbone tail is a linker, link its R2 -> sugar R1.\n this.addBond(chain, prev, sugar, 'backbone', { kind: 'numeric', r: 2 }, { kind: 'numeric', r: 1 });\n }\n\n const repeatAtoms: AtomBuilder[] = [sugar];\n if (base !== undefined) repeatAtoms.push(base);\n if (linker !== undefined) repeatAtoms.push(linker);\n this.maybeRepeatBracket(chain, repeatAtoms);\n }\n\n private canStartRnaLinker(): boolean {\n const k = this.cursor.peek().kind;\n return (\n k === 'identifier' ||\n k === 'inline-smiles' ||\n k === 'asterisk'\n );\n }\n\n private parseRnaSugar(chain: ChainBuilder, _isDna: boolean): AtomBuilder {\n const { symbol, isInlineSmiles, rawPayload, inlineSource, span } = this.consumeMonomerSymbol(false);\n const atom = this.makeAtom(chain, HelmTypes.SUGAR, symbol);\n if (inlineSource !== undefined) atom.inlineSource = inlineSource;\n if (isInlineSmiles) this.registerInlineSmiles(rawPayload, span, PolymerTypes.RNA);\n this.addToChain(chain, atom, /*isBackbone*/ true);\n return atom;\n }\n\n private parseRnaBaseSymbol(chain: ChainBuilder): AtomBuilder {\n const { symbol, isInlineSmiles, rawPayload, inlineSource, span } = this.consumeMonomerSymbol(false);\n const atom = this.makeAtom(chain, HelmTypes.BASE, symbol);\n if (inlineSource !== undefined) atom.inlineSource = inlineSource;\n if (isInlineSmiles) this.registerInlineSmiles(rawPayload, span, PolymerTypes.RNA);\n this.addToChain(chain, atom, /*isBackbone*/ false);\n return atom;\n }\n\n private parseRnaLinker(chain: ChainBuilder): AtomBuilder {\n // Standalone `*` linker -> pseudo-nucleotide marker.\n if (this.cursor.at('asterisk')) {\n const span = this.cursor.currentSpan();\n this.cursor.advance();\n const atom = this.makeAtom(chain, HelmTypes.LINKER, '*');\n this.addToChain(chain, atom, /*isBackbone*/ true);\n void span;\n return atom;\n }\n const { symbol, isInlineSmiles, rawPayload, inlineSource, span } = this.consumeMonomerSymbol(false);\n const atom = this.makeAtom(chain, HelmTypes.LINKER, symbol);\n if (inlineSource !== undefined) atom.inlineSource = inlineSource;\n if (isInlineSmiles) this.registerInlineSmiles(rawPayload, span, PolymerTypes.RNA);\n this.addToChain(chain, atom, /*isBackbone*/ true);\n return atom;\n }\n\n private parseRnaAlternation(chain: ChainBuilder, _isDna: boolean): void {\n // `(R(A)P. R(C)P. ...)'n-m'` or `(A,G,C)'2'`. We treat the inner as a\n // sub-sequence of full nucleotides if the body looks like one (contains a\n // dot or a paren); otherwise as a simple alternation. To keep things\n // simple here, we expand the inner sub-sequence into the current chain\n // and wrap the resulting atoms in a bracket group.\n const startIdx = chain.backboneAtoms.length;\n this.cursor.advance(); // consume '('\n // Probe the contents: if the very first token after `(` is an alternation\n // candidate (identifier without `(...)` body), treat as a flat AA-style\n // alternation; otherwise parse as RNA sub-sequence.\n if (this.looksLikeFlatAlternation()) {\n const candidates: { symbol: string; ratio?: number | '?' }[] = [];\n let separator: 'or' | 'and' | null = null;\n while (!this.cursor.at('rparen') && !this.cursor.isAtEnd()) {\n candidates.push(this.parseAlternationCandidate(PolymerTypes.RNA));\n if (this.cursor.at('comma')) { separator = 'or'; this.cursor.advance(); }\n else if (this.cursor.at('plus')) { separator = 'and'; this.cursor.advance(); }\n else break;\n }\n if (this.cursor.optional('rparen') === null)\n this.emit('error', 'unterminated-paren', `Expected ')' in RNA alternation`, this.cursor.currentSpan());\n const sep = separator === 'and' ? '+' : ',';\n const raw = `(${candidates.map((c) => c.symbol + (c.ratio !== undefined ? `:${String(c.ratio)}` : '')).join(sep)})`;\n const atom = this.makeAtom(chain, HelmTypes.BASE, '?');\n atom.bio.ambiguity = raw;\n atom.bio.ambiguityKind = separator === 'and' ? 'and' : 'or';\n this.addToChain(chain, atom, /*isBackbone*/ true);\n const prev = chain.backboneAtoms[chain.backboneAtoms.length - 2];\n if (prev !== undefined)\n this.addBond(chain, prev, atom, 'backbone', { kind: 'numeric', r: 2 }, { kind: 'numeric', r: 1 });\n this.maybeRepeatBracket(chain, [atom]);\n this.maybeAttachAnnotation(chain);\n return;\n }\n // RNA sub-sequence: parse inner items with the existing logic.\n this.parseRnaItem(chain, _isDna);\n while (this.cursor.at('dot')) {\n this.cursor.advance();\n if (this.cursor.at('rparen') || this.cursor.isAtEnd()) break;\n this.parseRnaItem(chain, _isDna);\n }\n if (this.cursor.optional('rparen') === null)\n this.emit('error', 'unterminated-paren', `Expected ')' in RNA repeat`, this.cursor.currentSpan());\n const repeatAtoms = chain.backboneAtoms.slice(startIdx);\n this.maybeRepeatBracket(chain, repeatAtoms);\n this.maybeAttachAnnotation(chain);\n }\n\n /**\n * Heuristic: peek into the parenthesised group to decide between flat\n * alternation `(A,G,C)` and an RNA sub-sequence `(R(A)P.R(G)P)`. A flat\n * alternation contains `,` or `+` at depth 1; never contains `(` or `.`.\n * A single-item paren `(X)` with no separator is treated as a\n * sub-sequence so `(X)'n'` round-trips through serialize→reparse without\n * accumulating extra paren layers.\n */\n private looksLikeFlatAlternation(): boolean {\n let depth = 1;\n let i = 0;\n let sawSeparator = false;\n while (true) {\n const t = this.cursor.peek(i);\n if (t.kind === 'eof') return sawSeparator;\n if (t.kind === 'rparen') {\n depth -= 1;\n if (depth === 0) return sawSeparator;\n } else if (t.kind === 'lparen') {\n return false;\n } else if (t.kind === 'dot') {\n return false;\n } else if (depth === 1 && (t.kind === 'comma' || t.kind === 'plus')) {\n sawSeparator = true;\n }\n i += 1;\n if (i > 256) return sawSeparator; // bail out on absurdly long groups\n }\n }\n\n // ---- CHEM / BLOB / G body parsing (T-0205) ----------------------------\n\n private parseChemBody(chain: ChainBuilder): void {\n let atom: AtomBuilder;\n if (this.cursor.at('asterisk')) {\n this.cursor.advance();\n atom = this.makeAtom(chain, HelmTypes.CHEM, '*');\n this.addToChain(chain, atom, /*isBackbone*/ true);\n } else {\n const { symbol, isInlineSmiles, rawPayload, inlineSource, span } = this.consumeMonomerSymbol(false);\n atom = this.makeAtom(chain, HelmTypes.CHEM, symbol);\n if (inlineSource !== undefined) atom.inlineSource = inlineSource;\n if (isInlineSmiles) this.registerInlineSmiles(rawPayload, span, PolymerTypes.CHEM);\n this.addToChain(chain, atom, /*isBackbone*/ true);\n }\n this.maybeAttachAnnotation(chain);\n // CHEM polymers cannot repeat — flag the apostrophe explicitly so the\n // diagnostic is `repeat-on-non-iterable-polymer` rather than the more\n // generic chem-multiple-monomers (which fires on additional monomers).\n if (this.cursor.at('apos')) {\n this.maybeRepeatBracket(chain, [atom]);\n }\n // After the chem atom there must be no more atoms (CHEM length == 1).\n if (!this.cursor.at('rbrace')) {\n this.emit('error', 'chem-multiple-monomers',\n `CHEM polymer '${chain.id}' must contain exactly one monomer`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['rbrace', 'eof']);\n }\n }\n\n private parseBlobBody(chain: ChainBuilder): void {\n let symbol: string;\n let blobtype: string;\n let isInlineSmiles = false;\n let rawPayload = '';\n let inlineSource: string | undefined;\n let span = this.cursor.currentSpan();\n if (this.cursor.at('inline-smiles')) {\n const t = this.cursor.advance();\n isInlineSmiles = looksLikeSmiles(t.value);\n rawPayload = t.value;\n symbol = t.value;\n blobtype = t.value;\n inlineSource = t.value;\n span = t.span;\n } else if (this.cursor.at('identifier')) {\n const t = this.cursor.advance();\n symbol = t.value;\n blobtype = t.value;\n span = t.span;\n } else {\n this.emit('error', 'unknown-blobtype',\n `Expected BLOB identifier`,\n this.cursor.currentSpan(),\n );\n // Try to recover.\n symbol = '?';\n blobtype = '?';\n }\n const atom = this.makeAtom(chain, HelmTypes.BLOB, symbol);\n atom.bio.blobtype = blobtype;\n if (inlineSource !== undefined) atom.inlineSource = inlineSource;\n if (isInlineSmiles) this.registerInlineSmiles(rawPayload, span, PolymerTypes.BLOB);\n this.addToChain(chain, atom, /*isBackbone*/ true);\n this.maybeAttachAnnotation(chain);\n }\n\n /** HELM 2.0 G-polymer bodies are empty; we accept whatever is inside. */\n private parseGroupBody(chain: ChainBuilder): void {\n // Drain until rbrace. Anything inside is legacy HELM 1.0 group body and\n // is ignored (membership lives in section 3).\n let depth = 0;\n while (true) {\n const t = this.cursor.peek();\n if (t.kind === 'eof') break;\n if (depth === 0 && t.kind === 'rbrace') break;\n if (t.kind === 'lbrace') depth += 1;\n if (t.kind === 'rbrace') depth -= 1;\n this.cursor.advance();\n }\n void chain;\n }\n\n // ---- Section 2: connections (T-0206) ----------------------------------\n\n private parseConnections(): void {\n if (this.cursor.at('dollar') || this.cursor.isAtEnd()) return;\n this.parseConnection();\n while (this.cursor.at('pipe')) {\n this.cursor.advance();\n if (this.cursor.at('dollar') || this.cursor.isAtEnd()) break;\n this.parseConnection();\n }\n }\n\n private parseConnection(): void {\n const startSpan = this.cursor.currentSpan();\n const id1 = this.cursor.optional('identifier');\n if (id1 === null) {\n this.emit('error', 'unexpected-token',\n `Expected chain id in connection`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n if (this.cursor.optional('comma') === null) {\n this.emit('error', 'unexpected-token',\n `Expected ',' in connection`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n const id2 = this.cursor.optional('identifier');\n if (id2 === null) {\n this.emit('error', 'unexpected-token',\n `Expected second chain id in connection`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n if (this.cursor.optional('comma') === null) {\n this.emit('error', 'unexpected-token',\n `Expected ',' before connection position`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n const pos1 = this.parsePosition();\n if (this.cursor.optional('colon') === null) {\n this.emit('error', 'unexpected-token',\n `Expected ':' between position and R-group`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n const r1 = this.parseRGroupSpec();\n if (this.cursor.optional('dash') === null) {\n this.emit('error', 'unexpected-token',\n `Expected '-' between connection endpoints`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n const pos2 = this.parsePosition();\n if (this.cursor.optional('colon') === null) {\n this.emit('error', 'unexpected-token',\n `Expected ':' before second R-group`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n const r2 = this.parseRGroupSpec();\n const annTok = this.cursor.optional('quote-string');\n const kind: BondKind = r1.kind === 'pair' && r2.kind === 'pair' ? 'hbond' : 'cross-polymer';\n const pending: PendingBond = {\n chain1: id1.value,\n pos1,\n r1,\n chain2: id2.value,\n pos2,\n r2,\n kind,\n span: { start: startSpan.start, end: annTok?.span.end ?? this.cursor.peek().span.start },\n ...(annTok !== null ? { tag: annTok.value } : {}),\n };\n this.pendingBonds.push(pending);\n }\n\n private parsePosition(): PositionRef {\n const t = this.cursor.peek();\n if (t.kind === 'integer') {\n this.cursor.advance();\n return { kind: 'index', value: parseInt(t.value, 10) };\n }\n if (t.kind === 'question') {\n this.cursor.advance();\n return { kind: 'any' };\n }\n if (t.kind === 'identifier') {\n this.cursor.advance();\n this.emit('info', 'symbol-position-reference',\n `Connection position uses monomer symbol '${t.value}' as chain-level ambiguity`,\n t.span,\n );\n return { kind: 'symbol', value: t.value };\n }\n this.emit('error', 'invalid-position',\n `Expected position (integer, '?', or symbol), got '${t.value}'`,\n t.span,\n );\n return { kind: 'any' };\n }\n\n /**\n * Parse an R-group specifier in a connection: `R<n>`, `?`, `*`, or the\n * literal `pair`. Lexer-wise these are: identifier `Rn`, question,\n * asterisk, identifier `pair`.\n */\n private parseRGroupSpec(): RGroupRef {\n const t = this.cursor.peek();\n if (t.kind === 'question') {\n this.cursor.advance();\n return { kind: 'unspecified' };\n }\n if (t.kind === 'asterisk') {\n this.cursor.advance();\n return { kind: 'wildcard' };\n }\n if (t.kind === 'identifier') {\n this.cursor.advance();\n if (t.value === 'pair') return { kind: 'pair' };\n const m = /^R([1-9][0-9]*)$/.exec(t.value);\n if (m === null) {\n this.emit('error', 'invalid-rgroup',\n `Expected R-group label, got '${t.value}'`,\n t.span,\n );\n return { kind: 'unspecified' };\n }\n return { kind: 'numeric', r: parseInt(m[1] as string, 10) };\n }\n this.emit('error', 'invalid-rgroup',\n `Expected R-group label, got '${t.value}'`,\n t.span,\n );\n return { kind: 'unspecified' };\n }\n\n // ---- Section 3: groups + bond ratios (T-0207) -------------------------\n\n private parseGroupsSection(): void {\n if (this.cursor.at('dollar') || this.cursor.isAtEnd()) return;\n this.parseGroupOrBondRatio();\n while (this.cursor.at('pipe')) {\n this.cursor.advance();\n if (this.cursor.at('dollar') || this.cursor.isAtEnd()) break;\n this.parseGroupOrBondRatio();\n }\n }\n\n private parseGroupOrBondRatio(): void {\n const id = this.cursor.optional('identifier');\n if (id === null) {\n this.emit('error', 'unexpected-token',\n `Expected group or bond-ratio identifier`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n // If next token is `(`, it's a group; else assume bond-ratio.\n if (this.cursor.at('lparen')) {\n this.parseGroupAfterId(id);\n } else if (this.cursor.at('plus')) {\n this.parseBondRatioAfterId(id);\n } else {\n this.emit('warning', 'unexpected-token',\n `Expected '(' or '+' after id '${id.value}' in section 3`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n }\n }\n\n private parseGroupAfterId(idTok: Token): void {\n // idTok looks like `G1`, `G2`, etc.\n const parts = classifyPolymerId(idTok.value);\n if (parts === null || !parts.isGroup) {\n this.emit('error', 'unknown-group-reference',\n `Group id must be 'G<n>', got '${idTok.value}'`,\n idTok.span,\n );\n }\n this.cursor.advance(); // consume '('\n const members: GroupMember[] = [];\n let kind: GroupKind = 'or';\n let sawSeparator: 'and' | 'or' | null = null;\n while (!this.cursor.at('rparen') && !this.cursor.isAtEnd()) {\n const m = this.parseGroupMember();\n if (m !== null) members.push(m);\n if (this.cursor.at('comma')) {\n if (sawSeparator === null) { sawSeparator = 'or'; kind = 'or'; }\n this.cursor.advance();\n } else if (this.cursor.at('plus')) {\n if (sawSeparator === null) { sawSeparator = 'and'; kind = 'and'; }\n this.cursor.advance();\n } else {\n break;\n }\n }\n if (this.cursor.optional('rparen') === null) {\n this.emit('error', 'unterminated-paren',\n `Expected ')' to close group`,\n this.cursor.currentSpan(),\n );\n }\n this.groups.push({ id: idTok.value, kind, members });\n }\n\n private parseGroupMember(): GroupMember | null {\n const id = this.cursor.optional('identifier');\n if (id === null) {\n this.emit('error', 'unexpected-token',\n `Expected group member id`, this.cursor.currentSpan());\n return null;\n }\n let ratio: number | '?' | undefined;\n if (this.cursor.optional('colon') !== null) {\n ratio = this.parseRatio();\n }\n return ratio === undefined ? { target: id.value } : { target: id.value, ratio };\n }\n\n /**\n * Parse a ratio value following `:`. Accepts integer, decimal, `?`, or\n * an integer-range `n-m` (the legacy editor uses this for positional\n * sub-ranges like `PEPTIDE1:20-34`; we capture the start as the ratio\n * and emit an info diagnostic).\n */\n private parseRatio(): number | '?' {\n const t = this.cursor.peek();\n if (t.kind === 'integer' || t.kind === 'decimal') {\n this.cursor.advance();\n const v = parseFloat(t.value);\n // Tolerate `n-m` range (legacy form).\n if (this.cursor.at('dash')) {\n const dashTok = this.cursor.peek();\n if (this.cursor.peek(1).kind === 'integer') {\n this.cursor.advance(); // consume dash\n const hi = this.cursor.advance();\n this.emit('info', 'ratio-range',\n `Ratio range ${t.value}-${hi.value}; using lower bound`,\n { start: t.span.start, end: hi.span.end },\n );\n void dashTok;\n }\n }\n return v;\n }\n if (t.kind === 'question') {\n this.cursor.advance();\n return '?';\n }\n this.emit('error', 'unexpected-token',\n `Expected ratio after ':', got '${t.value}'`,\n t.span,\n );\n return 0;\n }\n\n private parseBondRatioAfterId(id1: Token): void {\n // Already consumed id1; next is '+'.\n this.cursor.advance(); // consume '+'\n const id2 = this.cursor.optional('identifier');\n if (id2 === null) {\n this.emit('error', 'unexpected-token',\n `Expected second chain id in bond-ratio`,\n this.cursor.currentSpan(),\n );\n return;\n }\n let ratio: number | undefined;\n if (this.cursor.optional('colon') !== null) {\n const r = this.parseRatio();\n if (typeof r === 'number') ratio = r;\n }\n // Find the matching pending bond and attach the ratio.\n const match = this.pendingBonds.find((b) =>\n (b.chain1 === id1.value && b.chain2 === id2.value) ||\n (b.chain1 === id2.value && b.chain2 === id1.value),\n );\n if (match === undefined) {\n this.emit('warning', 'bond-ratio-no-matching-bond',\n `Bond-ratio for ${id1.value}+${id2.value} has no matching cross-polymer bond`,\n id1.span,\n );\n return;\n }\n if (ratio !== undefined) match.ratio = { numerator: ratio };\n }\n\n // ---- Section 4: annotations (T-0208) ----------------------------------\n\n private parseAnnotationsSection(): void {\n if (this.cursor.at('dollar') || this.cursor.isAtEnd()) return;\n const startIdx = this.cursor.position();\n // If the first token is `{`, treat as HELM 2.0 JSON.\n if (this.cursor.at('lbrace')) {\n this.parseAnnotation20();\n // If a `|` follows, we may have mixed HELM 1.0 + 2.0; emit info.\n if (this.cursor.at('pipe')) {\n this.emit('info', 'annotation-mixed-versions',\n `Mixed HELM 2.0 JSON and HELM 1.0 pipe annotations`,\n this.cursor.currentSpan(),\n );\n this.cursor.advance();\n this.parseAnnotation10Entries();\n }\n return;\n }\n // Otherwise HELM 1.0 pipe form.\n this.parseAnnotation10Entries();\n void startIdx;\n }\n\n /**\n * Parse a HELM 2.0 JSON annotation block. We slice the raw source\n * between the opening `{` and its matching close-brace and feed the\n * result to `JSON.parse`. We never use `eval` or `new Function`.\n */\n private parseAnnotation20(): void {\n const startSpan = this.cursor.currentSpan();\n // Find the matching close-brace by depth tracking on tokens.\n let depth = 0;\n let endSpanEnd = startSpan.end;\n while (!this.cursor.isAtEnd()) {\n const t = this.cursor.peek();\n if (t.kind === 'lbrace') depth += 1;\n else if (t.kind === 'rbrace') {\n depth -= 1;\n if (depth === 0) { endSpanEnd = t.span.end; this.cursor.advance(); break; }\n }\n this.cursor.advance();\n }\n const block = this.source.slice(startSpan.start, endSpanEnd);\n let parsed: unknown = null;\n try {\n parsed = JSON.parse(block);\n } catch {\n this.emit('warning', 'annotation-malformed-json',\n `Annotation block is not valid JSON`,\n { start: startSpan.start, end: endSpanEnd },\n );\n this.annotations = { perPolymer: this.annotations.perPolymer, version: this.annotations.version, raw: block };\n return;\n }\n if (parsed !== null && typeof parsed === 'object' && !Array.isArray(parsed)) {\n const map = new Map<string, Readonly<Record<string, unknown>>>(this.annotations.perPolymer);\n for (const [k, v] of Object.entries(parsed)) {\n if (v !== null && typeof v === 'object' && !Array.isArray(v)) {\n map.set(k, { ...(v as Record<string, unknown>) });\n if (!this.chainById.has(k))\n this.emit('warning', 'annotation-unknown-polymer',\n `Annotation references unknown polymer '${k}'`,\n startSpan,\n );\n } else {\n map.set(k, { value: v });\n }\n }\n this.annotations = { perPolymer: map, version: this.annotations.version };\n } else {\n this.emit('warning', 'annotation-malformed-json',\n `Annotation block parsed but is not an object`,\n { start: startSpan.start, end: endSpanEnd },\n );\n this.annotations = { perPolymer: this.annotations.perPolymer, version: this.annotations.version, raw: block };\n }\n }\n\n private parseAnnotation10Entries(): void {\n this.parseAnnotation10One();\n while (this.cursor.at('pipe')) {\n this.cursor.advance();\n if (this.cursor.at('dollar') || this.cursor.isAtEnd()) break;\n this.parseAnnotation10One();\n }\n }\n\n private parseAnnotation10One(): void {\n const id = this.cursor.optional('identifier');\n if (id === null) {\n this.emit('warning', 'annotation-malformed-json',\n `Expected polymer-id in HELM 1.0 annotation`,\n this.cursor.currentSpan(),\n );\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n if (this.cursor.optional('lbrace') === null) {\n this.emit('warning', 'annotation-malformed-json',\n `Expected '{' after polymer-id`, this.cursor.currentSpan());\n this.skipUntil(['pipe', 'dollar', 'eof']);\n return;\n }\n // Collect the key tokens until `}`.\n const parts: string[] = [];\n while (!this.cursor.at('rbrace') && !this.cursor.isAtEnd()) {\n parts.push(this.cursor.advance().value);\n }\n if (this.cursor.optional('rbrace') === null) {\n this.emit('error', 'unterminated-brace',\n `Expected '}' to close annotation`, this.cursor.currentSpan());\n return;\n }\n const key = parts.join('').trim();\n const map = new Map<string, Readonly<Record<string, unknown>>>(this.annotations.perPolymer);\n const existing = map.get(id.value) ?? {};\n if (key === 'ss' || key === 'as')\n map.set(id.value, { ...existing, strandtype: key });\n else\n map.set(id.value, { ...existing, [key]: true });\n if (!this.chainById.has(id.value))\n this.emit('warning', 'annotation-unknown-polymer',\n `Annotation references unknown polymer '${id.value}'`,\n id.span,\n );\n this.annotations = { perPolymer: map, version: this.annotations.version };\n }\n\n private parseVersionTrailer(): void {\n // Accept `V<int>.<int>` or any identifier+dot+int.\n const id = this.cursor.optional('identifier');\n if (id === null) {\n this.annotations = { ...this.annotations, version: '' };\n return;\n }\n let version = id.value;\n if (this.cursor.at('dot') && this.cursor.peek(1).kind === 'integer') {\n this.cursor.advance(); // dot\n const i = this.cursor.advance(); // integer\n version = `${id.value}.${i.value}`;\n }\n this.annotations = { ...this.annotations, version };\n }\n\n // ---- Common token helpers ---------------------------------------------\n\n /**\n * Skip tokens until one of the given terminators is the current token.\n * `eof` should always be included so the loop terminates.\n */\n private skipUntil(terminators: TokenKind[]): void {\n while (!this.cursor.isAtEnd()) {\n if (terminators.includes(this.cursor.peek().kind)) return;\n this.cursor.advance();\n }\n }\n\n /**\n * Consume one monomer-symbol token: either a bracketed payload\n * (`[meI]`, `[SMILES]`) or a single identifier / asterisk / underscore /\n * question. Returns the canonical symbol (e.g. `meI`) and flags. The\n * caller decides what biotype to assign.\n *\n * `inAlternation` adjusts error recovery: inside an alternation list we\n * stop on `,`/`+`/`)` rather than consuming them.\n */\n private consumeMonomerSymbol(_inAlternation: boolean): {\n symbol: string;\n annotation?: string;\n ambiguity?: string;\n ambiguityKind?: 'or' | 'and';\n isInlineSmiles: boolean;\n rawPayload: string;\n inlineSource?: string;\n span: TokenSpan;\n } {\n const t = this.cursor.peek();\n if (t.kind === 'inline-smiles') {\n this.cursor.advance();\n const sm = looksLikeSmiles(t.value);\n return { symbol: t.value, isInlineSmiles: sm, rawPayload: t.value, inlineSource: t.value, span: t.span };\n }\n if (t.kind === 'identifier') {\n this.cursor.advance();\n // Some legacy corpora carry bare hyphenated monomer symbols whose\n // lexical shape collides with the connection grammar:\n //\n // `D-2Pal` — `identifier=D dash integer=2 identifier=Pal`\n // `Oic_3aS-7aS` — `identifier=Oic_3aS dash integer=7 identifier=aS`\n //\n // The lexer is intentionally conservative (it stops identifiers at\n // `-<digit>` so `pair-9:pair` lexes as three tokens for the connection\n // parser). Here, inside a polymer body, we know the next token cannot\n // be a connection separator, so we glue `<id> dash integer <id>` back\n // together when it looks like a single bare symbol. We do NOT consume\n // a trailing `dash` that is followed by a non-identifier (that would\n // overrun into the next item).\n let symbol = t.value;\n let endSpan = t.span;\n while (\n this.cursor.peek().kind === 'dash'\n && this.cursor.peek(1).kind === 'integer'\n && (this.cursor.peek(2).kind === 'identifier' || this.cursor.peek(2).kind === 'dash')\n ) {\n const dashTok = this.cursor.advance();\n const intTok = this.cursor.advance();\n symbol = `${symbol}-${intTok.value}`;\n endSpan = intTok.span;\n if (this.cursor.peek().kind === 'identifier') {\n const idTok = this.cursor.advance();\n symbol = `${symbol}${idTok.value}`;\n endSpan = idTok.span;\n }\n void dashTok;\n }\n return { symbol, isInlineSmiles: false, rawPayload: symbol, span: { start: t.span.start, end: endSpan.end } };\n }\n if (t.kind === 'asterisk' || t.kind === 'underscore' || t.kind === 'question') {\n this.cursor.advance();\n return { symbol: t.value, isInlineSmiles: false, rawPayload: t.value, span: t.span };\n }\n // An integer at the start of a monomer symbol (`4Abz` etc.) is a corpus\n // authoring quirk — the spec says identifiers start with a letter — but\n // we accept it conservatively when followed by an identifier so legacy\n // strings keep round-tripping.\n if (t.kind === 'integer' && this.cursor.peek(1).kind === 'identifier') {\n const intTok = this.cursor.advance();\n const idTok = this.cursor.advance();\n const symbol = `${intTok.value}${idTok.value}`;\n return { symbol, isInlineSmiles: false, rawPayload: symbol, span: { start: intTok.span.start, end: idTok.span.end } };\n }\n this.emit('error', 'unexpected-token',\n `Expected monomer symbol, got '${t.value}'`,\n t.span,\n );\n return { symbol: '?', isInlineSmiles: false, rawPayload: '', span: t.span };\n }\n\n private maybeRepeatBracket(chain: ChainBuilder, atoms: AtomBuilder[]): void {\n if (!this.cursor.at('apos')) return;\n const startSpan = this.cursor.currentSpan();\n this.cursor.advance(); // first apos\n const loT = this.cursor.optional('integer');\n if (loT === null) {\n this.emit('error', 'unexpected-token',\n `Expected integer in repeat bracket`,\n this.cursor.currentSpan(),\n );\n this.cursor.optional('apos');\n return;\n }\n let min = parseInt(loT.value, 10);\n let max = min;\n if (this.cursor.at('dash')) {\n this.cursor.advance();\n const hiT = this.cursor.optional('integer');\n if (hiT === null) {\n this.emit('error', 'unexpected-token',\n `Expected integer after '-' in repeat bracket`,\n this.cursor.currentSpan(),\n );\n } else {\n max = parseInt(hiT.value, 10);\n }\n }\n if (this.cursor.optional('apos') === null) {\n this.emit('error', 'unterminated-apostrophe',\n `Expected closing apostrophe`,\n this.cursor.currentSpan(),\n );\n }\n if (atoms.length === 0) {\n this.emit('warning', 'repeat-on-empty-bracket',\n `Repeat bracket applied to empty content`,\n startSpan,\n );\n return;\n }\n if (max < min) {\n this.emit('warning', 'repeat-range-inverted',\n `Repeat range ${min}-${max} has max < min; swapping`,\n startSpan,\n );\n const t = min; min = max; max = t;\n }\n if (min === 0 && max === 0) {\n this.emit('warning', 'repeat-zero-count',\n `Repeat bracket with zero count`,\n startSpan,\n );\n return;\n }\n if (max > 10000) {\n this.emit('warning', 'bracket-repeat-too-large',\n `Repeat range upper bound ${max} > 10000`,\n startSpan,\n );\n }\n // CHEM polymers cannot repeat.\n if (chain.polymerType === PolymerTypes.CHEM) {\n this.emit('error', 'repeat-on-non-iterable-polymer',\n `Repeat bracket not allowed on CHEM polymer '${chain.id}'`,\n startSpan,\n );\n }\n this.groups.push({\n id: `${chain.id}/bracket@${atoms[0]?.id ?? 0}`,\n kind: 'bracket',\n members: atoms.map((a) => ({ target: String(a.id) })),\n repeat: { min, max },\n });\n }\n\n /**\n * If the next token is a quote string, attach it as the `tag`/annotation\n * of the most-recently-emitted backbone atom on `chain`.\n */\n private maybeAttachAnnotation(chain: ChainBuilder): void {\n const last = chain.backboneAtoms[chain.backboneAtoms.length - 1];\n if (last === undefined) return;\n this.maybeAttachAnnotationTo(last);\n }\n\n private maybeAttachAnnotationTo(atom: AtomBuilder | undefined): void {\n if (atom === undefined) return;\n const ann = this.cursor.optional('quote-string');\n if (ann === null) return;\n atom.tag = ann.value;\n }\n\n private registerInlineSmiles(payload: string, span: TokenSpan, polymerType: PolymerType): void {\n if (!looksLikeSmiles(payload)) return;\n if (this.lib === null) {\n this.emit('info', 'inline-smiles-no-lib',\n `Inline SMILES seen but no monomer library available for registration`,\n span,\n );\n return;\n }\n try {\n this.lib.addMonomer; // touch to keep tree-shaking honest\n // Use registerInlineSmilesMonomer when available — this is on the\n // concrete `MonomerLib` class, not `IMonomerLib`. Probe defensively.\n const reg = (this.lib as { registerInlineSmilesMonomer?: (pt: PolymerType, s: string) => unknown }).registerInlineSmilesMonomer;\n if (typeof reg === 'function') reg.call(this.lib, polymerType, payload);\n } catch (e) {\n const msg = e instanceof Error ? e.message : String(e);\n this.emit('warning', 'inline-smiles-without-r-groups',\n `Inline SMILES registration failed: ${msg}`,\n span,\n );\n }\n }\n\n // ---- Atom / chain helpers ---------------------------------------------\n\n private makeAtom(chain: ChainBuilder, biotype: HelmType, symbol: string): AtomBuilder {\n const id = this.atomIds.next();\n return {\n id,\n p: { x: 0, y: 0 },\n biotype,\n symbol,\n monomer: null,\n bio: {\n chainId: chain.id,\n positionInChain: 0, // filled by addToChain\n continuousId: 0, // filled by finalize\n },\n hidden: false,\n selected: false,\n highlighted: false,\n };\n }\n\n private addToChain(chain: ChainBuilder, atom: AtomBuilder, isBackbone: boolean): void {\n chain.allAtoms.push(atom);\n if (isBackbone) {\n chain.backboneAtoms.push(atom);\n atom.bio.positionInChain = chain.backboneAtoms.length;\n }\n }\n\n private addBond(chain: ChainBuilder, a1: AtomBuilder, a2: AtomBuilder, kind: BondKind, r1: RGroupRef, r2: RGroupRef): void {\n const id = this.bondIds.next();\n chain.bonds.push({ id, a1, a2, kind, r1, r2 });\n }\n\n // ---- Finalize ---------------------------------------------------------\n\n private finalize(): Mol {\n // 1. Resolve pending cross-polymer bonds.\n const xBonds: BondBuilder[] = [];\n for (const pb of this.pendingBonds) {\n const c1 = this.chainById.get(pb.chain1);\n const c2 = this.chainById.get(pb.chain2);\n if (c1 === undefined) {\n this.emit('error', 'unknown-chain-reference',\n `Connection references unknown chain '${pb.chain1}'`,\n pb.span,\n );\n continue;\n }\n if (c2 === undefined) {\n this.emit('error', 'unknown-chain-reference',\n `Connection references unknown chain '${pb.chain2}'`,\n pb.span,\n );\n continue;\n }\n let a1 = this.resolveAtomByPosition(c1, pb.pos1, pb.span);\n let a2 = this.resolveAtomByPosition(c2, pb.pos2, pb.span);\n if (a1 === null || a2 === null) continue;\n // Phase 34 (T-3401) — HELM 2.0 semantics: when a connection\n // uses `:pair-:pair` R-group references, the bond represents\n // a hydrogen bond between the BASES of the named monomers\n // (the H-bond between complementary Watson-Crick bases), NOT\n // between the sugar backbones that bear those bases. When a\n // resolved endpoint is a sugar with an attached base, route\n // the bond to the base atom so downstream consumers\n // (renderer hbond stroke, cloverleaf algorithm, antiparallel\n // duplex placement, golden SVGs) see the bond on the\n // biologically correct atoms.\n //\n // Round-trip: the serializer's `emitConnection` falls back to\n // the owning-sugar's position when a bond endpoint is a base\n // atom (atoms whose `bio.positionInChain === 0` are looked\n // up via the chain's `bases[]` parallel array). See\n // serializer.ts.\n if (pb.r1.kind === 'pair' && a1.branchAtom !== undefined)\n a1 = a1.branchAtom;\n if (pb.r2.kind === 'pair' && a2.branchAtom !== undefined)\n a2 = a2.branchAtom;\n const id = this.bondIds.next();\n const bond: BondBuilder = {\n id, a1, a2, kind: pb.kind, r1: pb.r1, r2: pb.r2,\n ...(pb.tag !== undefined ? { tag: pb.tag } : {}),\n ...(pb.ratio !== undefined ? { ratio: pb.ratio } : {}),\n };\n xBonds.push(bond);\n }\n\n // 2. Assemble final chain list and gather all atoms / bonds.\n //\n // Phase 33 (T-3301) — Resolve `strandType` from the section-3\n // annotation map so it becomes a first-class field on `Chain`.\n // Layout reads `chain.strandType` directly; the previous\n // \"stuff `5'ss` into the 5'-sugar's annotation\" hack is gone.\n const allAtoms: AtomBuilder[] = [];\n const allBonds: BondBuilder[] = [];\n const finalChains: Chain[] = [];\n for (const chain of this.chains) {\n for (const a of chain.allAtoms) allAtoms.push(a);\n for (const b of chain.bonds) allBonds.push(b);\n const polyAnn = this.annotations.perPolymer.get(chain.id);\n const rawStrand = polyAnn === undefined ? undefined : (polyAnn as { strandtype?: unknown }).strandtype;\n const strandType: 'ss' | 'as' | undefined =\n rawStrand === 'ss' || rawStrand === 'as' ? rawStrand : undefined;\n finalChains.push({\n id: chain.id,\n polymerType: chain.polymerType,\n backboneAtoms: chain.backboneAtoms as readonly Atom[],\n bonds: chain.bonds as readonly Bond[],\n ...(chain.annotation !== undefined ? { annotation: chain.annotation } : {}),\n ...(strandType !== undefined ? { strandType } : {}),\n });\n }\n for (const b of xBonds) allBonds.push(b);\n\n // 3. Assign continuous-id walking chains in source order.\n let counter = 0;\n for (const chain of this.chains) {\n for (const a of chain.backboneAtoms) {\n counter += 1;\n a.bio.continuousId = counter;\n if (a.branchAtom !== undefined) {\n counter += 1;\n a.branchAtom.bio.continuousId = counter;\n }\n }\n }\n\n // Phase 33 (T-3301) — `strandtype` is now resolved into\n // `chain.strandType` at step 2 above; the legacy\n // \"stuff `5'ss` into the 5'-sugar's atom annotation\" path is\n // removed. Layout + renderer read the structured field directly,\n // so the atom-annotation channel stays available for genuine\n // per-atom labels (e.g. `5'` prime-end markers themselves).\n\n // 5. Collect groups (filter out brackets for the `groups` field; brackets\n // are still stored so the serializer can find them).\n const finalGroups: Group[] = [];\n for (const g of this.groups) {\n finalGroups.push({\n id: g.id,\n kind: g.kind,\n members: g.members as readonly GroupMember[],\n ...(g.repeat !== undefined ? { repeat: g.repeat } : {}),\n });\n }\n\n return {\n atoms: allAtoms as readonly Atom[],\n bonds: allBonds as readonly Bond[],\n chains: finalChains as readonly Chain[],\n groups: finalGroups as readonly Group[],\n annotations: this.annotations,\n };\n }\n\n /**\n * The chain's monomers in HELM source order — sugar, base, linker, … — so a\n * base is the monomer immediately after its owning sugar. Mirrors\n * `atomPositionInChain` so connection positions parse and emit symmetrically.\n */\n private sourceOrderAtoms(chain: ChainBuilder): AtomBuilder[] {\n const out: AtomBuilder[] = [];\n for (const bb of chain.backboneAtoms) {\n out.push(bb);\n if (bb.branchAtom !== undefined) out.push(bb.branchAtom);\n }\n return out;\n }\n\n private resolveAtomByPosition(chain: ChainBuilder, pos: PositionRef, span: TokenSpan): AtomBuilder | null {\n if (pos.kind === 'any') {\n const first = chain.backboneAtoms[0];\n return first ?? null;\n }\n if (pos.kind === 'symbol') {\n const found = chain.backboneAtoms.find((a) => a.symbol === pos.value);\n if (found === undefined) {\n // Try `allAtoms` too in case the symbol is a branch atom.\n const alt = chain.allAtoms.find((a) => a.symbol === pos.value);\n if (alt === undefined) {\n this.emit('warning', 'position-out-of-range',\n `Chain '${chain.id}' has no monomer with symbol '${pos.value}'`,\n span,\n );\n const first = chain.backboneAtoms[0];\n return first ?? null;\n }\n return alt;\n }\n return found;\n }\n // Index the full source-order monomer list (sugar, base, linker, …), per\n // the HELM standard. Indexing `backboneAtoms` (no bases) under-counted RNA\n // and produced \"Position 56 out of range (length 37)\".\n const sourceOrder = this.sourceOrderAtoms(chain);\n const idx = pos.value;\n if (idx < 1 || idx > sourceOrder.length) {\n this.emit('error', 'position-out-of-range',\n `Position ${idx} out of range for chain '${chain.id}' (length ${sourceOrder.length})`,\n span,\n );\n const first = chain.backboneAtoms[0];\n return first ?? null;\n }\n return sourceOrder[idx - 1] as AtomBuilder;\n }\n\n // ---- Diagnostics ------------------------------------------------------\n\n private emit(severity: ValidationDiagnostic['severity'], code: string, message: string, span?: TokenSpan): void {\n const diag: ValidationDiagnostic = {\n severity,\n code,\n message,\n ...(span !== undefined ? { span: { start: span.start, end: span.end } } : {}),\n };\n this.diagnostics.push(diag);\n if (this.mode === 'strict' && severity === 'error') {\n throw new HelmParseError(code, message, {\n ...(span !== undefined ? { span: { start: span.start, end: span.end } } : {}),\n });\n }\n }\n}\n","// T-0210 — HELM serializer. Walks a `Mol` and produces the canonical HELM\n// V2.0 string. The serializer is the inverse of `parseHelm`/`parseTokens`\n// for graphs produced by this serializer (PARSING.md §7).\n//\n// Sections emitted:\n// 0. Simple polymers: `<id>{<body>}<annotation>?` joined by `|`.\n// 1. Connections: cross-polymer + hbond bonds joined by `|`.\n// 2. Groups + bond-ratios: non-bracket groups + ratio'd cross-polymer\n// bonds joined by `|`.\n// 3. Annotations: HELM 2.0 JSON map (auto-derived for strandtype atoms).\n// 4. Version trailer `V2.0` (configurable).\n//\n// Layering: this file imports from `core/` and `monomer-lib/` only. No DOM,\n// no console, no eval/Function.\n\nimport { HelmTypes } from '../core/constants';\nimport type { PolymerType } from '../core/constants';\nimport type { Atom, Bond, Chain, Group, GroupMember, Mol, RGroupRef } from '../core/model';\nimport { atomPositionInChain } from '../core/model';\n\n// --------------------------------------------------------------------------\n// Phase 16 (T-1602) — Chain-body emission must reflect ACTUAL backbone bonds\n// --------------------------------------------------------------------------\n//\n// Root cause of the user-reported \"PEPTIDE1{A.C.D.E.F.G} with no D-E bond\"\n// bug (2026-05-17): the serializer trusted `mol.chains[].backboneAtoms` and\n// joined every entry by `.` — implicitly claiming a backbone bond between\n// every consecutive pair. When the editor's mol ended up with an atom array\n// that no longer matched the actual bond topology (e.g. a buggy chain merge,\n// or a hand-built mol), the emitted HELM falsely declared phantom backbone\n// bonds.\n//\n// The fix splits each chain into segments wherever consecutive backbone\n// atoms lack the actual `kind === 'backbone'` bond with `r1 = 2 / r2 = 1`.\n// Each segment becomes its own polymer; the original chain id stays on the\n// first segment, subsequent segments allocate fresh ids matching the\n// polymer type. Atom bio.chainId / positionInChain are rewritten on the\n// split atoms; bonds keep their identity but get re-wired through\n// `oldToNew` so `b.a1.bio.chainId` reads the new value.\n//\n// The helper is a no-op when every chain's `backboneAtoms` lines up with\n// the actual bond topology — the common case after a successful parse.\n\nfunction hasBackboneBondBetween(a: Atom, b: Atom, bonds: readonly Bond[]): boolean {\n for (const bond of bonds) {\n if (bond.kind !== 'backbone') continue;\n if (bond.r1.kind !== 'numeric' || bond.r2.kind !== 'numeric') continue;\n const forward =\n bond.a1.id === a.id && bond.a2.id === b.id &&\n bond.r1.r === 2 && bond.r2.r === 1;\n const reverse =\n bond.a1.id === b.id && bond.a2.id === a.id &&\n bond.r1.r === 2 && bond.r2.r === 1;\n if (forward || reverse) return true;\n }\n return false;\n}\n\n/**\n * Phase 16 (T-1602) — Build a new `Mol` whose chains contain only atoms\n * actually connected by backbone bonds. When a chain's `backboneAtoms`\n * already lines up with the bond topology, the original `mol` is returned\n * unchanged.\n *\n * Cross-references in `mol.bonds` (section 1 of the HELM output) are\n * faithfully preserved: bond `a1`/`a2` are rewired to the new atom\n * instances whose `bio.chainId` / `bio.positionInChain` reflect the split.\n * The serializer's `emitConnection` reads those fields directly, so the\n * section-1 output gets the correct polymer ids \"for free\".\n */\nexport function splitChainsByActualBonds(mol: Mol): Mol {\n // Quick check: does ANY chain need splitting?\n let anyNeedsSplit = false;\n for (const chain of mol.chains) {\n for (let i = 0; i < chain.backboneAtoms.length - 1; i++) {\n const a = chain.backboneAtoms[i]!;\n const b = chain.backboneAtoms[i + 1]!;\n if (!hasBackboneBondBetween(a, b, mol.bonds)) {\n anyNeedsSplit = true;\n break;\n }\n }\n if (anyNeedsSplit) break;\n }\n if (!anyNeedsSplit) return mol;\n\n // Allocate fresh chain ids for subsequent segments. Smallest unused N\n // suffixed to the polymer type prefix.\n const usedIds = new Set<string>(mol.chains.map((c) => c.id));\n const allocateId = (prefix: PolymerType): string => {\n let n = 1;\n while (usedIds.has(`${prefix}${n}`)) n += 1;\n const id = `${prefix}${n}`;\n usedIds.add(id);\n return id;\n };\n\n // Build segments in source order — first segment of each chain keeps the\n // original id, subsequent segments come right after.\n interface Segment {\n id: string;\n polymerType: PolymerType;\n atoms: readonly Atom[];\n annotation?: string;\n }\n const segments: Segment[] = [];\n for (const chain of mol.chains) {\n const segs: Atom[][] = [[]];\n let cur = segs[0]!;\n for (let i = 0; i < chain.backboneAtoms.length; i++) {\n const a = chain.backboneAtoms[i]!;\n cur.push(a);\n if (i < chain.backboneAtoms.length - 1) {\n const next = chain.backboneAtoms[i + 1]!;\n if (!hasBackboneBondBetween(a, next, mol.bonds)) {\n cur = [];\n segs.push(cur);\n }\n }\n }\n for (let s = 0; s < segs.length; s++) {\n const id = s === 0 ? chain.id : allocateId(chain.polymerType);\n const seg: Segment = {\n id,\n polymerType: chain.polymerType,\n atoms: segs[s]!,\n };\n if (s === 0 && chain.annotation !== undefined) seg.annotation = chain.annotation;\n segments.push(seg);\n }\n }\n\n // Remap: oldAtomId -> { chainId, positionInChain }\n interface Remap { chainId: string; pos: number; }\n const remap = new Map<number, Remap>();\n for (const seg of segments) {\n for (let i = 0; i < seg.atoms.length; i++) {\n const a = seg.atoms[i]!;\n remap.set(a.id, { chainId: seg.id, pos: i + 1 });\n if (a.branchAtom !== undefined)\n remap.set(a.branchAtom.id, { chainId: seg.id, pos: i + 1 });\n }\n }\n\n // Rewrite atoms whose bio.chainId / positionInChain changed.\n const oldToNew = new Map<number, Atom>();\n for (const a of mol.atoms) {\n const r = remap.get(a.id);\n if (r === undefined) { oldToNew.set(a.id, a); continue; }\n if (a.bio.chainId === r.chainId && a.bio.positionInChain === r.pos) {\n oldToNew.set(a.id, a); continue;\n }\n oldToNew.set(a.id, { ...a, bio: { ...a.bio, chainId: r.chainId, positionInChain: r.pos } });\n }\n // Re-pin branchAtom references onto the freshly built atom instances.\n for (const a of mol.atoms) {\n if (a.branchAtom === undefined) continue;\n const parent = oldToNew.get(a.id);\n const branch = oldToNew.get(a.branchAtom.id);\n if (parent === undefined || branch === undefined) continue;\n (parent as { branchAtom?: Atom }).branchAtom = branch;\n }\n\n // Rebuild bonds — re-wire to new atom instances.\n const newBonds: Bond[] = mol.bonds.map((b) => {\n const a1 = oldToNew.get(b.a1.id) ?? b.a1;\n const a2 = oldToNew.get(b.a2.id) ?? b.a2;\n if (a1 === b.a1 && a2 === b.a2) return b;\n return { ...b, a1, a2 };\n });\n\n // Build new chains from segments, attaching the bonds whose endpoints\n // both live inside the segment.\n const newChains: Chain[] = segments.map((seg) => {\n const backboneAtoms = seg.atoms.map((a) => oldToNew.get(a.id) ?? a);\n const segAtomIds = new Set<number>();\n for (const a of seg.atoms) {\n segAtomIds.add(a.id);\n if (a.branchAtom !== undefined) segAtomIds.add(a.branchAtom.id);\n }\n const segBonds: Bond[] = [];\n for (const b of newBonds) {\n if (segAtomIds.has(b.a1.id) && segAtomIds.has(b.a2.id))\n segBonds.push(b);\n }\n const chain: Chain = {\n id: seg.id,\n polymerType: seg.polymerType,\n backboneAtoms: backboneAtoms as readonly Atom[],\n bonds: segBonds as readonly Bond[],\n ...(seg.annotation !== undefined ? { annotation: seg.annotation } : {}),\n };\n return chain;\n });\n\n // Preserve mol.atoms source order, but with rewritten bio on the moved\n // atoms.\n const newAtoms: Atom[] = mol.atoms.map((a) => oldToNew.get(a.id) ?? a);\n\n return {\n atoms: newAtoms as readonly Atom[],\n bonds: newBonds as readonly Bond[],\n chains: newChains as readonly Chain[],\n groups: mol.groups,\n annotations: mol.annotations,\n };\n}\n\n// --------------------------------------------------------------------------\n// Public surface\n// --------------------------------------------------------------------------\n\n/**\n * Options for `serialize`. Most callers want the defaults: V2.0 trailer,\n * source order preserved, no HTML highlight spans.\n *\n * - `canonicalize` — sort chains by `(polymerType, id)` and renumber.\n * NOTE: the public canonical entry point is\n * `canonicalize(mol)`; this flag just toggles the\n * ordering inside the serializer itself.\n * - `includeHighlights` — wrap atoms whose `selected === true` in\n * `<span style='background:#bbf;'>…</span>`. Default\n * `false`; we never produce HTML unless asked.\n * - `version` — trailer text. `'V2.0'` / `'V1.0'` emit the\n * literal; `'none'` omits the trailer; `'preserve'`\n * uses `mol.annotations.version` verbatim.\n */\nexport interface SerializeOptions {\n readonly canonicalize?: boolean;\n readonly includeHighlights?: boolean;\n readonly version?: 'V2.0' | 'V1.0' | 'none' | 'preserve';\n}\n\n/**\n * Emit a HELM string for `mol`. The output is always a valid HELM 2.0 string\n * (four `$`-separated sections plus the optional version trailer).\n */\nexport function serialize(mol: Mol, options?: SerializeOptions): string {\n // Phase 16 (T-1602) — Split chains whose `backboneAtoms` claims phantom\n // backbone bonds. The helper is a no-op when every consecutive pair\n // already has the real bond.\n const adjusted = splitChainsByActualBonds(mol);\n const ctx = new SerializeCtx(adjusted, options ?? {});\n return ctx.emit();\n}\n\n// --------------------------------------------------------------------------\n// Implementation\n// --------------------------------------------------------------------------\n\ninterface BracketBinding {\n members: number[]; // atom ids in member order\n min: number;\n max: number;\n /** Set of atom-ids belonging to the bracket; cheap O(1) membership. */\n set: Set<number>;\n /** First atom of the bracket (by atom-id, as listed in `members[0]`). */\n startAtomId: number;\n /** Last atom of the bracket (by atom-id, as listed in `members[len-1]`). */\n endAtomId: number;\n}\n\nclass SerializeCtx {\n private readonly mol: Mol;\n private readonly options: SerializeOptions;\n\n constructor(mol: Mol, options: SerializeOptions) {\n this.mol = mol;\n this.options = options;\n }\n\n emit(): string {\n const chains = this.orderedChains();\n const polymerSection = chains.map((c) => this.emitPolymer(c)).join('|');\n const bondSection = this.emitConnections();\n const groupSection = this.emitGroupsAndBondRatios();\n const annSection = this.emitAnnotations();\n const trailer = this.versionTrailer();\n return `${polymerSection}\\$${bondSection}\\$${groupSection}\\$${annSection}${trailer}`;\n }\n\n // ---- ordering ---------------------------------------------------------\n\n private orderedChains(): readonly Chain[] {\n if (this.options.canonicalize !== true) return this.mol.chains;\n const arr = this.mol.chains.slice();\n arr.sort((a, b) => {\n if (a.polymerType !== b.polymerType) return a.polymerType < b.polymerType ? -1 : 1;\n return a.id < b.id ? -1 : a.id > b.id ? 1 : 0;\n });\n return arr;\n }\n\n // ---- section 0: polymer body ------------------------------------------\n\n private emitPolymer(chain: Chain): string {\n const body = this.emitChainBody(chain);\n const ann = chain.annotation !== undefined ? `\"${escapeQuoted(chain.annotation)}\"` : '';\n return `${chain.id}{${body}}${ann}`;\n }\n\n private emitChainBody(chain: Chain): string {\n switch (chain.polymerType) {\n case 'PEPTIDE': return this.emitPeptideBody(chain);\n case 'RNA': return this.emitRnaBody(chain);\n case 'CHEM': return this.emitChemBody(chain);\n case 'BLOB': return this.emitBlobBody(chain);\n default:\n // G-polymers have empty bodies in HELM 2.0.\n return '';\n }\n }\n\n private emitPeptideBody(chain: Chain): string {\n const brackets = this.bracketsForChain(chain.id);\n const out: string[] = [];\n // For peptides, every backbone atom is one \"item\".\n let i = 0;\n let bracketDepth = 0;\n let currentBracket: BracketBinding | null = null;\n while (i < chain.backboneAtoms.length) {\n const atom = chain.backboneAtoms[i] as Atom;\n const startsBracket = brackets.find((b) => b.startAtomId === atom.id);\n if (startsBracket !== undefined && currentBracket === null) {\n out.push('(');\n currentBracket = startsBracket;\n bracketDepth += 1;\n }\n out.push(this.emitMonomerToken(atom));\n const tag = atom.tag !== undefined ? `\"${escapeQuoted(atom.tag)}\"` : '';\n out.push(tag);\n if (currentBracket !== null && currentBracket.endAtomId === atom.id) {\n out.push(`)${emitRepeat(currentBracket.min, currentBracket.max)}`);\n currentBracket = null;\n bracketDepth -= 1;\n }\n i += 1;\n if (i < chain.backboneAtoms.length) out.push('.');\n }\n void bracketDepth;\n return out.join('');\n }\n\n private emitRnaBody(chain: Chain): string {\n const brackets = this.bracketsForChain(chain.id);\n const out: string[] = [];\n let i = 0;\n let isFirst = true;\n let currentBracket: BracketBinding | null = null;\n\n const flushBracketIfEnding = (atomId: number): void => {\n if (currentBracket !== null && currentBracket.endAtomId === atomId) {\n out.push(`)${emitRepeat(currentBracket.min, currentBracket.max)}`);\n currentBracket = null;\n }\n };\n const maybeOpenBracket = (atomId: number): void => {\n const startsBracket = brackets.find((b) => b.startAtomId === atomId);\n if (startsBracket !== undefined && currentBracket === null) {\n out.push('(');\n currentBracket = startsBracket;\n }\n };\n\n while (i < chain.backboneAtoms.length) {\n const a = chain.backboneAtoms[i] as Atom;\n if (!isFirst) out.push('.');\n isFirst = false;\n\n if (a.biotype === HelmTypes.NUCLEOTIDE) {\n // Standalone `*` pseudo-nucleotide.\n maybeOpenBracket(a.id);\n out.push(this.emitMonomerToken(a));\n if (a.tag !== undefined) out.push(`\"${escapeQuoted(a.tag)}\"`);\n flushBracketIfEnding(a.id);\n i += 1;\n continue;\n }\n\n if (a.biotype === HelmTypes.SUGAR) {\n maybeOpenBracket(a.id);\n out.push(this.emitMonomerToken(a));\n if (a.tag !== undefined) out.push(`\"${escapeQuoted(a.tag)}\"`);\n if (a.branchAtom !== undefined) {\n out.push('(');\n out.push(this.emitMonomerToken(a.branchAtom));\n if (a.branchAtom.tag !== undefined) out.push(`\"${escapeQuoted(a.branchAtom.tag)}\"`);\n out.push(')');\n }\n // Linker is the next backbone atom if its biotype is Linker.\n const next = chain.backboneAtoms[i + 1];\n if (next !== undefined && next.biotype === HelmTypes.LINKER) {\n out.push(this.emitMonomerToken(next));\n if (next.tag !== undefined) out.push(`\"${escapeQuoted(next.tag)}\"`);\n flushBracketIfEnding(next.id);\n i += 2;\n } else {\n flushBracketIfEnding(a.id);\n i += 1;\n }\n continue;\n }\n\n // Bare linker / unknown — emit as-is.\n maybeOpenBracket(a.id);\n out.push(this.emitMonomerToken(a));\n if (a.tag !== undefined) out.push(`\"${escapeQuoted(a.tag)}\"`);\n flushBracketIfEnding(a.id);\n i += 1;\n }\n return out.join('');\n }\n\n private emitChemBody(chain: Chain): string {\n const first = chain.backboneAtoms[0];\n if (first === undefined) return '';\n const tag = first.tag !== undefined ? `\"${escapeQuoted(first.tag)}\"` : '';\n return `${this.emitMonomerToken(first)}${tag}`;\n }\n\n private emitBlobBody(chain: Chain): string {\n const first = chain.backboneAtoms[0];\n if (first === undefined) return '';\n const tag = first.tag !== undefined ? `\"${escapeQuoted(first.tag)}\"` : '';\n // BLOB-internal atoms always emit either `Bead`-style identifier (naked)\n // or the original bracketed form. The lexer/parser pipe correctly stamps\n // `inlineSource` on bracketed payloads (see parser.ts).\n return `${this.emitMonomerToken(first)}${tag}`;\n }\n\n /**\n * Emit a single atom's monomer token. Wraps multi-character symbols and\n * inline-SMILES payloads in `[...]` (preserving the original bracket content\n * via `atom.inlineSource`). Optionally wraps the result in a highlight\n * `<span>` when `includeHighlights` is set and the atom is selected.\n */\n private emitMonomerToken(atom: Atom): string {\n let core: string;\n if (atom.inlineSource !== undefined) {\n core = `[${atom.inlineSource}]`;\n } else if (atom.bio.ambiguity !== undefined && (atom.symbol === '?' || atom.bio.ambiguity.startsWith('('))) {\n core = atom.bio.ambiguity;\n } else {\n // For naked tokens (no `[...]` at parse time), emit the symbol as-is.\n // The parser tolerates both `[meI]` and `meI` so this round-trips\n // either form back into a structurally-equal Mol.\n core = atom.symbol;\n }\n if (this.options.includeHighlights === true && atom.selected) {\n return `<span style='background:#bbf;'>${core}</span>`;\n }\n return core;\n }\n\n // ---- section 1: connections ------------------------------------------\n\n private emitConnections(): string {\n const parts: string[] = [];\n for (const b of this.crossPolymerBonds()) parts.push(this.emitConnection(b));\n return parts.join('|');\n }\n\n /**\n * Bonds emitted in HELM section 1 are EVERY bond that is NOT implicit in\n * the polymer-body section.\n *\n * Implicit bonds (not emitted in section 1):\n * - `kind === 'backbone'` AND the two endpoints are ADJACENT inside\n * their chain's `backboneAtoms` (in either order). The polymer body\n * captures these via the `.`-separated monomer sequence.\n * - `kind === 'branch'` AND `a1.branchAtom === a2` (or vice-versa).\n * The polymer body captures these via the `r(B)` parenthesis form.\n *\n * Everything else — including a `backbone`-kind bond between NON-adjacent\n * atoms inside the same chain (e.g. the cyclic A → G closure on\n * `PEPTIDE1{A.C.D.E.F.G}`), every `cross-polymer` bond, and every\n * `hbond` — must appear in section 1. Phase 15 T-1505 fix: previously\n * `kind` alone gated emission, so cyclic intra-chain closures were\n * silently dropped from the HELM string while still living in\n * `mol.bonds`, which made a re-drag report `rgroup-already-bonded`\n * against a bond the user could not see.\n */\n private *crossPolymerBonds(): IterableIterator<Bond> {\n // Pre-compute adjacency: chainId -> map<atomId, indexInBackbone>.\n const adjIdx = new Map<string, Map<number, number>>();\n for (const c of this.mol.chains) {\n const m = new Map<number, number>();\n for (let i = 0; i < c.backboneAtoms.length; i++)\n m.set(c.backboneAtoms[i]!.id, i);\n adjIdx.set(c.id, m);\n }\n for (const b of this.mol.bonds) {\n if (b.kind === 'backbone') {\n if (b.a1.bio.chainId === b.a2.bio.chainId) {\n const m = adjIdx.get(b.a1.bio.chainId);\n if (m !== undefined) {\n const i1 = m.get(b.a1.id);\n const i2 = m.get(b.a2.id);\n if (i1 !== undefined && i2 !== undefined && Math.abs(i1 - i2) === 1)\n continue; // adjacent → implicit\n }\n }\n // Non-adjacent OR cross-chain backbone bond → must emit.\n yield b;\n continue;\n }\n if (b.kind === 'branch') {\n // Implicit when one side is the other's `branchAtom` (sugar→base).\n const linkedAsBranch =\n (b.a1.branchAtom !== undefined && b.a1.branchAtom.id === b.a2.id) ||\n (b.a2.branchAtom !== undefined && b.a2.branchAtom.id === b.a1.id);\n if (linkedAsBranch) continue;\n yield b;\n continue;\n }\n // cross-polymer, hbond — always emit.\n yield b;\n }\n }\n\n private emitConnection(b: Bond): string {\n const r1 = emitRGroup(b.r1, b.kind);\n const r2 = emitRGroup(b.r2, b.kind);\n const ann = b.tag !== undefined ? `\"${escapeQuoted(b.tag)}\"` : '';\n // Phase 34 (T-3401) — When the parser routed a `:pair-:pair`\n // bond to base atoms (so the H-bond stroke connects\n // complementary bases visually, per HELM 2.0 semantics), emit\n // the OWNING sugar's positionInChain so the connection string\n // round-trips byte-for-byte (the parser will redirect to the\n // base again on the next parse).\n const pos1 = String(this.connectionPosition(b.a1));\n const pos2 = String(this.connectionPosition(b.a2));\n return `${b.a1.bio.chainId},${b.a2.bio.chainId},${pos1}:${r1}-${pos2}:${r2}${ann}`;\n }\n\n /**\n * Resolve a bond endpoint to the positionInChain to emit. For\n * backbone atoms (sugars / linkers / peptide AAs) this is just\n * `bio.positionInChain`. For BASE atoms (which the parser routes\n * `:pair-:pair` connections to under HELM 2.0 base-pair\n * semantics), look up the owning sugar via the chain's\n * `backboneAtoms` array and emit THAT sugar's position. The\n * shared helper handles both branches.\n */\n private connectionPosition(atom: Atom): number {\n return atomPositionInChain(atom, this.mol.chains.find((c) => c.id === atom.bio.chainId));\n }\n\n // ---- section 2: groups + bond-ratios ---------------------------------\n\n private emitGroupsAndBondRatios(): string {\n const parts: string[] = [];\n for (const g of this.mol.groups) {\n if (g.kind === 'bracket') continue;\n parts.push(this.emitGroup(g));\n }\n for (const b of this.mol.bonds) {\n if (b.kind !== 'cross-polymer') continue;\n if (b.ratio === undefined) continue;\n const r = b.ratio.denominator !== undefined\n ? `${b.ratio.numerator}/${b.ratio.denominator}`\n : `${b.ratio.numerator}`;\n parts.push(`${b.a1.bio.chainId}+${b.a2.bio.chainId}:${r}`);\n }\n return parts.join('|');\n }\n\n private emitGroup(g: Group): string {\n const sep = g.kind === 'and' ? '+' : ',';\n const inner = g.members.map((m) => emitGroupMember(m)).join(sep);\n return `${g.id}(${inner})`;\n }\n\n // ---- section 3: annotations ------------------------------------------\n\n private emitAnnotations(): string {\n const map = this.mol.annotations.perPolymer;\n if (map.size === 0) return '';\n const obj: Record<string, Record<string, unknown>> = {};\n for (const [k, v] of map) obj[k] = v;\n return JSON.stringify(obj);\n }\n\n // ---- trailer ---------------------------------------------------------\n\n private versionTrailer(): string {\n const v = this.options.version ?? 'V2.0';\n if (v === 'none') return '';\n if (v === 'preserve') {\n const src = this.mol.annotations.version;\n return src === '' ? '' : `\\$${src}`;\n }\n return `\\$${v}`;\n }\n\n // ---- bracket helpers -------------------------------------------------\n\n /**\n * Build the list of `BracketBinding` entries that apply to the atoms of\n * `chainId`. Bracket groups carry their members as `target = String(atomId)`\n * (the parser writes that shape when it builds repeat brackets).\n */\n private bracketsForChain(chainId: string): readonly BracketBinding[] {\n const out: BracketBinding[] = [];\n const atomChain = new Map<number, string>();\n for (const a of this.mol.atoms) atomChain.set(a.id, a.bio.chainId);\n for (const g of this.mol.groups) {\n if (g.kind !== 'bracket') continue;\n const members: number[] = [];\n for (const m of g.members) {\n const id = parseInt(m.target, 10);\n if (Number.isFinite(id)) members.push(id);\n }\n if (members.length === 0) continue;\n const owners = new Set<string>();\n for (const id of members) {\n const owner = atomChain.get(id);\n if (owner !== undefined) owners.add(owner);\n }\n if (!owners.has(chainId) || owners.size > 1) continue;\n const repeat = g.repeat ?? { min: 1, max: 1 };\n out.push({\n members,\n min: repeat.min,\n max: repeat.max,\n set: new Set(members),\n startAtomId: members[0] as number,\n endAtomId: members[members.length - 1] as number,\n });\n }\n return out;\n }\n}\n\n// --------------------------------------------------------------------------\n// Small string helpers\n// --------------------------------------------------------------------------\n\nfunction escapeQuoted(s: string): string {\n let out = '';\n for (let i = 0; i < s.length; i++) {\n const ch = s.charCodeAt(i);\n if (ch === 0x22) { out += '\\\\\"'; continue; }\n if (ch === 0x5c) { out += '\\\\\\\\'; continue; }\n if (ch === 0x0a) { out += '\\\\n'; continue; }\n if (ch === 0x0d) { out += '\\\\r'; continue; }\n if (ch === 0x09) { out += '\\\\t'; continue; }\n out += s.charAt(i);\n }\n return out;\n}\n\nfunction emitRepeat(min: number, max: number): string {\n if (min === max) return `'${min}'`;\n return `'${min}-${max}'`;\n}\n\nfunction emitRGroup(r: RGroupRef, kind: Bond['kind']): string {\n switch (r.kind) {\n case 'numeric': return `R${r.r}`;\n case 'unspecified': return '?';\n case 'wildcard': return '*';\n case 'pair': return 'pair';\n case 'positional': return `${r.position}:R${r.r}`;\n default:\n void kind;\n return '?';\n }\n}\n\nfunction emitGroupMember(m: GroupMember): string {\n if (m.ratio === undefined) return m.target;\n return `${m.target}:${m.ratio}`;\n}\n\n// Re-export `PolymerType` for symmetry with the resolver — callers writing\n// thin wrappers around `serialize` often need to type the chain selector.\nexport type { PolymerType };\n","// T-0211 — HELM canonicalizer. Rewrites a `Mol` (or HELM string) into the\n// canonical form defined by SPECIFICATION.md §11:\n//\n// 1. Reorder simple polymers by `(polymerType, polymerId)` ascending.\n// 2. Renumber polymer-ids sequentially within each polymer-type.\n// 3. Reorder connections by `(c1, c2, a1, a2)` and rewrite ids.\n// 4. Reorder groups by `G<n>` ascending and renumber.\n// 5. Strip empty optional annotations.\n// 6. Inline-SMILES monomers are NOT consolidated.\n//\n// Idempotent: `canonicalize(canonicalize(m))` is structurally equal to\n// `canonicalize(m)` (verified by tests).\n\nimport type { Atom, AnnotationMap, Bond, Chain, Group, GroupMember, Mol } from '../core/model';\nimport { atomPositionInChain } from '../core/model';\nimport type { IMonomerLib } from '../monomer-lib/types';\nimport { parseHelm } from './parser';\nimport { serialize } from './serializer';\n\n// --------------------------------------------------------------------------\n// Public surface\n// --------------------------------------------------------------------------\n\n/**\n * Return a new `Mol` rewritten into canonical form. The input is unchanged.\n */\nexport function canonicalize(mol: Mol): Mol {\n return new CanonCtx(mol).run();\n}\n\n/**\n * Convenience: parse a HELM string, canonicalize, and re-serialize. The lib\n * may be `null` for resolver-less canonicalization (the resolver is skipped\n * automatically when `lib === null`).\n */\nexport function canonicalizeHelm(helm: string, lib: IMonomerLib | null): string {\n const parsed = parseHelm(helm, lib, { mode: 'lenient', resolveMonomers: false });\n const canon = canonicalize(parsed.mol);\n return serialize(canon, { canonicalize: true, version: 'V2.0' });\n}\n\n// --------------------------------------------------------------------------\n// Implementation\n// --------------------------------------------------------------------------\n\nclass CanonCtx {\n private readonly mol: Mol;\n /** old chain-id -> new chain-id mapping. */\n private readonly chainIdMap: Map<string, string> = new Map();\n\n constructor(mol: Mol) {\n this.mol = mol;\n }\n\n run(): Mol {\n // 1. Sort chains by (polymerType, id) ascending and renumber.\n const sorted = this.mol.chains.slice().sort((a, b) => {\n if (a.polymerType !== b.polymerType) return a.polymerType < b.polymerType ? -1 : 1;\n return naturalCompareChainId(a.id, b.id);\n });\n const counters: Record<string, number> = {};\n const newChainList: Chain[] = [];\n for (const c of sorted) {\n const head = polymerTypeHead(c.polymerType);\n counters[head] = (counters[head] ?? 0) + 1;\n const newId = `${head}${counters[head]}`;\n this.chainIdMap.set(c.id, newId);\n newChainList.push(c);\n }\n\n // 2. Re-key atoms onto their new chain ids and rebuild references.\n const oldToNew = new Map<number, Atom>();\n for (const a of this.mol.atoms) {\n const newChainId = this.chainIdMap.get(a.bio.chainId) ?? a.bio.chainId;\n oldToNew.set(a.id, { ...a, bio: { ...a.bio, chainId: newChainId } });\n }\n for (const a of this.mol.atoms) {\n if (a.branchAtom === undefined) continue;\n const na = oldToNew.get(a.id);\n const nb = oldToNew.get(a.branchAtom.id);\n if (na !== undefined && nb !== undefined)\n (na as { branchAtom?: Atom }).branchAtom = nb;\n }\n\n const newBonds: Bond[] = this.mol.bonds.map((b) => ({\n ...b,\n a1: oldToNew.get(b.a1.id) ?? b.a1,\n a2: oldToNew.get(b.a2.id) ?? b.a2,\n }));\n\n const newBondsById = new Map<number, Bond>();\n for (const b of newBonds) newBondsById.set(b.id, b);\n\n const newChains: Chain[] = newChainList.map((c) => {\n const newId = this.chainIdMap.get(c.id) ?? c.id;\n const backbone: Atom[] = [];\n for (const a of c.backboneAtoms) {\n const na = oldToNew.get(a.id);\n if (na !== undefined) backbone.push(na);\n }\n const bonds: Bond[] = [];\n for (const b of c.bonds) {\n const nb = newBondsById.get(b.id);\n if (nb !== undefined) bonds.push(nb);\n }\n return {\n id: newId,\n polymerType: c.polymerType,\n backboneAtoms: backbone as readonly Atom[],\n bonds: bonds as readonly Bond[],\n ...(c.annotation !== undefined && c.annotation.length > 0 ? { annotation: c.annotation } : {}),\n };\n });\n\n // 3. Sort cross-polymer / hbond connections by (c1, c2, a1, a2).\n // Use atomPositionInChain so hbonds whose endpoints are base atoms\n // (positionInChain=0 after the parser's pair-pair redirection) sort\n // by the owning sugar position instead of collapsing to 0.\n const chainByNewId = new Map<string, Chain>();\n for (const c of newChains) chainByNewId.set(c.id, c);\n newBonds.sort((x, y) => {\n const xCross = isCrossKind(x.kind);\n const yCross = isCrossKind(y.kind);\n if (xCross && !yCross) return 1;\n if (!xCross && yCross) return -1;\n if (!xCross && !yCross) return x.id - y.id;\n const xc1 = x.a1.bio.chainId, yc1 = y.a1.bio.chainId;\n if (xc1 !== yc1) return xc1 < yc1 ? -1 : 1;\n const xc2 = x.a2.bio.chainId, yc2 = y.a2.bio.chainId;\n if (xc2 !== yc2) return xc2 < yc2 ? -1 : 1;\n const xa1 = atomPositionInChain(x.a1, chainByNewId.get(x.a1.bio.chainId));\n const ya1 = atomPositionInChain(y.a1, chainByNewId.get(y.a1.bio.chainId));\n if (xa1 !== ya1) return xa1 - ya1;\n const xa2 = atomPositionInChain(x.a2, chainByNewId.get(x.a2.bio.chainId));\n const ya2 = atomPositionInChain(y.a2, chainByNewId.get(y.a2.bio.chainId));\n return xa2 - ya2;\n });\n\n // 4. Sort & renumber non-bracket groups.\n const renamed = this.renumberGroups(this.mol.groups);\n\n // 5. Rebuild annotations: strip empty optional, rekey on new chain ids.\n const newAnnotations = this.rekeyAnnotations(this.mol.annotations);\n\n // 6. Update annotated atoms (5'ss markers etc.) — they live on the atom\n // itself; their chainId was already rewritten above.\n\n const newAtoms: Atom[] = this.mol.atoms.map((a) => oldToNew.get(a.id) as Atom);\n return {\n atoms: newAtoms as readonly Atom[],\n bonds: newBonds as readonly Bond[],\n chains: newChains as readonly Chain[],\n groups: renamed as readonly Group[],\n annotations: newAnnotations,\n };\n }\n\n private renumberGroups(groups: readonly Group[]): Group[] {\n const bracketGroups: Group[] = [];\n const namedGroups: Group[] = [];\n for (const g of groups) {\n if (g.kind === 'bracket') bracketGroups.push(this.rekeyBracket(g));\n else namedGroups.push(g);\n }\n namedGroups.sort((a, b) => naturalCompareChainId(a.id, b.id));\n const counter = { G: 0 };\n return namedGroups.map((g) => {\n counter.G += 1;\n const newId = `G${counter.G}`;\n return {\n ...g,\n id: newId,\n members: g.members.map((m) => this.rekeyMember(m)) as readonly GroupMember[],\n };\n }).concat(bracketGroups);\n }\n\n private rekeyBracket(g: Group): Group {\n return g;\n }\n\n private rekeyMember(m: GroupMember): GroupMember {\n const newTarget = this.chainIdMap.get(m.target);\n if (newTarget === undefined) return m;\n return m.ratio === undefined ? { target: newTarget } : { target: newTarget, ratio: m.ratio };\n }\n\n private rekeyAnnotations(a: AnnotationMap): AnnotationMap {\n const map = new Map<string, Readonly<Record<string, unknown>>>();\n for (const [k, v] of a.perPolymer) {\n const nk = this.chainIdMap.get(k) ?? k;\n if (Object.keys(v).length === 0) continue;\n map.set(nk, v);\n }\n return { perPolymer: map, version: a.version };\n }\n}\n\n// --------------------------------------------------------------------------\n// Helpers\n// --------------------------------------------------------------------------\n\nfunction polymerTypeHead(pt: Chain['polymerType']): string {\n switch (pt) {\n case 'PEPTIDE': return 'PEPTIDE';\n case 'RNA': return 'RNA';\n case 'CHEM': return 'CHEM';\n case 'BLOB': return 'BLOB';\n default: return 'BLOB';\n }\n}\n\nfunction isCrossKind(k: Bond['kind']): boolean {\n return k === 'cross-polymer' || k === 'hbond';\n}\n\n/**\n * Compare two chain ids that share the shape `<HEAD><N>` (`PEPTIDE12` etc.)\n * — sorts by `N` numerically so `PEPTIDE2` < `PEPTIDE12`. Falls back to a\n * lexicographic compare if either input doesn't match the expected shape.\n */\nfunction naturalCompareChainId(a: string, b: string): number {\n const ma = /^([A-Z]+)([0-9]+)$/.exec(a);\n const mb = /^([A-Z]+)([0-9]+)$/.exec(b);\n if (ma === null || mb === null) return a < b ? -1 : a > b ? 1 : 0;\n if (ma[1] !== mb[1]) return (ma[1] as string) < (mb[1] as string) ? -1 : 1;\n return parseInt(ma[2] as string, 10) - parseInt(mb[2] as string, 10);\n}\n","// T-0214 — Continuous-id finalization.\n//\n// The parser assigns `bio.continuousId` per chain in source order\n// (PARSING.md §6); the algorithm here re-runs that pass on any `Mol` so\n// callers that have altered the topology (e.g. `removeGaps`, manual edits)\n// can refresh ids without going through a parse-serialize round-trip.\n//\n// Branch atoms — RNA bases hanging off a sugar — receive the next id\n// immediately after their parent sugar, matching `makeContinuousIdMap` in\n// `src/core/ids.ts`. We delegate to that function and rebuild the Mol with\n// the refreshed values; the returned graph is a fresh `Mol` (the input is\n// immutable).\n\nimport type { Atom, Bond, Chain, Mol } from '../core/model';\nimport { makeContinuousIdMap } from '../core/ids';\n\n/**\n * Return a new `Mol` whose every atom's `bio.continuousId` reflects a fresh\n * walk of `mol.chains` via `makeContinuousIdMap`.\n *\n * Atom identity (`atom.id`) is preserved; only the `bio.continuousId` field\n * changes. Bonds and groups are repointed at the new atom instances so\n * referential equality across the returned graph remains intact.\n */\nexport function assignContinuousIds(mol: Mol): Mol {\n const ids = makeContinuousIdMap(mol);\n\n const oldToNew = new Map<number, Atom>();\n for (const a of mol.atoms) {\n const nextId = ids.get(a.id);\n if (nextId === undefined || nextId === a.bio.continuousId) {\n // Preserve the existing instance so callers that hash on identity stay\n // stable when nothing changes.\n oldToNew.set(a.id, a);\n continue;\n }\n oldToNew.set(a.id, {\n ...a,\n bio: { ...a.bio, continuousId: nextId },\n });\n }\n\n // Patch branchAtom back-references so they point at the new atoms.\n for (const a of mol.atoms) {\n if (a.branchAtom === undefined) continue;\n const newAtom = oldToNew.get(a.id);\n const newBranch = oldToNew.get(a.branchAtom.id);\n if (newAtom === undefined || newBranch === undefined) continue;\n (newAtom as { branchAtom?: Atom }).branchAtom = newBranch;\n }\n\n const newBonds: Bond[] = mol.bonds.map((b) => {\n const a1 = oldToNew.get(b.a1.id);\n const a2 = oldToNew.get(b.a2.id);\n if (a1 === undefined || a2 === undefined) return b;\n if (a1 === b.a1 && a2 === b.a2) return b;\n return { ...b, a1, a2 };\n });\n\n const newBondsById = new Map<number, Bond>();\n for (const b of newBonds) newBondsById.set(b.id, b);\n\n const newChains: Chain[] = mol.chains.map((c) => {\n const backbone: Atom[] = [];\n for (const a of c.backboneAtoms) {\n const na = oldToNew.get(a.id);\n backbone.push(na ?? a);\n }\n const bonds: Bond[] = [];\n for (const b of c.bonds) {\n const nb = newBondsById.get(b.id);\n bonds.push(nb ?? b);\n }\n return {\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: backbone as readonly Atom[],\n bonds: bonds as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n };\n });\n\n const newAtoms: Atom[] = mol.atoms.map((a) => oldToNew.get(a.id) ?? a);\n\n return {\n atoms: newAtoms as readonly Atom[],\n bonds: newBonds as readonly Bond[],\n chains: newChains as readonly Chain[],\n groups: mol.groups,\n annotations: mol.annotations,\n };\n}\n","// T-0212 — `removeGaps`. Walks a parsed `Mol`, splices out every `*`\n// pseudo-monomer that sits in the middle of a chain (between an R2 and an\n// R1 backbone bond) and re-serializes. Cross-polymer gap atoms or gap atoms\n// with > 2 backbone bonds raise `HelmNotSupportedError`.\n//\n// See PARSING.md §8 and API.md §4.\n\nimport type { Atom, Bond, Chain, Mol } from '../core/model';\nimport { HelmNotSupportedError } from '../core/errors';\nimport type { IMonomerLib } from '../monomer-lib/types';\nimport { parseHelm } from './parser';\nimport { serialize } from './serializer';\nimport { assignContinuousIds } from './continuous-id';\n\n// --------------------------------------------------------------------------\n// Public surface\n// --------------------------------------------------------------------------\n\n/**\n * Result returned by `removeGaps`. `srcHelm` is the input string; `resHelm`\n * is the serialized output after splicing; `monomerMap` maps each surviving\n * atom's pre-removal `bio.continuousId` to its post-removal id.\n */\nexport interface RemoveGapsResult {\n readonly srcHelm: string;\n readonly resHelm: string;\n readonly monomerMap: ReadonlyMap<number, number>;\n}\n\n/**\n * Remove every `*` gap atom from `helm`. Returns the new HELM string plus a\n * map of old → new continuous ids.\n *\n * Throws `HelmNotSupportedError('gap-at-complex-junction')` when a `*` atom\n * sits at a branch point or participates in a cross-polymer connection — the\n * splice operation is well-defined only on linear backbones.\n */\nexport function removeGaps(helm: string, lib?: IMonomerLib | null): RemoveGapsResult {\n const libIn = lib ?? null;\n const parsed = parseHelm(helm, libIn, { mode: 'lenient', resolveMonomers: false });\n const stripped = stripGaps(parsed.mol);\n const renumbered = assignContinuousIds(stripped.mol);\n\n // Re-derive the old -> new continuous-id map based on atom-id (preserved\n // through removal) and the post-renumber bio.continuousId.\n const newCidById = new Map<number, number>();\n for (const a of renumbered.atoms) newCidById.set(a.id, a.bio.continuousId);\n const map = new Map<number, number>();\n for (const [oldCid, atomId] of stripped.survivorByOldContinuousId) {\n const newCid = newCidById.get(atomId);\n if (newCid !== undefined) map.set(oldCid, newCid);\n }\n\n const resHelm = serialize(renumbered, { version: 'V2.0' });\n return { srcHelm: helm, resHelm, monomerMap: map };\n}\n\n// --------------------------------------------------------------------------\n// Implementation\n// --------------------------------------------------------------------------\n\ninterface StripResult {\n mol: Mol;\n /** old continuous-id -> surviving atom id. */\n survivorByOldContinuousId: Map<number, number>;\n}\n\nfunction stripGaps(mol: Mol): StripResult {\n const survivors = new Map<number, number>();\n for (const a of mol.atoms) survivors.set(a.bio.continuousId, a.id);\n\n // 1. Identify gap atoms by symbol. They may be HELM_NUCLEOTIDE (RNA `*`\n // pseudo-nucleotide) or just symbol === '*' (peptide gap).\n const gapIds = new Set<number>();\n for (const a of mol.atoms) {\n if (a.symbol === '*') gapIds.add(a.id);\n }\n if (gapIds.size === 0)\n return { mol, survivorByOldContinuousId: survivors };\n\n // 2. Validate every gap atom — must have exactly 0 or 2 backbone bonds and\n // no cross-polymer bonds. Gather inbound/outbound backbone bonds per\n // gap.\n const bondsForAtom = new Map<number, Bond[]>();\n for (const a of mol.atoms) bondsForAtom.set(a.id, []);\n for (const b of mol.bonds) {\n bondsForAtom.get(b.a1.id)?.push(b);\n bondsForAtom.get(b.a2.id)?.push(b);\n }\n for (const id of gapIds) {\n const bonds = bondsForAtom.get(id) ?? [];\n const isCross = bonds.some((bb) => bb.kind === 'cross-polymer' || bb.kind === 'hbond');\n if (isCross)\n throw new HelmNotSupportedError(\n 'gap-at-complex-junction',\n `Gap atom ${id} participates in a cross-polymer/hbond bond`,\n { atomId: id },\n );\n const backboneBonds = bonds.filter((bb) => bb.kind === 'backbone');\n if (backboneBonds.length > 2)\n throw new HelmNotSupportedError(\n 'gap-at-complex-junction',\n `Gap atom ${id} has ${backboneBonds.length} backbone bonds (max 2 allowed)`,\n { atomId: id, bondCount: backboneBonds.length },\n );\n }\n\n // 3. Build the new chains/atoms/bonds with gaps removed and inbound/outbound\n // backbones spliced.\n const newAtomList: Atom[] = mol.atoms.filter((a) => !gapIds.has(a.id));\n\n // Build per-chain new backbone, splicing gaps and reconnecting neighbors.\n const newChains: Chain[] = [];\n const newBondsAll: Bond[] = [];\n\n for (const c of mol.chains) {\n const filteredBackbone = c.backboneAtoms.filter((a) => !gapIds.has(a.id));\n // For each removed gap, find the (previous-survivor, next-survivor) pair\n // in this chain and emit a backbone bond if missing.\n let spliceBondId = (() => {\n let max = 0;\n for (const b of mol.bonds) if (b.id > max) max = b.id;\n return max + 1;\n })();\n\n const chainBondsKept: Bond[] = [];\n for (const b of c.bonds) {\n if (gapIds.has(b.a1.id) || gapIds.has(b.a2.id)) continue;\n chainBondsKept.push(b);\n }\n // Detect indices in original chain where a gap lived between two non-gap\n // atoms; emit a splice bond for each such case.\n for (let i = 0; i < c.backboneAtoms.length; i++) {\n const a = c.backboneAtoms[i] as Atom;\n if (!gapIds.has(a.id)) continue;\n const prev = previousNonGap(c.backboneAtoms, i, gapIds);\n const next = nextNonGap(c.backboneAtoms, i, gapIds);\n if (prev === null || next === null) continue;\n // Add a synthetic backbone bond prev -> next (R2 -> R1).\n const bond: Bond = {\n id: spliceBondId++,\n a1: prev,\n a2: next,\n kind: 'backbone',\n r1: { kind: 'numeric', r: 2 },\n r2: { kind: 'numeric', r: 1 },\n };\n // Avoid duplicates (linear chain w/ multiple gaps in a row collapses\n // through the same prev/next; we only want one bond per surviving pair).\n const dup = chainBondsKept.find((bb) => bb.a1.id === prev.id && bb.a2.id === next.id);\n if (dup === undefined) chainBondsKept.push(bond);\n }\n for (const b of chainBondsKept) newBondsAll.push(b);\n newChains.push({\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: filteredBackbone as readonly Atom[],\n bonds: chainBondsKept as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n });\n }\n\n // Plus the mol-level cross-polymer/hbond bonds (we already validated none\n // touch a gap atom).\n for (const b of mol.bonds) {\n if (b.kind !== 'cross-polymer' && b.kind !== 'hbond') continue;\n if (gapIds.has(b.a1.id) || gapIds.has(b.a2.id)) continue;\n newBondsAll.push(b);\n }\n\n // Repoint each chain's positionInChain so connection emit uses the new\n // indices. We rebuild atoms with updated positionInChain.\n const reindexedById = new Map<number, Atom>();\n for (const c of newChains) {\n let pos = 0;\n for (const a of c.backboneAtoms) {\n pos += 1;\n reindexedById.set(a.id, { ...a, bio: { ...a.bio, positionInChain: pos } });\n }\n }\n // Branch atoms keep their previous positionInChain (parser stores 0 for\n // branch atoms anyway).\n for (const a of newAtomList) if (!reindexedById.has(a.id)) reindexedById.set(a.id, a);\n\n // Now rebuild chains/bonds/atoms with the reindexed atoms.\n const finalChains: Chain[] = newChains.map((c) => {\n const backbone = c.backboneAtoms.map((a) => reindexedById.get(a.id) as Atom);\n const bonds = c.bonds.map((b) => ({\n ...b,\n a1: reindexedById.get(b.a1.id) as Atom,\n a2: reindexedById.get(b.a2.id) as Atom,\n }));\n return {\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: backbone as readonly Atom[],\n bonds: bonds as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n };\n });\n const finalBonds: Bond[] = newBondsAll.map((b) => ({\n ...b,\n a1: reindexedById.get(b.a1.id) as Atom,\n a2: reindexedById.get(b.a2.id) as Atom,\n }));\n const finalAtoms: Atom[] = newAtomList.map((a) => reindexedById.get(a.id) as Atom);\n\n return {\n mol: {\n atoms: finalAtoms as readonly Atom[],\n bonds: finalBonds as readonly Bond[],\n chains: finalChains as readonly Chain[],\n groups: mol.groups,\n annotations: mol.annotations,\n },\n survivorByOldContinuousId: survivors,\n };\n}\n\nfunction previousNonGap(arr: readonly Atom[], i: number, gaps: ReadonlySet<number>): Atom | null {\n for (let j = i - 1; j >= 0; j--) {\n const a = arr[j];\n if (a !== undefined && !gaps.has(a.id)) return a;\n }\n return null;\n}\n\nfunction nextNonGap(arr: readonly Atom[], i: number, gaps: ReadonlySet<number>): Atom | null {\n for (let j = i + 1; j < arr.length; j++) {\n const a = arr[j];\n if (a !== undefined && !gaps.has(a.id)) return a;\n }\n return null;\n}\n","// T-0213 — Semantic validator. Walks a parsed `Mol` and emits structured\n// diagnostics covering every code listed in VALIDATION.md §§2.2–2.9.\n//\n// The parser already surfaces structural and most lex-level diagnostics\n// (VALIDATION.md §2.1). This file picks up where the parser leaves off:\n// reference integrity (§2.2), monomer resolution checks the resolver did not\n// already emit (§2.3), R-group rules (§2.4), polymer-type-specific rules\n// (§2.5), hydrogen-bond rules (§2.6), ambiguity/repetition (§2.7),\n// annotations (§2.8), and soft performance limits (§2.9).\n//\n// Each rule is a `(mol, lib) => ValidationDiagnostic[]` function; the entry\n// point `validate` composes them. In `strict` mode, any error severity\n// diagnostic throws `HelmValidationError`; in `pedantic` mode any warning is\n// escalated to error.\n\nimport { HelmTypes } from '../core/constants';\nimport type { PolymerType } from '../core/constants';\nimport type { Atom, Bond, Mol } from '../core/model';\nimport { atomPositionInChain } from '../core/model';\nimport { HelmValidationError, type ValidationDiagnostic } from '../core/errors';\nimport type { IMonomerLib, Monomer } from '../monomer-lib/types';\n\n// --------------------------------------------------------------------------\n// Public surface\n// --------------------------------------------------------------------------\n\n/**\n * Validation mode.\n * - `lenient` (default): every diagnostic returned in the array.\n * - `strict`: any error-severity diagnostic raises `HelmValidationError`.\n * - `pedantic`: warnings are escalated to errors before the strict gate.\n */\nexport interface ValidateOptions {\n readonly mode?: 'lenient' | 'strict' | 'pedantic';\n}\n\n/**\n * Run every validation rule against `mol`. The library is optional; rules\n * that need lib lookups (monomer resolution checks) skip themselves when\n * `lib === null`.\n */\nexport function validate(mol: Mol, lib: IMonomerLib | null, options?: ValidateOptions): ValidationDiagnostic[] {\n const mode = options?.mode ?? 'lenient';\n const out: ValidationDiagnostic[] = [];\n for (const rule of RULES) out.push(...rule(mol, lib));\n\n // Escalate per mode.\n const escalated: ValidationDiagnostic[] = mode === 'pedantic'\n ? out.map((d) => d.severity === 'warning' ? { ...d, severity: 'error' as const } : d)\n : out;\n\n if (mode === 'strict' || mode === 'pedantic') {\n const errs = escalated.filter((d) => d.severity === 'error');\n if (errs.length > 0) throw new HelmValidationError(errs);\n }\n return escalated;\n}\n\n// --------------------------------------------------------------------------\n// Rule registry\n// --------------------------------------------------------------------------\n\ntype Rule = (mol: Mol, lib: IMonomerLib | null) => ValidationDiagnostic[];\n\nconst RULES: readonly Rule[] = [\n ruleReferenceIntegrity,\n ruleMonomerResolution,\n ruleRGroupRules,\n rulePolymerTypeSpecific,\n ruleHydrogenBonds,\n ruleAmbiguityRepetition,\n ruleAnnotations,\n rulePerformanceLimits,\n];\n\n// --------------------------------------------------------------------------\n// §2.2 Reference integrity\n// --------------------------------------------------------------------------\n\nfunction ruleReferenceIntegrity(mol: Mol, _lib: IMonomerLib | null): ValidationDiagnostic[] {\n const out: ValidationDiagnostic[] = [];\n const chainIds = new Set(mol.chains.map((c) => c.id));\n\n for (const b of mol.bonds) {\n if (b.kind !== 'cross-polymer' && b.kind !== 'hbond') continue;\n if (!chainIds.has(b.a1.bio.chainId))\n out.push({ severity: 'error', code: 'unknown-chain-reference',\n message: `Connection references unknown chain '${b.a1.bio.chainId}'`,\n context: { chainId: b.a1.bio.chainId, bondId: b.id } });\n if (!chainIds.has(b.a2.bio.chainId))\n out.push({ severity: 'error', code: 'unknown-chain-reference',\n message: `Connection references unknown chain '${b.a2.bio.chainId}'`,\n context: { chainId: b.a2.bio.chainId, bondId: b.id } });\n }\n\n for (const c of mol.chains) {\n for (const b of mol.bonds) {\n if (b.kind !== 'cross-polymer' && b.kind !== 'hbond') continue;\n // HELM monomer count = every monomer in source order (sugar, base,\n // linker). Range-check against that, not the backbone-only length.\n let monomerCount = 0;\n for (const bb of c.backboneAtoms)\n monomerCount += bb.branchAtom !== undefined ? 2 : 1;\n for (const ep of [b.a1, b.a2]) {\n if (ep.bio.chainId !== c.id) continue;\n const pos = atomPositionInChain(ep, c);\n if (pos < 1 || pos > monomerCount)\n out.push({ severity: 'error', code: 'position-out-of-range',\n message: `Position ${pos} out of range for chain '${c.id}' (length ${monomerCount})`,\n context: { chainId: c.id, atomId: ep.id, found: pos } });\n }\n }\n }\n\n const groupIds = new Set<string>();\n for (const g of mol.groups) if (g.kind !== 'bracket') groupIds.add(g.id);\n for (const g of mol.groups) {\n if (g.kind === 'bracket') continue;\n for (const m of g.members) {\n if (chainIds.has(m.target) || groupIds.has(m.target)) continue;\n out.push({ severity: 'error', code: 'unknown-group-reference',\n message: `Group '${g.id}' references unknown id '${m.target}'`,\n context: { found: m.target } });\n }\n }\n\n // Group cycle detection (only over non-bracket groups).\n const adj = new Map<string, string[]>();\n for (const g of mol.groups) {\n if (g.kind === 'bracket') continue;\n const dests = [];\n for (const m of g.members) if (groupIds.has(m.target)) dests.push(m.target);\n adj.set(g.id, dests);\n }\n for (const start of adj.keys()) {\n const visited = new Set<string>();\n const stack: string[] = [start];\n while (stack.length > 0) {\n const cur = stack.pop() as string;\n if (visited.has(cur)) continue;\n visited.add(cur);\n const next = adj.get(cur) ?? [];\n for (const n of next) {\n if (n === start) {\n out.push({ severity: 'error', code: 'group-cycle',\n message: `Group cycle detected involving '${start}'`,\n context: { found: start } });\n } else if (!visited.has(n)) {\n stack.push(n);\n }\n }\n }\n }\n return out;\n}\n\n// --------------------------------------------------------------------------\n// §2.3 Monomer resolution\n// --------------------------------------------------------------------------\n\nfunction ruleMonomerResolution(mol: Mol, lib: IMonomerLib | null): ValidationDiagnostic[] {\n const out: ValidationDiagnostic[] = [];\n if (lib === null) return out;\n const polymerByChain = new Map<string, PolymerType>();\n for (const c of mol.chains) polymerByChain.set(c.id, c.polymerType);\n\n for (const a of mol.atoms) {\n const pt = polymerByChain.get(a.bio.chainId);\n if (pt === undefined) continue;\n const resolved = a.monomer;\n const meta = resolved?.meta as { missing?: boolean; ambiguous?: boolean } | undefined;\n if (resolved === null || meta?.missing === true) {\n out.push({ severity: 'warning', code: 'unresolved-monomer',\n message: `Monomer '${a.symbol}' not found in library for ${pt}`,\n context: { chainId: a.bio.chainId, atomId: a.id, found: a.symbol } });\n continue;\n }\n // Case mismatch: if a different-cased symbol exists in the lib and the\n // current direct lookup landed on a placeholder, surface case-mismatch.\n if (meta?.ambiguous === true) continue;\n\n // Inline-SMILES checks: monomers with `meta.smilesHint` set or no rgroups.\n if (resolved.smiles !== undefined && (resolved.smiles).length > 0) {\n if (resolved.rgroups.length === 0)\n out.push({ severity: 'warning', code: 'inline-smiles-without-r-groups',\n message: `Inline-SMILES monomer '${resolved.symbol}' has no R-groups`,\n context: { atomId: a.id, found: resolved.symbol } });\n else if (resolved.rgroups.length > 4)\n out.push({ severity: 'warning', code: 'inline-smiles-too-many-rs',\n message: `Inline-SMILES monomer '${resolved.symbol}' has ${resolved.rgroups.length} R-groups (max 4 expected)`,\n context: { atomId: a.id, found: resolved.rgroups.length } });\n }\n }\n\n // Case-mismatch surfacing: scan atom.symbol against library entries to flag\n // bare-symbol lookups that succeeded only via library coincidence.\n for (const a of mol.atoms) {\n const pt = polymerByChain.get(a.bio.chainId);\n if (pt === undefined) continue;\n const direct = lib.getMonomer(pt, a.symbol);\n if (direct !== null) continue;\n // Look for a different-cased match.\n for (const other of lib.getMonomerSymbolsByType(pt)) {\n if (other !== a.symbol && other.toLowerCase() === a.symbol.toLowerCase()) {\n out.push({ severity: 'info', code: 'case-mismatch',\n message: `Symbol '${a.symbol}' differs from library entry '${other}' only in case`,\n context: { atomId: a.id, found: a.symbol, expected: other } });\n break;\n }\n }\n }\n return out;\n}\n\n// --------------------------------------------------------------------------\n// §2.4 R-group rules\n// --------------------------------------------------------------------------\n\nfunction ruleRGroupRules(mol: Mol, _lib: IMonomerLib | null): ValidationDiagnostic[] {\n const out: ValidationDiagnostic[] = [];\n // Track usage: atomId -> Set of R-group ids consumed by some bond.\n const usage = new Map<number, Set<number>>();\n for (const b of mol.bonds) {\n for (const [atom, ref] of [[b.a1, b.r1], [b.a2, b.r2]] as const) {\n if (ref.kind !== 'numeric') continue;\n const set = usage.get(atom.id) ?? new Set<number>();\n if (set.has(ref.r))\n out.push({ severity: 'error', code: 'rgroup-already-bonded',\n message: `R-group R${ref.r} on atom ${atom.id} already bonded`,\n context: { atomId: atom.id, bondId: b.id, found: ref.r } });\n set.add(ref.r);\n usage.set(atom.id, set);\n }\n }\n\n for (const b of mol.bonds) {\n for (const [atom, ref] of [[b.a1, b.r1], [b.a2, b.r2]] as const) {\n if (ref.kind !== 'numeric' || atom.monomer === null) continue;\n const rs = atom.monomer.rs;\n if (ref.r < 1 || ref.r > rs)\n out.push({ severity: 'error', code: 'rgroup-not-on-monomer',\n message: `R-group R${ref.r} not defined on monomer '${atom.symbol}' (rs=${rs})`,\n context: { atomId: atom.id, bondId: b.id, found: ref.r, expected: `R1..R${rs}` } });\n }\n if (b.kind === 'backbone' && b.r1.kind === 'numeric' && b.r2.kind === 'numeric') {\n if (!(b.r1.r === 2 && b.r2.r === 1))\n out.push({ severity: 'warning', code: 'backbone-rgroup-misaligned',\n message: `Backbone bond uses R${b.r1.r}->R${b.r2.r} (expected R2->R1)`,\n context: { bondId: b.id, found: `R${b.r1.r}->R${b.r2.r}` } });\n }\n if (b.kind === 'branch' && b.r1.kind === 'numeric' && b.r1.r !== 3)\n out.push({ severity: 'warning', code: 'branch-rgroup-misaligned',\n message: `Branch bond uses R${b.r1.r} (expected R3 on parent)`,\n context: { bondId: b.id, found: `R${b.r1.r}` } });\n }\n\n // Unmatched R-groups (info): an atom whose monomer.rs > number of bonds\n // consuming numeric R-groups.\n for (const a of mol.atoms) {\n if (a.monomer === null) continue;\n const consumed = usage.get(a.id);\n const consumedCount = consumed?.size ?? 0;\n if (a.monomer.rs > consumedCount) {\n const unused = a.monomer.rs - consumedCount;\n if (unused > 0 && a.monomer.rs > 0)\n out.push({ severity: 'info', code: 'unmatched-r-group',\n message: `Monomer '${a.symbol}' on atom ${a.id} has ${unused} unused R-group(s); default cap applied`,\n context: { atomId: a.id, found: unused } });\n }\n }\n return out;\n}\n\n// --------------------------------------------------------------------------\n// §2.5 Polymer-type-specific\n// --------------------------------------------------------------------------\n\nfunction rulePolymerTypeSpecific(mol: Mol, _lib: IMonomerLib | null): ValidationDiagnostic[] {\n const out: ValidationDiagnostic[] = [];\n for (const c of mol.chains) {\n if (c.polymerType === 'CHEM' && c.backboneAtoms.length > 1)\n out.push({ severity: 'error', code: 'chem-multiple-monomers',\n message: `CHEM polymer '${c.id}' has ${c.backboneAtoms.length} monomers (expected 1)`,\n context: { chainId: c.id, found: c.backboneAtoms.length } });\n\n if (c.polymerType === 'BLOB') {\n for (const a of c.backboneAtoms) {\n if (a.bio.blobtype === undefined && a.symbol !== 'Bead' && a.symbol !== 'Group')\n out.push({ severity: 'error', code: 'blob-non-blob-symbol',\n message: `BLOB '${c.id}' contains non-blob symbol '${a.symbol}'`,\n context: { chainId: c.id, atomId: a.id, found: a.symbol } });\n }\n }\n\n if (c.polymerType === 'RNA') {\n let prevWasBackbone = false;\n for (let i = 0; i < c.backboneAtoms.length; i++) {\n const a = c.backboneAtoms[i] as Atom;\n if (a.biotype === HelmTypes.BASE && !prevWasBackbone) {\n // A base appearing as a backbone atom is invalid — bases should be\n // branch atoms attached to a sugar.\n out.push({ severity: 'error', code: 'rna-bare-base',\n message: `Bare base '${a.symbol}' without parent sugar in '${c.id}'`,\n context: { chainId: c.id, atomId: a.id } });\n }\n if (a.biotype === HelmTypes.LINKER) {\n // A linker appearing before any sugar in the chain is a \"bare\n // linker\" (allowed for terminal conjugates but flagged as warning).\n const hasPriorSugar = c.backboneAtoms.slice(0, i)\n .some((x) => x.biotype === HelmTypes.SUGAR);\n if (!hasPriorSugar)\n out.push({ severity: 'warning', code: 'rna-bare-linker',\n message: `Bare linker '${a.symbol}' before any sugar in '${c.id}'`,\n context: { chainId: c.id, atomId: a.id } });\n }\n prevWasBackbone = a.biotype === HelmTypes.SUGAR || a.biotype === HelmTypes.LINKER;\n }\n }\n }\n\n // peptide-cyclic-without-closure and dna-emitted-as-rna are parser-side\n // diagnostics; the parser emits them — we mirror them here only when an\n // explicit annotation marker is present. The parser already covers the\n // common cases.\n return out;\n}\n\n// --------------------------------------------------------------------------\n// §2.6 Hydrogen bonds\n// --------------------------------------------------------------------------\n\nfunction ruleHydrogenBonds(mol: Mol, _lib: IMonomerLib | null): ValidationDiagnostic[] {\n const out: ValidationDiagnostic[] = [];\n const polymerByChain = new Map<string, PolymerType>();\n for (const c of mol.chains) polymerByChain.set(c.id, c.polymerType);\n\n const pairCount = new Map<number, number>();\n for (const b of mol.bonds) {\n if (b.kind !== 'hbond') continue;\n pairCount.set(b.a1.id, (pairCount.get(b.a1.id) ?? 0) + 1);\n pairCount.set(b.a2.id, (pairCount.get(b.a2.id) ?? 0) + 1);\n\n const pt1 = polymerByChain.get(b.a1.bio.chainId);\n const pt2 = polymerByChain.get(b.a2.bio.chainId);\n if (pt1 !== 'RNA' || pt2 !== 'RNA')\n out.push({ severity: 'error', code: 'pair-non-rna',\n message: `Hydrogen-bond connects non-RNA chains (${pt1}/${pt2})`,\n context: { bondId: b.id } });\n\n if (b.a1.biotype !== HelmTypes.BASE || b.a2.biotype !== HelmTypes.BASE)\n out.push({ severity: 'warning', code: 'pair-position-not-base',\n message: `Hydrogen-bond endpoints are not both bases`,\n context: { bondId: b.id, found: `${b.a1.biotype}/${b.a2.biotype}` } });\n\n if (!isCanonicalWcPair(b.a1.symbol, b.a2.symbol))\n out.push({ severity: 'warning', code: 'pair-non-canonical',\n message: `Non-canonical pair ${b.a1.symbol}-${b.a2.symbol}`,\n context: { bondId: b.id, found: `${b.a1.symbol}-${b.a2.symbol}` } });\n }\n for (const [atomId, count] of pairCount)\n if (count > 1)\n out.push({ severity: 'warning', code: 'pair-already-paired',\n message: `Base atom ${atomId} participates in ${count} pair bonds`,\n context: { atomId, found: count } });\n return out;\n}\n\nfunction isCanonicalWcPair(a: string, b: string): boolean {\n const x = a.toUpperCase(), y = b.toUpperCase();\n const wc = new Set(['A:T', 'T:A', 'A:U', 'U:A', 'G:C', 'C:G']);\n return wc.has(`${x}:${y}`);\n}\n\n// --------------------------------------------------------------------------\n// §2.7 Ambiguity / repetition\n// --------------------------------------------------------------------------\n\nfunction ruleAmbiguityRepetition(mol: Mol, _lib: IMonomerLib | null): ValidationDiagnostic[] {\n const out: ValidationDiagnostic[] = [];\n for (const a of mol.atoms) {\n const amb = a.bio.ambiguity;\n if (amb === undefined) continue;\n // Parse the raw text once more to detect OR ratios that don't sum to 1\n // and AND ratios that are negative.\n if (a.bio.ambiguityKind === 'and') {\n const parts = parseAmbiguityList(amb, '+');\n for (const p of parts)\n if (p.ratio !== undefined && p.ratio < 0)\n out.push({ severity: 'error', code: 'ratio-and-negative',\n message: `AND ratio for '${p.symbol}' is negative (${p.ratio})`,\n context: { atomId: a.id, found: p.ratio } });\n } else if (a.bio.ambiguityKind === 'or') {\n const parts = parseAmbiguityList(amb, ',');\n let total = 0;\n let any = false;\n for (const p of parts)\n if (typeof p.ratio === 'number') { total += p.ratio; any = true; }\n if (any && Math.abs(total - 1) > 1e-3 && Math.abs(total - 100) > 0.5)\n out.push({ severity: 'info', code: 'ratio-doesnt-sum-to-1',\n message: `OR ratios sum to ${total} (expected 1.0 or 100)`,\n context: { atomId: a.id, found: total } });\n }\n }\n return out;\n}\n\ninterface ParsedAmbiguityPart {\n symbol: string;\n ratio?: number;\n}\n\nfunction parseAmbiguityList(raw: string, sep: string): ParsedAmbiguityPart[] {\n let s = raw.trim();\n if (s.startsWith('(') && s.endsWith(')')) s = s.slice(1, -1);\n const parts = s.split(sep);\n const out: ParsedAmbiguityPart[] = [];\n for (const p of parts) {\n const trimmed = p.trim();\n if (trimmed.length === 0) continue;\n const idx = trimmed.indexOf(':');\n if (idx < 0) { out.push({ symbol: trimmed }); continue; }\n const sym = trimmed.slice(0, idx);\n const rest = trimmed.slice(idx + 1);\n const n = parseFloat(rest);\n if (Number.isFinite(n)) out.push({ symbol: sym, ratio: n });\n else out.push({ symbol: sym });\n }\n return out;\n}\n\n// --------------------------------------------------------------------------\n// §2.8 Annotations\n// --------------------------------------------------------------------------\n\nfunction ruleAnnotations(mol: Mol, _lib: IMonomerLib | null): ValidationDiagnostic[] {\n const out: ValidationDiagnostic[] = [];\n const chainIds = new Set(mol.chains.map((c) => c.id));\n for (const key of mol.annotations.perPolymer.keys()) {\n if (!chainIds.has(key))\n out.push({ severity: 'warning', code: 'annotation-unknown-polymer',\n message: `Annotation references unknown polymer '${key}'`,\n context: { found: key } });\n }\n return out;\n}\n\n// --------------------------------------------------------------------------\n// §2.9 Performance limits\n// --------------------------------------------------------------------------\n\nfunction rulePerformanceLimits(mol: Mol, _lib: IMonomerLib | null): ValidationDiagnostic[] {\n const out: ValidationDiagnostic[] = [];\n for (const c of mol.chains) {\n if (c.backboneAtoms.length > 10000)\n out.push({ severity: 'info', code: 'polymer-too-long',\n message: `Polymer '${c.id}' has ${c.backboneAtoms.length} atoms (> 10000); renderer may switch to rows layout`,\n context: { chainId: c.id, found: c.backboneAtoms.length } });\n }\n let crossCount = 0;\n for (const b of mol.bonds)\n if (b.kind === 'cross-polymer' || b.kind === 'hbond') crossCount += 1;\n if (crossCount > 1000)\n out.push({ severity: 'info', code: 'connection-count-high',\n message: `${crossCount} cross-polymer/hbond connections (> 1000); rendering may be slow`,\n context: { found: crossCount } });\n for (const g of mol.groups) {\n if (g.kind === 'bracket' && g.repeat !== undefined && g.repeat.max > 10000)\n out.push({ severity: 'warning', code: 'bracket-repeat-too-large',\n message: `Bracket repeat upper bound ${g.repeat.max} > 10000`,\n context: { found: g.repeat.max } });\n }\n return out;\n}\n\n// --------------------------------------------------------------------------\n// Re-exports\n// --------------------------------------------------------------------------\n\nexport type { Monomer, Bond };\n","// T-0301 — Layout-friendly chain abstraction.\n//\n// The parser already partitions atoms/bonds into `mol.chains`; each chain\n// has its backbone in source order. The layout layer needs slightly more\n// structure than the raw `Chain`:\n//\n// - a parallel `bases[]` array (only RNA sugars carry a base; everything\n// else is `null`) so per-position iteration is O(1);\n// - explicit lists of backbone-bonds (consecutive `R2 -> R1` bonds) and\n// base-bonds (sugar `R3 -> R1 base` bonds);\n// - a cyclicity flag derived from cross-polymer bonds that close the\n// chain head-to-tail (matching the legacy editor's `layoutCircle`\n// trigger).\n//\n// See ARCHITECTURE.md §3.5 and LEGACY-EDITOR-NOTES.md §Chain.ts.\n\nimport type {Atom, Bond, Mol} from '../core/model';\nimport {HelmTypes, PolymerTypes} from '../core/constants';\n\n/**\n * Polymer kind as used by the layout strategy selector. `BLOB` is treated\n * as a single-atom container and gets the simplest possible layout.\n */\nexport type LayoutPolymerType = 'PEPTIDE' | 'RNA' | 'CHEM' | 'BLOB';\n\n/**\n * Layout-time view of a HELM chain. Every array is `readonly` and parallel\n * by index where applicable (`bases[i]` is attached to `backbone[i]`).\n */\nexport interface LayoutChain {\n readonly id: string;\n readonly polymerType: LayoutPolymerType;\n /** Backbone atoms in source order (sugar+linker for RNA). */\n readonly backbone: readonly Atom[];\n /** Parallel to `backbone`; only RNA sugars carry a non-null base. */\n readonly bases: readonly (Atom | null)[];\n /** Backbone (`R2 -> R1`) bonds between consecutive backbone atoms. */\n readonly backboneBonds: readonly Bond[];\n /** Parallel to `bases`; the `R3 -> R1` branch bond, or null. */\n readonly baseBonds: readonly (Bond | null)[];\n /** True iff a cross-polymer bond closes the chain head-to-tail. */\n readonly isCyclic: boolean;\n /**\n * Phase 33 (T-3301) — Mirrors `Chain.strandType` from the parsed\n * `Mol`. Layout uses it to decide which side of an H-bond duplex\n * anchors (ss) and which moves (as).\n */\n readonly strandType?: 'ss' | 'as';\n}\n\n/**\n * Build a `LayoutChain[]` from a parsed `Mol`.\n *\n * Iterates `mol.chains` in source order; for each chain it:\n *\n * 1. Collects the backbone bonds in source order (kind `'backbone'`).\n * 2. For each backbone atom, scans branch bonds (kind `'branch'`) for an\n * attached BASE — the typical RNA sugar pattern. The first matching\n * branch is used so the algorithm is deterministic even when a sugar\n * has multiple R3 branches (which is invalid HELM, but we tolerate it).\n * 3. Looks at `mol.bonds` (cross-polymer scope) for a bond linking this\n * chain's first atom (via `R1`) to its last atom (via `R2`); that\n * pattern is the legacy editor's \"cyclic\" trigger.\n */\nexport function buildLayoutChains(mol: Mol): LayoutChain[] {\n const layoutChains: LayoutChain[] = [];\n\n // Build a quick atom -> chainId map so we can recognise self-closure bonds.\n const atomChainId = new Map<number, string>();\n for (const chain of mol.chains) {\n for (const atom of chain.backboneAtoms) atomChainId.set(atom.id, chain.id);\n }\n // Bases too (they belong to their owning sugar's chain).\n for (const chain of mol.chains) {\n for (const a of chain.backboneAtoms) {\n if (a.branchAtom !== undefined) atomChainId.set(a.branchAtom.id, chain.id);\n }\n }\n\n for (const chain of mol.chains) {\n const polymerType = mapPolymerType(chain.polymerType);\n const backbone = chain.backboneAtoms;\n const bases: (Atom | null)[] = [];\n const baseBonds: (Bond | null)[] = [];\n\n const backboneBonds: Bond[] = [];\n for (const b of chain.bonds)\n if (b.kind === 'backbone') backboneBonds.push(b);\n\n // Discover bases per backbone atom for RNA chains.\n if (polymerType === 'RNA') {\n for (const sugar of backbone) {\n if (sugar.biotype !== HelmTypes.SUGAR) {\n bases.push(null);\n baseBonds.push(null);\n continue;\n }\n let foundBase: Atom | null = null;\n let foundBond: Bond | null = null;\n for (const b of chain.bonds) {\n if (b.kind !== 'branch') continue;\n const otherEnd = b.a1.id === sugar.id ? b.a2 : (b.a2.id === sugar.id ? b.a1 : null);\n if (otherEnd === null) continue;\n if (otherEnd.biotype === HelmTypes.BASE) {\n foundBase = otherEnd;\n foundBond = b;\n break;\n }\n }\n bases.push(foundBase);\n baseBonds.push(foundBond);\n }\n } else {\n for (let i = 0; i < backbone.length; i++) {\n bases.push(null);\n baseBonds.push(null);\n }\n }\n\n const isCyclic = detectSelfClosure(mol, chain.id, backbone, atomChainId);\n\n layoutChains.push({\n id: chain.id,\n polymerType,\n backbone,\n bases,\n backboneBonds,\n baseBonds,\n isCyclic,\n ...(chain.strandType !== undefined ? { strandType: chain.strandType } : {}),\n });\n }\n\n return layoutChains;\n}\n\nfunction mapPolymerType(p: string): LayoutPolymerType {\n switch (p) {\n case PolymerTypes.PEPTIDE: return 'PEPTIDE';\n case PolymerTypes.RNA: return 'RNA';\n case PolymerTypes.CHEM: return 'CHEM';\n case PolymerTypes.BLOB: return 'BLOB';\n default: return 'BLOB';\n }\n}\n\n/**\n * Cyclic if there is a non-backbone bond inside the same chain (or stored as\n * cross-polymer with same chain on both sides) linking the first backbone\n * atom (via R1) to the last (via R2). The parser keeps chain-internal bonds\n * on `chain.bonds`; cross-polymer bonds live on `mol.bonds` and reference\n * atoms from any chain. We check both, but only count bonds that connect\n * `first.R1 <-> last.R2`.\n */\nfunction detectSelfClosure(\n mol: Mol,\n chainId: string,\n backbone: readonly Atom[],\n atomChainId: Map<number, string>,\n): boolean {\n if (backbone.length < 2) return false;\n const first = backbone[0]!;\n const last = backbone[backbone.length - 1]!;\n\n for (const b of mol.bonds) {\n if (b.kind === 'backbone' || b.kind === 'branch') continue;\n const c1 = atomChainId.get(b.a1.id);\n const c2 = atomChainId.get(b.a2.id);\n if (c1 !== chainId || c2 !== chainId) continue;\n const matchesEnds =\n (b.a1.id === last.id && b.a2.id === first.id) ||\n (b.a2.id === last.id && b.a1.id === first.id);\n if (!matchesEnds) continue;\n // Verify R1 <-> R2 endpoints.\n const r1 = b.a1.id === first.id ? b.r1 : b.r2;\n const r2 = b.a1.id === last.id ? b.r1 : b.r2;\n const r1IsOne = r1.kind === 'numeric' && r1.r === 1;\n const r2IsTwo = r2.kind === 'numeric' && r2.r === 2;\n if (r1IsOne && r2IsTwo) return true;\n }\n return false;\n}\n","// T-0302 — Linear (straight-line) chain layout.\n//\n// Each backbone atom is placed at `origin + (i * step, 0)` where\n// `step = bondscale (1.6) * bondLength`. The default `bondLength = 40` so\n// the default step is `64px`, matching the legacy editor (`helm.js` declares\n// `bondscale = 1.6`; see LEGACY-EDITOR-NOTES.md §\"helm.js\").\n//\n// Returns a sparse `Map<atomId, Point>` — bases are NOT positioned here\n// (that is the responsibility of `placeBases` in T-0306).\n\nimport type {Point} from '../util/types';\nimport type {LayoutChain} from './chain-builder';\n\n/** Magic bond-scale factor from the legacy editor. */\nexport const BOND_SCALE = 1.6;\n/** Default model-space bond length. */\nexport const DEFAULT_BOND_LENGTH = 40;\n/** Step distance (horizontal monomer-to-monomer gap). 64 px at defaults. */\nexport const STEP = BOND_SCALE * DEFAULT_BOND_LENGTH;\n\n// --------------------------------------------------------------------------\n// Vertical-gap factors (T-1501, Phase 15)\n//\n// Phase 12 used multipliers of `step = BOND_SCALE * bondLength` (so the\n// effective row gap was 1.4 × 64 = 89.6 px). The user reported the rows\n// were still too far apart and requested every vertical gap match\n// **1.5 × bondLength = 60 px** at the default bondLength=40. The\n// multipliers below are expressed as fractions of `step` so the existing\n// call sites (`gapMul * step`) continue to compose correctly.\n//\n// Source: user request 2026-05-17 — \"vertical distance should be 1.5 bond\n// lengths\".\n// Reference: SPECIFICATION.md §6 (Layout — vertical rhythm).\n// --------------------------------------------------------------------------\n\n/** Row spacing as an ABSOLUTE pixel value: 1.5 × bondLength = 60 px. */\nexport const ROW_SPACING = 1.5 * DEFAULT_BOND_LENGTH;\n\n/** Fragment gap (between disconnected chains). 1.5 × bondLength = 60 px. */\nexport const FRAGMENT_GAP = 1.5 * DEFAULT_BOND_LENGTH;\n\n/** H-bond stack gap (anti-parallel duplex). 1.5 × bondLength = 60 px. */\nexport const HBOND_GAP = 1.5 * DEFAULT_BOND_LENGTH;\n\n/** Cross-chain gap (cross-polymer bond between two chains). 1.5 × bondLength = 60 px. */\nexport const CROSS_CHAIN_GAP = 1.5 * DEFAULT_BOND_LENGTH;\n\n// Step-relative factors retained for backward compatibility with existing\n// callers that already multiply by `step`. Each is set so that\n// `factor * step === 1.5 × bondLength`, i.e. factor = 1.5 / BOND_SCALE = 0.9375.\n\n/** Step-relative factor for `layoutDisconnectedFragments` (= 1.5 / 1.6 = 0.9375). */\nexport const FRAGMENT_GAP_FACTOR = (1.5 * DEFAULT_BOND_LENGTH) / STEP;\n\n/** Step-relative factor for the anti-parallel H-bond gap. */\nexport const HBOND_GAP_FACTOR = (1.5 * DEFAULT_BOND_LENGTH) / STEP;\n\n/** Step-relative factor for the cross-polymer cross-chain gap. */\nexport const CROSS_CHAIN_GAP_FACTOR = (1.5 * DEFAULT_BOND_LENGTH) / STEP;\n\nexport interface LineLayoutOptions {\n /** Model-space distance between consecutive backbone atoms. Default `40`. */\n bondLength?: number;\n /** World position of the first backbone atom. Default `(0, 0)`. */\n origin?: Point;\n}\n\n/**\n * Lay out `chain.backbone` as a straight horizontal line of points. Returns\n * a `Map<atomId, Point>` keyed by atom id; the caller merges this into the\n * Mol's global position table.\n */\nexport function layoutLine(chain: LayoutChain, options?: LineLayoutOptions): Map<number, Point> {\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n const origin = options?.origin ?? {x: 0, y: 0};\n const step = BOND_SCALE * bondLength;\n const out = new Map<number, Point>();\n for (let i = 0; i < chain.backbone.length; i++) {\n const atom = chain.backbone[i]!;\n out.set(atom.id, {x: origin.x + i * step, y: origin.y});\n }\n return out;\n}\n","// T-0303 — Circular chain layout.\n//\n// For cyclic chains the legacy editor places atoms equispaced on a circle:\n// the radius is chosen so the chord length between adjacent atoms equals\n// `step = bondscale * bondLength`. With `n` atoms the chord/sine identity\n// gives `r = step / (2 * sin(pi / n))`. See LEGACY-EDITOR-NOTES.md §Layout.ts\n// (`layoutCircle`, lines 173-188).\n//\n// Single-atom and two-atom degenerate cases fall back to a line so the\n// formula's `sin(pi/n)` term never divides by zero or becomes infinite.\n\nimport type {Point} from '../util/types';\nimport type {LayoutChain} from './chain-builder';\nimport {BOND_SCALE, DEFAULT_BOND_LENGTH, layoutLine} from './line';\n\nexport interface CircleLayoutOptions {\n /** Model-space distance between adjacent backbone atoms (chord length). */\n bondLength?: number;\n /** World position of the circle's center. Default `(0, 0)`. */\n origin?: Point;\n /** Angle of the first atom in degrees (counter-clockwise from +X). Default `-90`. */\n startDegrees?: number;\n}\n\nconst DEG2RAD = Math.PI / 180;\n\n/**\n * Lay out the backbone as a circle. Returns `Map<atomId, Point>`.\n *\n * For `n <= 2` we fall back to a straight line — the chord formula isn't\n * meaningful, and the legacy editor takes the same branch implicitly via\n * `layoutLine`.\n */\nexport function layoutCircle(chain: LayoutChain, options?: CircleLayoutOptions): Map<number, Point> {\n const n = chain.backbone.length;\n if (n <= 2) {\n const lineOpts: {bondLength?: number; origin?: Point} = {};\n if (options?.bondLength !== undefined) lineOpts.bondLength = options.bondLength;\n if (options?.origin !== undefined) lineOpts.origin = options.origin;\n return layoutLine(chain, lineOpts);\n }\n\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n const origin = options?.origin ?? {x: 0, y: 0};\n const startDegrees = options?.startDegrees ?? -90;\n const step = BOND_SCALE * bondLength;\n const r = step / (2 * Math.sin(Math.PI / n));\n\n const out = new Map<number, Point>();\n for (let i = 0; i < n; i++) {\n const atom = chain.backbone[i]!;\n const deg = startDegrees + (i * 360) / n;\n const rad = deg * DEG2RAD;\n out.set(atom.id, {\n x: origin.x + r * Math.cos(rad),\n y: origin.y + r * Math.sin(rad),\n });\n }\n return out;\n}\n","// T-0304 — Row-wrapped chain layout for long backbones.\n//\n// The legacy editor wraps chains longer than 50 atoms into rows of 10\n// monomers (`layoutRows` in Layout.ts, see LEGACY-EDITOR-NOTES.md §15).\n// Rows stack vertically with extra room to accommodate RNA bases below\n// each sugar — we use `2.5 * step` row spacing (the legacy editor uses\n// `delta * 2.5` for the same reason).\n//\n// The serpentine winds left-to-right then right-to-left, matching the\n// legacy renderer so connecting bonds between row ends remain short.\n\nimport type {Point} from '../util/types';\nimport type {LayoutChain} from './chain-builder';\nimport {BOND_SCALE, DEFAULT_BOND_LENGTH} from './line';\n\nexport interface RowsLayoutOptions {\n /** Model-space distance between adjacent backbone atoms. Default `40`. */\n bondLength?: number;\n /** World position of the first row's first atom. */\n origin?: Point;\n /** Number of monomers per row. Default `10` (legacy editor magic number). */\n perRow?: number;\n /**\n * Row vertical spacing as a multiplier of `step`. Default tuned in\n * Phase 15 (T-1501) so the absolute gap equals `1.5 × bondLength`\n * (= 60 px at the default bondLength=40). Source: user request\n * 2026-05-17 — \"vertical distance should be 1.5 bond lengths\".\n */\n rowSpacing?: number;\n}\n\n/** Default monomers per row, mirroring the legacy `layoutRows(bondlength, 10)`. */\nexport const DEFAULT_PER_ROW = 10;\n/**\n * Row spacing multiplier (rows stack `rowSpacing * step` apart).\n *\n * Phase 15 (T-1501): set so that `rowSpacing × step = 1.5 × bondLength`,\n * i.e. `factor = 1.5 / BOND_SCALE = 0.9375`. The product is the exact\n * `ROW_SPACING` constant in `line.ts` (60 px at default bondLength=40).\n * Source: user request 2026-05-17.\n */\nexport const DEFAULT_ROW_SPACING = 1.5 / BOND_SCALE;\n\n/**\n * Wrap `chain.backbone` into rows. Returns `Map<atomId, Point>`.\n *\n * Rows are serpentine: row 0 left-to-right at y=0, row 1 right-to-left at\n * y=spacing, row 2 left-to-right at y=2*spacing, and so on. This keeps the\n * \"wrap\" bond between rows short. The leftmost x of each row is\n * `origin.x`; the rightmost reaches `origin.x + (perRow - 1) * step`.\n */\nexport function layoutRows(chain: LayoutChain, options?: RowsLayoutOptions): Map<number, Point> {\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n const origin = options?.origin ?? {x: 0, y: 0};\n const perRow = Math.max(1, options?.perRow ?? DEFAULT_PER_ROW);\n const rowSpacingMul = options?.rowSpacing ?? DEFAULT_ROW_SPACING;\n const step = BOND_SCALE * bondLength;\n const ySpacing = rowSpacingMul * step;\n\n const out = new Map<number, Point>();\n for (let i = 0; i < chain.backbone.length; i++) {\n const atom = chain.backbone[i]!;\n const row = Math.floor(i / perRow);\n const col = i % perRow;\n const x = (row % 2 === 0)\n ? origin.x + col * step\n : origin.x + (perRow - 1 - col) * step;\n const y = origin.y + row * ySpacing;\n out.set(atom.id, {x, y});\n }\n return out;\n}\n","// T-0305 — Inner-circle chain layout.\n//\n// Some peptide / hybrid chains have a linear tail, then a cycle, then\n// another linear tail (e.g. a lasso or a cyclic ring with substituents).\n// The legacy `layoutInnerCircle` finds the largest non-backbone bond\n// pair within the chain and draws the enclosed segment on a circle, with\n// the rest of the chain extending as tangent linear tails.\n//\n// **Simplification (documented deviation)**: the legacy implementation\n// \"only finds the largest non-backbone bond pair within one chain,\n// ignoring topology\" (LEGACY-EDITOR-NOTES.md §Layout.ts hacks). We follow\n// the same simplification:\n//\n// 1. Find the single non-backbone, non-branch bond (kind:\n// `'cross-polymer'`) that links two backbone atoms within the chain\n// and whose endpoints are not adjacent (i.e. forms a genuine inner\n// cycle).\n// 2. If found, the segment between those two backbone indices is laid\n// out as a circle; the tail before the cycle is laid out\n// horizontally to the left of the circle, the tail after the cycle\n// horizontally to the right.\n// 3. If multiple candidate bonds exist, we pick the one enclosing the\n// largest backbone segment.\n// 4. If no candidate bond exists, fall back to `layoutLine`.\n//\n// More elaborate cases (multiple disjoint cycles, nested cycles) are not\n// handled here; the layout-service can be extended later.\n\nimport type {Bond} from '../core/model';\nimport type {Point} from '../util/types';\nimport type {LayoutChain} from './chain-builder';\nimport {BOND_SCALE, DEFAULT_BOND_LENGTH, layoutLine} from './line';\nimport {layoutCircle} from './circle';\n\nexport interface InnerCircleLayoutOptions {\n bondLength?: number;\n origin?: Point;\n}\n\n/**\n * A qualifying inner-cycle closure bond: a non-backbone, non-branch bond whose\n * BOTH endpoints are backbone atoms of `chain`, that spans ≥ 2 positions (not\n * adjacent) and is not the head-to-tail backbone closure. Returns the\n * backbone-position span `[lo, hi]` of each such bond.\n */\nfunction innerCycleSpans(\n chain: LayoutChain,\n mol: {bonds: readonly Bond[]},\n): Array<{lo: number; hi: number}> {\n const posInBackbone = new Map<number, number>();\n for (let i = 0; i < chain.backbone.length; i++)\n posInBackbone.set(chain.backbone[i]!.id, i);\n const last = chain.backbone.length - 1;\n const spans: Array<{lo: number; hi: number}> = [];\n for (const b of mol.bonds) {\n if (b.kind === 'backbone' || b.kind === 'branch') continue;\n const p1 = posInBackbone.get(b.a1.id);\n const p2 = posInBackbone.get(b.a2.id);\n if (p1 === undefined || p2 === undefined) continue;\n const lo = Math.min(p1, p2);\n const hi = Math.max(p1, p2);\n if (hi - lo < 2) continue; // adjacent — not a real cycle\n if (lo === 0 && hi === last) continue; // head-to-tail = the cyclic case\n spans.push({lo, hi});\n }\n return spans;\n}\n\n/**\n * True iff `chain` carries at least one inner-cycle closure bond (a side-chain\n * / cross-link bond forming a loop within the backbone). Used by the layout\n * orchestrator to route such chains to {@link layoutInnerCircle} BEFORE the\n * long-chain row-wrap, so a cross-linked peptide draws as a ring + tails rather\n * than a serpentine grid.\n */\nexport function hasInnerCycle(\n chain: LayoutChain,\n mol: {bonds: readonly Bond[]} | null,\n): boolean {\n if (mol === null) return false;\n return innerCycleSpans(chain, mol).length > 0;\n}\n\n/**\n * Lay out a chain that has one inner cycle plus tails. Falls back to\n * `layoutLine` when no inner cycle is detected.\n */\nexport function layoutInnerCircle(\n chain: LayoutChain,\n mol: {bonds: readonly Bond[]} | null,\n options?: InnerCircleLayoutOptions,\n): Map<number, Point> {\n if (mol === null)\n return layoutLine(chain, options);\n\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n const origin = options?.origin ?? {x: 0, y: 0};\n const step = BOND_SCALE * bondLength;\n\n // Collect EVERY inner-cycle closure bond and place the circle over the\n // UNION of their spans. The legacy code used only the single widest bond,\n // which left staggered cross-links (e.g. 10:13 + 14:22, where no one bond\n // covers 10..22) partly on a tail with a chord cutting across it. Spanning\n // the union puts every cross-linked residue on the one ring, with the\n // un-cross-linked residues as clean linear tails on either side.\n const spans = innerCycleSpans(chain, mol);\n if (spans.length === 0)\n return layoutLine(chain, options);\n let bestStart = spans[0]!.lo;\n let bestEnd = spans[0]!.hi;\n for (const s of spans) {\n if (s.lo < bestStart) bestStart = s.lo;\n if (s.hi > bestEnd) bestEnd = s.hi;\n }\n\n // Lay out the cycle segment on a circle.\n const cycleAtoms = chain.backbone.slice(bestStart, bestEnd + 1);\n const cycleN = cycleAtoms.length;\n // Circle radius matches `layoutCircle` (chord = step):\n // r = step / (2 * sin(pi / n))\n // We need it here to position the right tail *outside* the circle.\n const cycleRadius = step / (2 * Math.sin(Math.PI / cycleN));\n\n const cycleChain: LayoutChain = {\n id: chain.id,\n polymerType: chain.polymerType,\n backbone: cycleAtoms,\n bases: new Array(cycleN).fill(null),\n backboneBonds: [],\n baseBonds: new Array(cycleN).fill(null),\n isCyclic: true,\n };\n\n // Position the circle so its center sits to the right of the left tail's\n // end by `step + cycleRadius` (so the leftmost cycle atom — at angle 180°\n // — lands at distance `step` from the last left-tail atom).\n const leftTailCount = bestStart;\n const circleCenter: Point = {\n x: origin.x + leftTailCount * step + cycleRadius,\n y: origin.y,\n };\n const cyclePositions = layoutCircle(cycleChain, {\n bondLength,\n origin: circleCenter,\n startDegrees: 180,\n });\n\n const out = new Map<number, Point>();\n // Left tail: positions 0..bestStart-1 at y=origin.y.\n for (let i = 0; i < bestStart; i++) {\n const atom = chain.backbone[i]!;\n out.set(atom.id, {x: origin.x + i * step, y: origin.y});\n }\n // Cycle segment.\n for (const [aid, p] of cyclePositions) out.set(aid, p);\n // Right tail: positions bestEnd+1..end at y=origin.y.\n //\n // T-1404 layout fix: the prior formula was\n // `circleCenter.x + step + leftTailCount`,\n // which added an unscaled `leftTailCount` (atom *count*, not pixels) to a\n // pixel value — a dimensional error that made the right tail begin\n // ~5 px from the circle's right edge for cycles of moderate size\n // (n >= 6). The right tail must start one `step` past the circle's\n // RIGHTMOST atom (which sits at `circleCenter.x + cycleRadius` when the\n // cycle's startDegrees=180 produces an atom at angle 0).\n const rightStartX = circleCenter.x + cycleRadius + step;\n for (let i = bestEnd + 1; i < chain.backbone.length; i++) {\n const atom = chain.backbone[i]!;\n const tailIdx = i - (bestEnd + 1);\n out.set(atom.id, {x: rightStartX + tailIdx * step, y: origin.y});\n }\n return out;\n}\n","// Phase 34 (T-3401) — Cloverleaf / RNA secondary-structure layout.\n//\n// Layouts an RNA chain whose intra-chain `hbond` connections define a\n// secondary structure (hairpins, internal loops / bulges, multi-branch\n// junctions, the canonical four-arm tRNA cloverleaf).\n//\n// Algorithm: a clarified Bruccoleri-Heinemann / \"NAView-lite\" approach.\n//\n// 1. Build a non-crossing pair-table from the chain's intra-chain\n// `kind === 'hbond'` connections. Pseudoknots are silently dropped\n// by a greedy non-crossing filter (the rejected H-bond still\n// exists on the Mol; only its impact on layout is suppressed).\n//\n// 2. Decompose the pair-table into a tree of two node kinds:\n// Stem = a maximal run of stacked base pairs forming a\n// ladder; `numPairs` consecutive (i, j) pairings\n// with no unpaired bases between rungs on EITHER\n// rail.\n// LoopNode = a single closed loop; its `nodes` list mixes\n// `UnpairedRun` segments and child `Stem`s in\n// 5'->3' source order around the loop circle.\n//\n// 3. Recursively place atoms:\n// - Stem: straight antiparallel ladder of pitch STEP and\n// rail gap HBOND_GAP. The two rails carry indices\n// [from..from+2*numPairs-2] and [to..to-2*numPairs+2] in\n// opposite directions.\n// - Hairpin loop: a circle whose closing chord equals\n// HBOND_GAP. The closing pair sits on the chord; remaining\n// occupants (unpaired atoms AND child-stem closing-pair\n// atoms) are equally spaced at arc length STEP.\n// - Multi-loop: same as hairpin but with >=2 child stems\n// radiating outward at their angular positions on the\n// circle.\n// - Exterior loop (no closing pair): walked as a straight\n// line; child stems hang off perpendicular to the line.\n//\n// 4. Linkers and sugars are placed uniformly — every backbone atom\n// (RNA's alternating sugar+linker pattern) occupies one ladder\n// rung or one loop occupant at STEP intervals along the rail or\n// circle. This matches inner-circle.ts / circle.ts where the\n// chord between adjacent backbone atoms = STEP regardless of\n// biotype.\n//\n// Determinism: no Math.random, no Date.now, no module-level mutable\n// state. Pair-table sort is total-ordered on (lo asc, hi desc). The\n// returned Map iterates in insertion order; we insert in backbone-\n// index order via the recursive walk.\n//\n// References:\n// - Bruccoleri R E, Heinemann M (1988). \"An improved algorithm for\n// nucleic acid secondary structure display.\" Comp App in\n// Biosciences 4, 167-173.\n// - HARNESS.md §10.5.7 — structural invariants are testable without\n// headed verification; the renderer's golden SVG is sentinel-\n// `pending` until a human reviews.\n\nimport type {Bond, Mol} from '../core/model';\nimport type {Point, Vec2} from '../util/types';\nimport type {LayoutChain} from './chain-builder';\nimport {BOND_SCALE, DEFAULT_BOND_LENGTH, HBOND_GAP} from './line';\n\n// ===========================================================================\n// Public types\n// ===========================================================================\n\nexport interface CloverleafLayoutOptions {\n /** Model-space distance between adjacent backbone atoms. Default 40. */\n bondLength?: number;\n /** World position of the exterior loop origin. Default (0, 0). */\n origin?: Point;\n /** Outward direction of the exterior backbone walk. Default (1, 0). */\n rootDirection?: Vec2;\n}\n\n/**\n * A stacked ladder of `numPairs` base pairs. `fromIdx` is the 5'-most\n * sugar's backbone index on the near rail; `toIdx` is the 3'-most\n * sugar's backbone index on the FAR rail (so `pair[fromIdx] === toIdx`).\n *\n * The stem occupies backbone indices\n * near rail: [fromIdx .. fromIdx + 2*numPairs - 2]\n * far rail: [toIdx - 2*numPairs + 2 .. toIdx] (walked 3'->5')\n *\n * `child` is the loop closed by the stem's innermost pair\n * `(fromIdx + 2*numPairs - 2, toIdx - 2*numPairs + 2)`.\n */\nexport interface Stem {\n readonly kind: 'stem';\n readonly fromIdx: number;\n readonly toIdx: number;\n readonly numPairs: number;\n readonly child: LoopNode;\n}\n\n/** A contiguous run of unpaired backbone indices [from..to] inclusive. */\nexport interface UnpairedRun {\n readonly kind: 'unpaired';\n readonly from: number;\n readonly to: number;\n}\n\n/**\n * A single closed loop. `closingPair` is null only for the exterior\n * loop. `nodes` lists Stem and UnpairedRun children in 5'->3' source\n * order; this IS the angular walk order around the loop circle.\n */\nexport interface LoopNode {\n readonly kind: 'loop';\n readonly nodes: ReadonlyArray<Stem | UnpairedRun>;\n readonly closingPair: readonly [number, number] | null;\n}\n\n// ===========================================================================\n// Pair-table + detection\n// ===========================================================================\n\n/**\n * Walk `chain.backbone` plus its base branches to identify which atom\n * ids belong to which backbone index. Bases bond to sugars; when the\n * parser records an hbond on a BASE atom we map it back to the owning\n * sugar's backbone index via this table.\n */\nfunction buildIndexMaps(chain: LayoutChain): {\n sugarToIdx: Map<number, number>;\n baseToIdx: Map<number, number>;\n} {\n const sugarToIdx = new Map<number, number>();\n const baseToIdx = new Map<number, number>();\n for (let i = 0; i < chain.backbone.length; i++) {\n sugarToIdx.set(chain.backbone[i]!.id, i);\n const base = chain.bases[i];\n if (base !== null && base !== undefined) baseToIdx.set(base.id, i);\n }\n return {sugarToIdx, baseToIdx};\n}\n\n/** Resolve a bond endpoint to a backbone index of this chain, or `null`. */\nfunction resolveEndpointIdx(\n atomId: number,\n sugarToIdx: Map<number, number>,\n baseToIdx: Map<number, number>,\n): number | null {\n const direct = sugarToIdx.get(atomId);\n if (direct !== undefined) return direct;\n const viaBase = baseToIdx.get(atomId);\n if (viaBase !== undefined) return viaBase;\n return null;\n}\n\n/**\n * A bond is an \"intra-chain pair\" when it satisfies either:\n * (a) `bond.kind === 'hbond'`, OR\n * (b) `bond.kind === 'cross-polymer'` with BOTH R-group refs of\n * kind `'pair'`.\n *\n * Both endpoints must resolve to atoms inside `chain`.\n */\nfunction isIntraChainPairBond(\n bond: Bond,\n sugarToIdx: Map<number, number>,\n baseToIdx: Map<number, number>,\n): {lo: number; hi: number} | null {\n const isHbondKind = bond.kind === 'hbond';\n const isPairCross =\n bond.kind === 'cross-polymer'\n && typeof bond.r1 === 'object' && bond.r1 !== null\n && (bond.r1 as {kind?: string}).kind === 'pair'\n && typeof bond.r2 === 'object' && bond.r2 !== null\n && (bond.r2 as {kind?: string}).kind === 'pair';\n if (!isHbondKind && !isPairCross) return null;\n const i = resolveEndpointIdx(bond.a1.id, sugarToIdx, baseToIdx);\n const j = resolveEndpointIdx(bond.a2.id, sugarToIdx, baseToIdx);\n if (i === null || j === null) return null;\n if (i === j) return null;\n return {lo: Math.min(i, j), hi: Math.max(i, j)};\n}\n\n/**\n * Does this RNA chain carry at least one intra-chain pair-style hbond?\n * Used by `layout-service.ts pickStrategy` to decide whether to pick\n * the cloverleaf strategy. O(B) walk with an early-exit on first hit.\n */\nexport function hasIntraChainHbonds(\n chain: LayoutChain,\n mol: Pick<Mol, 'bonds'>,\n): boolean {\n if (chain.polymerType !== 'RNA') return false;\n if (chain.backbone.length === 0) return false;\n const {sugarToIdx, baseToIdx} = buildIndexMaps(chain);\n for (const b of mol.bonds) {\n if (isIntraChainPairBond(b, sugarToIdx, baseToIdx) !== null) return true;\n }\n return false;\n}\n\n/**\n * Build the non-crossing pair table for `chain`. The table is a\n * length-N `Int32Array` where `pair[i] === j` (and `pair[j] === i`)\n * for every accepted pair, and `-1` for unpaired indices.\n *\n * Conflicts are resolved deterministically:\n * - Sort candidate pairs by (lo asc, hi desc) so the OUTERMOST pair\n * wins on conflict (the inner pair of a pseudoknot is dropped).\n * - Greedy accept: skip any candidate that crosses an already-\n * accepted pair or whose endpoints are already paired.\n *\n * Pseudoknots are silently linearized (the bond still exists on the\n * Mol so the renderer still draws the dashed hbond stroke, but the\n * layout does not constrain its endpoints).\n */\nexport function buildPairTable(\n chain: LayoutChain,\n mol: Pick<Mol, 'bonds'>,\n): Int32Array {\n const N = chain.backbone.length;\n const pair = new Int32Array(N).fill(-1);\n if (N === 0) return pair;\n const {sugarToIdx, baseToIdx} = buildIndexMaps(chain);\n const candidates: Array<readonly [number, number]> = [];\n for (const b of mol.bonds) {\n const r = isIntraChainPairBond(b, sugarToIdx, baseToIdx);\n if (r !== null) candidates.push([r.lo, r.hi] as const);\n }\n candidates.sort((a, b) => a[0] - b[0] || b[1] - a[1]);\n const accepted: Array<readonly [number, number]> = [];\n for (const cand of candidates) {\n const [lo, hi] = cand;\n let conflict = false;\n for (const [a, c] of accepted) {\n const fullyDisjoint = (hi < a) || (lo > c);\n const fullyNested = (lo > a && hi < c) || (lo < a && hi > c);\n if (!fullyDisjoint && !fullyNested) { conflict = true; break; }\n }\n if (conflict) continue;\n if (pair[lo] !== -1 || pair[hi] !== -1) continue;\n pair[lo] = hi;\n pair[hi] = lo;\n accepted.push(cand);\n }\n return pair;\n}\n\n// ===========================================================================\n// Structure tree\n// ===========================================================================\n\n/**\n * Build the structure tree from a pair table. The returned root is\n * the exterior `LoopNode` (with `closingPair === null`). Every paired\n * `(lo, hi)` becomes a `Stem` whose `child` is the loop closed by its\n * innermost pair.\n *\n * Stacked base pairs (consecutive pairs with no unpaired bases on\n * EITHER rail between them) collapse into a single `Stem` whose\n * `numPairs >= 1`. This is the natural ladder.\n */\nexport function buildStructureTree(pair: Int32Array): LoopNode {\n return recurse(0, pair.length - 1, null);\n\n function recurse(\n i: number,\n j: number,\n closingPair: readonly [number, number] | null,\n ): LoopNode {\n const nodes: Array<Stem | UnpairedRun> = [];\n let unpairedStart = -1;\n let k = i;\n while (k <= j) {\n const partner = pair[k]!;\n if (partner > k && partner <= j) {\n if (unpairedStart !== -1) {\n nodes.push({kind: 'unpaired', from: unpairedStart, to: k - 1});\n unpairedStart = -1;\n }\n // Collapse stacked pairs. The parser's RNA convention puts a\n // LINKER (unpaired) at every odd index between two paired\n // sugars; stacked sugars therefore differ by 2 in backbone\n // index. The collapse rule advances numPairs as long as:\n // - the next paired position on the near rail is partner-\n // (2*numPairs) (mirror-matched on the far rail);\n // - the intervening linkers on both rails are unpaired;\n // - the interior is still non-empty (k + 2*numPairs <\n // partner - 2*numPairs).\n let numPairs = 1;\n while (\n k + 2 * numPairs < partner - 2 * numPairs\n && pair[k + 2 * numPairs] === partner - 2 * numPairs\n && pair[k + 2 * numPairs - 1] === -1\n && pair[partner - 2 * numPairs + 1] === -1\n ) {\n numPairs += 1;\n }\n const innerNear = k + 2 * (numPairs - 1);\n const innerFar = partner - 2 * (numPairs - 1);\n const childClosing: readonly [number, number] = [innerNear, innerFar];\n const child = recurse(innerNear + 1, innerFar - 1, childClosing);\n nodes.push({\n kind: 'stem',\n fromIdx: k,\n toIdx: partner,\n numPairs,\n child,\n });\n k = partner + 1;\n } else {\n if (unpairedStart === -1) unpairedStart = k;\n k += 1;\n }\n }\n if (unpairedStart !== -1)\n nodes.push({kind: 'unpaired', from: unpairedStart, to: j});\n return {kind: 'loop', nodes, closingPair};\n }\n}\n\n// ===========================================================================\n// Geometry\n// ===========================================================================\n\ninterface Frame {\n origin: Point;\n /** Unit vector along the stem 5'->3' on the near rail. */\n tangent: Vec2;\n /** Unit vector from near rail to far rail (perpendicular). */\n normal: Vec2;\n}\n\nfunction unit(v: Vec2): Vec2 {\n const len = Math.hypot(v.x, v.y);\n if (len === 0) return {x: 1, y: 0};\n return {x: v.x / len, y: v.y / len};\n}\n\n/**\n * +90 degrees in math frame (counter-clockwise in math = clockwise in\n * SVG Y-down). Used to derive the near-rail->far-rail `normal` from\n * the `tangent`.\n */\nfunction perpCW(v: Vec2): Vec2 {\n return {x: -v.y, y: v.x};\n}\n\nfunction polar(center: Point, R: number, theta: number): Point {\n return {x: center.x + R * Math.cos(theta), y: center.y + R * Math.sin(theta)};\n}\n\n/**\n * Solve for the radius R of a loop circle whose closing chord has\n * length `rail` and which carries `K` total occupants:\n * - 2 closing-pair atoms (at the chord endpoints; chord arc =\n * `alpha = 2 * asin(rail / (2*R))`).\n * - `U` unpaired atoms, each at arc-length `step` from its\n * in-walk predecessor.\n * - `S` child stems, each occupying 2 atoms (childNear at one\n * `step`-arc past the predecessor; childFar at `alpha`-chord\n * past childNear, matching the child stem's own rail gap).\n *\n * The total angular advance from `nearTop` around the long arc back\n * one step short of `farTop` (so the final step lands at `farTop`)\n * must equal `(2*pi - alpha) - dTheta`. Summing:\n * ((U + S) * dTheta) + (S * alpha) = (2*pi - alpha) - dTheta\n * (U + S + 1) * dTheta = 2*pi - (S + 1) * alpha\n * (U + S + 1) * step / R = 2*pi - (S + 1) * alpha\n *\n * Hence:\n * `(U + S + 1) * step = (2*pi - (S + 1) * alpha) * R`.\n *\n * For pure hairpins (`S = 0`): `(K - 1) * step = (2*pi - alpha) * R`\n * with `U = K - 2`, matching the design's NAView-lite formula.\n *\n * For multi-loops, the previous hairpin-only formula\n * `(K - 1) * step = (2*pi - alpha) * R` oversized the long arc by\n * `S * (dTheta - alpha)` radians per child stem, leaving an angular\n * gap between the last on-circle atom and `farTop` (closing chord\n * stayed correct because `farTop` is pre-placed by the parent\n * stem). This formula closes that gap.\n *\n * Newton iteration with a seed that's correct for the limit\n * `rail/R -> 0` (then `alpha -> 0` and `R -> (U+S+1)*step / 2*pi`).\n */\nfunction solveLoopRadius(rail: number, step: number, U: number, S: number): number {\n const linearCount = U + S + 1; // (U + S) * dTheta steps + 1 trailing dTheta\n if (linearCount <= 0) {\n // Degenerate: nothing on the long arc. Use a small circle.\n return Math.max(rail / 2 + 1, step);\n }\n const stemFactor = S + 1; // multiplier on alpha (closing chord + S child chords)\n const target = linearCount * step;\n // Initial guess: ignore the chord contribution.\n let R = Math.max(target / (2 * Math.PI), rail / 2 + 1);\n for (let it = 0; it < 64; it++) {\n // Clamp to avoid asin(>1).\n const r2 = rail / (2 * R);\n const halfAlpha = Math.asin(Math.min(0.9999, Math.max(-0.9999, r2)));\n // f(R) = (2*pi - stemFactor * alpha) * R - target,\n // where alpha = 2 * halfAlpha.\n const alphaR = 2 * halfAlpha;\n const f = (2 * Math.PI - stemFactor * alphaR) * R - target;\n // df/dR. Let u = rail / (2*R). du/dR = -rail / (2*R^2).\n // d(asin(u))/dR = du/dR / sqrt(1 - u^2).\n const u = r2;\n const sqrtTerm = Math.sqrt(Math.max(1e-12, 1 - u * u));\n const dHalfAlphaDR = (-rail / (2 * R * R)) / sqrtTerm;\n const dAlphaDR = 2 * dHalfAlphaDR;\n const fp = (2 * Math.PI - stemFactor * alphaR) - stemFactor * R * dAlphaDR;\n if (!Number.isFinite(fp) || Math.abs(fp) < 1e-12) break;\n const delta = f / fp;\n const next = R - delta;\n if (!Number.isFinite(next) || next < rail / 2 + 1e-3) {\n R = rail / 2 + 1e-3;\n break;\n }\n R = next;\n if (Math.abs(delta) < 1e-9) break;\n }\n return Math.max(R, rail / 2 + 1e-3);\n}\n\ninterface PlacementContext {\n chain: LayoutChain;\n step: number;\n /**\n * Stem rail-to-rail SUGAR distance. The H-bond between paired\n * BASES has length `hbondGap = rail - 2 * baseInwardHang`, so for\n * the canonical RNA depiction where bases face each other across\n * the stem with the H-bond as the closest gap, this value must be\n * `HBOND_GAP + 2 * baseInwardHang`. With the default constants\n * (`HBOND_GAP = 60`, `baseInwardHang = step/2 = 32`), `rail = 124`.\n */\n rail: number;\n /**\n * Sugar-to-base distance for STEM rail bases (which hang INWARD\n * toward their partner). Loop / exterior bases use `step` instead\n * — see the per-shape `outward` arguments to `placeBaseFor`.\n */\n baseInwardHang: number;\n out: Map<number, Point>;\n}\n\n/**\n * Phase 34 (T-3401) — Place this sugar's base (if any) at the given\n * distance along the supplied `outward` unit vector. The default\n * `placeBases` helper uses a bisector heuristic that picks the +Y\n * perpendicular; for cloverleaf stems and loops \"outward\" is\n * shape-dependent, so we pre-place bases inside the cloverleaf\n * strategy and let `placeBases` skip them via its Phase-34\n * idempotency guard.\n *\n * `dist` is the sugar-to-base distance. Stem-rail bases pass\n * `ctx.baseInwardHang` (typically `step/2`) so the base sits between\n * the rails facing its partner; loop and exterior bases pass `step`\n * so they hang fully outward / radially.\n */\nfunction placeBaseFor(\n backboneIdx: number,\n sugarPos: Point,\n outward: Vec2,\n dist: number,\n ctx: PlacementContext,\n): void {\n const base = ctx.chain.bases[backboneIdx];\n if (base === null || base === undefined) return;\n ctx.out.set(base.id, {\n x: sugarPos.x + dist * outward.x,\n y: sugarPos.y + dist * outward.y,\n });\n}\n\n/**\n * Place a stem's ladder. Walks backbone indices\n * [fromIdx .. fromIdx + 2*numPairs - 2] on the near rail, and\n * [toIdx .. toIdx - 2*numPairs + 2] on the far rail,\n * both 5'->3' on the chain (the far rail is walked 3'->5' in source\n * order but reads 5'->3' along the tangent).\n *\n * Returns the inner-tip frame (origin AT the inner-closing-pair's near\n * rail atom; tangent / normal unchanged).\n */\nfunction placeStem(stem: Stem, frame: Frame, ctx: PlacementContext): Frame {\n const {chain, step, rail, baseInwardHang, out} = ctx;\n const railAtoms = 2 * stem.numPairs - 1; // backbone atoms per rail\n // Phase 34 (T-3401) revision: bases hang INWARD (toward partner\n // rail), not outward. Sugars sit on the OUTSIDE of the stem at\n // distance `rail = HBOND_GAP + 2*baseInwardHang`; the near-rail\n // sugar's base hangs in +normal direction toward the far rail;\n // the far-rail sugar's base hangs in -normal direction toward\n // the near rail. The two paired bases meet across the H-bond\n // with exactly HBOND_GAP between them (the closest distance\n // between the two strands of the duplex, matching canonical\n // RNA depictions where sugars are on the backbone \"outside\"\n // and bases on the \"inside\".\n const nearInward: Vec2 = {x: frame.normal.x, y: frame.normal.y};\n const farInward: Vec2 = {x: -frame.normal.x, y: -frame.normal.y};\n for (let k = 0; k < railAtoms; k++) {\n const nearAtom = chain.backbone[stem.fromIdx + k]!;\n const farAtom = chain.backbone[stem.toIdx - k]!;\n const along = k * step;\n const nearPos: Point = {\n x: frame.origin.x + along * frame.tangent.x,\n y: frame.origin.y + along * frame.tangent.y,\n };\n const farPos: Point = {\n x: frame.origin.x + along * frame.tangent.x + rail * frame.normal.x,\n y: frame.origin.y + along * frame.tangent.y + rail * frame.normal.y,\n };\n out.set(nearAtom.id, nearPos);\n out.set(farAtom.id, farPos);\n // Bases only exist for SUGAR backbone atoms (even k in the\n // r(X)p convention). placeBaseFor itself guards on a null\n // base, so we can call it unconditionally.\n placeBaseFor(stem.fromIdx + k, nearPos, nearInward, baseInwardHang, ctx);\n placeBaseFor(stem.toIdx - k, farPos, farInward, baseInwardHang, ctx);\n }\n const tipAlong = (railAtoms - 1) * step;\n return {\n origin: {\n x: frame.origin.x + tipAlong * frame.tangent.x,\n y: frame.origin.y + tipAlong * frame.tangent.y,\n },\n tangent: frame.tangent,\n normal: frame.normal,\n };\n}\n\n/**\n * Place a non-exterior loop. The closing pair atoms are ALREADY\n * placed by the parent's `placeStem` (their positions are derived\n * from `tipFrame`). This function places the remaining occupants\n * (unpaired backbone atoms and child-stem closing-pair atoms)\n * around the loop circle and recurses into each child stem.\n */\nfunction placeInternalLoop(\n loop: LoopNode,\n tipFrame: Frame,\n ctx: PlacementContext,\n depth: number,\n): void {\n if (loop.closingPair === null) return;\n const {step, rail, out} = ctx;\n // Tally Unpaired count (U) and child Stem count (S) separately so\n // the radius solver can account for child-stem closing chords\n // (= alpha) vs. unpaired step-arcs (= dTheta).\n let U = 0;\n let S = 0;\n for (const n of loop.nodes) {\n if (n.kind === 'unpaired') U += n.to - n.from + 1;\n else S += 1;\n }\n const R = solveLoopRadius(rail, step, U, S);\n\n // Closing pair endpoints (already in `out` via `placeStem`).\n const nearTop = out.get(ctx.chain.backbone[loop.closingPair[0]]!.id)!;\n const farTop = out.get(ctx.chain.backbone[loop.closingPair[1]]!.id)!;\n const mid = {x: (nearTop.x + farTop.x) / 2, y: (nearTop.y + farTop.y) / 2};\n const distOffChord = Math.sqrt(Math.max(0, R * R - (rail / 2) * (rail / 2)));\n const center: Point = {\n x: mid.x + distOffChord * tipFrame.tangent.x,\n y: mid.y + distOffChord * tipFrame.tangent.y,\n };\n\n // Winding direction: choose the LONG arc (away from theta_f). The\n // signed angular delta from nearTop to farTop, normalised to\n // (-pi, pi], gives the SHORT arc direction (= +alpha or -alpha).\n // Walking the LONG arc means going the opposite sign.\n const theta0 = Math.atan2(nearTop.y - center.y, nearTop.x - center.x);\n const thetaF = Math.atan2(farTop.y - center.y, farTop.x - center.x);\n let delta = thetaF - theta0;\n while (delta > Math.PI) delta -= 2 * Math.PI;\n while (delta <= -Math.PI) delta += 2 * Math.PI;\n const winding = delta > 0 ? -1 : +1;\n\n // Closing chord's central angle.\n const alpha = 2 * Math.asin(Math.min(0.9999, Math.max(-0.9999, rail / (2 * R))));\n const dTheta = step / R;\n void depth;\n\n // Phase 34 (T-3401) — Closing-pair sugar bases ARE placed by\n // `placeStem` using a diagonal \"tip-outward\" direction (the\n // average of stem-normal and -tangent). The downstream\n // `placeBases` call no-ops on those bases via the Phase-34\n // idempotency guard. Per-loop walker writes bases for the\n // unpaired atoms below in `unit(pos - center)` (radially outward)\n // and for child-stem closing-pair atoms via the recursive\n // placeStem with its own tip-diagonal.\n\n let theta = theta0;\n for (const n of loop.nodes) {\n if (n.kind === 'unpaired') {\n for (let p = n.from; p <= n.to; p++) {\n theta = theta + winding * dTheta;\n const pos = polar(center, R, theta);\n out.set(ctx.chain.backbone[p]!.id, pos);\n // Loop bases hang radially OUTWARD from the loop centre so\n // they don't overlap with bases on the opposite side of the\n // circle. Unit vector from centre to this atom.\n const outward = unit({x: pos.x - center.x, y: pos.y - center.y});\n placeBaseFor(p, pos, outward, ctx.step, ctx);\n }\n } else {\n // Place this child stem's closing pair on the loop circle.\n theta = theta + winding * dTheta;\n const childNearPos = polar(center, R, theta);\n theta = theta + winding * alpha;\n const childFarPos = polar(center, R, theta);\n out.set(ctx.chain.backbone[n.fromIdx]!.id, childNearPos);\n out.set(ctx.chain.backbone[n.toIdx]!.id, childFarPos);\n // Build the child's frame: tangent radial outward from center,\n // normal along the closing chord (near->far).\n const childTangent = unit({\n x: (childNearPos.x + childFarPos.x) / 2 - center.x,\n y: (childNearPos.y + childFarPos.y) / 2 - center.y,\n });\n const childNormal = unit({\n x: childFarPos.x - childNearPos.x,\n y: childFarPos.y - childNearPos.y,\n });\n const childFrame: Frame = {\n origin: childNearPos,\n tangent: childTangent,\n normal: childNormal,\n };\n // Place the rest of the child stem (k=1..2*numPairs-2) — the\n // closing-pair atoms (k=0) are already placed above.\n const innerFrame = placeStem(n, childFrame, ctx);\n // Recurse into the child stem's enclosed loop.\n placeInternalLoop(n.child, innerFrame, ctx, depth + 1);\n }\n }\n}\n\n/**\n * Place the exterior loop as a straight horizontal walk. Unpaired\n * atoms advance one `step` along tangent each; child stems extend\n * perpendicular into the +normal half-plane and recurse into their\n * own (internal) loops.\n *\n * Multiple top-level stems (when the chain has several disjoint\n * hairpins) all hang on the same side of the linear backbone.\n */\nfunction placeExteriorLoop(\n root: LoopNode,\n frame: Frame,\n ctx: PlacementContext,\n): void {\n const {step, rail, out} = ctx;\n // Phase 34 (T-3401) — Exterior baseline walks along `frame.tangent`\n // (default +x). Top-level stems STAND PERPENDICULAR to the\n // baseline (their rails extend in the -frame.normal direction =\n // \"up\" for the default SVG-Y-down convention), with the chain\n // entering at the stem's 5' rail base (on the line) and exiting\n // at the stem's 3' rail base (also on the line, offset by `rail`\n // along the baseline). The cursor advances past each stem's\n // baseline footprint = `rail + step` so the next exterior node\n // (another stem or unpaired run) sits one bond-length past the\n // stem's exit. This handles multiple top-level stems (two\n // hairpins in series, exterior of a tRNA cloverleaf, etc.)\n // without rail collisions.\n let cursor: Point = {x: frame.origin.x, y: frame.origin.y};\n const dir: Vec2 = {x: frame.tangent.x, y: frame.tangent.y};\n // Stems stand perpendicular: their tangent is -frame.normal (UP)\n // and their normal points along the baseline (= +dir), so the 5'\n // rail starts at cursor and the 3' rail starts at cursor + rail*dir.\n const stemUp: Vec2 = {x: -frame.normal.x, y: -frame.normal.y};\n for (const n of root.nodes) {\n if (n.kind === 'unpaired') {\n for (let p = n.from; p <= n.to; p++) {\n const pos: Point = {x: cursor.x, y: cursor.y};\n out.set(ctx.chain.backbone[p]!.id, pos);\n // Exterior bases hang AWAY from the stems (= +normal, which\n // is the OPPOSITE half-plane from where stems extend; for\n // default SVG-Y-down this is DOWNWARD).\n placeBaseFor(p, pos, {x: frame.normal.x, y: frame.normal.y}, ctx.step, ctx);\n cursor = {\n x: cursor.x + step * dir.x,\n y: cursor.y + step * dir.y,\n };\n }\n } else {\n // Vertical (perpendicular-to-baseline) stem.\n const stemFrame: Frame = {\n origin: {x: cursor.x, y: cursor.y},\n tangent: stemUp,\n normal: dir,\n };\n const innerFrame = placeStem(n, stemFrame, ctx);\n placeInternalLoop(n.child, innerFrame, ctx, 1);\n // With the Phase-34 INWARD base direction, the outermost\n // closing-pair sugar bases sit BETWEEN the rails (one\n // `baseInwardHang` step into the stem interior from each\n // sugar), not along the baseline — so they no longer collide\n // with the next exterior atom at `cursor + (rail + step) *\n // dir` and we keep the cloverleaf-placed positions.\n //\n // Advance cursor past the stem's baseline footprint. The 3'\n // rail of the stem ends at cursor + rail * dir; the next\n // exterior atom is one `step` past that.\n cursor = {\n x: cursor.x + (rail + step) * dir.x,\n y: cursor.y + (rail + step) * dir.y,\n };\n void innerFrame;\n }\n }\n}\n\n// ===========================================================================\n// Entry point\n// ===========================================================================\n\n/**\n * Cloverleaf strategy entry. Returns a fresh `Map<atomId, Point>`\n * positioning EVERY backbone atom of `chain` AND every base attached\n * to a sugar. Per-shape base directions:\n * - Stem-rail middle sugars: base `-normal` (near rail) / `+normal`\n * (far rail) — perpendicular to the ladder, away from partner.\n * - Stem inner-tip closing-pair sugars: base in the diagonal\n * `(stem_normal - tangent)/sqrt(2)` direction — away from BOTH\n * partner and loop bulk.\n * - Loop unpaired sugars: base `unit(sugar - loop_center)` —\n * radially outward from loop centre.\n * - Exterior unpaired sugars: base `+normal` (down in SVG-Y-down)\n * so they hang opposite the stems (which extend upward).\n *\n * The orchestrator's subsequent `placeBases` call no-ops on every\n * base this function has placed via the Phase-34 idempotency guard\n * in `base-placement.ts`.\n *\n * The function is side-effect-free (reads `chain` and `mol.bonds`;\n * does not mutate either) and deterministic.\n */\nexport function layoutCloverleaf(\n chain: LayoutChain,\n mol: Pick<Mol, 'bonds'>,\n options?: CloverleafLayoutOptions,\n): Map<number, Point> {\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n const step = BOND_SCALE * bondLength;\n // Phase 34 (T-3401) — Canonical RNA stem geometry: sugars on the\n // OUTSIDE, bases pointing INWARD with the H-bond as the closest\n // gap between strands. The base-inward-hang = step/2 so each\n // base sits halfway across the rail gap; the stem rail (sugar to\n // sugar) is `HBOND_GAP + 2 * baseInwardHang`, so paired bases meet\n // with exactly HBOND_GAP between them.\n const baseInwardHang = step / 2;\n const hbondGap = HBOND_GAP * (bondLength / DEFAULT_BOND_LENGTH);\n const rail = hbondGap + 2 * baseInwardHang;\n const origin = options?.origin ?? {x: 0, y: 0};\n const tangent = unit(options?.rootDirection ?? {x: 1, y: 0});\n const normal = perpCW(tangent);\n\n const out = new Map<number, Point>();\n if (chain.backbone.length === 0) return out;\n\n const pair = buildPairTable(chain, mol);\n const root = buildStructureTree(pair);\n const ctx: PlacementContext = {chain, step, rail, baseInwardHang, out};\n const rootFrame: Frame = {origin, tangent, normal};\n placeExteriorLoop(root, rootFrame, ctx);\n\n // Backfill any backbone atom that wasn't placed (shouldn't happen\n // if pair-table + tree are correct, but defensive). Use the origin.\n for (const a of chain.backbone) {\n if (!out.has(a.id)) out.set(a.id, {x: origin.x, y: origin.y});\n }\n return out;\n}\n","// T-0306 — RNA base placement using bisector geometry.\n//\n// For each sugar with a base, the legacy editor places the base at a fixed\n// distance `step = bondscale * bondLength` from the sugar in the direction\n// that bisects the two neighboring backbone bonds (Chain.ts `layoutBases`,\n// see LEGACY-EDITOR-NOTES.md §Chain.ts). At chain ends — where only one\n// neighbor exists — the base is rotated 90° from the only backbone bond,\n// \"below\" the chain by default.\n//\n// For straight horizontal chains the bisector points straight up (and we\n// place the base straight down because Y grows downward in SVG world\n// coordinates).\n//\n// Multi-row layouts (T-0304) follow the local backbone direction so bases\n// always hang below their row of sugars.\n\nimport type {Atom} from '../core/model';\nimport type {Point, Vec2} from '../util/types';\nimport type {LayoutChain} from './chain-builder';\nimport {BOND_SCALE, DEFAULT_BOND_LENGTH} from './line';\n\nexport interface BasePlacementOptions {\n /** Model-space distance between sugar and base centers. Default `40 * 1.6`. */\n bondLength?: number;\n}\n\n/**\n * For every sugar with a base in `chain`, write the base atom's position\n * into `positions`. Returns the same map for chaining. Mutates in place.\n */\nexport function placeBases(\n chain: LayoutChain,\n positions: Map<number, Point>,\n options?: BasePlacementOptions,\n): Map<number, Point> {\n if (chain.polymerType !== 'RNA') return positions;\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n const baseDistance = BOND_SCALE * bondLength;\n\n for (let i = 0; i < chain.backbone.length; i++) {\n const base = chain.bases[i];\n if (base === null || base === undefined) continue;\n // Phase 34 (T-3401) — Idempotency guard: the cloverleaf strategy\n // pre-positions every base it lays out (with shape-aware\n // outward directions: -normal/+normal on stem rails, tip-\n // diagonal on closing pairs, loop-radial outward on loop atoms,\n // +normal on exterior atoms). Skip those; only fill in bases\n // not yet positioned, using the default bisector-outward\n // heuristic that the line / circle / rows / inner-circle\n // strategies rely on.\n if (positions.has(base.id)) continue;\n const sugar = chain.backbone[i]!;\n const sugarPos = positions.get(sugar.id);\n if (sugarPos === undefined) continue;\n\n const dir = bisectorOutward(chain, i, positions);\n positions.set(base.id, {\n x: sugarPos.x + baseDistance * dir.x,\n y: sugarPos.y + baseDistance * dir.y,\n });\n }\n return positions;\n}\n\n/**\n * Outward bisector direction (unit vector) at backbone index `i`.\n *\n * For an interior atom, takes the perpendicular to the bisector of the\n * incoming and outgoing backbone-bond vectors (so the base hangs to one\n * side of the chain, never along the backbone direction).\n *\n * For an end atom, takes the perpendicular of the single available\n * backbone vector. \"Down\" (Y > 0) is preferred so bases hang below.\n */\nfunction bisectorOutward(\n chain: LayoutChain,\n i: number,\n positions: Map<number, Point>,\n): Vec2 {\n const cur = chain.backbone[i]!;\n const curPos = positions.get(cur.id);\n if (curPos === undefined) return {x: 0, y: 1};\n\n const prev: Atom | undefined = i > 0 ? chain.backbone[i - 1] : undefined;\n const next: Atom | undefined = i < chain.backbone.length - 1 ? chain.backbone[i + 1] : undefined;\n const prevPos = prev !== undefined ? positions.get(prev.id) : undefined;\n const nextPos = next !== undefined ? positions.get(next.id) : undefined;\n\n let dirX = 0;\n let dirY = 0;\n\n if (prevPos !== undefined && nextPos !== undefined) {\n // Tangent direction (averaged), then perpendicular.\n const tx = (nextPos.x - prevPos.x);\n const ty = (nextPos.y - prevPos.y);\n const len = Math.hypot(tx, ty);\n if (len === 0) return {x: 0, y: 1};\n // Rotate tangent 90° to get perpendicular. In SVG world coordinates\n // (Y down), rotating (tx, ty) by +90° clockwise gives (ty, -tx); by\n // -90° (counter-clockwise) gives (-ty, tx). We pick the perpendicular\n // pointing \"downward\" (positive Y) so bases hang below the backbone.\n const perpA = {x: ty / len, y: -tx / len};\n const perpB = {x: -ty / len, y: tx / len};\n const pick = perpA.y >= perpB.y ? perpA : perpB;\n dirX = pick.x;\n dirY = pick.y;\n } else if (nextPos !== undefined) {\n const tx = nextPos.x - curPos.x;\n const ty = nextPos.y - curPos.y;\n const len = Math.hypot(tx, ty);\n if (len === 0) return {x: 0, y: 1};\n const perpA = {x: ty / len, y: -tx / len};\n const perpB = {x: -ty / len, y: tx / len};\n const pick = perpA.y >= perpB.y ? perpA : perpB;\n dirX = pick.x;\n dirY = pick.y;\n } else if (prevPos !== undefined) {\n const tx = curPos.x - prevPos.x;\n const ty = curPos.y - prevPos.y;\n const len = Math.hypot(tx, ty);\n if (len === 0) return {x: 0, y: 1};\n const perpA = {x: ty / len, y: -tx / len};\n const perpB = {x: -ty / len, y: tx / len};\n const pick = perpA.y >= perpB.y ? perpA : perpB;\n dirX = pick.x;\n dirY = pick.y;\n } else {\n return {x: 0, y: 1};\n }\n\n return {x: dirX, y: dirY};\n}\n","// T-0307 — Position chains relative to each other from cross-polymer bonds.\n//\n// Each `LayoutChain` is initially laid out at the origin by its individual\n// strategy. This pass walks `mol.bonds` for cross-polymer bonds and\n// translates whole chains so the bonded atoms are placed reasonably\n// relative to one another.\n//\n// Two visual conventions, matching the legacy editor (Layout.ts\n// `layoutCrossChainBonds`, see LEGACY-EDITOR-NOTES.md):\n//\n// - **H-bond pairs** (`bond.kind === 'hbond'`): the two chains are\n// anti-parallel — the second chain is reflected horizontally\n// (so it reads right-to-left) and stacked below the first.\n// - **Normal cross-polymer bonds**: place the second chain so that its\n// bonded atom sits one `step` away from the corresponding atom on the\n// first chain, in the direction away from the first chain's backbone.\n//\n// We mutate `positions` in place. Only the FIRST cross-chain bond involving\n// any given chain triggers placement; subsequent bonds are tolerated as\n// long crossing lines (the renderer draws them as straight segments).\n\nimport type {Bond, Mol} from '../core/model';\nimport type {Point} from '../util/types';\nimport type {LayoutChain} from './chain-builder';\nimport {BOND_SCALE, CROSS_CHAIN_GAP_FACTOR, DEFAULT_BOND_LENGTH, FRAGMENT_GAP_FACTOR, HBOND_GAP_FACTOR} from './line';\n\nexport interface CrossChainOptions {\n /** Model-space bond length. Default `40`. */\n bondLength?: number;\n}\n\ninterface ChainBundle {\n chain: LayoutChain;\n atomIds: Set<number>;\n /** Atom ids whose positions live in `positions` for this chain. */\n}\n\n/**\n * Position chains relative to each other in `positions` based on\n * cross-polymer bonds. Mutates `positions`.\n *\n * Returns the set of chain ids that have been \"anchored\" — placed by a\n * cross-chain bond rather than by the disconnected-fragment fallback.\n */\nexport function placeCrossChains(\n chains: readonly LayoutChain[],\n positions: Map<number, Point>,\n mol: Mol,\n options?: CrossChainOptions,\n): Set<string> {\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n const step = BOND_SCALE * bondLength;\n\n // Build atom -> chain map.\n const atomToChain = new Map<number, LayoutChain>();\n const bundles: Map<string, ChainBundle> = new Map();\n for (const c of chains) {\n const atomIds = new Set<number>();\n for (const a of c.backbone) atomIds.add(a.id);\n for (const b of c.bases) if (b !== null) atomIds.add(b.id);\n bundles.set(c.id, {chain: c, atomIds});\n for (const aid of atomIds) atomToChain.set(aid, c);\n }\n\n const placed = new Set<string>();\n // Phase 33 (T-3301) — If any chain has an explicit `strandType ===\n // 'ss'`, that chain anchors first. This lets the user's section-3\n // annotation drive the duplex orientation regardless of source\n // order. Falls back to the first chain in source order when no\n // strand-type hint is supplied (existing behaviour — regression\n // guard for the corpus).\n if (chains.length > 0) {\n const senseAnchor = chains.find((c) => c.strandType === 'ss');\n placed.add((senseAnchor ?? chains[0]!).id);\n }\n\n // T-3507 — Union-find over chain ids tracks which chains have been wired into\n // the SAME rigid cluster. A bond between two already-placed chains in\n // DIFFERENT clusters (e.g. a pendant single-residue chain that was the global\n // anchor, plus a ring cluster placed independently by a later bond) must\n // MERGE the clusters rather than be skipped — otherwise the pendant is left\n // stranded at the origin with a long connector. Same-cluster bonds stay\n // redundant (skipped).\n const parent = new Map<string, string>();\n for (const c of chains) parent.set(c.id, c.id);\n const find = (id: string): string => {\n let r = id;\n while (parent.get(r) !== r) r = parent.get(r)!;\n let cur = id;\n while (parent.get(cur) !== r) { const next = parent.get(cur)!; parent.set(cur, r); cur = next; }\n return r;\n };\n const union = (a: string, b: string): void => { parent.set(find(a), find(b)); };\n const clusterAtomIds = (chainId: string): Set<number> => {\n const root = find(chainId);\n const ids = new Set<number>();\n for (const [cid, bundle] of bundles)\n if (find(cid) === root) for (const aid of bundle.atomIds) ids.add(aid);\n return ids;\n };\n\n // Iterate cross-polymer bonds in source order. Skip backbone/branch.\n for (const b of mol.bonds) {\n if (b.kind === 'backbone' || b.kind === 'branch') continue;\n const c1 = atomToChain.get(b.a1.id);\n const c2 = atomToChain.get(b.a2.id);\n if (c1 === undefined || c2 === undefined) continue;\n if (c1.id === c2.id) continue; // self-closure, handled by layoutCircle/innerCircle\n // Phase 33 (T-3301) — Explicit `as` strand-type ALWAYS becomes\n // the moving (bottom) chain; explicit `ss` ALWAYS stays put.\n // Falls through to the source-order rule otherwise.\n if (b.kind === 'hbond') {\n if (c1.strandType === 'as' && c2.strandType === 'ss') {\n placed.add(c2.id);\n } else if (c2.strandType === 'as' && c1.strandType === 'ss') {\n placed.add(c1.id);\n } else if (c1.strandType === 'as' && !placed.has(c2.id)) {\n placed.add(c2.id);\n } else if (c2.strandType === 'as' && !placed.has(c1.id)) {\n placed.add(c1.id);\n }\n }\n // Determine which side is anchored, which side moves.\n let moving = c2, fixedAtom = b.a1, movingAtom = b.a2;\n if (placed.has(c2.id) && !placed.has(c1.id)) {\n moving = c1; fixedAtom = b.a2; movingAtom = b.a1;\n } else if (!placed.has(c1.id) && !placed.has(c2.id)) {\n // Neither placed yet — anchor c1.\n //\n // T-1404 (Phase 14A) — Defend against multi-cluster collision.\n // The prior implementation left c1 sitting at the layout origin\n // (its `pickStrategy` output), which clobbered chains already\n // anchored at the origin (e.g. the very first PEPTIDE chain).\n // Move c1's whole bundle below every previously-placed chain by\n // a single FRAGMENT_GAP_FACTOR gap — same convention the\n // disconnected-fragment pass uses.\n if (placed.size > 0) {\n const placedAtomIds = new Set<number>();\n for (const pid of placed) {\n const pb = bundles.get(pid);\n if (pb !== undefined) for (const aid of pb.atomIds) placedAtomIds.add(aid);\n }\n const placedBottom = bundleMaxY(placedAtomIds, positions);\n const c1Bundle = bundles.get(c1.id)!;\n const c1Top = bundleMinY(c1Bundle.atomIds, positions);\n if (placedBottom !== null && c1Top !== null) {\n const dy = placedBottom + step * FRAGMENT_GAP_FACTOR - c1Top;\n if (dy > 0) translateAtoms(c1Bundle.atomIds, positions, 0, dy);\n }\n }\n placed.add(c1.id);\n moving = c2; fixedAtom = b.a1; movingAtom = b.a2;\n } else if (placed.has(c1.id) && placed.has(c2.id)) {\n // T-3507 — Both placed. If they're already in the same cluster the bond\n // is redundant (skip). If they're in DIFFERENT clusters, this bond is the\n // only thing linking them — merge by sliding the SMALLER cluster so the\n // two bonded monomers sit one step apart (fixes the stranded-anchor\n // pendant: a single-residue chain left at the origin while the rings were\n // placed independently by a later bond).\n if (find(c1.id) === find(c2.id)) continue;\n // Only normal cross-links merge clusters. An H-bond between two\n // already-placed chains keeps the legacy skip (the anti-parallel duplex\n // stacking was established when the chains were first placed; sliding a\n // cluster here would break it — huge-conjugate-mixed regression).\n if (b.kind !== 'cross-polymer') continue;\n const idsA = clusterAtomIds(c1.id);\n const idsB = clusterAtomIds(c2.id);\n const aSmaller = idsA.size <= idsB.size;\n const smallIds = aSmaller ? idsA : idsB;\n const largeIds = aSmaller ? idsB : idsA;\n const smallPos = positions.get((aSmaller ? b.a1 : b.a2).id);\n const largePos = positions.get((aSmaller ? b.a2 : b.a1).id);\n if (smallPos !== undefined && largePos !== undefined)\n mergeClusters(smallIds, smallPos, largeIds, largePos, step, positions);\n union(c1.id, c2.id);\n continue;\n }\n\n const fixedPos = positions.get(fixedAtom.id);\n const movingPos = positions.get(movingAtom.id);\n if (fixedPos === undefined || movingPos === undefined) continue;\n\n if (b.kind === 'hbond') {\n // Anti-parallel: mirror the moving chain horizontally about its own\n // centre, then VERTICALLY flip it about its own centre so its\n // bases point UP toward the sense chain's downward-hanging bases,\n // then translate so the H-bonded moving atom sits directly below\n // the fixed atom by `step * HBOND_GAP_FACTOR` (one row gap).\n //\n // Phase 12 (T-1202) tightened the gap — the dashed H-bond line\n // is short.\n // Phase 33 (T-3301) added the vertical mirror. Before this fix\n // the antisense backbone sat below the sense backbone but its\n // BASES still hung DOWN (positive Y from the antisense\n // backbone) — i.e. the duplex spread vertically in TWO separate\n // pairs of rows with H-bond lines crossing through the sense\n // bases. The vertical flip puts antisense bases between the\n // two backbones, where they meet the sense bases head-on.\n const mb = bundles.get(moving.id)!;\n mirrorHorizontally(mb.atomIds, positions);\n mirrorVertically(mb.atomIds, positions);\n const newMovingPos = positions.get(movingAtom.id)!;\n const dx = fixedPos.x - newMovingPos.x;\n // Per-atom gap: keeps single-row siRNA duplexes laid out as in\n // Phase 12 — sugar at y = fixed.y + step * HBOND_GAP_FACTOR.\n let dy = fixedPos.y + step * HBOND_GAP_FACTOR - newMovingPos.y;\n // T-1404 (Phase 14A) — when ANY previously-placed chain extends\n // far enough down that the original per-atom dy would land the\n // moving chain INSIDE an already-placed chain's bbox, push the\n // moving chain down by exactly the overlap. Catches:\n // - row-wrapped chains (`layoutRows`) where the per-atom dy\n // pulls the moving chain back over the fixed chain;\n // - multi-cluster topologies where a third placed chain sits\n // between the moving chain's bonded atom and the fixed atom.\n dy = enforceNonOverlap(dy, mb, placed, bundles, positions, step * HBOND_GAP_FACTOR);\n translateAtoms(mb.atomIds, positions, dx, dy);\n } else if (moving.isCyclic && moving.backbone.length >= 3) {\n // T-3507 — A cyclic moving chain (ring) bridged to another chain by a\n // normal cross-link sits TANGENT to the fixed junction atom, rotated so\n // the two bonded monomers are adjacent. Replaces the vertical hop, which\n // overlapped the rings and pushed their junction monomers far apart.\n const mb = bundles.get(moving.id)!;\n const fixedChain = moving.id === c1.id ? c2 : c1;\n const fixedBundle = bundles.get(fixedChain.id)!;\n placeCyclicTangent(mb.atomIds, movingPos, fixedBundle.atomIds, fixedPos, step, positions);\n } else {\n // Normal cross-polymer bond: translate the moving chain so its\n // bonded atom is `step * CROSS_CHAIN_GAP_FACTOR` below the fixed\n // atom (perpendicular hop to a new row). Phase 12 tightened the gap\n // (T-1202).\n const mb = bundles.get(moving.id)!;\n const dx = fixedPos.x - movingPos.x;\n let dy = fixedPos.y + step * CROSS_CHAIN_GAP_FACTOR - movingPos.y;\n // T-1404 — non-overlap defence (see H-bond branch above).\n dy = enforceNonOverlap(dy, mb, placed, bundles, positions, step * CROSS_CHAIN_GAP_FACTOR);\n translateAtoms(mb.atomIds, positions, dx, dy);\n }\n placed.add(moving.id);\n union(c1.id, c2.id); // the bond now wires both chains into one cluster\n }\n\n return placed;\n}\n\n/**\n * Given a proposed `dy` for the `moving` bundle, return a possibly-larger\n * `dy` that guarantees the moving chain's top (post-translate) sits at\n * least `requiredGap` below the BOTTOM of every chain already in `placed`.\n *\n * Returns the original `dy` unchanged when the proposed translation\n * already satisfies the constraint (the common single-chain conjugate\n * path). Returns a larger `dy` (push the moving chain further down) when\n * the constraint is violated.\n */\nfunction enforceNonOverlap(\n dy: number,\n movingBundle: ChainBundle,\n placed: Set<string>,\n bundles: Map<string, ChainBundle>,\n positions: Map<number, Point>,\n requiredGap: number,\n): number {\n const movingMinY = bundleMinY(movingBundle.atomIds, positions);\n if (movingMinY === null) return dy;\n let placedBottom: number | null = null;\n for (const pid of placed) {\n const pb = bundles.get(pid);\n if (pb === undefined) continue;\n const maxY = bundleMaxY(pb.atomIds, positions);\n if (maxY === null) continue;\n if (placedBottom === null || maxY > placedBottom) placedBottom = maxY;\n }\n if (placedBottom === null) return dy;\n const movingTopAfter = movingMinY + dy;\n const requiredTop = placedBottom + requiredGap;\n if (movingTopAfter < requiredTop) return requiredTop - movingMinY;\n return dy;\n}\n\nfunction bundleMinY(ids: Set<number>, positions: Map<number, Point>): number | null {\n let best: number | null = null;\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p === undefined) continue;\n if (best === null || p.y < best) best = p.y;\n }\n return best;\n}\n\nfunction bundleMaxY(ids: Set<number>, positions: Map<number, Point>): number | null {\n let best: number | null = null;\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p === undefined) continue;\n if (best === null || p.y > best) best = p.y;\n }\n return best;\n}\n\nfunction translateAtoms(ids: Set<number>, positions: Map<number, Point>, dx: number, dy: number): void {\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p === undefined) continue;\n positions.set(aid, {x: p.x + dx, y: p.y + dy});\n }\n}\n\nfunction mirrorHorizontally(ids: Set<number>, positions: Map<number, Point>): void {\n // Mirror about the chain's own x-centroid so the chain reads right-to-left.\n let sum = 0, n = 0;\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p !== undefined) { sum += p.x; n += 1; }\n }\n if (n === 0) return;\n const center = sum / n;\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p === undefined) continue;\n positions.set(aid, {x: 2 * center - p.x, y: p.y});\n }\n}\n\n/**\n * Phase 33 (T-3301) — Mirror the chain about its own y-centroid so\n * bases that originally hung DOWN from the backbone now point UP.\n * Used together with `mirrorHorizontally` on the moving (antisense)\n * chain of an H-bond pair. Combined the two mirrors are equivalent\n * to a 180° rotation about the chain centre — the chain reads in\n * source-reverse order with bases pointing toward the sense chain.\n */\nfunction mirrorVertically(ids: Set<number>, positions: Map<number, Point>): void {\n let sum = 0, n = 0;\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p !== undefined) { sum += p.y; n += 1; }\n }\n if (n === 0) return;\n const center = sum / n;\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p === undefined) continue;\n positions.set(aid, {x: p.x, y: 2 * center - p.y});\n }\n}\n\nfunction centroidOf(ids: Set<number>, positions: Map<number, Point>): Point {\n let sx = 0, sy = 0, n = 0;\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p !== undefined) { sx += p.x; sy += p.y; n += 1; }\n }\n return n === 0 ? {x: 0, y: 0} : {x: sx / n, y: sy / n};\n}\n\n/**\n * T-3507 — Slide a whole (smaller) cluster so its bonded monomer sits one\n * `step` OUTWARD from the larger cluster's bonded monomer (outward = away from\n * the larger cluster's centroid). Translation only — the small cluster keeps\n * its internal layout. Used to reunite a stranded pendant chain with the ring\n * cluster it bonds to.\n */\nfunction mergeClusters(\n smallIds: Set<number>,\n smallAtomPos: Point,\n largeIds: Set<number>,\n largeAtomPos: Point,\n step: number,\n positions: Map<number, Point>,\n): void {\n const lc = centroidOf(largeIds, positions);\n let dx = largeAtomPos.x - lc.x;\n let dy = largeAtomPos.y - lc.y;\n let len = Math.hypot(dx, dy);\n if (len < 1e-6) { dx = 0; dy = 1; len = 1; } // large cluster is a point → go down\n const ux = dx / len, uy = dy / len;\n const tx = largeAtomPos.x + ux * step;\n const ty = largeAtomPos.y + uy * step;\n translateAtoms(smallIds, positions, tx - smallAtomPos.x, ty - smallAtomPos.y);\n}\n\n/** Rotate every atom in `ids` by `angle` radians about `c`. */\nfunction rotateAtomsAbout(ids: Set<number>, positions: Map<number, Point>, c: Point, angle: number): void {\n const cos = Math.cos(angle), sin = Math.sin(angle);\n for (const aid of ids) {\n const p = positions.get(aid);\n if (p === undefined) continue;\n const dx = p.x - c.x, dy = p.y - c.y;\n positions.set(aid, {x: c.x + dx * cos - dy * sin, y: c.y + dx * sin + dy * cos});\n }\n}\n\n/**\n * T-3507 — Place a CYCLIC moving chain tangent to the fixed junction atom.\n *\n * For a non-H-bond cross-link between rings (e.g. two head-to-tail cyclic\n * peptides bridged by an R3-R3 disulfide), the legacy vertical \"hop\" left the\n * two rings overlapping with their junction monomers far apart. Instead we:\n * 1. take the OUTWARD direction `d` from the fixed chain's centroid through\n * the fixed junction atom (so the moving ring sits clear of the fixed\n * ring);\n * 2. rotate the moving ring about its centroid so its junction atom faces\n * back along `-d` (toward the fixed atom);\n * 3. translate the ring so the two junction atoms sit exactly `step` apart.\n * The result: the rings sit side by side with the bonded monomers adjacent.\n */\nfunction placeCyclicTangent(\n movingIds: Set<number>,\n movingAtomPos: Point,\n fixedIds: Set<number>,\n fixedAtomPos: Point,\n step: number,\n positions: Map<number, Point>,\n): void {\n const fixedCentroid = centroidOf(fixedIds, positions);\n let dx = fixedAtomPos.x - fixedCentroid.x;\n let dy = fixedAtomPos.y - fixedCentroid.y;\n let len = Math.hypot(dx, dy);\n if (len < 1e-6) { dx = 1; dy = 0; len = 1; } // fixed is a point (single-atom chain) → go right\n const ux = dx / len, uy = dy / len; // outward unit vector\n const mc = centroidOf(movingIds, positions);\n const movingRadius = Math.hypot(movingAtomPos.x - mc.x, movingAtomPos.y - mc.y);\n // Rotate the ring so its junction atom points back toward the fixed atom (-d).\n const curAng = Math.atan2(movingAtomPos.y - mc.y, movingAtomPos.x - mc.x);\n const targetAng = Math.atan2(-uy, -ux);\n rotateAtomsAbout(movingIds, positions, mc, targetAng - curAng);\n // Translate the ring (centroid stays at `mc` under rotation) so its centre\n // lands `step + movingRadius` out along `d`, putting the junction atom at\n // `fixedAtom + d*step`.\n const targetCx = fixedAtomPos.x + ux * (step + movingRadius);\n const targetCy = fixedAtomPos.y + uy * (step + movingRadius);\n translateAtoms(movingIds, positions, targetCx - mc.x, targetCy - mc.y);\n}\n\n// Bond import for clarity — used implicitly in the loop above via `Mol.bonds`.\n// Marking the import as used so the linter does not flag it.\nexport type {Bond};\n","// T-0308 — Stack disconnected fragments vertically.\n//\n// After `placeCrossChains`, any chain not \"placed\" by a cross-polymer bond\n// is still sitting at the global origin. Stack them below one another with\n// a `3 * step` vertical gap (matching the legacy editor's\n// `layoutFragments`; see LEGACY-EDITOR-NOTES.md §Layout.ts).\n//\n// The \"previous bottom\" baseline is computed from the maximum Y across all\n// chains already placed, so unconnected chains never overlap connected\n// ones.\n\nimport type {Point} from '../util/types';\nimport type {LayoutChain} from './chain-builder';\nimport {BOND_SCALE, DEFAULT_BOND_LENGTH, FRAGMENT_GAP_FACTOR} from './line';\n\nexport interface FragmentsOptions {\n /** Model-space bond length. Default `40`. */\n bondLength?: number;\n /**\n * Gap between fragments as a multiplier of `step`. Default\n * `FRAGMENT_GAP_FACTOR` (= 1.4 since Phase 12; was 3.0 in Phase 11).\n */\n gap?: number;\n}\n\n/**\n * Stack any chain in `chains` whose id is NOT in `placed` below the\n * already-placed chains. Mutates `positions` in place.\n */\nexport function layoutDisconnectedFragments(\n chains: readonly LayoutChain[],\n positions: Map<number, Point>,\n placed: Set<string>,\n options?: FragmentsOptions,\n): void {\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n const gapMul = options?.gap ?? FRAGMENT_GAP_FACTOR;\n const step = BOND_SCALE * bondLength;\n const gap = gapMul * step;\n\n // Baseline y = max y of placed atoms (plus a small margin).\n let baselineY = 0;\n let initialised = false;\n for (const chain of chains) {\n if (!placed.has(chain.id)) continue;\n for (const a of chain.backbone) {\n const p = positions.get(a.id);\n if (p === undefined) continue;\n if (!initialised) { baselineY = p.y; initialised = true; }\n else if (p.y > baselineY) baselineY = p.y;\n }\n for (const base of chain.bases) {\n if (base === null) continue;\n const p = positions.get(base.id);\n if (p === undefined) continue;\n if (p.y > baselineY) baselineY = p.y;\n }\n }\n if (!initialised) baselineY = 0;\n\n let cursorY = baselineY + gap;\n for (const chain of chains) {\n if (placed.has(chain.id)) continue;\n // Find this chain's current bounding box.\n let minY = Number.POSITIVE_INFINITY;\n let maxY = Number.NEGATIVE_INFINITY;\n for (const a of chain.backbone) {\n const p = positions.get(a.id);\n if (p === undefined) continue;\n if (p.y < minY) minY = p.y;\n if (p.y > maxY) maxY = p.y;\n }\n for (const base of chain.bases) {\n if (base === null) continue;\n const p = positions.get(base.id);\n if (p === undefined) continue;\n if (p.y < minY) minY = p.y;\n if (p.y > maxY) maxY = p.y;\n }\n if (minY === Number.POSITIVE_INFINITY) {\n placed.add(chain.id);\n continue;\n }\n const dy = cursorY - minY;\n for (const a of chain.backbone) {\n const p = positions.get(a.id);\n if (p === undefined) continue;\n positions.set(a.id, {x: p.x, y: p.y + dy});\n }\n for (const base of chain.bases) {\n if (base === null) continue;\n const p = positions.get(base.id);\n if (p === undefined) continue;\n positions.set(base.id, {x: p.x, y: p.y + dy});\n }\n cursorY = maxY + dy + gap;\n placed.add(chain.id);\n }\n}\n","// T-0309 — Layout orchestrator.\n//\n// Given a parsed `Mol`, compute 2D positions for every atom and return a\n// new `Mol` whose atoms carry the resulting `p` field. The strategy\n// selection follows the legacy editor:\n//\n// - Cyclic chains up to 20 backbone atoms → `layoutCircle`.\n// - Backbones longer than 30 atoms → `layoutRows` (10 per row).\n// - Everything else → `layoutLine`, with `layoutInnerCircle` as the\n// specialised path when an inner cycle is detected.\n//\n// For RNA chains, `placeBases` runs after the backbone strategy so each\n// base is positioned along the bisector of its sugar's neighbors.\n//\n// Cross-polymer bonds drive `placeCrossChains` (anti-parallel for H-bond\n// pairs); disconnected fragments are stacked below by\n// `layoutDisconnectedFragments`.\n//\n// Mol is immutable — we build a new `Mol` whose atoms and bonds reference\n// freshly-allocated atom objects with the same identity and updated `p`.\n\nimport type {Atom, Bond, Chain, Mol} from '../core/model';\nimport type {Point} from '../util/types';\nimport {buildLayoutChains} from './chain-builder';\nimport type {LayoutChain} from './chain-builder';\nimport {layoutLine, DEFAULT_BOND_LENGTH} from './line';\nimport {layoutCircle} from './circle';\nimport {layoutRows} from './rows';\nimport {layoutInnerCircle, hasInnerCycle} from './inner-circle';\nimport {layoutCloverleaf, hasIntraChainHbonds} from './cloverleaf';\nimport {placeBases} from './base-placement';\nimport {placeCrossChains} from './cross-chain';\nimport {layoutDisconnectedFragments} from './fragments';\n\n// Per-polymer serpentine wrap width (T-3501, user request 2026-06-15).\n//\n// Peptides wrap every 20 residues. RNA wraps every 40 BACKBONE atoms — an RNA\n// backbone alternates sugar/phosphate, so ~40 backbone atoms ≈ 20 nucleotides,\n// keeping the per-row visual width comparable to a 20-residue peptide row. The\n// wrap THRESHOLD equals the per-row width per type, so a chain that exactly\n// fills one row does not wrap (n > threshold is false at n === perRow).\nexport const PEPTIDE_PER_ROW = 20;\nexport const RNA_PER_ROW = 40;\n\nexport interface LayoutOptions {\n /** Model-space bond length. Default `40`. */\n bondLength?: number;\n /** Monomers per row when wrapping. Default: 20 (peptide) / 40 (RNA) per chain. */\n perRow?: number;\n /** Threshold above which rows-wrap kicks in. Default: 20 (peptide) / 40 (RNA). */\n rowsThreshold?: number;\n /** Threshold below which a cyclic chain is laid out as a circle. Default `20`. */\n circleThreshold?: number;\n}\n\n/**\n * Lay out every atom of `mol` and return a new immutable `Mol`. The result\n * has the same identity (same atom ids, bond ids, chain ids) and the same\n * topology — only `atom.p` values change.\n */\nexport function layoutMol(mol: Mol, options?: LayoutOptions): Mol {\n const bondLength = options?.bondLength ?? DEFAULT_BOND_LENGTH;\n // `undefined` here means \"use the per-polymer default\" — resolved per chain\n // in pickStrategy so peptide (20) and RNA (40) chains wrap at different widths.\n const perRow = options?.perRow;\n const rowsThreshold = options?.rowsThreshold;\n const circleThreshold = options?.circleThreshold ?? 20;\n\n const chains = buildLayoutChains(mol);\n\n // 1. Per-chain strategy. Each chain is laid out at its own origin.\n const positions = new Map<number, Point>();\n for (const chain of chains) {\n const sub = pickStrategy(chain, mol, bondLength, perRow, rowsThreshold, circleThreshold);\n for (const [aid, p] of sub) positions.set(aid, p);\n // Base placement after backbone.\n if (chain.polymerType === 'RNA') placeBases(chain, positions, {bondLength});\n }\n\n // 2. Cross-chain placement.\n const placed = placeCrossChains(chains, positions, mol, {bondLength});\n\n // 3. Disconnected fragments.\n layoutDisconnectedFragments(chains, positions, placed, {bondLength});\n\n // 4. Backfill any atom we missed (shouldn't happen, but defend against\n // weird parser output by leaving such atoms at the origin).\n for (const a of mol.atoms)\n if (!positions.has(a.id)) positions.set(a.id, {x: 0, y: 0});\n\n // 5. Build a new Mol with updated atom.p — preserving atom identity\n // requires rebuilding bonds (their `a1`/`a2` references must point at\n // the new atom objects). Use a map from old.id to new atom.\n return rebuildMol(mol, positions);\n}\n\nfunction pickStrategy(\n chain: LayoutChain,\n mol: Mol,\n bondLength: number,\n perRow: number | undefined,\n rowsThreshold: number | undefined,\n circleThreshold: number,\n): Map<number, Point> {\n const n = chain.backbone.length;\n if (n === 0) return new Map();\n // Per-polymer wrap width (T-3501): peptide 20, RNA 40, unless overridden.\n // The threshold mirrors the width so a chain that exactly fills one row\n // does not wrap.\n const isRna = chain.polymerType === 'RNA';\n const effPerRow = perRow ?? (isRna ? RNA_PER_ROW : PEPTIDE_PER_ROW);\n const effThreshold = rowsThreshold ?? effPerRow;\n // Phase 34 (T-3401) — Cloverleaf / RNA secondary structure layout\n // preempts every other strategy for RNA chains that carry at least\n // one intra-chain hbond. Hairpins, internal loops / bulges, multi-\n // branch junctions, and tRNA cloverleaves are all handled by the\n // recursive structure-tree algorithm in cloverleaf.ts. Without\n // this branch, layoutInnerCircle picks the single widest hbond and\n // draws one circle, producing a partial and wrong picture.\n if (chain.polymerType === 'RNA' && hasIntraChainHbonds(chain, mol))\n return layoutCloverleaf(chain, mol, {bondLength});\n if (chain.isCyclic && n <= circleThreshold)\n return layoutCircle(chain, {bondLength});\n // Inner-cycle (side-chain cross-link) chains draw as a ring + tails. This\n // MUST take priority over the long-chain row-wrap: a cross-linked peptide\n // longer than the wrap threshold should still ring, not serpentine into a\n // grid that scatters its cross-link partners across rows (T-3504).\n if (!chain.isCyclic && hasInnerCycle(chain, mol))\n return layoutInnerCircle(chain, mol, {bondLength});\n if (n > effThreshold) {\n // Phase 15 (T-1501) — RNA needs a wider row gap because each sugar\n // has a base hanging at +step (=64 px) below it; using the 60 px\n // peptide row spacing would let a row-0 base overlap a row-1 sugar.\n // For RNA we keep the legacy 2.0 × step factor (= 128 px) so the\n // base-to-next-row-sugar distance stays one full step. Peptides use\n // the new `1.5 × bondLength` rhythm (= 60 px) — no bases to fit.\n const rowSpacing = isRna ? 2.0 : undefined;\n return layoutRows(chain, rowSpacing !== undefined\n ? {bondLength, perRow: effPerRow, rowSpacing}\n : {bondLength, perRow: effPerRow});\n }\n // Otherwise try inner-circle (it falls back to line if no inner cycle).\n if (!chain.isCyclic)\n return layoutInnerCircle(chain, mol, {bondLength});\n return layoutLine(chain, {bondLength});\n}\n\nfunction rebuildMol(mol: Mol, positions: Map<number, Point>): Mol {\n const idToNewAtom = new Map<number, Atom>();\n const newAtoms: Atom[] = [];\n for (const old of mol.atoms) {\n const p = positions.get(old.id) ?? old.p;\n const next: Atom = {...old, p: {x: p.x, y: p.y}};\n idToNewAtom.set(old.id, next);\n newAtoms.push(next);\n }\n // Patch branchAtom pointers — they reference Atom objects.\n for (let i = 0; i < newAtoms.length; i++) {\n const orig = mol.atoms[i]!;\n if (orig.branchAtom !== undefined) {\n const newBranch = idToNewAtom.get(orig.branchAtom.id);\n if (newBranch !== undefined)\n newAtoms[i] = {...newAtoms[i]!, branchAtom: newBranch};\n // The map must be updated so subsequent lookups return the patched copy.\n idToNewAtom.set(newAtoms[i]!.id, newAtoms[i]!);\n }\n }\n\n const newBonds: Bond[] = [];\n for (const b of mol.bonds) {\n const a1 = idToNewAtom.get(b.a1.id);\n const a2 = idToNewAtom.get(b.a2.id);\n if (a1 === undefined || a2 === undefined) continue;\n newBonds.push({...b, a1, a2});\n }\n\n const newChains: Chain[] = [];\n for (const c of mol.chains) {\n const newBackbone = c.backboneAtoms.map((a) => idToNewAtom.get(a.id) ?? a);\n const newChainBonds = c.bonds.map((b) => {\n const a1 = idToNewAtom.get(b.a1.id) ?? b.a1;\n const a2 = idToNewAtom.get(b.a2.id) ?? b.a2;\n return {...b, a1, a2};\n });\n newChains.push({\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: newBackbone,\n bonds: newChainBonds,\n ...(c.annotation !== undefined ? {annotation: c.annotation} : {}),\n // Phase 33 (T-3301) — Preserve `strandType` across layout's\n // chain rebuild (the legacy code copied just the topology).\n // Without this the field would survive the parser only to be\n // dropped here, so `chain.strandType` would be `undefined` for\n // every consumer downstream of `layoutMol`.\n ...(c.strandType !== undefined ? {strandType: c.strandType} : {}),\n });\n }\n\n return {\n atoms: newAtoms,\n bonds: newBonds,\n chains: newChains,\n groups: mol.groups,\n annotations: mol.annotations,\n };\n}\n","// Primitive value types and pure geometry helpers shared by every layer of the\n// library. These are intentionally simple, allocation-friendly shapes used at\n// boundaries everywhere; the helpers here are dependency-free and side-effect\n// free. See ARCHITECTURE.md §3.1.\n\n/** A 2D point in SVG world coordinates (origin top-left, Y grows downward). */\nexport interface Point {\n x: number;\n y: number;\n}\n\n/** Axis-aligned rectangle (top-left origin, positive width/height). */\nexport interface Rect {\n x: number;\n y: number;\n width: number;\n height: number;\n}\n\n/** Free 2D vector. Distinct from `Point` to express geometric intent at call-sites. */\nexport interface Vec2 {\n x: number;\n y: number;\n}\n\n/** Disposer returned by every event subscription in the public API. */\nexport type Unsubscribe = () => void;\n\n/**\n * Axis-aligned bounding box. A semantic alias of `Rect` used at call sites\n * where the rectangle is computed from a set of points (a \"bounding\" box) as\n * opposed to a user-specified region.\n */\nexport interface BBox extends Rect {}\n\n/** Euclidean distance between two points. */\nexport function pointDistance(a: Readonly<Point>, b: Readonly<Point>): number {\n const dx = a.x - b.x;\n const dy = a.y - b.y;\n return Math.sqrt(dx * dx + dy * dy);\n}\n\n/** Structural equality on points. Exact (no epsilon). */\nexport function pointEquals(a: Readonly<Point>, b: Readonly<Point>): boolean {\n return a.x === b.x && a.y === b.y;\n}\n\n/**\n * Build the tightest axis-aligned bounding box covering every input point.\n *\n * Returns a zero-size box at the origin when `points` is empty — callers that\n * need to distinguish \"no input\" from \"single point\" should check length up\n * front.\n */\nexport function bboxFromPoints(points: Iterable<Readonly<Point>>): BBox {\n let initialised = false;\n let minX = 0;\n let minY = 0;\n let maxX = 0;\n let maxY = 0;\n for (const p of points) {\n if (!initialised) {\n minX = maxX = p.x;\n minY = maxY = p.y;\n initialised = true;\n continue;\n }\n if (p.x < minX) minX = p.x;\n if (p.x > maxX) maxX = p.x;\n if (p.y < minY) minY = p.y;\n if (p.y > maxY) maxY = p.y;\n }\n if (!initialised) return { x: 0, y: 0, width: 0, height: 0 };\n return { x: minX, y: minY, width: maxX - minX, height: maxY - minY };\n}\n\n/** Union of two bounding boxes (the smallest box covering both). */\nexport function bboxUnion(a: Readonly<BBox>, b: Readonly<BBox>): BBox {\n const minX = Math.min(a.x, b.x);\n const minY = Math.min(a.y, b.y);\n const maxX = Math.max(a.x + a.width, b.x + b.width);\n const maxY = Math.max(a.y + a.height, b.y + b.height);\n return { x: minX, y: minY, width: maxX - minX, height: maxY - minY };\n}\n","// T-0401 — Pure SVG path generators for the seven HELM monomer shapes plus\n// bond strokes and a tiny bounding-box helper.\n//\n// Every path is centered at the caller-supplied `Point` (`p`) and uses the\n// SVG convention that y grows downward. All functions are deterministic and\n// allocation-light: they build a single path-data string from a fixed-arity\n// vertex list. The renderer wraps the result in a `<path>` element and the\n// hit-tester reads `shapeBBox` to seed its broad-phase.\n//\n// References:\n// - RENDERING.md §3 (shape conventions)\n// - LEGACY-EDITOR-NOTES.md §\"helm/Interface.ts\" `drawMonomer` (canonical\n// mapping from biotype to shape)\n//\n// Layering: this module imports only from `util/`. No DOM, no console.\n\nimport type {Point} from '../util/types';\n\n// --------------------------------------------------------------------------\n// Tiny number formatter — keeps SVG strings short and deterministic.\n// --------------------------------------------------------------------------\n\n/**\n * Format a number with up to three decimal places, collapsing `-0` to `0`\n * and any non-finite input to `0`. The renderer cares about deterministic\n * output above all (snapshot tests compare strings byte-for-byte).\n *\n * T-0902 PROFILING NOTES (Phase 9): a 100-monomer render emits ~5 shape\n * paths per atom and each path contains 6-12 `fmt()` calls — so the function\n * is invoked thousands of times per render. Inlining a `Number.isInteger`\n * fast path skips the multiply/divide for the (frequent) zero-radius and\n * integer-coordinate cases that arise after layout snapping.\n */\nfunction fmt(n: number): string {\n if (Number.isInteger(n)) return n === 0 ? '0' : n.toString();\n if (!Number.isFinite(n)) return '0';\n if (Object.is(n, -0)) return '0';\n const r = Math.round(n * 1000) / 1000;\n return r === 0 ? '0' : r.toString();\n}\n\n// --------------------------------------------------------------------------\n// Polygon helpers\n// --------------------------------------------------------------------------\n\n/**\n * Concatenate a list of polygon vertices into an SVG path that\n * closes back to the first vertex with an explicit `L` (and then `Z`). The\n * explicit return-line is more verbose than the shorter `M v0 L v1 ... Z`\n * form, but it gives a stable count of `L` commands equal to the number of\n * vertices — useful for renderer snapshot tests and for the hit-tester's\n * polygon-walk helper.\n */\nfunction polygonPath(points: ReadonlyArray<Point>): string {\n if (points.length === 0) return '';\n const first = points[0] as Point;\n let out = `M ${fmt(first.x)} ${fmt(first.y)}`;\n for (let i = 1; i < points.length; i++) {\n const pt = points[i] as Point;\n out += ` L ${fmt(pt.x)} ${fmt(pt.y)}`;\n }\n // Close back to the first vertex with an explicit L, then Z.\n out += ` L ${fmt(first.x)} ${fmt(first.y)} Z`;\n return out;\n}\n\n/**\n * Sample `n` evenly-spaced vertices of a regular polygon inscribed in a\n * circle of `radius` centered at `p`, with the first vertex at angle\n * `rotationDeg` (SVG convention: 0° points right, 90° points down). Returns\n * a freshly-allocated `Point[]`.\n */\nfunction regularPolygonPoints(\n p: Point, n: number, radius: number, rotationDeg: number,\n): Point[] {\n const out: Point[] = [];\n const step = 360 / n;\n for (let i = 0; i < n; i++) {\n const angle = (rotationDeg + i * step) * Math.PI / 180;\n out.push({x: p.x + radius * Math.cos(angle), y: p.y + radius * Math.sin(angle)});\n }\n return out;\n}\n\n// --------------------------------------------------------------------------\n// Per-shape generators\n// --------------------------------------------------------------------------\n\n/**\n * Hexagonal `HELM_AA` shape. The default `-30°` rotation matches the legacy\n * editor's \"pointy-side\" orientation (vertices at top and bottom of the\n * bbox). `size` is the circumradius.\n */\nexport function hexagonPath(p: Point, size: number, rotationDeg: number = -30): string {\n return polygonPath(regularPolygonPoints(p, 6, size, rotationDeg));\n}\n\n/**\n * Diamond (rhombus) for `HELM_BASE`. The four vertices sit on the axes at\n * `±size`, producing a square rotated 45° in screen coordinates.\n */\nexport function diamondPath(p: Point, size: number): string {\n const pts: Point[] = [\n {x: p.x, y: p.y - size},\n {x: p.x + size, y: p.y},\n {x: p.x, y: p.y + size},\n {x: p.x - size, y: p.y},\n ];\n return polygonPath(pts);\n}\n\n/**\n * Pentagonal `HELM_NUCLEOTIDE` shape (the gap base-pair marker). The default\n * `-90°` rotation puts the first vertex at the top so the pentagon \"points\n * up\" — matching the legacy editor.\n */\nexport function pentagonPath(p: Point, size: number, rotationDeg: number = -90): string {\n return polygonPath(regularPolygonPoints(p, 5, size, rotationDeg));\n}\n\n/**\n * Rounded axis-aligned rectangle centered at `p` with width `w`, height\n * `h`, and corner radius `r`. The radius is clamped to half the shorter\n * side so callers can pass arbitrary values without producing degenerate\n * arcs.\n */\nexport function roundedRectPath(p: Point, w: number, h: number, r: number): string {\n const halfW = Math.abs(w) / 2;\n const halfH = Math.abs(h) / 2;\n const radius = Math.max(0, Math.min(r, halfW, halfH));\n const x = p.x - halfW;\n const y = p.y - halfH;\n const right = x + halfW * 2;\n const bottom = y + halfH * 2;\n let out = `M ${fmt(x + radius)} ${fmt(y)}`;\n out += ` L ${fmt(right - radius)} ${fmt(y)}`;\n out += ` A ${fmt(radius)} ${fmt(radius)} 0 0 1 ${fmt(right)} ${fmt(y + radius)}`;\n out += ` L ${fmt(right)} ${fmt(bottom - radius)}`;\n out += ` A ${fmt(radius)} ${fmt(radius)} 0 0 1 ${fmt(right - radius)} ${fmt(bottom)}`;\n out += ` L ${fmt(x + radius)} ${fmt(bottom)}`;\n out += ` A ${fmt(radius)} ${fmt(radius)} 0 0 1 ${fmt(x)} ${fmt(bottom - radius)}`;\n out += ` L ${fmt(x)} ${fmt(y + radius)}`;\n out += ` A ${fmt(radius)} ${fmt(radius)} 0 0 1 ${fmt(x + radius)} ${fmt(y)}`;\n out += ' Z';\n return out;\n}\n\n/**\n * Closed ellipse centered at `p` with x-radius `rx` and y-radius `ry`. We\n * emit two half-arcs to keep the path explicitly closed (SVG's `<path>`\n * with `Z` works for circles even when described this way, and avoids the\n * need for a separate `<circle>` element type at the call site).\n */\nexport function ellipsePath(p: Point, rx: number, ry: number): string {\n const ax = Math.abs(rx);\n const ay = Math.abs(ry);\n return (\n `M ${fmt(p.x - ax)} ${fmt(p.y)} ` +\n `A ${fmt(ax)} ${fmt(ay)} 0 1 0 ${fmt(p.x + ax)} ${fmt(p.y)} ` +\n `A ${fmt(ax)} ${fmt(ay)} 0 1 0 ${fmt(p.x - ax)} ${fmt(p.y)} Z`\n );\n}\n\n/**\n * A `HELM_BLOB` rectangle — same as `roundedRectPath` but typically called\n * with a larger size and corner radius. Aliased rather than re-implemented\n * so consumers can write call-site intent.\n */\nexport function blobPath(p: Point, w: number, h: number, r: number): string {\n return roundedRectPath(p, w, h, r);\n}\n\n/**\n * Circle path used to draw a gap atom (`*`). The dashed appearance is\n * applied at draw time via `stroke-dasharray`; the path itself is a plain\n * circle so hit-testing and bbox computation stay simple.\n */\nexport function dashedCirclePath(p: Point, r: number): string {\n return ellipsePath(p, r, r);\n}\n\n// --------------------------------------------------------------------------\n// Bond strokes\n// --------------------------------------------------------------------------\n\n/**\n * Straight `M..L..` bond stroke between two atom centers. The renderer is\n * responsible for any per-bond-kind decoration (dash, colour, hash marks).\n */\nexport function bondLinePath(a: Point, b: Point): string {\n return `M ${fmt(a.x)} ${fmt(a.y)} L ${fmt(b.x)} ${fmt(b.y)}`;\n}\n\n/**\n * Two short perpendicular hash marks straddling the midpoint of `a..b`, the\n * canonical H-bond decoration. Both hashes are emitted in a single path so\n * the renderer can stroke them together (one `<path>` per bond).\n *\n * When `a` and `b` coincide we still emit a non-empty (degenerate) path so\n * downstream SVG parsers do not choke.\n */\nexport function bondHashPath(a: Point, b: Point, hashLength: number = 6): string {\n const dx = b.x - a.x;\n const dy = b.y - a.y;\n const len = Math.sqrt(dx * dx + dy * dy);\n if (len === 0)\n return `M ${fmt(a.x)} ${fmt(a.y)} L ${fmt(a.x)} ${fmt(a.y)}`;\n const ux = dx / len;\n const uy = dy / len;\n const px = -uy;\n const py = ux;\n const mx = (a.x + b.x) / 2;\n const my = (a.y + b.y) / 2;\n const half = hashLength / 2;\n // Offset hashes a quarter of the bond length on either side of the midpoint\n // — far enough apart to read as two ticks, close enough to remain close.\n const offset = Math.min(hashLength * 0.6, len * 0.25);\n const c1x = mx - ux * offset;\n const c1y = my - uy * offset;\n const c2x = mx + ux * offset;\n const c2y = my + uy * offset;\n return (\n `M ${fmt(c1x - px * half)} ${fmt(c1y - py * half)} L ${fmt(c1x + px * half)} ${fmt(c1y + py * half)} ` +\n `M ${fmt(c2x - px * half)} ${fmt(c2y - py * half)} L ${fmt(c2x + px * half)} ${fmt(c2y + py * half)}`\n );\n}\n\n// --------------------------------------------------------------------------\n// Bounding box helper\n// --------------------------------------------------------------------------\n\n/**\n * One of the seven shape families the renderer knows how to draw. Used as\n * the discriminant for `shapeBBox` so callers can request a tight bbox for\n * any registered shape without re-implementing the trig per-shape.\n */\nexport type ShapeKind = 'hexagon' | 'diamond' | 'pentagon' | 'rounded-rect' | 'ellipse' | 'blob' | 'circle';\n\n/**\n * Return the axis-aligned bounding box of a centered shape. `w` carries the\n * primary size (radius for hexagon/diamond/pentagon/circle, full width for\n * rounded-rect/blob, x-radius for ellipse). `h` is required for ellipse\n * (y-radius) and rounded-rect/blob (height); for the regular polygons it is\n * ignored.\n *\n * The bbox is tight: it covers the actual geometry, not just the\n * circumradius. Hit-tests use this as the broad-phase rectangle.\n */\nexport function shapeBBox(\n kind: ShapeKind, p: Point, w: number, h?: number,\n): {x: number; y: number; width: number; height: number} {\n switch (kind) {\n case 'hexagon': {\n // Rotation -30° → vertices at angles -30, 30, 90, 150, 210, 270.\n // x-extremes share |cos(30)| = √3/2; y-extremes at 90°/270° are ±size.\n const hw = w * Math.sqrt(3) / 2;\n const hh = w;\n return {x: p.x - hw, y: p.y - hh, width: hw * 2, height: hh * 2};\n }\n case 'diamond': {\n return {x: p.x - w, y: p.y - w, width: w * 2, height: w * 2};\n }\n case 'pentagon': {\n // Rotation -90° → first vertex straight up at (0, -w); lower vertices at\n // angles 18°, 162° from x-axis... but our convention is offset by -90,\n // so the second pair sits at angles -18° (≡ 342°) and 198°, and the bottom\n // pair at 54° / 126°. Extremes: top y = -w, bottom y = sin(54°)*w,\n // x-extremes = ±cos(18°)*w.\n const halfW = Math.cos(18 * Math.PI / 180) * w;\n const top = -w;\n const bottom = Math.sin(54 * Math.PI / 180) * w;\n return {x: p.x - halfW, y: p.y + top, width: halfW * 2, height: bottom - top};\n }\n case 'rounded-rect':\n case 'blob': {\n const _h = h ?? w;\n const hw = Math.abs(w) / 2;\n const hh = Math.abs(_h) / 2;\n return {x: p.x - hw, y: p.y - hh, width: hw * 2, height: hh * 2};\n }\n case 'ellipse': {\n const rx = Math.abs(w);\n const ry = Math.abs(h ?? w);\n return {x: p.x - rx, y: p.y - ry, width: rx * 2, height: ry * 2};\n }\n case 'circle': {\n const r = Math.abs(w);\n return {x: p.x - r, y: p.y - r, width: r * 2, height: r * 2};\n }\n }\n}\n","// T-0402 — Renderer theme contract.\n//\n// A `Theme` collects every visual constant the renderer needs (background,\n// stroke / fill, font sizing, selection/highlight colours, per-biotype shape\n// styles, plus a `ColorTheme` palette for monomer colour resolution). Two\n// built-in themes (`lightTheme`, `darkTheme`) cover the common case;\n// `defineTheme(base, overrides)` composes custom variants.\n//\n// References:\n// - RENDERING.md §3 (shape sizing), §11 (theme contract), §12 (selection)\n// - MONOMER-LIBRARY.md §6 (colour resolution via `ColorTheme`)\n//\n// Layering: imports from `core/`, `monomer-lib/` only. No DOM, no console.\n\nimport {HelmTypes, type HelmType} from '../core/constants';\nimport {DEFAULT_BOND_LENGTH} from '../layout/line';\nimport {lightPalette, darkPalette, type ColorTheme} from '../monomer-lib/color-rules';\n\n/**\n * Per-shape sizing — kept tiny on purpose so themes are easy to override.\n *\n * `size` is the shape's primary dimension at zoom 1: the circumradius for\n * regular polygons (hexagon, diamond, pentagon), the side for rounded\n * squares (sugar/chem), the width/height for the blob rectangle, and the\n * radius for the linker ellipse. The renderer interprets it consistently\n * with the shape generators in `./shapes`.\n */\nexport interface ShapeStyle {\n /** Primary dimension (radius / side / width) in CSS pixels at zoom 1. */\n size: number;\n /** Stroke width in CSS pixels. */\n strokeWidth: number;\n /** Corner radius for rounded shapes (sugar, chem, blob). */\n cornerRadius?: number;\n}\n\n/**\n * Renderer theme. Everything the SVG and canvas backends paint is sourced\n * from one of these fields — there are no other style knobs. Custom themes\n * compose via `defineTheme(base, overrides)`.\n */\nexport interface Theme {\n /** Stable theme name. Used as part of cache keys. */\n readonly name: string;\n /** Canvas background colour (CSS). */\n readonly background: string;\n /** Default stroke colour for shapes and bonds. */\n readonly defaultStroke: string;\n /** Default fill colour when a monomer has no resolved colour. */\n readonly defaultFill: string;\n /** Stroke colour for selected atoms in the selection pass. */\n readonly selectionColor: string;\n /** Stroke colour for highlighted atoms in the highlight pass. */\n readonly highlightColor: string;\n /** Stroke colour used for missing-monomer outlines. */\n readonly errorColor: string;\n /** Default label font size in CSS pixels at zoom 1. */\n readonly fontSize: number;\n /** Default label font family. */\n readonly fontFamily: string;\n /** Model-space distance between consecutive backbone atoms. */\n readonly bondLength: number;\n /** Default text colour for monomer labels. */\n readonly textColor: string;\n /** Optional vertical offset (CSS px) for the label baseline. */\n readonly labelOffsetY?: number;\n /** Colour for the optional continuous-id overlay. */\n readonly idColor: string;\n /** Colour for the annotation overlay (5'/n/c markers). */\n readonly annotationColor: string;\n /** Fill colour of the small tag dot on tagged atoms. */\n readonly tagDotColor: string;\n /** Stroke colour for canonical Watson-Crick H-bonds. */\n readonly hbondColor: string;\n /** Stroke colour for mismatched / non-canonical H-bonds. */\n readonly nonCanonicalHbondColor: string;\n /** Stroke colour for bonds that cross between two polymers. */\n readonly crossPolymerBondColor: string;\n /** Monomer-colour palette consumed by `resolveMonomerColors`. */\n readonly colorTheme: ColorTheme;\n /**\n * Optional palette tuning. `softenCanvas`, when `true`, instructs renderers\n * to soften (pastel) the resolved monomer colour on the main canvas — the\n * palette tiles always soften by default. Default `false`: canvas keeps the\n * saturated legacy colours per RENDERING.md §11.\n */\n readonly palette?: {\n readonly softenCanvas?: boolean;\n };\n /** Per-biotype shape styles keyed on a stable short tag. */\n readonly shapes: Record<\n 'aa' | 'sugar' | 'base' | 'linker' | 'chem' | 'blob' | 'nucleotide',\n ShapeStyle\n >;\n}\n\n// --------------------------------------------------------------------------\n// Built-in shape sizing\n// --------------------------------------------------------------------------\n\nconst DEFAULT_FONT_SIZE = 14;\nconst DEFAULT_FONT_FAMILY = '\"Helvetica Neue\", Helvetica, Arial, sans-serif';\n\n/**\n * Build the per-biotype shape styles from a single font-size constant.\n *\n * Phase 13a (T-1301a Bug 9) — equal-area multipliers. The Phase 12\n * multipliers compared shape `size` numerically, but `size` means\n * different things for different shapes (circumradius for regular\n * polygons, side for squares, radius for circles, half-width for blobs),\n * so equal `size` produced VERY unequal painted area. The Phase 13a\n * multipliers retarget every biotype to render at ~600 px² of painted\n * area at fontSize=14 — except blob (~1080 px²) which stays slightly\n * larger by design for visual emphasis.\n *\n * Derivation (each shape's true area as a function of its `size`):\n * hexagon (regular, circumradius s): A = (3√3/2) · s² ≈ 2.598 · s²\n * → for A=600, s≈15.2 → mult ≈ 15.2 / 14 ≈ 1.08\n * diamond (rhombus, half-diagonal d): A = 2 · d²\n * → for A=600, d≈17.32 → mult ≈ 17.32 / 14 ≈ 1.24\n * rounded square (side s; we treat A ≈ s² since the radius rounds off\n * only the corners): A = s²\n * → for A=600 (sugar), s≈24.49 → mult ≈ 24.49 / 14 ≈ 1.75\n * → for A=679 (chem, slightly chunkier), s≈26.06 → mult ≈ 1.85\n * circle (radius r): A = π · r²\n * → for A=600, r≈13.82 → mult ≈ 13.82 / 14 ≈ 0.99\n * pentagon (regular, circumradius r):\n * A = (5/2) · r² · sin(72°) ≈ 5 · sin(72°) / 2 · r² ≈ 2.378 · r²\n * → for A=600, r≈15.88 → mult ≈ 15.88 / 14 ≈ 1.13 (cross-check)\n * We use 1.34 instead, targeting A≈836 px²; pentagon sits between\n * hex and chem so it reads as a distinct nucleotide marker.\n * blob (rounded square, side ≈ 2 · size · cos45° span on the bbox):\n * We keep the visual-emphasis target ~1080 px² → mult ≈ 2.0.\n *\n * Phase 13a multipliers:\n * aa hexagon: 1.08 (was 1.25)\n * sugar rounded square: 1.75 (was 1.25)\n * base diamond: 1.24 (was 1.15)\n * linker circle: 0.99 (was 1.05)\n * chem rounded square: 1.85 (was 1.35)\n * blob: 2.00 (was 1.80)\n * nucleotide pentagon: 1.34 (was 1.25)\n */\nfunction buildShapes(fontSize: number): Theme['shapes'] {\n // Phase 29 (T-2902) -- Round every shape's corners by giving each\n // shape a 5 px self-coloured stroke with `stroke-linejoin: round`.\n // The stroke is painted in the SAME colour as the fill so it blends\n // visually -- the only effect is rounded vertices (polygons) and a\n // slightly chunkier outline on already-curved shapes. User request\n // 2026-05-19: \"I like the rounded edges on the sugars, but I would\n // like them just a bit more rounded, and similarly rounded shapes\n // on hexagons, nucleotides, etc. you can set the stroke to same\n // colour and have stroke-linejoin round property. lets say stroke\n // of 5 px should be good. don't forget to readjust the size and\n // also readjust hover/selected states\".\n //\n // Because the 5 px stroke straddles the path (half inside, half\n // outside), each shape's visual extent grows by ~5 px in every\n // direction unless we shrink the path. To keep visual areas close\n // to the Phase 22 equal-area target (~600 px²), every `size` value\n // is reduced by `5 / fontSize` (so 5 px less along the characteristic\n // dimension). New multipliers:\n //\n // aa hex: 1.08 -> 0.72 ((15.12 - 5) / 14)\n // sugar rounded square: 1.75 -> 1.39 ((24.50 - 5) / 14)\n // base diamond: 1.24 -> 0.88 ((17.36 - 5) / 14)\n // linker circle: 0.99 -> 0.63 ((13.86 - 5) / 14)\n // chem rounded square: 1.85 -> 1.49 ((25.90 - 5) / 14)\n // blob: 2.00 -> 1.64 ((28.00 - 5) / 14)\n // nucleotide pentagon: 1.34 -> 0.98 ((18.76 - 5) / 14)\n //\n // All seven shapes adopt a uniform 5 px strokeWidth; blob no longer\n // needs its old 1 px monomer outline because the self-coloured 5 px\n // stroke already provides a visible (rounded) edge.\n return {\n aa: {size: fontSize * 0.72, strokeWidth: 5},\n sugar: {size: fontSize * 1.39, strokeWidth: 5, cornerRadius: fontSize * 0.3},\n base: {size: fontSize * 0.88, strokeWidth: 5},\n linker: {size: fontSize * 0.63, strokeWidth: 5},\n chem: {size: fontSize * 1.49, strokeWidth: 5, cornerRadius: fontSize * 0.5},\n blob: {size: fontSize * 1.64, strokeWidth: 5, cornerRadius: fontSize * 0.8},\n nucleotide: {size: fontSize * 0.98, strokeWidth: 5},\n };\n}\n\n// --------------------------------------------------------------------------\n// Built-in themes\n// --------------------------------------------------------------------------\n\n/**\n * Light theme — white canvas, dark strokes, the legacy Pistoia colour\n * palette for monomer fills. Matches the default appearance of the legacy\n * HELM Web Editor.\n */\nexport const lightTheme: Theme = {\n name: 'light',\n background: '#ffffff',\n defaultStroke: '#202020',\n defaultFill: '#ffffff',\n // Phase 18 (T-1801 / T-1803) — yellow outline for selected atoms, teal\n // outline for hover-highlighted ones. The previous Phase 4 colours\n // (`#FFD29B` peach, `#FFB2B2` pink) were too close to the legacy\n // monomer-fill palette to read as a \"this monomer is selected\" cue —\n // the user reported \"I can't tell what's selected.\" Material-design\n // amber + teal both achieve > 4.5:1 contrast against the white canvas\n // and against every default fill.\n selectionColor: '#FFC107',\n // Phase 22 (T-2205) -- \"Light Tiffany\" hover ring. The previous\n // teal #26A69A read as heavy and matched some monomer fills too\n // closely; the new #A4E2DC sits on the lighter Tiffany blue spectrum\n // and visibly differentiates the highlight pass from any monomer\n // fill in the lightPalette.\n highlightColor: '#A4E2DC',\n errorColor: '#cc0000',\n fontSize: DEFAULT_FONT_SIZE,\n fontFamily: DEFAULT_FONT_FAMILY,\n bondLength: DEFAULT_BOND_LENGTH,\n textColor: '#000000',\n idColor: '#00aa00',\n annotationColor: '#FFA500',\n tagDotColor: '#dd2222',\n hbondColor: '#888888',\n nonCanonicalHbondColor: '#cc8800',\n crossPolymerBondColor: '#1f5fcd',\n colorTheme: lightPalette,\n palette: {softenCanvas: false},\n shapes: buildShapes(DEFAULT_FONT_SIZE),\n};\n\n/**\n * Dark theme — slate canvas, light strokes, desaturated monomer fills.\n * Derived from `lightTheme` so consumers only see overrides that actually\n * change for dark mode.\n */\nexport const darkTheme: Theme = {\n name: 'dark',\n background: '#1a1d23',\n defaultStroke: '#e0e0e0',\n defaultFill: '#2b2f37',\n // Phase 18 (T-1801 / T-1803) — lighter yellow + cyan-teal so the\n // selection / hover rings still clear ≥ 4.5:1 against the slate\n // background. Mirrors the Material amber 300 / cyan 300 swatches.\n selectionColor: '#FFD54F',\n // Phase 22 (T-2205) -- Dark-mode counterpart to the light Tiffany\n // tone (lightTheme uses #A4E2DC). Slightly more saturated so it\n // still reads against the slate background.\n highlightColor: '#7DD8CC',\n errorColor: '#ff5050',\n fontSize: DEFAULT_FONT_SIZE,\n fontFamily: DEFAULT_FONT_FAMILY,\n bondLength: DEFAULT_BOND_LENGTH,\n textColor: '#ffffff',\n idColor: '#33ff33',\n annotationColor: '#FFB84D',\n tagDotColor: '#ff6464',\n hbondColor: '#aaaaaa',\n nonCanonicalHbondColor: '#ffaa44',\n crossPolymerBondColor: '#6699ff',\n colorTheme: darkPalette,\n palette: {softenCanvas: false},\n shapes: buildShapes(DEFAULT_FONT_SIZE),\n};\n\n// --------------------------------------------------------------------------\n// Composition helper\n// --------------------------------------------------------------------------\n\n/**\n * Compose a new theme by shallow-merging `overrides` on top of `base`. The\n * `shapes` map is merged shallowly too so callers can override just one\n * biotype without having to restate the others. Other nested objects\n * (`colorTheme`) are taken from the override outright when present.\n */\nexport function defineTheme(base: Theme, overrides: Partial<Theme>): Theme {\n const shapes =\n overrides.shapes === undefined\n ? base.shapes\n : {...base.shapes, ...overrides.shapes};\n return {...base, ...overrides, shapes};\n}\n\n/**\n * Pick the appropriate `ShapeStyle` for an atom's `biotype`. Every concrete\n * `HelmType` maps to exactly one entry in `theme.shapes`; the switch is\n * exhaustive so TypeScript guarantees no missing cases.\n */\nexport function shapeStyleFor(theme: Theme, biotype: HelmType): ShapeStyle {\n switch (biotype) {\n case HelmTypes.AA:\n return theme.shapes.aa;\n case HelmTypes.SUGAR:\n return theme.shapes.sugar;\n case HelmTypes.BASE:\n return theme.shapes.base;\n case HelmTypes.LINKER:\n return theme.shapes.linker;\n case HelmTypes.CHEM:\n return theme.shapes.chem;\n case HelmTypes.BLOB:\n return theme.shapes.blob;\n case HelmTypes.NUCLEOTIDE:\n return theme.shapes.nucleotide;\n }\n}\n","// Shared helpers used by `svg-renderer.ts`, `selection-overlay.ts`, and\n// `hit-test.ts` so each of them computes per-atom geometry the same way.\n//\n// These functions encapsulate two concerns:\n// 1. The biotype → shape-kind mapping (which generator function to call).\n// 2. The shape-style + atom position → path data + bbox composition.\n//\n// Layering: imports from `core/`, `util/`, plus the local `./shapes` and\n// `./theme` modules. No DOM, no console.\n\nimport type {Atom} from '../core/model';\nimport {HelmTypes, type HelmType} from '../core/constants';\nimport type {BBox} from '../util/types';\nimport {\n blobPath,\n dashedCirclePath,\n diamondPath,\n ellipsePath,\n hexagonPath,\n pentagonPath,\n roundedRectPath,\n shapeBBox,\n type ShapeKind,\n} from './shapes';\nimport {shapeStyleFor, type ShapeStyle, type Theme} from './theme';\n\n/** Sentinel symbol used by the parser/resolver for gap atoms (HELM `*`). */\nconst GAP_SYMBOL = '*';\n\n/**\n * Subset of `ShapeKind`s that are reachable from an atom's `biotype` — the\n * shape lookup never produces a generic 'ellipse' (linker uses a circle of\n * equal radii). Narrowing the return type lets callers' switches stay\n * exhaustive without dead branches.\n */\nexport type AtomShapeKind = Exclude<ShapeKind, 'ellipse'>;\n\n/**\n * Map an atom's `biotype` to one of the registered `ShapeKind`s in\n * `./shapes`. CHEM and SUGAR both use rounded rectangles — they differ\n * only in size / corner radius, which the caller pulls from the\n * `ShapeStyle` separately.\n */\nexport function shapeKindFor(biotype: HelmType): AtomShapeKind {\n switch (biotype) {\n case HelmTypes.AA:\n return 'hexagon';\n case HelmTypes.SUGAR:\n return 'rounded-rect';\n case HelmTypes.BASE:\n return 'diamond';\n case HelmTypes.LINKER:\n return 'circle';\n case HelmTypes.CHEM:\n return 'rounded-rect';\n case HelmTypes.BLOB:\n return 'blob';\n case HelmTypes.NUCLEOTIDE:\n return 'pentagon';\n }\n}\n\n/**\n * Build the SVG `d` attribute for an atom's shape under the given theme.\n * Gap atoms (`atom.symbol === '*'`) always render as a circle; the dashed\n * stroke is applied by the caller via `stroke-dasharray`.\n *\n * Phase 31 (T-3002) — `outset` (px) shifts every edge of the shape\n * outward by that perpendicular distance. The highlight / selection\n * ring builders pass a positive `outset` so the ring's inner edge sits\n * flush against the atom's outer edge instead of overlapping it.\n *\n * The per-shape math derives from the apothem formula for a regular\n * n-gon: the minimum-distance edge (apothem) is `radius * cos(π / n)`.\n * To move the edge outward by `d` perpendicular pixels, the\n * circumradius grows by `d / cos(π / n)`. For a circle (the\n * degenerate ∞-gon) `cos(π / n) → 1` so the radius grows by `d`. For\n * a rounded rectangle whose `size` is the **full** width/height, each\n * side moves outward by `d` so width and height grow by `2d`; the\n * corner radius gains `d` to keep the corners concentric.\n */\nexport function atomShapePath(atom: Atom, theme: Theme, outset: number = 0): string {\n const style = shapeStyleFor(theme, atom.biotype);\n if (atom.symbol === GAP_SYMBOL)\n return dashedCirclePath(atom.p, style.size + outset);\n const kind = shapeKindFor(atom.biotype);\n switch (kind) {\n case 'hexagon': {\n // -30° rotation → apothem at angle 0; cos(π/6) ≈ 0.866.\n const grow = outset === 0 ? 0 : outset / Math.cos(Math.PI / 6);\n return hexagonPath(atom.p, style.size + grow);\n }\n case 'diamond': {\n // n = 4; cos(π/4) = √2/2 ≈ 0.707.\n const grow = outset === 0 ? 0 : outset / Math.cos(Math.PI / 4);\n return diamondPath(atom.p, style.size + grow);\n }\n case 'pentagon': {\n // n = 5; cos(π/5) ≈ 0.809.\n const grow = outset === 0 ? 0 : outset / Math.cos(Math.PI / 5);\n return pentagonPath(atom.p, style.size + grow);\n }\n case 'rounded-rect':\n return roundedRectPath(\n atom.p,\n style.size + 2 * outset,\n style.size + 2 * outset,\n (style.cornerRadius ?? 0) + outset,\n );\n case 'blob':\n return blobPath(\n atom.p,\n style.size + 2 * outset,\n style.size + 2 * outset,\n (style.cornerRadius ?? 0) + outset,\n );\n case 'circle':\n return ellipsePath(atom.p, style.size + outset, style.size + outset);\n }\n}\n\n/**\n * Tight axis-aligned bbox for an atom's shape, including stroke half-width\n * padding so the bbox covers the visible ink. Used by the renderer to size\n * the canvas and by the hit-tester as a broad-phase rect.\n */\nexport function atomBBox(atom: Atom, theme: Theme): BBox {\n const style = shapeStyleFor(theme, atom.biotype);\n const kind: AtomShapeKind = atom.symbol === GAP_SYMBOL ? 'circle' : shapeKindFor(atom.biotype);\n let bbox: BBox;\n switch (kind) {\n case 'hexagon':\n case 'diamond':\n case 'pentagon':\n case 'circle':\n bbox = shapeBBox(kind, atom.p, style.size);\n break;\n case 'rounded-rect':\n case 'blob':\n bbox = shapeBBox(kind, atom.p, style.size, style.size);\n break;\n }\n const pad = style.strokeWidth / 2;\n return {\n x: bbox.x - pad,\n y: bbox.y - pad,\n width: bbox.width + 2 * pad,\n height: bbox.height + 2 * pad,\n };\n}\n\n/**\n * Hit-test radius used by the broad-phase / nearest-atom logic. We adopt\n * the legacy editor's convention of `atomscale * fontSize / 2` (the inner\n * circumradius of the atom's bounding circle), giving a single scalar per\n * atom that's cheap to compare against an Euclidean distance.\n */\nexport function atomHitRadius(atom: Atom, theme: Theme): number {\n const style = shapeStyleFor(theme, atom.biotype);\n return style.size;\n}\n\n/**\n * Convenience: re-export the per-atom `ShapeStyle` resolution so render\n * call sites can grab style + path with a single import.\n */\nexport function atomStyle(atom: Atom, theme: Theme): ShapeStyle {\n return shapeStyleFor(theme, atom.biotype);\n}\n","// T-0403 — Tiny string-based SVG element builder.\n//\n// The renderer produces an SVG document as a single string (no DOM\n// traversal, no `innerHTML` parsing). This builder exists so attribute\n// escaping happens in exactly one place and number formatting is\n// consistent with `./shapes` (3-decimal rounding, `-0` collapsed).\n//\n// The API is deliberately minimal: a single `tag(name, attrs?, children?)`\n// helper plus the two escape primitives. Higher-level call sites assemble\n// elements by concatenation.\n//\n// Layering: imports nothing. No DOM, no console.\n//\n// T-0902 PROFILING NOTES (Phase 9): a 100-monomer cold render performs\n// ~5-7 `tag(...)` calls per atom (path, label, optional ambiguity / id / tag\n// dot, outer `<g>`), and almost every attribute value passes through\n// `escapeAttr` or `formatNumber`. The bench results showed both functions in\n// the top 5 self-time frames. Optimizations applied below — all purely\n// algorithmic, no API change:\n// 1. `escapeAttr` / `escapeText` short-circuit when no escapable char is\n// present (the common case for atom labels like \"A\", \"C\", \"meI\" and for\n// generated class names). `String#test`-style ASCII scans dwarf five\n// chained `.replace(/g, ...)` calls, the latter of which always allocate\n// a result string even when nothing matches.\n// 2. `formatNumber` adds a small-integer fast path. Most coordinates pass\n// through `Math.round`'d already-integer values; `Number.isInteger` is\n// a microsecond check that skips the multiply/divide + `Object.is(-0)`\n// branch when applicable.\n// 3. `tag(...)` checks `attrs === undefined` and short-circuits the loop\n// entirely; the rendered output is unchanged because the keys-loop was\n// already a no-op in that case but the `Object.keys()` allocation was\n// not.\n\n/**\n * Allowed attribute value types: strings (HTML-escaped on emit), numbers\n * (formatted with 3-decimal precision), booleans (presence/absence flags),\n * and `undefined` (skipped). Other types are rejected at the call site by\n * the type system.\n */\nexport type SvgAttrValue = string | number | boolean | undefined;\n\n/** Attribute map for the `tag` builder. */\nexport type SvgAttrs = Record<string, SvgAttrValue>;\n\n// Module-level scan regexes — kept as constants so they aren't recompiled\n// per call. The `test()` returns false for the common monomer-symbol /\n// generated-class-name case, in which case we can return the input as-is.\nconst ATTR_NEEDS_ESCAPE = /[&\"'<>]/;\nconst TEXT_NEEDS_ESCAPE = /[&<>]/;\n\n/**\n * Escape a string for use as an XML attribute value. Quotes are doubled\n * (`\"`) so callers can wrap attribute values in `\"…\"` without worrying\n * about embedded characters.\n *\n * Fast path: if the string contains none of `&\"'<>`, the input is returned\n * unchanged. This dominates the hot path because attribute values are\n * generated from monomer symbols and class names — neither contains XML\n * metacharacters in practice.\n */\nexport function escapeAttr(s: string): string {\n if (!ATTR_NEEDS_ESCAPE.test(s)) return s;\n return s\n .replace(/&/g, '&amp;')\n .replace(/\"/g, '&quot;')\n .replace(/'/g, '&apos;')\n .replace(/</g, '&lt;')\n .replace(/>/g, '&gt;');\n}\n\n/**\n * Escape a string for use as XML text content. Only `&`, `<`, and `>`\n * matter inside text nodes — quotes pass through.\n */\nexport function escapeText(s: string): string {\n if (!TEXT_NEEDS_ESCAPE.test(s)) return s;\n return s.replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;');\n}\n\n/**\n * Format a number with up to three decimal places. Mirrors the formatting\n * used by `./shapes` so attribute values and path data round identically.\n *\n * Integer fast path: every value passed through the renderer's surface\n * transform ends up close to an integer (pixel grid); when the input is\n * already an exact integer we can skip the multiply/divide entirely and\n * fall straight to `Number#toString`.\n */\nexport function formatNumber(n: number): string {\n if (Number.isInteger(n)) return n === 0 ? '0' : n.toString();\n if (!Number.isFinite(n)) return '0';\n if (Object.is(n, -0)) return '0';\n const r = Math.round(n * 1000) / 1000;\n return r === 0 ? '0' : r.toString();\n}\n\n/**\n * Build a single SVG element as a string. If `children` is undefined the\n * tag is emitted self-closing (`<g/>`); otherwise the children are\n * concatenated and wrapped in matching open/close tags.\n *\n * Attribute encoding rules:\n * - `undefined` → attribute omitted\n * - `false` → attribute omitted\n * - `true` → bare attribute name (no value)\n * - `number` → formatted via `formatNumber`\n * - `string` → escaped via `escapeAttr`\n */\nexport function tag(name: string, attrs?: SvgAttrs, children?: string | ReadonlyArray<string>): string {\n let out = `<${name}`;\n if (attrs !== undefined) {\n // Inline the attribute loop. We iterate `for...in` rather than\n // `Object.keys(...).forEach` so we don't allocate a temporary key array\n // per tag call (called O(atoms * 5) per render).\n for (const k in attrs) {\n const v = attrs[k];\n if (v === undefined || v === false) continue;\n if (v === true) {\n out += ` ${k}`;\n continue;\n }\n if (typeof v === 'number') {\n out += ` ${k}=\"${formatNumber(v)}\"`;\n } else {\n out += ` ${k}=\"${escapeAttr(v)}\"`;\n }\n }\n }\n if (children === undefined) return `${out}/>`;\n if (typeof children === 'string') return `${out}>${children}</${name}>`;\n return `${out}>${children.join('')}</${name}>`;\n}\n","// T-0403 — SVG renderer.\n//\n// Builds a single self-contained `<svg>` document for a `Mol`. The structure\n// follows RENDERING.md §8 (rect background → highlight layer → selection\n// layer → bonds → atoms → annotations). All output is concatenated as a\n// string via `./svg-builder`; we never touch `innerHTML`.\n//\n// The renderer is deterministic — given the same `Mol`, theme, and options\n// it produces the same string byte-for-byte. Snapshot tests rely on that.\n//\n// Layering: imports from `core/`, `util/`, `monomer-lib/`, and `./` only.\n// No DOM, no console. `document` is consulted only via `options.documentImpl`\n// when the host wants a `Document` round-trip; the default path stays string-\n// based.\n//\n// References:\n// - RENDERING.md §3 (shapes), §4 (bonds), §5 (labels), §6 (passes),\n// §8 (SVG structure), §11 (theme), §12 (selection)\n\nimport type {Atom, Bond, Mol} from '../core/model';\nimport {HelmTypes} from '../core/constants';\nimport type {BBox} from '../util/types';\nimport {bboxUnion} from '../util/types';\nimport {resolveMonomerColors} from '../monomer-lib/color-rules';\n\nimport {atomBBox, atomShapePath, atomStyle} from './atom-shape';\nimport {bondHashPath, bondLinePath} from './shapes';\nimport {escapeText, formatNumber, tag} from './svg-builder';\nimport {lightTheme, type Theme} from './theme';\n\n// --------------------------------------------------------------------------\n// Public API\n// --------------------------------------------------------------------------\n\n/** Options accepted by `renderSvg`. See RENDERING.md §8 for semantics. */\nexport interface RenderOptions {\n /** Output canvas width in CSS pixels. Default `400`. */\n width?: number;\n /** Output canvas height in CSS pixels. Default `100`. */\n height?: number;\n /** Background colour. Defaults to `theme.background`. */\n backColor?: string;\n /** Theme used for colours and shape sizing. Default `lightTheme`. */\n theme?: Theme;\n /** Padding around the drawn content in surface pixels. Default `16`. */\n padding?: number;\n /** Show the continuous-id overlay on each atom. Default `false`. */\n showIds?: boolean;\n /** Show per-atom / per-bond annotation text. Default `true`. */\n showAnnotations?: boolean;\n /** Show R-group labels on bond endpoints. Default `false`. */\n showRGroupLabels?: boolean;\n /** Override the theme's `bondLength`. Default `theme.bondLength`. */\n bondLength?: number;\n /** Override the theme's `fontSize`. Default `theme.fontSize`. */\n fontSize?: number;\n /**\n * Maximum up-scale factor when fitting the model into the surface. Default\n * `1` — the renderer never enlarges past native monomer size, so a small\n * drawing leaves empty space (the historical behaviour every snapshot\n * golden assumes). Datagrok consumers pass `Infinity` (or a large number)\n * so a single cell / editor pane is filled by scaling the drawing UP to\n * the available width/height. The fit still preserves aspect ratio and\n * never shrinks below what is needed to fit (down-scaling is always on).\n */\n maxScale?: number;\n /** Atom ids that should render in the selection pass. */\n selectedAtomIds?: ReadonlySet<number>;\n /** Atom ids that should render in the highlight pass. */\n highlightedAtomIds?: ReadonlySet<number>;\n /**\n * Optional `Document` implementation for headless callers that want to\n * parse the resulting SVG. Defaults to `globalThis.document` when\n * available. The renderer never *requires* a Document — output is a\n * string — but exposes the hook so callers can pin behaviour.\n */\n documentImpl?: Document;\n /**\n * T-1704 — Override the auto-fit. When supplied, the renderer skips\n * `computeModelBbox(mol)` and uses this bbox for the transform math.\n * The interactive editor uses this to keep the canvas transform stable\n * across mutations: after each `mol:changed` the view re-renders with\n * the bbox captured at the most recent layout (`setHelm` /\n * `cleanLayout`), so adding / removing / moving atoms does NOT cause a\n * visible re-fit. Headless callers can omit it for the auto-fit\n * behaviour.\n */\n fixedModelBbox?: { x: number; y: number; width: number; height: number };\n}\n\n/** Result returned by `renderSvg`. */\nexport interface RenderResult {\n /** The full `<svg>…</svg>` document as a string. */\n readonly svg: string;\n /** Tight bbox of the drawn content in model space. */\n readonly bbox: {x: number; y: number; width: number; height: number};\n /** Where that bbox sits inside the surface in surface-space pixels. */\n readonly drawBox: {x: number; y: number; width: number; height: number};\n}\n\n// --------------------------------------------------------------------------\n// Renderer entry point\n// --------------------------------------------------------------------------\n\nconst SVG_NS = 'http://www.w3.org/2000/svg';\n\n/**\n * Continuous-id (monomer index) overlay geometry, shared by the svg + canvas\n * renderers so both place the number identically. The offset is a FIXED\n * multiple of the font size (independent of each shape's `size`) so every\n * monomer's number sits at the same height — a sugar (size 1.39×fs) and a\n * phosphate linker (0.63×fs) align. `1.5×fs` clears every RNA/peptide shape.\n */\nexport const ID_OFFSET_FACTOR = 1.5;\n/** Id-label font size as a multiple of the base font size (was 0.6). */\nexport const ID_FONT_FACTOR = 0.8;\n\nconst EMBEDDED_CSS =\n '.hw-atom{transition:stroke-width 120ms,filter 120ms;}' +\n '.hw-atom:focus{outline:none;}' +\n '.hw-atom__shape{shape-rendering:geometricPrecision;}' +\n '.hw-bond__stroke{stroke-linecap:round;}';\n\nconst CANONICAL_PAIRS: ReadonlyArray<[string, string]> = [\n ['A', 'T'],\n ['A', 'U'],\n ['G', 'C'],\n];\n\n/**\n * Render a `Mol` to a self-contained SVG document. The result includes the\n * model bbox (in model coordinates) and a draw box (in surface coordinates)\n * so consumers can remap hit-test points without re-running the renderer.\n *\n * When `options.documentImpl` is supplied AND no global `document` is\n * available, the renderer still produces a string but skips any future\n * DOM-aware enhancements (no current call site requires DOM access; the\n * option exists for forward-compatibility).\n */\nexport function renderSvg(mol: Mol, options: RenderOptions = {}): RenderResult {\n const theme = options.theme ?? lightTheme;\n const width = options.width ?? 400;\n const height = options.height ?? 100;\n const padding = options.padding ?? 16;\n const backColor = options.backColor ?? theme.background;\n const showIds = options.showIds ?? false;\n const showAnnotations = options.showAnnotations ?? true;\n const fontSize = options.fontSize ?? theme.fontSize;\n const selected = options.selectedAtomIds ?? new Set<number>();\n const highlighted = options.highlightedAtomIds ?? new Set<number>();\n // `documentImpl` is accepted for API symmetry; the string path doesn't\n // need it but a future enhancement (DOM-returning variant) will. We only\n // touch globals lazily — never at module init — and only when the caller\n // didn't supply one. Reference it here so tests can confirm the option\n // is at least inspected.\n const docImpl = options.documentImpl ?? (typeof globalThis !== 'undefined' && typeof (globalThis as {document?: Document}).document !== 'undefined'\n ? (globalThis as {document: Document}).document\n : undefined);\n void docImpl;\n\n // -----------------------------------------------------------------------\n // Compute model-space bbox + surface transform\n // T-1704 — Honour `fixedModelBbox` (if supplied) so the auto-fit\n // transform stays stable across interactive mutations. The interactive\n // editor pins this to the bbox captured at the most recent layout so\n // adding / removing / moving atoms doesn't visibly rescale the canvas.\n // -----------------------------------------------------------------------\n const modelBbox = options.fixedModelBbox ?? computeModelBbox(mol, theme);\n const drawBox = fitToSurface(modelBbox, width, height, padding, options.maxScale ?? 1);\n const tx = drawBox.x - modelBbox.x * drawBox.scale;\n const ty = drawBox.y - modelBbox.y * drawBox.scale;\n\n // -----------------------------------------------------------------------\n // Layers\n //\n // Phase 19 (T-1901) — Paint order changed: highlights/selections now\n // come AFTER atoms so the rings actually paint ON TOP of the atom\n // shape (painter's algorithm). Previously the rings were drawn\n // beneath atoms and were occluded by the atom's fill, which made\n // selection invisible and hover indistinguishable from the CSS\n // `:hover` outline. The new order is: bonds → atoms → annotations →\n // highlights → selections. Selections are LAST so a selected+hovered\n // atom shows the yellow ring (selection wins over highlight when\n // both are present).\n // -----------------------------------------------------------------------\n const highlightsLayer = buildHighlightLayer(mol, theme, highlighted);\n const selectionsLayer = buildSelectionLayer(mol, theme, selected);\n const bondsLayer = buildBondsLayer(mol, theme);\n const atomsLayer = buildAtomsLayer(mol, theme, fontSize, showIds);\n const annotationsLayer = showAnnotations ? buildAnnotationsLayer(mol, theme, fontSize) : '';\n\n const transformValue =\n `translate(${formatNumber(tx)} ${formatNumber(ty)}) scale(${formatNumber(drawBox.scale)})`;\n\n const inner = tag(\n 'g',\n {class: 'hw-content', transform: transformValue},\n [bondsLayer, atomsLayer, annotationsLayer, highlightsLayer, selectionsLayer].join(''),\n );\n\n const defs = tag('defs', undefined, `<style>${EMBEDDED_CSS}</style>`);\n const bg = tag('rect', {class: 'hw-bg', x: 0, y: 0, width, height, fill: backColor});\n\n const svg = tag(\n 'svg',\n {\n xmlns: SVG_NS,\n viewBox: `0 0 ${formatNumber(width)} ${formatNumber(height)}`,\n width,\n height,\n 'data-hw-theme': theme.name,\n },\n [defs, bg, inner].join(''),\n );\n\n return {\n svg,\n bbox: {x: modelBbox.x, y: modelBbox.y, width: modelBbox.width, height: modelBbox.height},\n drawBox: {x: drawBox.x, y: drawBox.y, width: drawBox.width, height: drawBox.height},\n };\n}\n\n// --------------------------------------------------------------------------\n// Geometry helpers\n// --------------------------------------------------------------------------\n\n/**\n * Tight bbox covering every atom's shape (with stroke half-width). Empty\n * `Mol` yields a zero-size bbox at the origin.\n */\n/**\n * Compute the tight model-space bbox for `mol` (the union of every\n * atom's drawn shape). Exposed so the interactive editor can capture\n * the bbox of one rendered state and pin subsequent renders to it\n * (T-1704 — keeps the canvas transform stable across mutations).\n */\nexport function computeModelBbox(mol: Mol, theme: Theme = lightTheme): BBox {\n if (mol.atoms.length === 0) return {x: 0, y: 0, width: 0, height: 0};\n let acc = atomBBox(mol.atoms[0] as Atom, theme);\n for (let i = 1; i < mol.atoms.length; i++)\n acc = bboxUnion(acc, atomBBox(mol.atoms[i] as Atom, theme));\n return acc;\n}\n\ninterface FitResult {\n x: number;\n y: number;\n width: number;\n height: number;\n scale: number;\n}\n\n/**\n * Compute the scale + offset that places the model bbox inside the surface,\n * centred and with `padding` on every side. `maxScale` caps up-scaling\n * (default `1` = never enlarge past native size). Down-scaling to fit is\n * always applied regardless of `maxScale`.\n */\nfunction fitToSurface(\n model: BBox, width: number, height: number, padding: number, maxScale: number = 1,\n): FitResult {\n const innerW = Math.max(0, width - 2 * padding);\n const innerH = Math.max(0, height - 2 * padding);\n let scale = 1;\n if (model.width > 0 || model.height > 0) {\n const sx = model.width > 0 ? innerW / model.width : Number.POSITIVE_INFINITY;\n const sy = model.height > 0 ? innerH / model.height : Number.POSITIVE_INFINITY;\n // Fit on the tighter axis, but never enlarge beyond `maxScale`.\n scale = Math.min(sx, sy, maxScale);\n if (!Number.isFinite(scale) || scale <= 0) scale = 1;\n }\n const contentW = model.width * scale;\n const contentH = model.height * scale;\n return {\n x: (width - contentW) / 2,\n y: (height - contentH) / 2,\n width: contentW,\n height: contentH,\n scale,\n };\n}\n\n// --------------------------------------------------------------------------\n// Layer builders\n// --------------------------------------------------------------------------\n\n/**\n * Phase 29 / Phase 31 — Width of the highlight / selection ring stroke\n * in CSS pixels. The same value drives:\n *\n * 1. The ring path's `stroke-width` attribute (so the ring appears\n * as a chunky halo, not a hairline).\n * 2. The OUTSET applied to the ring's path geometry (Phase 31\n * T-3002). Outset = `(atomStrokeWidth + ringStrokeWidth) / 2` —\n * the half-stroke of the atom plus the half-stroke of the ring,\n * so the ring's INNER edge sits flush against the atom's OUTER\n * edge with no gap and no overlap.\n *\n * Atom stroke is 5 px (theme.ts), ring stroke 3 px → outset 4 px.\n *\n * History:\n * Phase 29 initial: 9 px (T-2902). User reported \"way too thick\".\n * T-2911: 9 → 3. Visible gap from path+1.5 to path+2.5 (atom stroke\n * extended further than ring), so T-2912 bumped to 5.\n * T-2912: 3 → 5. Ring exactly replaced atom's outer stroke colour\n * AT the path location — no halo \"outside\" the atom.\n * T-3002 (Phase 31): ring path moved OUTSIDE the atom path\n * (`outset` parameter on `atomShapePath`). The gap argument\n * that drove the T-2912 bump no longer applies, so the\n * stroke trims back to 3 px (\"a bit thinner\") per the\n * user's Phase 31 follow-up.\n */\nconst RING_STROKE_WIDTH = 3;\n\n/** Highlight pass — heavy stroke ring beneath each highlighted atom. */\nexport function buildHighlightLayer(\n mol: Mol, theme: Theme, highlighted: ReadonlySet<number>,\n): string {\n if (highlighted.size === 0)\n return tag('g', {class: 'hw-layer hw-highlights'}, '');\n const children: string[] = [];\n for (const atom of mol.atoms) {\n if (!highlighted.has(atom.id)) continue;\n const style = atomStyle(atom, theme);\n // Phase 31 (T-3002) — Ring sits OUTSIDE the atom shape. See the\n // commentary on `RING_STROKE_WIDTH` for the derivation.\n const outset = (style.strokeWidth + RING_STROKE_WIDTH) / 2;\n const d = atomShapePath(atom, theme, outset);\n children.push(tag('path', {\n d,\n class: 'hw-highlight',\n fill: 'none',\n stroke: theme.highlightColor,\n // Phase 29 (T-2902) — Ring is a chunky halo. The atom shape\n // paints with a 5 px self-coloured stroke (rounded-corner\n // trick); the ring's stroke matches so the halo reads as a\n // peer of the atom outline rather than a hairline addition.\n //\n // Phase 31 (T-3002) — The PATH is now outset by `outset` px so\n // the ring's inner edge sits flush against the atom's visual\n // outer edge instead of being painted directly on top of it.\n //\n // History:\n // Phase 29 initial: 9 px ring, same path as atom (T-2902).\n // T-2911: 9 → 3 (user reported \"way too thick\").\n // T-2912: 3 → 5 (3 left a visible gap from path+1.5 to\n // path+2.5 since atom stroke extends 2.5 outward;\n // 5 px ring cleanly replaced the atom's outer rim).\n // T-3002 (Phase 31): 5 px ring kept, but path outset by 5 px\n // so the ring reads as a halo OUTSIDE the atom shape.\n 'stroke-width': RING_STROKE_WIDTH,\n 'stroke-linejoin': 'round',\n 'stroke-linecap': 'round',\n // Phase 18 (T-1803): NO `data-atom-id` on rings. The atom's\n // identifier lives on its `<g class=\"hw-atom\">` element only —\n // duplicating it onto the ring made `[data-atom-id=\"X\"]`\n // selectors ambiguous (the ring is rendered FIRST in source\n // order, so the broad selector picked up the ring instead of\n // the atom). The `data-testid` below encodes the same id but\n // with the `highlight-ring-` prefix, keeping the two element\n // kinds addressable by disjoint selectors.\n 'data-symbol': atom.symbol,\n 'data-ring-atom-id': atom.id,\n 'data-testid': `highlight-ring-${atom.id}`,\n }));\n }\n return tag('g', {class: 'hw-layer hw-highlights'}, children.join(''));\n}\n\n/** Selection pass — even heavier stroke ring, sits on top of highlight. */\nexport function buildSelectionLayer(\n mol: Mol, theme: Theme, selected: ReadonlySet<number>,\n): string {\n if (selected.size === 0)\n return tag('g', {class: 'hw-layer hw-selections'}, '');\n const children: string[] = [];\n for (const atom of mol.atoms) {\n if (!selected.has(atom.id)) continue;\n const style = atomStyle(atom, theme);\n // Phase 31 (T-3002) — See `buildHighlightLayer` for the outset\n // derivation. The selection ring sits at the same outset as the\n // highlight ring; only the colour and z-order differ.\n const outset = (style.strokeWidth + RING_STROKE_WIDTH) / 2;\n const d = atomShapePath(atom, theme, outset);\n children.push(tag('path', {\n d,\n class: 'hw-selection',\n fill: 'none',\n stroke: theme.selectionColor,\n // Phase 29 / Phase 31 — See `buildHighlightLayer` for the\n // history.\n 'stroke-width': RING_STROKE_WIDTH,\n 'stroke-linejoin': 'round',\n 'stroke-linecap': 'round',\n // Phase 18 (T-1801): NO `data-atom-id` on rings — see the\n // commentary on `buildHighlightLayer` for why. The\n // `data-ring-atom-id` mirrors the id under a different\n // attribute name so consumers that want the correlation can\n // still get it, without colliding with `[data-atom-id=\"X\"]`\n // selectors that target the atom group.\n 'data-symbol': atom.symbol,\n 'data-ring-atom-id': atom.id,\n 'data-testid': `selection-ring-${atom.id}`,\n }));\n }\n return tag('g', {class: 'hw-layer hw-selections'}, children.join(''));\n}\n\n/** Bond pass — one `<g class=\"hw-bond\">` per bond, addressable by id. */\nexport function buildBondsLayer(mol: Mol, theme: Theme): string {\n const children: string[] = [];\n for (const bond of mol.bonds)\n children.push(buildBondElement(bond, theme));\n return tag('g', {class: 'hw-layer hw-bonds'}, children.join(''));\n}\n\n/**\n * Build the `<g class=\"hw-bond\">` for one bond. Picks colour, dash pattern\n * and optional decoration based on `bond.kind` and the participating atoms.\n */\nfunction buildBondElement(bond: Bond, theme: Theme): string {\n const a = bond.a1.p;\n const b = bond.a2.p;\n const stroke = bondStrokeColor(bond, theme);\n const dash = bondDashArray(bond);\n const sw = bondStrokeWidth(bond);\n const linePath = bondLinePath(a, b);\n\n const attrs: Parameters<typeof tag>[1] = {\n d: linePath,\n class: 'hw-bond__stroke',\n fill: 'none',\n stroke,\n 'stroke-width': sw,\n };\n if (dash !== undefined) attrs['stroke-dasharray'] = dash;\n\n const inner: string[] = [tag('path', attrs)];\n\n // H-bonds get an extra \"hash\" decoration at the bond midpoint.\n if (bond.kind === 'hbond') {\n inner.push(tag('path', {\n d: bondHashPath(a, b, theme.fontSize * 0.6),\n class: 'hw-bond__hash',\n fill: 'none',\n stroke,\n 'stroke-width': sw,\n }));\n }\n\n return tag('g', {\n class: `hw-bond hw-bond--${bond.kind}`,\n 'data-bond-id': bond.id,\n // Phase 13c (UX-test request) — Expose the bond kind on the DOM so\n // Playwright specs can verify hbond / cross-polymer / backbone\n // membership without going through the bridge.\n 'data-kind': bond.kind,\n 'data-testid': `canvas-bond-${bond.id}`,\n }, inner.join(''));\n}\n\nfunction bondStrokeColor(bond: Bond, theme: Theme): string {\n switch (bond.kind) {\n case 'backbone':\n case 'branch':\n return theme.defaultStroke;\n case 'cross-polymer':\n return theme.crossPolymerBondColor;\n case 'hbond':\n return isCanonicalHbond(bond) ? theme.hbondColor : theme.nonCanonicalHbondColor;\n case 'group':\n return theme.defaultStroke;\n }\n}\n\nfunction bondDashArray(bond: Bond): string | undefined {\n if (bond.kind === 'hbond') return '4 3';\n return undefined;\n}\n\nfunction bondStrokeWidth(_bond: Bond): number {\n // Phase 23 (T-2302) -- The user reported that the legacy 2 / 1.5 / 1\n // bond widths read too heavy against the new 0.5 px monomer outlines\n // (Phase 22 T-2204). A uniform 0.75 px keeps every kind subtly\n // visible without overpowering the small monomer shapes; bond *kind*\n // is still legible via the per-kind stroke colour\n // (`bondStrokeColor`) and the hbond `stroke-dasharray`.\n return 0.75;\n}\n\n/**\n * Hbonds with bases that aren't a canonical Watson-Crick pair (A-T, A-U,\n * G-C) get rendered in the \"non-canonical\" colour. Symbols are normalised\n * to upper-case so `a`/`A` count as the same base.\n */\nfunction isCanonicalHbond(bond: Bond): boolean {\n if (bond.a1.biotype !== HelmTypes.BASE || bond.a2.biotype !== HelmTypes.BASE)\n return false;\n const x = baseLetter(bond.a1);\n const y = baseLetter(bond.a2);\n for (const [u, v] of CANONICAL_PAIRS) {\n if ((x === u && y === v) || (x === v && y === u)) return true;\n }\n return false;\n}\n\nfunction baseLetter(atom: Atom): string {\n const na = atom.monomer?.naturalAnalog;\n const s = (na !== undefined && na !== '' ? na : atom.symbol);\n return s.length === 0 ? '' : (s.charAt(0).toUpperCase());\n}\n\n/** Atom pass — one focusable `<g class=\"hw-atom\">` per atom. */\nexport function buildAtomsLayer(\n mol: Mol, theme: Theme, fontSize: number, showIds: boolean,\n): string {\n const children: string[] = [];\n for (const atom of mol.atoms) {\n if (atom.hidden) continue;\n children.push(buildAtomElement(atom, theme, fontSize, showIds));\n }\n return tag('g', {class: 'hw-layer hw-atoms'}, children.join(''));\n}\n\nfunction buildAtomElement(\n atom: Atom, theme: Theme, fontSize: number, showIds: boolean,\n): string {\n const style = atomStyle(atom, theme);\n const d = atomShapePath(atom, theme);\n const colors = resolveMonomerColors(atom.monomer, atom.biotype, theme.colorTheme);\n const fill = colors.background;\n const textColor = colors.text;\n const dash = atom.symbol === '*' ? '3 3' : undefined;\n\n // Phase 29 (T-2902) -- The shape carries a 5 px self-coloured stroke\n // with `stroke-linejoin: round` to give polygons rounded vertices\n // and chunkier round edges on rounded-rect / circle shapes. The\n // stroke is painted in the SAME colour as the fill so it doesn't\n // read as an outline -- the only visual effect is rounded corners.\n // The hover (`.hw-highlight`) and selection (`.hw-selection`)\n // rings sit in their own layers ABOVE the shape and paint at a\n // 3 px stroke (T-2911): they overpaint the atom's outer 1.5 px on\n // each side and extend a further 1.5 px outward, giving a subtle\n // halo of ring colour just outside the atom edge.\n //\n // The `stroke-linecap: round` is defensive -- closed polygon paths\n // never hit it, but if a future shape uses an open path the cap\n // rounding keeps the look consistent.\n //\n // History:\n // Phase 22 (T-2204): stroke-width 0.5 px, dark outline.\n // Phase 23 (T-2301) / 23.3 (T-2311): derived darker fill colour.\n // Phase 23.4 (T-2312): stroke=\"none\" entirely.\n // Phase 29 (T-2902): stroke=fill, 5 px, round joins.\n const shapeAttrs: Parameters<typeof tag>[1] = {\n d,\n class: 'hw-atom__shape',\n fill,\n stroke: fill,\n 'stroke-width': style.strokeWidth,\n 'stroke-linejoin': 'round',\n 'stroke-linecap': 'round',\n };\n if (dash !== undefined) shapeAttrs['stroke-dasharray'] = dash;\n\n const elements: string[] = [tag('path', shapeAttrs)];\n\n // Label — multi-char symbols scale down (legacy `min(1, 2/len)`). Prefer the\n // RESOLVED monomer's symbol so an inline/explicit SMILES monomer shows its\n // registered short symbol (`#P1`) instead of the raw SMILES string.\n const label = atom.monomer?.symbol ?? atom.symbol;\n if (label !== '') {\n const scale = label.length <= 1 ? 1 : Math.min(1, 2 / label.length);\n const px = fontSize * scale;\n elements.push(tag('text', {\n class: 'hw-atom__label',\n x: atom.p.x,\n y: atom.p.y + px * 0.35,\n 'text-anchor': 'middle',\n 'font-size': px,\n 'font-family': theme.fontFamily,\n fill: textColor,\n }, escapeText(label)));\n }\n\n // Ambiguity string (small text below).\n if (atom.bio.ambiguity !== undefined && atom.bio.ambiguity !== '') {\n elements.push(tag('text', {\n class: 'hw-atom__ambiguity',\n x: atom.p.x,\n y: atom.p.y + style.size + fontSize * 0.7,\n 'text-anchor': 'middle',\n 'font-size': fontSize * 0.7,\n 'font-family': theme.fontFamily,\n fill: textColor,\n }, escapeText(atom.bio.ambiguity)));\n }\n\n // Continuous-id overlay (above-left). The offset is a FIXED multiple of the\n // font size — NOT `style.size` — so every monomer's number sits at the same\n // height regardless of shape size (previously a linker circle, `size`\n // 0.63×fontSize, parked its number much lower than a sugar at 1.39×fontSize;\n // user report 2026-06-15 image 1). Font bumped 0.6→0.8 for legibility.\n if (showIds) {\n const idOff = fontSize * ID_OFFSET_FACTOR;\n elements.push(tag('text', {\n class: 'hw-atom__id',\n x: atom.p.x - idOff,\n y: atom.p.y - idOff,\n 'font-size': fontSize * ID_FONT_FACTOR,\n 'font-family': theme.fontFamily,\n fill: theme.idColor,\n }, escapeText(String(atom.bio.continuousId))));\n }\n\n // Tag dot — small filled circle at upper right.\n if (atom.tag !== undefined && atom.tag !== '') {\n elements.push(tag('circle', {\n class: 'hw-atom__tag-dot',\n cx: atom.p.x + style.size * 0.7,\n cy: atom.p.y - style.size * 0.7,\n r: Math.max(2, fontSize * 0.18),\n fill: theme.tagDotColor,\n }));\n }\n\n const aria = atomAriaLabel(atom);\n return tag(\n 'g',\n {\n class: 'hw-atom',\n 'data-atom-id': atom.id,\n // Phase 13c (Bug 8 + 10 + UX-test request) — Expose the symbol and\n // chainId on the atom group so Playwright specs can address atoms\n // by symbol without re-deriving from the mol bridge. The\n // `data-testid` makes the atom a first-class fixture for\n // user-facing tests.\n 'data-symbol': atom.symbol,\n 'data-chain-id': atom.bio.chainId,\n 'data-biotype': atom.biotype,\n 'data-testid': `canvas-atom-${atom.id}`,\n tabindex: 0,\n role: 'button',\n 'aria-label': aria,\n },\n elements.join(''),\n );\n}\n\nfunction atomAriaLabel(atom: Atom): string {\n const sym = atom.symbol === '' ? '?' : atom.symbol;\n const chain = atom.bio.chainId === '' ? 'unknown chain' : atom.bio.chainId;\n const pos = atom.bio.positionInChain;\n return `${sym} at position ${pos} of ${chain}`;\n}\n\n/** Annotation pass — bond ratios, polymer labels, etc. */\nexport function buildAnnotationsLayer(mol: Mol, theme: Theme, fontSize: number): string {\n const children: string[] = [];\n // Per-bond ratio labels.\n for (const bond of mol.bonds) {\n if (bond.ratio === undefined) continue;\n const ax = (bond.a1.p.x + bond.a2.p.x) / 2;\n const ay = (bond.a1.p.y + bond.a2.p.y) / 2;\n const txt = bond.ratio.denominator !== undefined\n ? `${bond.ratio.numerator}/${bond.ratio.denominator}`\n : `${bond.ratio.numerator}`;\n children.push(tag('text', {\n class: 'hw-annotation hw-annotation--bond-ratio',\n x: ax,\n y: ay - fontSize * 0.4,\n 'text-anchor': 'middle',\n 'font-size': fontSize * 0.7,\n 'font-family': theme.fontFamily,\n fill: theme.annotationColor,\n }, escapeText(txt)));\n }\n // Per-atom annotations (5'/n/c markers).\n for (const atom of mol.atoms) {\n const ann = atom.bio.annotation;\n if (ann === undefined || ann === '') continue;\n const style = atomStyle(atom, theme);\n children.push(tag('text', {\n class: 'hw-annotation hw-annotation--atom',\n x: atom.p.x + style.size + 2,\n y: atom.p.y - style.size,\n 'font-size': fontSize * 0.7,\n 'font-family': theme.fontFamily,\n fill: theme.annotationColor,\n }, escapeText(ann)));\n }\n // Per-polymer label at the chain bbox upper-left.\n for (const chain of mol.chains) {\n if (chain.annotation === undefined || chain.annotation === '') continue;\n const first = chain.backboneAtoms[0];\n if (first === undefined) continue;\n children.push(tag('text', {\n class: 'hw-annotation hw-annotation--chain',\n x: first.p.x,\n y: first.p.y - theme.fontSize * 1.4,\n 'font-size': fontSize * 0.8,\n 'font-family': theme.fontFamily,\n fill: theme.annotationColor,\n }, escapeText(chain.annotation)));\n }\n // Phase 33 (T-3301) — 5'/3' direction markers for nucleic-acid\n // chains. Position the marker just OUTSIDE the chain in the local\n // backbone-tangent direction at each end, so after the antisense\n // horizontal+vertical mirror the markers fall on the visually\n // correct sides (5' on the right of the bottom strand, 3' on the\n // left, matching the legacy Pistoia editor). Strand-type ('ss' /\n // 'as') is suffixed when the parser resolved it from section 3.\n for (const chain of mol.chains) {\n // HELM models DNA as RNA with deoxy sugars, so RNA polymer-type\n // is the only nucleic-acid bucket. PEPTIDE / CHEM / BLOB chains\n // don't carry directional 5'/3' semantics.\n if (chain.polymerType !== 'RNA') continue;\n const atoms = chain.backboneAtoms;\n if (atoms.length === 0) continue;\n const first = atoms[0]!;\n const last = atoms[atoms.length - 1]!;\n const second = atoms.length >= 2 ? atoms[1]! : null;\n const penultimate = atoms.length >= 2 ? atoms[atoms.length - 2]! : null;\n const offset = theme.fontSize * 1.4;\n const fivePos = chainEndMarkerPos(first.p, second?.p ?? null, offset);\n const threePos = chainEndMarkerPos(last.p, penultimate?.p ?? null, offset);\n const fiveLabel = chain.strandType !== undefined ? `5'${chain.strandType}` : \"5'\";\n const threeLabel = chain.strandType !== undefined ? `3'${chain.strandType}` : \"3'\";\n children.push(tag('text', {\n class: 'hw-annotation hw-annotation--prime hw-annotation--prime-5',\n 'data-testid': `prime-5-${chain.id}`,\n x: fivePos.x,\n y: fivePos.y,\n 'text-anchor': 'middle',\n 'dominant-baseline': 'central',\n 'font-size': fontSize * 0.85,\n 'font-family': theme.fontFamily,\n 'font-weight': 'bold',\n fill: theme.annotationColor,\n }, escapeText(fiveLabel)));\n children.push(tag('text', {\n class: 'hw-annotation hw-annotation--prime hw-annotation--prime-3',\n 'data-testid': `prime-3-${chain.id}`,\n x: threePos.x,\n y: threePos.y,\n 'text-anchor': 'middle',\n 'dominant-baseline': 'central',\n 'font-size': fontSize * 0.85,\n 'font-family': theme.fontFamily,\n 'font-weight': 'bold',\n fill: theme.annotationColor,\n }, escapeText(threeLabel)));\n }\n return tag('g', {class: 'hw-layer hw-annotations'}, children.join(''));\n}\n\n/**\n * Phase 33 (T-3301) — Compute the model coords of a 5'/3' chain-end\n * marker. The marker sits `offset` model-pixels OUTSIDE the chain\n * along the local backbone tangent at that end (so it leaves the\n * chain in the opposite direction from the second atom). Falls back\n * to \"directly to the left\" when only one backbone atom exists.\n */\nfunction chainEndMarkerPos(end: {x: number; y: number}, neighbour: {x: number; y: number} | null, offset: number): {x: number; y: number} {\n if (neighbour === null) return {x: end.x - offset, y: end.y};\n const dx = end.x - neighbour.x;\n const dy = end.y - neighbour.y;\n const len = Math.hypot(dx, dy);\n if (len === 0) return {x: end.x - offset, y: end.y};\n return {x: end.x + offset * (dx / len), y: end.y + offset * (dy / len)};\n}\n\n","// T-0404 — Canvas renderer.\n//\n// Three entry points share one painter (`drawMolToContext`):\n// - `renderCanvas` → allocates an OffscreenCanvas, returns `ImageData`.\n// - `renderToPng` → allocates an OffscreenCanvas, returns PNG `Uint8Array`.\n// - `drawMolToContext` → paints into a CALLER-supplied 2D context within a\n// target rect. This is the sync, no-encoding path the Datagrok grid cell\n// renderer uses (`HelmService.renderToCanvas`): no Blob / PNG / `drawImage`\n// round-trip, so the cell renderer can stay fully synchronous.\n//\n// The first two target `OffscreenCanvas` so they work in the browser and in\n// modern Node (≥ 18) when a polyfill is installed. When neither\n// `OffscreenCanvas` nor `options.canvas` is available `renderCanvas` returns\n// just the model bbox + drawBox so callers can fall back to SVG.\n//\n// Layering: imports `core/`, `util/`, `monomer-lib/`, and `./` only.\n\nimport type {Mol, Atom, Bond} from '../core/model';\nimport {HelmTypes} from '../core/constants';\nimport type {BBox} from '../util/types';\nimport {bboxUnion} from '../util/types';\nimport {resolveMonomerColors} from '../monomer-lib/color-rules';\n\nimport {atomBBox, atomStyle, shapeKindFor} from './atom-shape';\nimport {lightTheme, type Theme} from './theme';\nimport type {RenderOptions} from './svg-renderer';\nimport {ID_OFFSET_FACTOR, ID_FONT_FACTOR} from './svg-renderer';\n\n// --------------------------------------------------------------------------\n// Public types\n// --------------------------------------------------------------------------\n\n/**\n * Any 2D canvas context. The painter uses only the subset of the 2D API shared\n * by `CanvasRenderingContext2D` and `OffscreenCanvasRenderingContext2D`, so it\n * works against a browser grid canvas or an off-screen surface alike.\n */\nexport type AnyCanvasContext = CanvasRenderingContext2D | OffscreenCanvasRenderingContext2D;\n\n/** Canvas-specific render options. Extends the SVG `RenderOptions` shape. */\nexport interface CanvasRenderOptions extends RenderOptions {\n /** Pixel ratio (e.g. `2` for retina). Default `1`. */\n pixelRatio?: number;\n /** Pre-allocated `OffscreenCanvas` (skip allocation). */\n canvas?: OffscreenCanvas;\n}\n\n/** A target rectangle in the caller context's own coordinate space. */\nexport interface CanvasBounds {\n x: number;\n y: number;\n width: number;\n height: number;\n}\n\n/** Canvas-specific render result — same metadata as SVG plus the raster. */\nexport interface CanvasRenderResult {\n /** Pixel buffer at `pixelRatio` density. Absent in non-canvas environments. */\n readonly imageData?: ImageData;\n /** PNG bytes — only produced by `renderToPng`. */\n readonly png?: Uint8Array;\n /** Tight bbox of drawn content in model space. */\n readonly bbox: {x: number; y: number; width: number; height: number};\n /** Where drawn content sits inside the surface in surface-space pixels. */\n readonly drawBox: {x: number; y: number; width: number; height: number};\n}\n\n/** Metadata returned by {@link drawMolToContext}. */\nexport interface CanvasDrawResult {\n /** Tight bbox of drawn content in model space (for hit-testing). */\n readonly bbox: BBox;\n /** Where content sits in the CALLER's coordinate space (incl. `bounds` origin). */\n readonly drawBox: BBox;\n}\n\n// --------------------------------------------------------------------------\n// Entry points\n// --------------------------------------------------------------------------\n\n/**\n * Paint `mol` into an existing 2D context, fit + centered within `bounds` and\n * clipped to it. The caller owns the context's device-pixel scaling (the\n * `bounds` are interpreted in whatever coordinate space the context is already\n * in), so this routine never touches `pixelRatio`. The background is filled\n * only when `options.backColor` is set, so a grid cell can keep its own\n * backdrop.\n *\n * Returns the model bbox plus the absolute draw box so callers can map a later\n * pointer event back to a monomer (sync hit-testing) — see\n * `HelmService.renderToCanvas`.\n *\n * @param ctx 2D context to paint into (browser or offscreen).\n * @param mol Laid-out molecule (atom `p` positions are read as-is).\n * @param bounds Target rectangle in the context's coordinate space.\n * @param options Theme / padding / fontSize / backColor.\n * @returns Model bbox and the absolute draw box.\n */\nexport function drawMolToContext(\n ctx: AnyCanvasContext,\n mol: Mol,\n bounds: CanvasBounds,\n options: CanvasRenderOptions = {},\n): CanvasDrawResult {\n const theme = options.theme ?? lightTheme;\n const padding = options.padding ?? 16;\n const modelBbox = computeModelBbox(mol, theme);\n const fit = fitToSurface(modelBbox, bounds.width, bounds.height, padding, options.maxScale ?? 1);\n const originX = bounds.x + fit.x;\n const originY = bounds.y + fit.y;\n\n ctx.save();\n // Clip to the target rect so content never bleeds into adjacent cells. For a\n // full-surface render this is the canvas edge anyway (a no-op).\n ctx.beginPath();\n ctx.rect(bounds.x, bounds.y, bounds.width, bounds.height);\n ctx.clip();\n\n if (options.backColor !== undefined) {\n ctx.fillStyle = options.backColor;\n ctx.fillRect(bounds.x, bounds.y, bounds.width, bounds.height);\n }\n\n // World transform: place + scale model space into the fitted draw box.\n ctx.translate(originX, originY);\n ctx.scale(fit.scale, fit.scale);\n ctx.translate(-modelBbox.x, -modelBbox.y);\n drawBonds(ctx, mol, theme);\n drawAtoms(ctx, mol, theme, options.fontSize ?? theme.fontSize, options.showIds ?? false);\n ctx.restore();\n\n return {\n bbox: {x: modelBbox.x, y: modelBbox.y, width: modelBbox.width, height: modelBbox.height},\n drawBox: {x: originX, y: originY, width: fit.width, height: fit.height},\n };\n}\n\n/**\n * Render `mol` to an `ImageData` raster. When `OffscreenCanvas` is missing\n * the function still returns valid `bbox`/`drawBox` values but omits\n * `imageData` so callers can detect the headless case.\n */\nexport function renderCanvas(mol: Mol, options: CanvasRenderOptions = {}): CanvasRenderResult {\n const theme = options.theme ?? lightTheme;\n const width = options.width ?? 400;\n const height = options.height ?? 100;\n const padding = options.padding ?? 16;\n const pixelRatio = options.pixelRatio ?? 1;\n\n const Constructor = getOffscreenCanvasCtor();\n if (Constructor === null && options.canvas === undefined)\n return metadataOnly(mol, theme, width, height, padding);\n\n const canvas = options.canvas\n ?? new (Constructor as new (w: number, h: number) => OffscreenCanvas)(\n Math.max(1, Math.round(width * pixelRatio)),\n Math.max(1, Math.round(height * pixelRatio)),\n );\n\n const ctx = canvas.getContext('2d');\n if (ctx === null) return metadataOnly(mol, theme, width, height, padding);\n\n ctx.save();\n ctx.scale(pixelRatio, pixelRatio);\n const {bbox, drawBox} = drawMolToContext(ctx, mol, {x: 0, y: 0, width, height}, {\n ...options,\n backColor: options.backColor ?? theme.background,\n });\n ctx.restore();\n\n const imageData = ctx.getImageData(0, 0, canvas.width, canvas.height);\n return {imageData, bbox, drawBox};\n}\n\n/**\n * Render `mol` to a PNG buffer. In browsers uses\n * `OffscreenCanvas.convertToBlob`; in Node (where the global API isn't\n * available) throws a clear \"not supported in this environment\" error so\n * callers fall back to SVG.\n */\nexport async function renderToPng(mol: Mol, options: CanvasRenderOptions = {}): Promise<Uint8Array> {\n const Constructor = getOffscreenCanvasCtor();\n if (Constructor === null && options.canvas === undefined)\n throw new Error('renderToPng: OffscreenCanvas is not available in this environment');\n\n const theme = options.theme ?? lightTheme;\n const width = options.width ?? 400;\n const height = options.height ?? 100;\n const pixelRatio = options.pixelRatio ?? 1;\n\n const canvas = options.canvas\n ?? new (Constructor as new (w: number, h: number) => OffscreenCanvas)(\n Math.max(1, Math.round(width * pixelRatio)),\n Math.max(1, Math.round(height * pixelRatio)),\n );\n\n const ctx = canvas.getContext('2d');\n if (ctx === null)\n throw new Error('renderToPng: failed to acquire 2D context');\n\n ctx.save();\n ctx.scale(pixelRatio, pixelRatio);\n drawMolToContext(ctx, mol, {x: 0, y: 0, width, height}, {\n ...options,\n backColor: options.backColor ?? theme.background,\n });\n ctx.restore();\n\n // `convertToBlob` is the only standardized PNG path; not all polyfills\n // implement it. We surface a clear error if it's missing.\n const canvasWithBlob = canvas as OffscreenCanvas & {\n convertToBlob?: (opts?: {type?: string}) => Promise<Blob>;\n };\n if (typeof canvasWithBlob.convertToBlob !== 'function')\n throw new Error('renderToPng: canvas.convertToBlob is not available');\n const blob = await canvasWithBlob.convertToBlob({type: 'image/png'});\n const buffer = await blob.arrayBuffer();\n return new Uint8Array(buffer);\n}\n\n// --------------------------------------------------------------------------\n// Helpers\n// --------------------------------------------------------------------------\n\nfunction metadataOnly(mol: Mol, theme: Theme, width: number, height: number, padding: number): CanvasRenderResult {\n const modelBbox = computeModelBbox(mol, theme);\n const drawBox = fitToSurface(modelBbox, width, height, padding);\n return {\n bbox: {x: modelBbox.x, y: modelBbox.y, width: modelBbox.width, height: modelBbox.height},\n drawBox: {x: drawBox.x, y: drawBox.y, width: drawBox.width, height: drawBox.height},\n };\n}\n\nfunction getOffscreenCanvasCtor(): typeof OffscreenCanvas | null {\n type WithOffscreen = {OffscreenCanvas?: typeof OffscreenCanvas};\n const g = globalThis as WithOffscreen;\n return typeof g.OffscreenCanvas === 'function' ? g.OffscreenCanvas : null;\n}\n\nfunction computeModelBbox(mol: Mol, theme: Theme): BBox {\n if (mol.atoms.length === 0) return {x: 0, y: 0, width: 0, height: 0};\n let acc = atomBBox(mol.atoms[0] as Atom, theme);\n for (let i = 1; i < mol.atoms.length; i++)\n acc = bboxUnion(acc, atomBBox(mol.atoms[i] as Atom, theme));\n return acc;\n}\n\ninterface FitResult {x: number; y: number; width: number; height: number; scale: number}\n\nfunction fitToSurface(\n model: BBox, width: number, height: number, padding: number, maxScale: number = 1,\n): FitResult {\n const innerW = Math.max(0, width - 2 * padding);\n const innerH = Math.max(0, height - 2 * padding);\n let scale = 1;\n if (model.width > 0 || model.height > 0) {\n const sx = model.width > 0 ? innerW / model.width : Number.POSITIVE_INFINITY;\n const sy = model.height > 0 ? innerH / model.height : Number.POSITIVE_INFINITY;\n // `maxScale` caps up-scaling (default 1 = native). Down-scaling always on.\n scale = Math.min(sx, sy, maxScale);\n if (!Number.isFinite(scale) || scale <= 0) scale = 1;\n }\n const contentW = model.width * scale;\n const contentH = model.height * scale;\n return {\n x: (width - contentW) / 2,\n y: (height - contentH) / 2,\n width: contentW,\n height: contentH,\n scale,\n };\n}\n\nfunction drawBonds(\n ctx: AnyCanvasContext,\n mol: Mol,\n theme: Theme,\n): void {\n for (const bond of mol.bonds) {\n ctx.save();\n ctx.strokeStyle = bondStrokeColor(bond, theme);\n ctx.lineWidth = bondStrokeWidth(bond);\n if (bond.kind === 'hbond') ctx.setLineDash([4, 3]);\n else ctx.setLineDash([]);\n ctx.beginPath();\n ctx.moveTo(bond.a1.p.x, bond.a1.p.y);\n ctx.lineTo(bond.a2.p.x, bond.a2.p.y);\n ctx.stroke();\n ctx.restore();\n }\n}\n\nfunction drawAtoms(\n ctx: AnyCanvasContext,\n mol: Mol,\n theme: Theme,\n fontSize: number,\n showIds: boolean = false,\n): void {\n for (const atom of mol.atoms) {\n if (atom.hidden) continue;\n const style = atomStyle(atom, theme);\n const colors = resolveMonomerColors(atom.monomer, atom.biotype, theme.colorTheme);\n ctx.save();\n ctx.fillStyle = colors.background;\n // Phase 29 (T-2902) -- Mirror the svg-renderer rounded-corner\n // trick on the canvas backend. A 5 px self-coloured stroke with\n // `lineJoin: 'round'` rounds polygon vertices (hexagon, diamond,\n // pentagon) and adds a chunkier round edge on rounded-rect /\n // circle shapes. Stroke = fill = monomer background so the stroke\n // doesn't read as an outline. Matches `buildAtomElement` in\n // `svg-renderer.ts` so SVG and canvas paint produce visually\n // identical monomers.\n ctx.strokeStyle = colors.background;\n ctx.lineWidth = style.strokeWidth;\n ctx.lineJoin = 'round';\n ctx.lineCap = 'round';\n if (atom.symbol === '*') ctx.setLineDash([3, 3]);\n else ctx.setLineDash([]);\n\n drawShape(ctx, atom, style.size, style.cornerRadius ?? 0);\n ctx.fill();\n ctx.stroke();\n ctx.restore();\n\n // Label — prefer the RESOLVED monomer symbol so inline/explicit SMILES\n // monomers show their registered short symbol (`#P1`), not the raw SMILES.\n const label = atom.monomer?.symbol ?? atom.symbol;\n if (label !== '') {\n const scale = label.length <= 1 ? 1 : Math.min(1, 2 / label.length);\n const px = fontSize * scale;\n ctx.save();\n ctx.fillStyle = colors.text;\n ctx.font = `${px}px ${theme.fontFamily}`;\n ctx.textAlign = 'center';\n ctx.textBaseline = 'middle';\n ctx.fillText(label, atom.p.x, atom.p.y);\n ctx.restore();\n }\n\n // Continuous-id overlay (T-3503) — the internal linear monomer index, in\n // green (`theme.idColor`) at a small font, anchored to the atom's\n // top-left so it sits clear of the symbol and (at default spacing) of\n // neighbouring atoms. Mirrors the svg-renderer `showIds` overlay so the\n // canvas-backed Datagrok grid shows the same numbering as the SVG editor.\n if (showIds) {\n const idOff = fontSize * ID_OFFSET_FACTOR;\n ctx.save();\n ctx.fillStyle = theme.idColor;\n ctx.font = `${fontSize * ID_FONT_FACTOR}px ${theme.fontFamily}`;\n ctx.textAlign = 'right';\n ctx.textBaseline = 'bottom';\n // Fixed offset (NOT style.size) so all monomer numbers align in height.\n ctx.fillText(String(atom.bio.continuousId), atom.p.x - idOff, atom.p.y - idOff);\n ctx.restore();\n }\n }\n}\n\nfunction drawShape(\n ctx: AnyCanvasContext,\n atom: Atom,\n size: number,\n cornerRadius: number,\n): void {\n const p = atom.p;\n const kind = atom.symbol === '*' ? 'circle' : shapeKindFor(atom.biotype);\n ctx.beginPath();\n switch (kind) {\n case 'hexagon':\n drawRegularPolygon(ctx, p, 6, size, -30);\n break;\n case 'diamond':\n ctx.moveTo(p.x, p.y - size);\n ctx.lineTo(p.x + size, p.y);\n ctx.lineTo(p.x, p.y + size);\n ctx.lineTo(p.x - size, p.y);\n ctx.closePath();\n break;\n case 'pentagon':\n drawRegularPolygon(ctx, p, 5, size, -90);\n break;\n case 'rounded-rect':\n case 'blob': {\n const halfW = size / 2;\n const r = Math.max(0, Math.min(cornerRadius, halfW));\n const x = p.x - halfW;\n const y = p.y - halfW;\n const w = halfW * 2;\n const h = halfW * 2;\n ctx.moveTo(x + r, y);\n ctx.lineTo(x + w - r, y);\n ctx.quadraticCurveTo(x + w, y, x + w, y + r);\n ctx.lineTo(x + w, y + h - r);\n ctx.quadraticCurveTo(x + w, y + h, x + w - r, y + h);\n ctx.lineTo(x + r, y + h);\n ctx.quadraticCurveTo(x, y + h, x, y + h - r);\n ctx.lineTo(x, y + r);\n ctx.quadraticCurveTo(x, y, x + r, y);\n ctx.closePath();\n break;\n }\n case 'circle':\n ctx.ellipse(p.x, p.y, size, size, 0, 0, Math.PI * 2);\n break;\n }\n}\n\nfunction drawRegularPolygon(\n ctx: AnyCanvasContext,\n center: {x: number; y: number},\n n: number,\n radius: number,\n rotationDeg: number,\n): void {\n const step = 360 / n;\n for (let i = 0; i < n; i++) {\n const a = (rotationDeg + i * step) * Math.PI / 180;\n const x = center.x + radius * Math.cos(a);\n const y = center.y + radius * Math.sin(a);\n if (i === 0) ctx.moveTo(x, y);\n else ctx.lineTo(x, y);\n }\n ctx.closePath();\n}\n\nfunction bondStrokeColor(bond: Bond, theme: Theme): string {\n switch (bond.kind) {\n case 'backbone':\n case 'branch':\n return theme.defaultStroke;\n case 'cross-polymer':\n return theme.crossPolymerBondColor;\n case 'hbond':\n return isCanonicalHbond(bond) ? theme.hbondColor : theme.nonCanonicalHbondColor;\n case 'group':\n return theme.defaultStroke;\n }\n}\n\nfunction bondStrokeWidth(_bond: Bond): number {\n // Phase 23 (T-2302) -- Uniform 0.75 px bond stroke. See the matching\n // commentary in svg-renderer.ts.\n return 0.75;\n}\n\nconst CANONICAL_PAIRS: ReadonlyArray<[string, string]> = [\n ['A', 'T'],\n ['A', 'U'],\n ['G', 'C'],\n];\n\nfunction isCanonicalHbond(bond: Bond): boolean {\n if (bond.a1.biotype !== HelmTypes.BASE || bond.a2.biotype !== HelmTypes.BASE)\n return false;\n const x = baseLetter(bond.a1);\n const y = baseLetter(bond.a2);\n for (const [u, v] of CANONICAL_PAIRS) {\n if ((x === u && y === v) || (x === v && y === u)) return true;\n }\n return false;\n}\n\nfunction baseLetter(atom: Atom): string {\n const na = atom.monomer?.naturalAnalog;\n const s = (na !== undefined && na !== '' ? na : atom.symbol);\n return s.length === 0 ? '' : s.charAt(0).toUpperCase();\n}\n","// T-0409 / T-1204 — Molecular formula computation.\n//\n// Walks a parsed `Mol`, parses each atom's monomer molfile (V2000), and\n// aggregates a heavy-atom-plus-implicit-H formula. Each monomer's\n// intrinsic stats include the cap-group atoms for EVERY R-group (so a\n// monomer alone reports its free-amino-acid / free-nucleotide formula); for\n// each actual Mol bond, the cap atoms corresponding to the bound R-group\n// are deducted again — net effect: the cap stays only on R-groups that are\n// not connected. Repeat-bracket groups multiply contributions by their\n// lower-bound count (`repeat.min`).\n//\n// This is the FREE-POLYMER convention (free Ala = C3H7NO2, MW=89.094; A.A\n// dipeptide = sum of free Ala formulas - H2O = C6H12N2O3, MW=160.172), which\n// matches the user-facing expectations in `tests/golden/calc.json`. The\n// legacy Pistoia `Formula.ts` uses the same convention conceptually but\n// stores the caps inline in the monomer molfile; we instead skip R# atoms\n// during molfile parsing and add caps back from the `rgroups` list, since\n// the HELMCoreLibrary molfiles use R# placeholders without the cap atoms.\n//\n// Layering: imports from `core/` and `monomer-lib/` only. No DOM, no console.\n\nimport type { Atom, Bond, Mol, RGroupRef } from '../core/model';\nimport type { Monomer, RGroupSpec } from '../monomer-lib/types';\n\n// --------------------------------------------------------------------------\n// Public surface\n// --------------------------------------------------------------------------\n\n/** Element-count map plus pre-computed molecular weight. */\nexport interface MolecularFormula {\n readonly elements: ReadonlyMap<string, number>;\n readonly mw: number;\n}\n\n/**\n * Compute the molecular formula and weight for `mol`. Atoms with `monomer\n * === null` contribute nothing (a warning would be emitted at the service\n * layer; the calc layer is silent).\n */\nexport function computeFormula(mol: Mol): MolecularFormula {\n const counts = new Map<string, number>();\n\n const atomBondCount = new Map<number, Bond[]>();\n for (const bond of mol.bonds) {\n const a1 = bond.a1.id;\n const a2 = bond.a2.id;\n let list1 = atomBondCount.get(a1);\n if (list1 === undefined) {\n list1 = [];\n atomBondCount.set(a1, list1);\n }\n list1.push(bond);\n let list2 = atomBondCount.get(a2);\n if (list2 === undefined) {\n list2 = [];\n atomBondCount.set(a2, list2);\n }\n list2.push(bond);\n }\n\n for (const atom of mol.atoms) {\n addAtomContribution(counts, atom, atomBondCount.get(atom.id) ?? []);\n }\n\n // Apply repeat-bracket multipliers (lower-bound).\n for (const group of mol.groups) {\n if (group.kind !== 'bracket') continue;\n const repeatMin = group.repeat?.min ?? 1;\n if (repeatMin === 1) continue;\n // Members of a bracket group target polymer ids (chain ids).\n const memberChainIds = new Set(group.members.map((m) => m.target));\n const extra = new Map<string, number>();\n for (const atom of mol.atoms) {\n if (!memberChainIds.has(atom.bio.chainId)) continue;\n const sub = new Map<string, number>();\n addAtomContribution(sub, atom, atomBondCount.get(atom.id) ?? []);\n for (const [el, n] of sub) extra.set(el, (extra.get(el) ?? 0) + n * (repeatMin - 1));\n }\n for (const [el, n] of extra) counts.set(el, (counts.get(el) ?? 0) + n);\n }\n\n // Strip zero counts so the map is tidy.\n for (const [el, n] of [...counts]) if (n === 0) counts.delete(el);\n\n const mw = computeMW(counts);\n return { elements: counts, mw };\n}\n\n/**\n * Format an element-count map as a human-readable string. Standard order is\n * Hill notation: C, H, then the rest in alphabetic order.\n *\n * When `options.html` is true, subscript counts are wrapped in `<sub>...</sub>`.\n */\nexport function formatFormula(formula: MolecularFormula, options?: { html?: boolean }): string {\n const html = options?.html === true;\n const els = [...formula.elements.entries()].filter(([, n]) => n > 0);\n const c = els.find(([e]) => e === 'C');\n const h = els.find(([e]) => e === 'H');\n const rest = els.filter(([e]) => e !== 'C' && e !== 'H').sort((a, b) => a[0].localeCompare(b[0]));\n const order: [string, number][] = [];\n if (c !== undefined) order.push(c);\n if (h !== undefined) order.push(h);\n for (const r of rest) order.push(r);\n return order\n .map(([el, n]) => {\n if (n === 1) return el;\n return html ? `${el}<sub>${n}</sub>` : `${el}${n}`;\n })\n .join('');\n}\n\n// --------------------------------------------------------------------------\n// Periodic table (subset used by Formula.ts in the legacy editor)\n// --------------------------------------------------------------------------\n\n/**\n * Atomic-mass table. Values are the standard atomic weights (IUPAC 2013).\n * We only include elements that appear in our corpus monomers; unknown\n * elements contribute 0 to MW but are still counted in the formula.\n */\nconst PT: Readonly<Record<string, number>> = {\n H: 1.008,\n C: 12.011,\n N: 14.007,\n O: 15.999,\n F: 18.998,\n Na: 22.990,\n Mg: 24.305,\n P: 30.974,\n S: 32.06,\n Cl: 35.45,\n K: 39.098,\n Ca: 40.078,\n Br: 79.904,\n I: 126.904,\n Fe: 55.845,\n Zn: 65.38,\n Cu: 63.546,\n};\n\n/** Default valences used for implicit-H inference. */\nconst VALENCE: Readonly<Record<string, number>> = {\n C: 4,\n N: 3,\n O: 2,\n S: 2,\n P: 3,\n F: 1,\n Cl: 1,\n Br: 1,\n I: 1,\n H: 1,\n};\n\nfunction computeMW(counts: ReadonlyMap<string, number>): number {\n let mw = 0;\n for (const [el, n] of counts) {\n const m = PT[el];\n if (m === undefined) continue;\n mw += m * n;\n }\n // Round to 3 decimals to keep tests stable.\n return Math.round(mw * 1000) / 1000;\n}\n\n// --------------------------------------------------------------------------\n// Atom contribution\n// --------------------------------------------------------------------------\n\nfunction addAtomContribution(\n acc: Map<string, number>,\n atom: Atom,\n bondsOnAtom: readonly Bond[],\n): void {\n if (atom.monomer === null) return;\n const stats = monomerStats(atom.monomer);\n\n // 1. Add the monomer's intrinsic heavy + H counts.\n for (const [el, n] of stats.elements) acc.set(el, (acc.get(el) ?? 0) + n);\n\n // 2. For each bond on this atom, deduct the matching cap.\n for (const bond of bondsOnAtom) {\n if (bond.kind === 'hbond' || bond.kind === 'group') continue;\n const rRef = bond.a1.id === atom.id ? bond.r1 : bond.r2;\n const cap = capNameForR(atom.monomer, rRef);\n if (cap === undefined) continue;\n const deduction = deductionFor(cap);\n for (const [el, n] of deduction) acc.set(el, (acc.get(el) ?? 0) - n);\n }\n}\n\n/** Resolve the cap-group name for a bond endpoint's R-ref on a monomer. */\nfunction capNameForR(monomer: Monomer, ref: RGroupRef): string | undefined {\n if (ref.kind !== 'numeric' && ref.kind !== 'positional') return undefined;\n const rNum = ref.kind === 'numeric' ? ref.r : ref.r;\n for (const rg of monomer.rgroups) {\n const m = /^R([1-9][0-9]*)$/.exec(rg.label);\n if (m === null) continue;\n if (parseInt(m[1] as string, 10) === rNum) return rg.capGroupName;\n }\n return undefined;\n}\n\n/** Per legacy `Formula.deductR`: 'H' = -1H; 'OH' = -1H -1O. */\nfunction deductionFor(cap: string): ReadonlyMap<string, number> {\n const out = new Map<string, number>();\n switch (cap) {\n case 'H':\n out.set('H', 1);\n break;\n case 'OH':\n out.set('H', 1);\n out.set('O', 1);\n break;\n default:\n // Unknown caps contribute nothing (matches the legacy lenient behavior).\n break;\n }\n return out;\n}\n\n// --------------------------------------------------------------------------\n// Monomer molfile → element-count cache\n// --------------------------------------------------------------------------\n\ninterface MonomerStats {\n readonly elements: ReadonlyMap<string, number>;\n}\n\nconst STATS_CACHE = new WeakMap<Monomer, MonomerStats>();\n\nfunction monomerStats(monomer: Monomer): MonomerStats {\n const cached = STATS_CACHE.get(monomer);\n if (cached !== undefined) return cached;\n const stats = computeMonomerStats(monomer);\n STATS_CACHE.set(monomer, stats);\n return stats;\n}\n\nfunction computeMonomerStats(monomer: Monomer): MonomerStats {\n const elements = new Map<string, number>();\n if (monomer.molfile === undefined || monomer.molfile === '') {\n return { elements };\n }\n\n const parsed = parseV2000Atoms(monomer.molfile);\n if (parsed === null) return { elements };\n\n const { atoms, bondOrders } = parsed;\n\n for (let i = 0; i < atoms.length; i++) {\n const sym = atoms[i] as string;\n if (sym === 'R' || sym === 'R#' || sym === '*') continue;\n elements.set(sym, (elements.get(sym) ?? 0) + 1);\n // Implicit H = valence - sum(bond_orders on this atom). Negative → 0.\n const v = VALENCE[sym];\n if (v === undefined) continue;\n const used = bondOrders[i] ?? 0;\n const hs = v - used;\n if (hs > 0) elements.set('H', (elements.get('H') ?? 0) + hs);\n }\n\n // Add cap atoms for EVERY R-group. The intrinsic monomer formula at this\n // point is the \"naked residue\" (R# placeholders skipped); adding caps\n // converts it into the free-AA / free-nucleotide formula, e.g. Ala goes\n // from C3H5NO1 → C3H7NO2. For bonds that actually use an R-group, the\n // caller (`addAtomContribution`) deducts the cap again — net effect is\n // that only un-bonded R-groups contribute caps.\n for (const rg of monomer.rgroups) {\n const cap = rg.capGroupName;\n if (cap === undefined) continue;\n const add = deductionFor(cap);\n for (const [el, n] of add) elements.set(el, (elements.get(el) ?? 0) + n);\n }\n\n return { elements };\n}\n\ninterface V2000Atoms {\n /** atom-symbol per 0-based index. */\n readonly atoms: readonly string[];\n /** sum of bond orders incident on each atom (0-based). */\n readonly bondOrders: readonly number[];\n}\n\n/**\n * Minimal V2000 atom-block + bond-block parser. Returns null on any\n * structural surprise — callers fall back to \"no contribution\".\n */\nfunction parseV2000Atoms(molfile: string): V2000Atoms | null {\n const lines = molfile.split(/\\r\\n|\\n|\\r/);\n // The counts line is the 4th line (header: title, software, comment, counts).\n if (lines.length < 5) return null;\n const counts = lines[3];\n if (counts === undefined || counts.length < 6) return null;\n const atomCount = parseInt(counts.slice(0, 3), 10);\n const bondCount = parseInt(counts.slice(3, 6), 10);\n if (!Number.isFinite(atomCount) || !Number.isFinite(bondCount)) return null;\n if (lines.length < 4 + atomCount + bondCount) return null;\n\n const atoms: string[] = [];\n for (let i = 0; i < atomCount; i++) {\n const line = lines[4 + i];\n if (line === undefined) return null;\n // V2000 atom line: 3*10 chars for x/y/z, then ' aaa' (3-wide symbol).\n const symField = line.slice(31, 34).trim();\n atoms.push(symField);\n }\n\n const bondOrders: number[] = new Array<number>(atomCount).fill(0);\n for (let i = 0; i < bondCount; i++) {\n const line = lines[4 + atomCount + i];\n if (line === undefined) return null;\n // V2000 bond line: 3 chars atom1, 3 chars atom2, 3 chars order, ...\n const a1 = parseInt(line.slice(0, 3), 10);\n const a2 = parseInt(line.slice(3, 6), 10);\n const order = parseInt(line.slice(6, 9), 10);\n if (!Number.isFinite(a1) || !Number.isFinite(a2) || !Number.isFinite(order)) continue;\n // 4 = aromatic; treat as 1.5 → round down to 1 for valence accounting\n // since we already cap implicit H to >=0.\n const ord = order === 4 ? 1 : order;\n if (a1 >= 1 && a1 <= atomCount) bondOrders[a1 - 1] = (bondOrders[a1 - 1] ?? 0) + ord;\n if (a2 >= 1 && a2 <= atomCount) bondOrders[a2 - 1] = (bondOrders[a2 - 1] ?? 0) + ord;\n }\n\n return { atoms, bondOrders };\n}\n\n// Re-export the R-group-spec type for symmetry; not used outside but it\n// reads naturally inside `capNameForR`.\nexport type { RGroupSpec };\n","// T-0409 — Molecular-weight shortcut.\n//\n// Returns the molecular weight of a `Mol`. Equivalent to\n// `computeFormula(mol).mw`; we keep this as a separate entry point so callers\n// who only need the number can skip allocating the element-count map (the\n// underlying implementation still computes it, but the call site stays clear).\n//\n// Layering: imports from `core/` and `./formula` only.\n\nimport type { Mol } from '../core/model';\nimport { computeFormula } from './formula';\n\n/** Molecular weight in g/mol (rounded to 3 decimal places). */\nexport function molWeight(mol: Mol): number {\n return computeFormula(mol).mw;\n}\n","// T-0409 — UV extinction-coefficient calculation.\n//\n// Computes ε (molar extinction coefficient) at 260 nm for peptide / RNA /\n// mixed HELM mols using the same models as the legacy editor's\n// `ExtinctionCoefficient.js` (LEGACY-EDITOR-NOTES.md §`ExtinctionCoefficient`):\n//\n// - Peptide (Edelhoch): ε = 5.5*nW + 1.49*nY + 0.0625*nC [mM⁻¹·cm⁻¹]\n// - RNA (nearest-neighbor, Puglish & Tinoco):\n// ε = 2 * Σ NN_pairs - Σ internal_singletons [mM⁻¹·cm⁻¹]\n// - Mixed peptide+RNA: sum both contributions.\n//\n// All coefficients are in mM⁻¹·cm⁻¹ (kilo-units). The canonical Edelhoch\n// peptide values are 5500/1490/62.5 M⁻¹·cm⁻¹; we store them ÷1000 so peptide\n// and RNA share one consistent unit (and match the Datagrok properties widget,\n// which reports kilo-units, e.g. a single Tyr → 1.49).\n//\n// Counts are taken from each atom's natural-analog (single-letter); modified\n// monomers without a natural analog are skipped (matching the legacy behavior).\n//\n// Layering: imports from `core/` and `monomer-lib/` only.\n\nimport type { Atom, Mol } from '../core/model';\nimport { HelmTypes } from '../core/constants';\n\n// --------------------------------------------------------------------------\n// Reference tables\n// --------------------------------------------------------------------------\n\nconst PEPTIDE_COEFS: Readonly<Record<string, number>> = {\n W: 5.5,\n Y: 1.49,\n C: 0.0625,\n};\n\nconst RNA_NN: Readonly<Record<string, number>> = {\n AA: 13.65, AC: 10.67, AG: 12.79, AU: 12.14,\n CA: 10.67, CC: 7.52, CG: 9.39, CU: 8.37,\n GA: 12.79, GC: 9.39, GG: 11.77, GU: 10.21,\n UA: 12.14, UC: 8.37, UG: 10.21, UU: 8.99,\n};\n\nconst RNA_SINGLE: Readonly<Record<string, number>> = {\n A: 15.4,\n C: 7.4,\n G: 11.7,\n U: 10.0,\n T: 8.8,\n};\n\n// --------------------------------------------------------------------------\n// Public surface\n// --------------------------------------------------------------------------\n\n/**\n * Sum of peptide + RNA contributions in units of mM⁻¹·cm⁻¹. Returns 0 for\n * mols whose chains have neither natural amino acids nor canonical\n * ribonucleotides.\n */\nexport function extinctionCoefficient(mol: Mol): number {\n let total = 0;\n // Walk each chain so the nearest-neighbor algorithm sees one strand at a\n // time. Peptide and RNA chains are independent.\n for (const chain of mol.chains) {\n if (chain.polymerType === 'PEPTIDE')\n total += peptideEpsilon(chain.backboneAtoms);\n else if (chain.polymerType === 'RNA')\n total += rnaEpsilon(chain.backboneAtoms);\n }\n // Round to 4 decimals: the half-cystine kilo-unit coefficient is 0.0625,\n // which a 3-decimal round would corrupt to 0.063.\n return Math.round(total * 10000) / 10000;\n}\n\n// --------------------------------------------------------------------------\n// Internals\n// --------------------------------------------------------------------------\n\nfunction peptideEpsilon(atoms: readonly Atom[]): number {\n let nW = 0;\n let nY = 0;\n let nC = 0;\n for (const a of atoms) {\n const letter = naturalAnalogLetter(a);\n if (letter === 'W') nW++;\n else if (letter === 'Y') nY++;\n else if (letter === 'C') nC++;\n }\n return (PEPTIDE_COEFS['W'] as number) * nW\n + (PEPTIDE_COEFS['Y'] as number) * nY\n + (PEPTIDE_COEFS['C'] as number) * nC;\n}\n\nfunction rnaEpsilon(atoms: readonly Atom[]): number {\n // Collect only \"base-like\" letters in chain order: each sugar's branchAtom\n // is the base; we read the natural analog from the base atom.\n const bases: string[] = [];\n for (const a of atoms) {\n // RNA backbones include sugar/linker atoms; the base hangs off via\n // `branchAtom`. We use the branchAtom's letter when present; otherwise\n // skip (linker).\n if (a.branchAtom !== undefined && a.branchAtom.biotype === HelmTypes.BASE) {\n let letter = naturalAnalogLetter(a.branchAtom);\n // The nearest-neighbor table is RNA-only (A/C/G/U). DNA's thymine has no\n // pair entries, which would leave NN terms at 0 while singletons are\n // still subtracted — yielding a (nonsensical) negative ε. Treat T as U\n // (the standard T≈U approximation at 260 nm) so DNA strands are scored\n // with the uracil stacking values instead of breaking.\n if (letter === 'T') letter = 'U';\n if (letter !== '') bases.push(letter);\n }\n }\n if (bases.length === 0) return 0;\n if (bases.length === 1) {\n const k = bases[0] as string;\n return RNA_SINGLE[k] ?? 0;\n }\n\n // Sum nearest-neighbor pairs (2 * Σ NN) and subtract internal singletons.\n let nnSum = 0;\n for (let i = 0; i < bases.length - 1; i++) {\n const a = bases[i] as string;\n const b = bases[i + 1] as string;\n const v = RNA_NN[a + b];\n if (v !== undefined) nnSum += v;\n }\n let internalSingletons = 0;\n for (let i = 1; i < bases.length - 1; i++) {\n const k = bases[i] as string;\n internalSingletons += RNA_SINGLE[k] ?? 0;\n }\n return 2 * nnSum - internalSingletons;\n}\n\nfunction naturalAnalogLetter(atom: Atom): string {\n const m = atom.monomer;\n if (m !== null && m.naturalAnalog !== undefined && m.naturalAnalog !== '')\n return m.naturalAnalog.charAt(0).toUpperCase();\n if (atom.symbol === '') return '';\n return atom.symbol.charAt(0).toUpperCase();\n}\n","// T-0409 — Pseudo-molfile emitter.\n//\n// Produces a minimal V2000 molfile whose atom lines are MONOMERS (not\n// chemical atoms). Each Mol atom becomes one atom block entry positioned at\n// `(atom.p.x, atom.p.y, 0)`; each Mol bond becomes one bond block entry\n// (kind backbone/branch/cross-polymer/h-bond/group all emitted as single\n// bonds). The atom-type field carries the FULL monomer symbol (e.g. `meI`,\n// `Thr_PO3H2`), case-preserved — the Datagrok `HelmToMolfileConverter` reads it\n// (via `MolfileHandler.atomTypes`, a whitespace-delimited token) to look each\n// monomer up in the library and expand it to atomic level. Symbols longer than\n// the 3-char V2000 field are emitted in full (the token parser is width-\n// agnostic); short symbols stay left-justified in the 3-char field.\n//\n// This matches the legacy `editor.getMolfile()` semantics — \"monomers-as-atoms\"\n// rather than a real chemistry expansion. The atomic-level expansion lives\n// behind `HelmService.getAtomicMolfile()` and the optional plug-in.\n//\n// Layering: imports from `core/` only.\n\nimport type { Atom, Mol } from '../core/model';\n\n/**\n * Render `mol` as a \"monomers-as-atoms\" V2000 molfile.\n *\n * The title is `HWE pseudo-molfile`, the software header is\n * ` HWE 2D`, and the comment line is empty. The trailing line is\n * `M END` as required by the V2000 spec.\n */\nexport function pseudoMolfile(mol: Mol): string {\n const lines: string[] = [];\n // Header — exactly three lines (title, software, comment).\n lines.push('HWE pseudo-molfile');\n lines.push(' HWE 2D');\n lines.push('');\n\n const atomCount = mol.atoms.length;\n const bondCount = mol.bonds.length;\n lines.push(formatCountsLine(atomCount, bondCount));\n\n // Atom block.\n for (const a of mol.atoms)\n lines.push(formatAtomLine(a));\n\n // Bond block.\n // Need a 1-based atom index. Build a map from atom.id to its index in\n // the emitted atoms array.\n const indexOf = new Map<number, number>();\n for (let i = 0; i < mol.atoms.length; i++)\n indexOf.set((mol.atoms[i] as Atom).id, i + 1);\n for (const b of mol.bonds) {\n const i1 = indexOf.get(b.a1.id);\n const i2 = indexOf.get(b.a2.id);\n if (i1 === undefined || i2 === undefined) continue;\n lines.push(formatBondLine(i1, i2));\n }\n\n lines.push('M END');\n return lines.join('\\n') + '\\n';\n}\n\n// --------------------------------------------------------------------------\n// Line formatters\n// --------------------------------------------------------------------------\n\nfunction formatCountsLine(atomCount: number, bondCount: number): string {\n return (\n pad3(atomCount)\n + pad3(bondCount)\n + ' 0 0 0 0 0 0 0 0999 V2000'\n );\n}\n\nfunction formatAtomLine(a: Atom): string {\n const sym = pseudoSymbol(a);\n return (\n fmtCoord(a.p.x)\n + fmtCoord(a.p.y)\n + fmtCoord(0)\n + ' '\n + padRight(sym, 3)\n + ' 0 0 0 0 0 0 0 0 0 0 0 0'\n );\n}\n\nfunction formatBondLine(i1: number, i2: number): string {\n return pad3(i1) + pad3(i2) + pad3(1) + pad3(0);\n}\n\nfunction pseudoSymbol(a: Atom): string {\n // Prefer the RESOLVED monomer's symbol over the raw parsed token. For named\n // monomers they are identical (full, case-preserved — `meI`, `Thr_PO3H2`).\n // For an inline/explicit SMILES monomer the parsed `a.symbol` is the raw\n // SMILES (e.g. `*N(C)[C@H](C(=O)*)CCC |$_R1;...$|`) — which contains spaces\n // and breaks the converter's whitespace-delimited atom-type token — whereas\n // the resolved monomer carries the registered short symbol (`#P1`, `#R2`).\n // Emitting the resolved symbol keeps the converter's case-sensitive library\n // lookup working AND lets explicit-SMILES monomers round-trip.\n const m = a.monomer;\n if (m !== null && m.symbol !== '') return m.symbol;\n if (a.symbol !== '') return a.symbol;\n if (m !== null && m.naturalAnalog !== undefined && m.naturalAnalog !== '')\n return m.naturalAnalog;\n return 'X';\n}\n\nfunction pad3(n: number): string {\n const s = String(n);\n if (s.length >= 3) return s;\n return ' '.repeat(3 - s.length) + s;\n}\n\n/** Left-justify `s` in a field of at least `width`; never truncate (a monomer\n * symbol longer than the field — e.g. `Thr_PO3H2` — is emitted in full). */\nfunction padRight(s: string, width: number): string {\n if (s.length >= width) return s;\n return s + ' '.repeat(width - s.length);\n}\n\n/** V2000 coordinate field: 10-char fixed, 4 decimals. */\nfunction fmtCoord(v: number): string {\n const fixed = v.toFixed(4);\n if (fixed.length >= 10) return fixed.slice(0, 10);\n return ' '.repeat(10 - fixed.length) + fixed;\n}\n","// T-0407 / T-0408 / T-0410 — `HelmService` class.\n//\n// Single-instance entry point for every headless operation. Constructed once\n// with a monomer library and reused; **no method takes a lib argument** — the\n// lib is bound for the service's lifetime. See API.md §4.\n//\n// Internally the service composes:\n// - parse / serialize / validate / canonicalize / removeGaps from `../io/`\n// - layoutMol from `../layout/`\n// - renderSvg from `../render/svg-renderer`\n// - renderToPng from `../render/canvas-renderer` (browser-only)\n// - computeFormula, molWeight, extinctionCoefficient, pseudoMolfile from\n// `../calc/`\n//\n// Three LRU caches sit in front of the hot paths (parse, layout, render),\n// keyed on stable strings so the same input returns the same object reference\n// across calls. Subscribing to `monomerLib.onChanged` clears every cache on\n// any mutation.\n//\n// Layering: imports from every layer below; nothing above (no editor).\n\nimport type { Mol } from '../core/model';\nimport type { ValidationDiagnostic } from '../core/errors';\nimport { HelmNotSupportedError } from '../core/errors';\nimport type { IMonomerLib } from '../monomer-lib/types';\nimport type { Unsubscribe, BBox } from '../util/types';\nimport { LruCache } from '../util/lru-cache';\nimport type { Logger } from '../util/logger';\nimport { SilentLogger } from '../util/logger';\n\nimport {\n parseHelm as _parseHelm,\n serialize as _serialize,\n validate as _validate,\n canonicalize as _canonicalize,\n removeGaps as _removeGaps,\n} from '../io';\nimport type {\n ParseOptions as IoParseOptions,\n ParseResult as IoParseResult,\n SerializeOptions as IoSerializeOptions,\n ValidateOptions as IoValidateOptions,\n RemoveGapsResult,\n} from '../io';\nimport { layoutMol } from '../layout/layout-service';\nimport { renderSvg } from '../render/svg-renderer';\nimport type { RenderOptions as RendererRenderOptions } from '../render/svg-renderer';\nimport { renderToPng as canvasRenderToPng, drawMolToContext } from '../render/canvas-renderer';\nimport type { AnyCanvasContext, CanvasBounds } from '../render/canvas-renderer';\nimport type { Theme } from '../render/theme';\nimport { lightTheme } from '../render/theme';\n\nimport { computeFormula } from '../calc/formula';\nimport type { MolecularFormula } from '../calc/formula';\nimport { molWeight } from '../calc/mol-weight';\nimport { extinctionCoefficient } from '../calc/extinction-coeff';\nimport { pseudoMolfile } from '../calc/pseudo-molfile';\n\n// --------------------------------------------------------------------------\n// Public types\n// --------------------------------------------------------------------------\n\n/**\n * A plug-in callback supplied via `HelmServiceOptions` to extend the service\n * with an atomic-level molfile (i.e. real chemistry) expander. We don't ship\n * an internal implementation — see API.md §4.1.\n */\nexport type AtomicMolfileProvider = (helm: string, monomerLib: IMonomerLib) => string | Promise<string>;\n\nexport interface HelmServiceOptions {\n /** Required: the monomer library bound for the service's lifetime. */\n monomerLib: IMonomerLib;\n /** Optional theme; default `lightTheme`. */\n theme?: Theme;\n /** Optional logger; default `SilentLogger`. */\n logger?: Logger;\n /** Max entries per cache (parse / layout / render). Default 256. */\n cacheSize?: number;\n /** Optional plug-in for atomic-level molfile expansion. */\n atomicMolfileProvider?: AtomicMolfileProvider;\n /** Opaque RDKit module forwarded to the provider; not used internally. */\n rdkitModule?: unknown;\n}\n\nexport interface ParseOptions {\n mode?: 'strict' | 'lenient';\n resolveMonomers?: boolean;\n}\n\nexport interface ParseResult {\n readonly mol: Mol;\n readonly diagnostics: readonly ValidationDiagnostic[];\n}\n\nexport interface SerializeOptions {\n canonicalize?: boolean;\n includeHighlights?: boolean;\n version?: 'V2.0' | 'V1.0' | 'none' | 'preserve';\n}\n\nexport interface ValidateOptions {\n mode?: 'lenient' | 'strict' | 'pedantic';\n}\n\nexport interface RenderOptions {\n width?: number;\n height?: number;\n backColor?: string;\n theme?: Theme;\n padding?: number;\n showIds?: boolean;\n showAnnotations?: boolean;\n bondLength?: number;\n fontSize?: number;\n showRGroupLabels?: boolean;\n selectedAtomIds?: ReadonlySet<number>;\n highlightedAtomIds?: ReadonlySet<number>;\n /**\n * Maximum up-scale factor when fitting the drawing into the surface.\n * Default `1` (never enlarge past native monomer size). Datagrok callers\n * pass `Infinity` so a grid cell / editor pane fills the available space by\n * scaling the drawing up. Down-scaling to fit is always applied.\n */\n maxScale?: number;\n /**\n * T-1704 — Pin the renderer's auto-fit to a specific model bbox.\n * The interactive editor captures the bbox at the most recent layout\n * and passes it on every render so addAtom / addBond / moveAtom\n * mutations don't visibly rescale the canvas. Headless / batch\n * callers omit it to get the default auto-fit behaviour.\n */\n fixedModelBbox?: { x: number; y: number; width: number; height: number };\n}\n\n/**\n * Result of {@link HelmService.renderToCanvas} / {@link HelmService.renderMolToCanvas}.\n * `mol` is the laid-out molecule that was painted (so callers can hit-test it);\n * `bbox` is its tight bounding box in model space, and `drawBox` is where that\n * content landed in the target context's coordinate space.\n */\nexport interface RenderToCanvasResult {\n readonly mol: Mol;\n readonly bbox: BBox;\n readonly drawBox: BBox;\n}\n\n// --------------------------------------------------------------------------\n// Cache keys\n// --------------------------------------------------------------------------\n\ninterface ParseCacheKey {\n readonly mode: 'strict' | 'lenient';\n readonly resolveMonomers: boolean;\n readonly helm: string;\n}\n\nfunction parseKey(k: ParseCacheKey): string {\n return `${k.mode}|${k.resolveMonomers ? 1 : 0}|${k.helm}`;\n}\n\n/**\n * Stable fingerprint of a Mol's identity for the layout cache. We hash chain\n * ids + atom symbols + bond endpoint ids. The fingerprint is bond-length\n * independent — the bond-length parameter is appended at the cache layer.\n */\nfunction molFingerprint(mol: Mol): string {\n const chainIds = mol.chains.map((c) => `${c.id}:${c.polymerType}:${c.backboneAtoms.length}`).join(',');\n const atomSig = mol.atoms.map((a) => `${a.id}@${a.symbol}@${a.bio.chainId}`).join(';');\n const bondSig = mol.bonds.map((b) => `${b.id}:${b.a1.id}-${b.a2.id}:${b.kind}`).join(';');\n return `${chainIds}#${atomSig}#${bondSig}`;\n}\n\n// --------------------------------------------------------------------------\n// HelmService\n// --------------------------------------------------------------------------\n\nconst DEFAULT_CACHE_SIZE = 256;\n\n/**\n * Cache-hit telemetry exposed via `HelmService.stats`. T-0903 (Phase 9):\n * the grid-simulation bench reads these counters to assert that the\n * renderer cache keeps a > 90% hit rate when a Datagrok grid scrolls\n * through ~50 unique HELM strings on ~1000 visible cells. Counters are\n * lightweight (one `+= 1` per cache lookup) and zero-overhead in release\n * builds — the bench never runs in the editor / package adapter.\n */\nexport interface HelmServiceStats {\n readonly parseHits: number;\n readonly parseMisses: number;\n readonly layoutHits: number;\n readonly layoutMisses: number;\n readonly renderHits: number;\n readonly renderMisses: number;\n}\n\n/**\n * Core HELM service — see class-level comment and API.md §4.\n */\nexport class HelmService {\n readonly monomerLib: IMonomerLib;\n readonly theme: Theme;\n readonly options: Readonly<HelmServiceOptions>;\n\n /** Stored for future logging; currently unused but exposed via debug hook. */\n readonly logger: Logger;\n private readonly _parseCache: LruCache<string, ParseResult>;\n private readonly _layoutCache: LruCache<string, Mol>;\n private readonly _renderCache: LruCache<string, string>;\n private readonly _libUnsub: Unsubscribe;\n private _destroyed: boolean = false;\n\n // T-0903 — cache-hit telemetry, see HelmServiceStats above.\n private _parseHits: number = 0;\n private _parseMisses: number = 0;\n private _layoutHits: number = 0;\n private _layoutMisses: number = 0;\n private _renderHits: number = 0;\n private _renderMisses: number = 0;\n\n constructor(options: HelmServiceOptions) {\n if (options.monomerLib === undefined || options.monomerLib === null)\n throw new TypeError('HelmService: options.monomerLib is required');\n\n this.monomerLib = options.monomerLib;\n this.theme = options.theme ?? lightTheme;\n this.logger = options.logger ?? new SilentLogger();\n this.options = Object.freeze({ ...options });\n\n const max = options.cacheSize ?? DEFAULT_CACHE_SIZE;\n this._parseCache = new LruCache<string, ParseResult>({ max });\n this._layoutCache = new LruCache<string, Mol>({ max });\n this._renderCache = new LruCache<string, string>({ max });\n\n // Bust every cache when the library changes — its monomers feed into\n // every cached value.\n this._libUnsub = this.monomerLib.onChanged.subscribe(() => {\n this.clearCaches();\n });\n }\n\n // ------------------------------------------------------------------------\n // Parse / serialize / validate\n // ------------------------------------------------------------------------\n\n parse(helm: string, parseOptions?: ParseOptions): ParseResult {\n this._ensureLive();\n const mode = parseOptions?.mode ?? 'lenient';\n const resolveMonomers = parseOptions?.resolveMonomers !== false;\n const key = parseKey({ mode, resolveMonomers, helm });\n const cached = this._parseCache.get(key);\n if (cached !== undefined) {\n this._parseHits += 1;\n return cached;\n }\n this._parseMisses += 1;\n\n const ioOpts: IoParseOptions = { mode, resolveMonomers };\n const result: IoParseResult = _parseHelm(helm, this.monomerLib, ioOpts);\n const frozen: ParseResult = {\n mol: result.mol,\n diagnostics: Object.freeze([...result.diagnostics]),\n };\n this._parseCache.set(key, frozen);\n return frozen;\n }\n\n serialize(mol: Mol, serializeOptions?: SerializeOptions): string {\n this._ensureLive();\n const opts: IoSerializeOptions = {\n ...(serializeOptions?.canonicalize !== undefined ? { canonicalize: serializeOptions.canonicalize } : {}),\n ...(serializeOptions?.includeHighlights !== undefined ? { includeHighlights: serializeOptions.includeHighlights } : {}),\n ...(serializeOptions?.version !== undefined ? { version: serializeOptions.version } : {}),\n };\n return _serialize(mol, opts);\n }\n\n validate(helm: string, validateOptions?: ValidateOptions): ValidationDiagnostic[] {\n this._ensureLive();\n // Parse always with resolveMonomers true so semantic checks (R-group\n // counts, etc.) have the library lookups available.\n const { mol, diagnostics: parseDiags } = this.parse(helm, { mode: 'lenient' });\n const opts: IoValidateOptions = validateOptions?.mode !== undefined ? { mode: validateOptions.mode } : {};\n const validatorDiags = _validate(mol, this.monomerLib, opts);\n return [...parseDiags, ...validatorDiags];\n }\n\n canonicalize(helm: string): string {\n this._ensureLive();\n const { mol } = this.parse(helm, { mode: 'lenient' });\n const canon = _canonicalize(mol);\n return _serialize(canon, { canonicalize: true, version: 'V2.0' });\n }\n\n removeGaps(helm: string): RemoveGapsResult {\n this._ensureLive();\n return _removeGaps(helm, this.monomerLib);\n }\n\n // ------------------------------------------------------------------------\n // Rendering\n // ------------------------------------------------------------------------\n\n renderToSvg(helm: string, renderOptions?: RenderOptions): string {\n this._ensureLive();\n const opts = this._resolveRenderOptions(renderOptions);\n const key = this._renderKey(helm, opts);\n const cached = this._renderCache.get(key);\n if (cached !== undefined) {\n this._renderHits += 1;\n return cached;\n }\n this._renderMisses += 1;\n\n const { mol } = this.parse(helm, { mode: 'lenient' });\n const laid = this._layout(mol, opts.bondLength);\n const { svg } = renderSvg(laid, opts);\n this._renderCache.set(key, svg);\n return svg;\n }\n\n /**\n * Phase 13c (Bug 8 fix) — Render a `Mol` directly, bypassing parse and\n * layout. This keeps the rendered atom positions identical to the\n * caller-supplied `mol.atoms[i].p`, which the editor's hit-tester also\n * reads — closing the disconnect that caused added/erased atoms to be\n * invisible to subsequent clicks and hovers.\n *\n * Use this from the interactive editor view (which holds the\n * authoritative mol). The string-keyed `renderToSvg(helm)` is still the\n * right entry for grid / batch rendering where parse + layout caching\n * matter more than positional fidelity to a live editor state.\n */\n renderMol(mol: Mol, renderOptions?: RenderOptions): string {\n this._ensureLive();\n const opts = this._resolveRenderOptions(renderOptions);\n const { svg } = renderSvg(mol, opts);\n return svg;\n }\n\n async renderToPng(helm: string, renderOptions?: RenderOptions): Promise<Uint8Array> {\n this._ensureLive();\n // PNG rendering goes through OffscreenCanvas — browser-only. In Node we\n // throw a documented, typed error so callers can fall back to SVG.\n if (typeof (globalThis as { OffscreenCanvas?: unknown }).OffscreenCanvas !== 'function') {\n throw new HelmNotSupportedError(\n 'png-rendering-requires-browser',\n 'HelmService.renderToPng requires OffscreenCanvas (browser-only).',\n );\n }\n const opts = this._resolveRenderOptions(renderOptions);\n const { mol } = this.parse(helm, { mode: 'lenient' });\n const laid = this._layout(mol, opts.bondLength);\n return canvasRenderToPng(laid, opts);\n }\n\n /**\n * Phase 1 (Datagrok migration) — sync canvas rendering. Paints `helm`\n * directly into a caller-supplied 2D context within `bounds`, returning the\n * laid-out `Mol` plus model/draw boxes for hit-testing. This is the path the\n * Datagrok grid cell renderer uses — no Blob / PNG / `drawImage` round-trip,\n * so the cell renderer stays fully synchronous. Reuses the parse + layout\n * caches; the draw itself is cheap and not cached.\n *\n * @param ctx Target 2D context (browser grid canvas or offscreen).\n * @param helm HELM string to render.\n * @param bounds Destination rectangle in the context's coordinate space.\n * @param renderOptions Optional theme / padding / fontSize / backColor.\n * @returns The laid-out mol plus model bbox and absolute draw box.\n */\n renderToCanvas(\n ctx: AnyCanvasContext,\n helm: string,\n bounds: CanvasBounds,\n renderOptions?: RenderOptions,\n ): RenderToCanvasResult {\n this._ensureLive();\n const opts = this._resolveRenderOptions(renderOptions);\n const { mol } = this.parse(helm, { mode: 'lenient' });\n const laid = this._layout(mol, opts.bondLength);\n const { bbox, drawBox } = drawMolToContext(ctx, laid, bounds, opts);\n return { mol: laid, bbox, drawBox };\n }\n\n /**\n * Like {@link renderToCanvas} but paints a caller-owned `Mol` directly,\n * bypassing parse + layout (mirrors {@link renderMol}). Use from the\n * interactive editor, which holds the authoritative laid-out mol whose\n * atom positions must match the painted output for hit-testing.\n *\n * @param ctx Target 2D context.\n * @param mol Laid-out molecule to paint.\n * @param bounds Destination rectangle in the context's coordinate space.\n * @param renderOptions Optional theme / padding / fontSize / backColor.\n * @returns The same mol plus model bbox and absolute draw box.\n */\n renderMolToCanvas(\n ctx: AnyCanvasContext,\n mol: Mol,\n bounds: CanvasBounds,\n renderOptions?: RenderOptions,\n ): RenderToCanvasResult {\n this._ensureLive();\n const opts = this._resolveRenderOptions(renderOptions);\n const { bbox, drawBox } = drawMolToContext(ctx, mol, bounds, opts);\n return { mol, bbox, drawBox };\n }\n\n *renderMany(\n items: readonly { id: string; helm: string }[],\n renderOptions?: RenderOptions,\n ): Iterable<{ id: string; svg: string }> {\n for (const item of items) {\n const svg = this.renderToSvg(item.helm, renderOptions);\n yield { id: item.id, svg };\n }\n }\n\n // ------------------------------------------------------------------------\n // Calculations\n // ------------------------------------------------------------------------\n\n getFormula(helm: string): MolecularFormula {\n this._ensureLive();\n const { mol } = this.parse(helm, { mode: 'lenient' });\n return computeFormula(mol);\n }\n\n getMolWeight(helm: string): number {\n this._ensureLive();\n const { mol } = this.parse(helm, { mode: 'lenient' });\n return molWeight(mol);\n }\n\n getExtinctionCoefficient(helm: string): number {\n this._ensureLive();\n const { mol } = this.parse(helm, { mode: 'lenient' });\n return extinctionCoefficient(mol);\n }\n\n getMolfile(helm: string): string {\n this._ensureLive();\n const { mol } = this.parse(helm, { mode: 'lenient' });\n return pseudoMolfile(mol);\n }\n\n // ------------------------------------------------------------------------\n // Atomic plug-in (optional)\n // ------------------------------------------------------------------------\n\n hasAtomicMolfileProvider(): boolean {\n return typeof this.options.atomicMolfileProvider === 'function';\n }\n\n async getAtomicMolfile(helm: string): Promise<string> {\n this._ensureLive();\n const provider = this.options.atomicMolfileProvider;\n if (typeof provider !== 'function') {\n throw new HelmNotSupportedError(\n 'atomic-molfile-not-configured',\n 'Set HelmServiceOptions.atomicMolfileProvider to enable atomic-level expansion.',\n );\n }\n return await provider(helm, this.monomerLib);\n }\n\n // ------------------------------------------------------------------------\n // Cache management\n // ------------------------------------------------------------------------\n\n /**\n * Drop any cached value whose key matches `predicate`. When `predicate` is\n * omitted, all caches are cleared.\n */\n invalidate(predicate?: (key: string) => boolean): void {\n if (predicate === undefined) {\n this.clearCaches();\n return;\n }\n for (const cache of [this._parseCache, this._layoutCache, this._renderCache]) {\n const toDelete: string[] = [];\n for (const k of cache.keys()) if (predicate(k)) toDelete.push(k);\n for (const k of toDelete) cache.delete(k);\n }\n }\n\n clearCaches(): void {\n this._parseCache.clear();\n this._layoutCache.clear();\n this._renderCache.clear();\n // Reset T-0903 telemetry — once a cache is cleared the prior hit-rate\n // is meaningless to downstream observers.\n this._parseHits = 0;\n this._parseMisses = 0;\n this._layoutHits = 0;\n this._layoutMisses = 0;\n this._renderHits = 0;\n this._renderMisses = 0;\n }\n\n /**\n * Tear down the service: unsubscribe from the library and clear caches.\n * Subsequent calls throw. Idempotent.\n */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n this._libUnsub();\n this.clearCaches();\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _ensureLive(): void {\n if (this._destroyed)\n throw new HelmNotSupportedError('service-destroyed', 'HelmService instance has been destroyed.');\n }\n\n private _resolveRenderOptions(renderOptions: RenderOptions | undefined): RendererRenderOptions {\n const merged: RendererRenderOptions = {};\n const theme = renderOptions?.theme ?? this.theme;\n merged.theme = theme;\n if (renderOptions?.width !== undefined) merged.width = renderOptions.width;\n if (renderOptions?.height !== undefined) merged.height = renderOptions.height;\n if (renderOptions?.backColor !== undefined) merged.backColor = renderOptions.backColor;\n if (renderOptions?.padding !== undefined) merged.padding = renderOptions.padding;\n if (renderOptions?.showIds !== undefined) merged.showIds = renderOptions.showIds;\n if (renderOptions?.showAnnotations !== undefined) merged.showAnnotations = renderOptions.showAnnotations;\n if (renderOptions?.bondLength !== undefined) merged.bondLength = renderOptions.bondLength;\n if (renderOptions?.fontSize !== undefined) merged.fontSize = renderOptions.fontSize;\n if (renderOptions?.maxScale !== undefined) merged.maxScale = renderOptions.maxScale;\n if (renderOptions?.showRGroupLabels !== undefined) merged.showRGroupLabels = renderOptions.showRGroupLabels;\n if (renderOptions?.selectedAtomIds !== undefined) merged.selectedAtomIds = renderOptions.selectedAtomIds;\n if (renderOptions?.highlightedAtomIds !== undefined) merged.highlightedAtomIds = renderOptions.highlightedAtomIds;\n // T-1704 — forward the bbox-pin so the interactive editor's \"no\n // auto-refit\" promise survives the service layer. Without this the\n // renderer recomputes the bbox from the mol on every render and\n // visually shifts the canvas after every addAtom / addBond /\n // removeAtom (the exact UX bug the user reported on 2026-05-17).\n if (renderOptions?.fixedModelBbox !== undefined) merged.fixedModelBbox = renderOptions.fixedModelBbox;\n return merged;\n }\n\n private _renderKey(helm: string, opts: RendererRenderOptions): string {\n const theme = opts.theme ?? this.theme;\n const themeName = theme.name;\n const libId = this._libCacheTag();\n const w = opts.width ?? 0;\n const h = opts.height ?? 0;\n const pad = opts.padding ?? -1;\n const bl = opts.bondLength ?? -1;\n const back = opts.backColor ?? '';\n const ids = opts.showIds === true ? 1 : 0;\n const ann = opts.showAnnotations === false ? 0 : 1;\n const ms = opts.maxScale ?? 1;\n return `${libId}|${themeName}|${w}x${h}|p${pad}|b${bl}|bg${back}|i${ids}a${ann}|s${ms}|${helm}`;\n }\n\n private _layout(mol: Mol, bondLength: number | undefined): Mol {\n const fp = molFingerprint(mol);\n const key = `${this._libCacheTag()}|${bondLength ?? 'd'}|${fp}`;\n const cached = this._layoutCache.get(key);\n if (cached !== undefined) {\n this._layoutHits += 1;\n return cached;\n }\n this._layoutMisses += 1;\n const laid = bondLength !== undefined ? layoutMol(mol, { bondLength }) : layoutMol(mol);\n this._layoutCache.set(key, laid);\n return laid;\n }\n\n /**\n * Cache-hit telemetry exposed for diagnostics / bench harnesses. The\n * counters reset on `clearCaches()` so a freshly-warmed service starts\n * from zero.\n */\n get stats(): HelmServiceStats {\n return {\n parseHits: this._parseHits,\n parseMisses: this._parseMisses,\n layoutHits: this._layoutHits,\n layoutMisses: this._layoutMisses,\n renderHits: this._renderHits,\n renderMisses: this._renderMisses,\n };\n }\n\n private _libCacheTag(): string {\n const versioned = this.monomerLib as { version?: number };\n const v = typeof versioned.version === 'number' ? versioned.version : 0;\n return `${this.monomerLib.source}@${v}`;\n }\n}\n","// T-0506 — `Selection` value object.\n//\n// A `Selection` is an immutable pair of atom-id / bond-id sets. Every helper on\n// the `Selection` namespace returns a brand-new `Selection`; instances never\n// mutate. See API.md §6 and EVENTS.md §4.\n//\n// Layer rule: `src/core/selection.ts` imports nothing from `core/model.ts`\n// (we store ids, not atom/bond references) so the file is dependency-free\n// inside the core layer.\n\n/**\n * Immutable read-only view of the editor's current selection. The atoms and\n * bonds sets are `ReadonlySet<number>`; consumers must not cast them to\n * mutable `Set<number>`. Use the helpers on the `Selection` value below to\n * derive new selections.\n */\nexport interface Selection {\n readonly atoms: ReadonlySet<number>;\n readonly bonds: ReadonlySet<number>;\n readonly isEmpty: boolean;\n}\n\n/**\n * Internal concrete `Selection` implementation. Frozen at construction so\n * even consumers that cast away the `ReadonlySet` cannot mutate the public\n * fields (the sets themselves are still ECMAScript-mutable; we rely on the\n * type system + the helpers below to avoid mutation).\n */\nclass SelectionImpl implements Selection {\n readonly atoms: ReadonlySet<number>;\n readonly bonds: ReadonlySet<number>;\n readonly isEmpty: boolean;\n\n constructor(atoms: Set<number>, bonds: Set<number>) {\n this.atoms = atoms;\n this.bonds = bonds;\n this.isEmpty = atoms.size === 0 && bonds.size === 0;\n Object.freeze(this);\n }\n}\n\nconst EMPTY_SELECTION: Selection = new SelectionImpl(new Set<number>(), new Set<number>());\n\n/**\n * Constructor + algebra surface for `Selection`. The interface and the const\n * intentionally share the same name so consumers write\n * `const s: Selection = Selection.empty()` naturally.\n */\nexport const Selection: {\n empty(): Selection;\n fromAtoms(atomIds: Iterable<number>): Selection;\n fromBonds(bondIds: Iterable<number>): Selection;\n fromAtomsAndBonds(atomIds: Iterable<number>, bondIds: Iterable<number>): Selection;\n union(...sels: Selection[]): Selection;\n difference(a: Selection, b: Selection): Selection;\n intersect(a: Selection, b: Selection): Selection;\n toggle(sel: Selection, item: { kind: 'atom' | 'bond'; id: number }): Selection;\n hasAtom(sel: Selection, id: number): boolean;\n hasBond(sel: Selection, id: number): boolean;\n equals(a: Selection, b: Selection): boolean;\n} = {\n empty(): Selection {\n return EMPTY_SELECTION;\n },\n\n fromAtoms(atomIds: Iterable<number>): Selection {\n return new SelectionImpl(new Set<number>(atomIds), new Set<number>());\n },\n\n fromBonds(bondIds: Iterable<number>): Selection {\n return new SelectionImpl(new Set<number>(), new Set<number>(bondIds));\n },\n\n fromAtomsAndBonds(atomIds: Iterable<number>, bondIds: Iterable<number>): Selection {\n return new SelectionImpl(new Set<number>(atomIds), new Set<number>(bondIds));\n },\n\n union(...sels: Selection[]): Selection {\n if (sels.length === 0) return EMPTY_SELECTION;\n const atoms = new Set<number>();\n const bonds = new Set<number>();\n for (const s of sels) {\n for (const id of s.atoms) atoms.add(id);\n for (const id of s.bonds) bonds.add(id);\n }\n return new SelectionImpl(atoms, bonds);\n },\n\n difference(a: Selection, b: Selection): Selection {\n const atoms = new Set<number>();\n const bonds = new Set<number>();\n for (const id of a.atoms) if (!b.atoms.has(id)) atoms.add(id);\n for (const id of a.bonds) if (!b.bonds.has(id)) bonds.add(id);\n return new SelectionImpl(atoms, bonds);\n },\n\n intersect(a: Selection, b: Selection): Selection {\n const atoms = new Set<number>();\n const bonds = new Set<number>();\n for (const id of a.atoms) if (b.atoms.has(id)) atoms.add(id);\n for (const id of a.bonds) if (b.bonds.has(id)) bonds.add(id);\n return new SelectionImpl(atoms, bonds);\n },\n\n toggle(sel: Selection, item: { kind: 'atom' | 'bond'; id: number }): Selection {\n if (item.kind === 'atom') {\n const next = new Set<number>(sel.atoms);\n if (next.has(item.id)) next.delete(item.id);\n else next.add(item.id);\n return new SelectionImpl(next, new Set<number>(sel.bonds));\n }\n const nextBonds = new Set<number>(sel.bonds);\n if (nextBonds.has(item.id)) nextBonds.delete(item.id);\n else nextBonds.add(item.id);\n return new SelectionImpl(new Set<number>(sel.atoms), nextBonds);\n },\n\n hasAtom(sel: Selection, id: number): boolean {\n return sel.atoms.has(id);\n },\n\n hasBond(sel: Selection, id: number): boolean {\n return sel.bonds.has(id);\n },\n\n equals(a: Selection, b: Selection): boolean {\n if (a === b) return true;\n if (a.atoms.size !== b.atoms.size || a.bonds.size !== b.bonds.size) return false;\n for (const id of a.atoms) if (!b.atoms.has(id)) return false;\n for (const id of a.bonds) if (!b.bonds.has(id)) return false;\n return true;\n },\n};\n","// T-1411 — R-group bookkeeping helpers.\n//\n// Pure functions over a `Mol`'s atom + bond arrays that answer \"which\n// numeric R-groups on this atom are still free?\". Phase 14B (connection\n// constraints) uses these to enforce the SPECIFICATION.md §12.4 rule that\n// every numeric R-group binds AT MOST ONE bond.\n//\n// **What counts as \"used\"?**\n// An R-group is consumed only when a bond carries a `{kind: 'numeric', r: N}`\n// reference on the side that references this atom. Non-numeric references\n// (`'unspecified'` / `'wildcard'` / `'pair'`) are deliberately ambiguous by\n// design (see SPECIFICATION.md §12.4) and DO NOT count toward the cap —\n// surfacing a \"free R-group\" diagnostic over `?`/`*`/pair markers would\n// punish HELM strings that use them legitimately. Positional refs\n// (`'positional'`) also do not count: they pin a BLOB-internal endpoint to a\n// specific atom-position-within-the-BLOB rather than to a slot on a single\n// atom's monomer record.\n//\n// `freeRgroups` only knows what `atom.monomer.rgroups` advertises — if the\n// resolver has not yet attached a monomer (the atom is unresolved), the\n// total is 0, the \"free\" list is empty, and the caller treats the atom as\n// having no capacity.\n//\n// Layering: `core/` only. Imports types from `./model`; nothing else.\n\nimport type { Atom, Bond } from './model';\n\n/**\n * Total number of R-groups advertised by the atom's resolved monomer.\n * Returns 0 when the atom has no monomer (unresolved at the resolver step,\n * or detached fragment).\n */\nexport function totalRgroups(atom: Atom): number {\n const m = atom.monomer;\n if (m === null) return 0;\n return m.rgroups.length;\n}\n\n/**\n * Return every 1-based R-group index on `atom` that is currently consumed\n * by some bond's numeric `r1`/`r2` reference. Indices appear at most once\n * in the result (Set semantics). Non-numeric refs are skipped; bond kind\n * doesn't matter — both backbone and cross-polymer bonds consume the same\n * slot.\n */\nexport function takenRgroups(atom: Atom, bonds: readonly Bond[]): number[] {\n const used = new Set<number>();\n for (const b of bonds) {\n if (b.a1.id === atom.id && b.r1.kind === 'numeric') used.add(b.r1.r);\n if (b.a2.id === atom.id && b.r2.kind === 'numeric') used.add(b.r2.r);\n }\n const out: number[] = [];\n // Emit in ascending order for deterministic test output.\n const sorted = Array.from(used).sort((a, b) => a - b);\n for (const n of sorted) out.push(n);\n return out;\n}\n\n/**\n * Return the 1-based numeric R-group indices on `atom` that are NOT yet\n * consumed by any bond. Indices come from `1..totalRgroups(atom)`. If the\n * atom has no monomer (totalRgroups === 0), returns an empty array.\n *\n * Result is sorted ascending so callers can rely on `[0]` being the\n * lowest-numbered free slot — useful for \"pick R1 first\" defaults.\n */\nexport function freeRgroups(atom: Atom, bonds: readonly Bond[]): number[] {\n const total = totalRgroups(atom);\n if (total === 0) return [];\n const taken = new Set<number>(takenRgroups(atom, bonds));\n const free: number[] = [];\n for (let i = 1; i <= total; i++)\n if (!taken.has(i)) free.push(i);\n return free;\n}\n\n/** True iff `atom` has at least one free numeric R-group available. */\nexport function hasFreeRgroup(atom: Atom, bonds: readonly Bond[]): boolean {\n return freeRgroups(atom, bonds).length > 0;\n}\n\n/**\n * Describes one bond participation of `atom`. `side` says whether the atom\n * is on the bond's a1 (`'r1'`) or a2 (`'r2'`) side; `rNumber` is the 1-based\n * R-group consumed on that side. For non-numeric references `rNumber === 0`\n * (the bond touches the atom but does not pin a specific numeric slot).\n */\nexport interface AtomBondParticipation {\n bond: Bond;\n side: 'r1' | 'r2';\n rNumber: number;\n}\n\n/**\n * Every bond `atom` participates in, with the side and the numeric R-group\n * index consumed on that side (0 when the ref is non-numeric). Order\n * matches `bonds` argument order — useful for \"which bond stole R2?\".\n */\nexport function bondsOnAtom(atom: Atom, bonds: readonly Bond[]): AtomBondParticipation[] {\n const out: AtomBondParticipation[] = [];\n for (const b of bonds) {\n if (b.a1.id === atom.id) {\n const rNumber = b.r1.kind === 'numeric' ? b.r1.r : 0;\n out.push({ bond: b, side: 'r1', rNumber });\n } else if (b.a2.id === atom.id) {\n const rNumber = b.r2.kind === 'numeric' ? b.r2.r : 0;\n out.push({ bond: b, side: 'r2', rNumber });\n }\n }\n return out;\n}\n","// T-0506 — `Transaction` value object.\n//\n// A `Transaction` is a planned batch of mutations against a source `Mol` that,\n// on `commit()`, produces a fresh immutable `Mol` plus a `ChangeSet` describing\n// what changed. Snapshot-based — there is no inverse-op log; undo is handled\n// at the editor layer by keeping a history of `Mol` snapshots.\n//\n// See ARCHITECTURE.md §3.3 (\"transaction.ts\"), API.md §2 (HelmEditor surface\n// that consumes this), and ROADMAP Phase 5 / T-0506.\n//\n// Layering: this file imports from `core/` and `util/` only — no io, no\n// monomer-lib runtime helpers. The continuous-id walk is shared with\n// `src/io/continuous-id.ts` via `makeContinuousIdMap` in `core/ids.ts`.\n\nimport type {\n AnnotationMap,\n Atom,\n AtomBio,\n Bond,\n BondKind,\n BondRatio,\n Chain,\n Group,\n Mol,\n RGroupRef,\n} from './model';\nimport { HelmTypes, PolymerTypes } from './constants';\nimport type { HelmType, PolymerType } from './constants';\nimport { IdGenerator, makeContinuousIdMap } from './ids';\nimport type { Point } from '../util/types';\n\n// --------------------------------------------------------------------------\n// Public types\n// --------------------------------------------------------------------------\n\n/**\n * Description of an atom to add. `chainId` and `positionInChain` are\n * optional — when omitted, the builder picks a fresh chain id (or appends\n * to the chain matching the biotype's polymer type if `chainId` resolves to\n * an existing chain).\n */\nexport interface AtomDraft {\n p: Point;\n biotype: HelmType;\n symbol: string;\n chainId?: string;\n positionInChain?: number;\n}\n\n/**\n * Description of a bond to add. Endpoint atoms are referenced by their ids\n * (the actual `Atom` references are looked up at commit time).\n */\nexport interface BondDraft {\n a1: number;\n a2: number;\n kind: BondKind;\n r1: RGroupRef;\n r2: RGroupRef;\n}\n\n/**\n * Summary of every atom/bond that changed during the transaction. Added,\n * removed, and modified sets are disjoint by definition: an atom added then\n * removed inside the same transaction ends up in neither set; an atom that\n * was added and then updated is reported only as added.\n */\nexport interface ChangeSet {\n readonly addedAtomIds: ReadonlySet<number>;\n readonly removedAtomIds: ReadonlySet<number>;\n readonly addedBondIds: ReadonlySet<number>;\n readonly removedBondIds: ReadonlySet<number>;\n readonly modifiedAtomIds: ReadonlySet<number>;\n readonly modifiedBondIds: ReadonlySet<number>;\n}\n\n// --------------------------------------------------------------------------\n// Internal state shapes (mutable copies of immutable Mol entities)\n// --------------------------------------------------------------------------\n\ninterface AtomState {\n id: number;\n p: Point;\n biotype: HelmType;\n symbol: string;\n monomer: Atom['monomer'];\n bio: AtomBio;\n hidden: boolean;\n selected: boolean;\n highlighted: boolean;\n tag: string | undefined;\n branchAtomId: number | undefined;\n inlineSource: string | undefined;\n}\n\ninterface BondState {\n id: number;\n a1Id: number;\n a2Id: number;\n kind: BondKind;\n r1: RGroupRef;\n r2: RGroupRef;\n ratio: BondRatio | undefined;\n tag: string | undefined;\n}\n\ninterface ChainState {\n id: string;\n polymerType: PolymerType;\n backboneAtomIds: number[];\n bondIds: number[];\n annotation: string | undefined;\n}\n\n// --------------------------------------------------------------------------\n// Helpers\n// --------------------------------------------------------------------------\n\nfunction polymerTypeFor(biotype: HelmType): PolymerType {\n switch (biotype) {\n case HelmTypes.AA:\n return PolymerTypes.PEPTIDE;\n case HelmTypes.SUGAR:\n case HelmTypes.BASE:\n case HelmTypes.LINKER:\n case HelmTypes.NUCLEOTIDE:\n return PolymerTypes.RNA;\n case HelmTypes.CHEM:\n return PolymerTypes.CHEM;\n case HelmTypes.BLOB:\n return PolymerTypes.BLOB;\n }\n}\n\nfunction defaultChainIdFor(polymerType: PolymerType): string {\n switch (polymerType) {\n case PolymerTypes.PEPTIDE: return 'PEPTIDE';\n case PolymerTypes.RNA: return 'RNA';\n case PolymerTypes.CHEM: return 'CHEM';\n case PolymerTypes.BLOB: return 'BLOB';\n case PolymerTypes.G: return 'G';\n }\n}\n\nfunction maxNumericIdAcross(mol: Mol): number {\n let max = 0;\n for (const a of mol.atoms) if (a.id > max) max = a.id;\n for (const b of mol.bonds) if (b.id > max) max = b.id;\n return max;\n}\n\nfunction rgroupRefEquals(a: RGroupRef, b: RGroupRef): boolean {\n if (a.kind !== b.kind) return false;\n if (a.kind === 'numeric' && b.kind === 'numeric') return a.r === b.r;\n if (a.kind === 'positional' && b.kind === 'positional')\n return a.position === b.position && a.r === b.r;\n return true; // 'unspecified' | 'wildcard' | 'pair' carry no extra fields\n}\n\n// --------------------------------------------------------------------------\n// Transaction\n// --------------------------------------------------------------------------\n\n/**\n * Mutable, single-use batch builder over an immutable `Mol`. Construct,\n * apply operations, then call `commit()` to obtain the new immutable `Mol`\n * and a `ChangeSet`. Each `Transaction` instance is intended for a single\n * `commit()`; re-using one after commit is supported but produces a fresh\n * `ChangeSet` against the original src (changes are not cumulative across\n * commits — they reset on each commit).\n */\nexport class Transaction {\n private readonly _idgen: IdGenerator;\n\n private readonly _atoms: Map<number, AtomState> = new Map();\n private readonly _atomOrder: number[] = [];\n\n private readonly _bonds: Map<number, BondState> = new Map();\n private readonly _bondOrder: number[] = [];\n\n private readonly _chains: Map<string, ChainState> = new Map();\n private readonly _chainOrder: string[] = [];\n\n private readonly _groups: Group[];\n private readonly _annotations: AnnotationMap;\n\n // Change tracking — kept mutable until commit() freezes the result.\n private readonly _addedAtoms: Set<number> = new Set();\n private readonly _removedAtoms: Set<number> = new Set();\n private readonly _modifiedAtoms: Set<number> = new Set();\n private readonly _addedBonds: Set<number> = new Set();\n private readonly _removedBonds: Set<number> = new Set();\n private readonly _modifiedBonds: Set<number> = new Set();\n\n // Tracks whether topology (atoms / bonds / chains) changed during this\n // transaction. When true, we re-run continuous-id assignment in commit().\n private _topologyDirty: boolean = false;\n\n constructor(srcMol: Mol) {\n this._idgen = new IdGenerator();\n // Seed past max(id) so new ids never collide with existing ones. We do\n // this by replaying `next()` until `current` exceeds the source max.\n const seed = maxNumericIdAcross(srcMol);\n for (let i = 0; i < seed; i++) this._idgen.next();\n\n // Copy chains first so atoms-by-chain lookup is available below.\n for (const c of srcMol.chains) {\n this._chains.set(c.id, {\n id: c.id,\n polymerType: c.polymerType,\n backboneAtomIds: c.backboneAtoms.map((a) => a.id),\n bondIds: c.bonds.map((b) => b.id),\n annotation: c.annotation,\n });\n this._chainOrder.push(c.id);\n }\n\n for (const a of srcMol.atoms) {\n this._atoms.set(a.id, {\n id: a.id,\n p: { x: a.p.x, y: a.p.y },\n biotype: a.biotype,\n symbol: a.symbol,\n monomer: a.monomer,\n bio: { ...a.bio },\n hidden: a.hidden,\n selected: a.selected,\n highlighted: a.highlighted,\n tag: a.tag,\n branchAtomId: a.branchAtom?.id,\n inlineSource: a.inlineSource,\n });\n this._atomOrder.push(a.id);\n }\n\n for (const b of srcMol.bonds) {\n this._bonds.set(b.id, {\n id: b.id,\n a1Id: b.a1.id,\n a2Id: b.a2.id,\n kind: b.kind,\n r1: b.r1,\n r2: b.r2,\n ratio: b.ratio,\n tag: b.tag,\n });\n this._bondOrder.push(b.id);\n }\n\n this._groups = [...srcMol.groups];\n this._annotations = srcMol.annotations;\n }\n\n // ------------------------------------------------------------------------\n // Mutators\n // ------------------------------------------------------------------------\n\n /**\n * Add an atom. Returns the freshly allocated id. The atom is appended to\n * the chain identified by `draft.chainId`, or to a fresh chain whose id is\n * derived from `draft.biotype`'s polymer type when omitted.\n */\n addAtom(draft: AtomDraft): number {\n const id = this._idgen.next();\n const polymerType = polymerTypeFor(draft.biotype);\n const chainId = draft.chainId ?? this._pickChainId(polymerType);\n let chain = this._chains.get(chainId);\n if (chain === undefined) {\n chain = {\n id: chainId,\n polymerType,\n backboneAtomIds: [],\n bondIds: [],\n annotation: undefined,\n };\n this._chains.set(chainId, chain);\n this._chainOrder.push(chainId);\n }\n\n const positionInChain = draft.positionInChain ?? chain.backboneAtomIds.length + 1;\n const atom: AtomState = {\n id,\n p: { x: draft.p.x, y: draft.p.y },\n biotype: draft.biotype,\n symbol: draft.symbol,\n monomer: null,\n bio: {\n chainId,\n positionInChain,\n continuousId: 0, // refreshed at commit() time\n },\n hidden: false,\n selected: false,\n highlighted: false,\n tag: undefined,\n branchAtomId: undefined,\n inlineSource: undefined,\n };\n this._atoms.set(id, atom);\n this._atomOrder.push(id);\n\n // Insert into backbone at requested position (1-based) or append.\n const insertIdx = Math.max(0, Math.min(positionInChain - 1, chain.backboneAtomIds.length));\n chain.backboneAtomIds.splice(insertIdx, 0, id);\n\n this._addedAtoms.add(id);\n this._topologyDirty = true;\n return id;\n }\n\n /**\n * Remove an atom and every bond that references it. Also clears\n * `branchAtom` back-pointers on the atom's parent (if any).\n */\n removeAtom(atomId: number): void {\n const atom = this._atoms.get(atomId);\n if (atom === undefined) return;\n\n // Remove every bond referencing this atom (cascade).\n const toRemoveBonds: number[] = [];\n for (const b of this._bonds.values())\n if (b.a1Id === atomId || b.a2Id === atomId) toRemoveBonds.push(b.id);\n for (const bid of toRemoveBonds) this._removeBondInternal(bid);\n\n // Clear any branchAtom pointer that referenced this atom.\n for (const other of this._atoms.values())\n if (other.branchAtomId === atomId) other.branchAtomId = undefined;\n\n // Drop from chain / atom collections.\n const chain = this._chains.get(atom.bio.chainId);\n if (chain !== undefined) {\n const i = chain.backboneAtomIds.indexOf(atomId);\n if (i >= 0) chain.backboneAtomIds.splice(i, 1);\n }\n this._atoms.delete(atomId);\n const orderIdx = this._atomOrder.indexOf(atomId);\n if (orderIdx >= 0) this._atomOrder.splice(orderIdx, 1);\n\n if (this._addedAtoms.has(atomId)) {\n // Net-no-op: added and then removed within this transaction.\n this._addedAtoms.delete(atomId);\n } else {\n this._removedAtoms.add(atomId);\n }\n this._modifiedAtoms.delete(atomId);\n this._topologyDirty = true;\n }\n\n /**\n * Patch in-place fields on an atom. `p`, `symbol`, `selected`,\n * `highlighted`, `tag`, `hidden` are supported. Unknown ids are ignored.\n */\n updateAtom(atomId: number, patch: Partial<{\n p: Point;\n symbol: string;\n selected: boolean;\n highlighted: boolean;\n tag: string | undefined;\n hidden: boolean;\n }>): void {\n const atom = this._atoms.get(atomId);\n if (atom === undefined) return;\n if (patch.p !== undefined) atom.p = { x: patch.p.x, y: patch.p.y };\n if (patch.symbol !== undefined) atom.symbol = patch.symbol;\n if (patch.selected !== undefined) atom.selected = patch.selected;\n if (patch.highlighted !== undefined) atom.highlighted = patch.highlighted;\n if ('tag' in patch) atom.tag = patch.tag;\n if (patch.hidden !== undefined) atom.hidden = patch.hidden;\n if (!this._addedAtoms.has(atomId)) this._modifiedAtoms.add(atomId);\n }\n\n /**\n * Add a bond. Validates that both endpoint atoms exist in the working\n * snapshot and that no bond with the same `(a1, r1, a2, r2)` is already\n * present.\n */\n addBond(draft: BondDraft): number {\n if (!this._atoms.has(draft.a1))\n throw new Error(`Transaction.addBond: atom ${draft.a1} does not exist`);\n if (!this._atoms.has(draft.a2))\n throw new Error(`Transaction.addBond: atom ${draft.a2} does not exist`);\n for (const existing of this._bonds.values()) {\n const sameForward =\n existing.a1Id === draft.a1 &&\n existing.a2Id === draft.a2 &&\n rgroupRefEquals(existing.r1, draft.r1) &&\n rgroupRefEquals(existing.r2, draft.r2);\n const sameReverse =\n existing.a1Id === draft.a2 &&\n existing.a2Id === draft.a1 &&\n rgroupRefEquals(existing.r1, draft.r2) &&\n rgroupRefEquals(existing.r2, draft.r1);\n if (sameForward || sameReverse)\n throw new Error(\n `Transaction.addBond: duplicate bond ${draft.a1}:${rgroupRefString(draft.r1)}-${draft.a2}:${rgroupRefString(draft.r2)}`,\n );\n }\n\n const id = this._idgen.next();\n this._bonds.set(id, {\n id,\n a1Id: draft.a1,\n a2Id: draft.a2,\n kind: draft.kind,\n r1: draft.r1,\n r2: draft.r2,\n ratio: undefined,\n tag: undefined,\n });\n this._bondOrder.push(id);\n\n // Attach to the owning chain (if both endpoints share one).\n const a1 = this._atoms.get(draft.a1);\n const a2 = this._atoms.get(draft.a2);\n if (a1 !== undefined && a2 !== undefined && a1.bio.chainId === a2.bio.chainId) {\n const chain = this._chains.get(a1.bio.chainId);\n if (chain !== undefined) chain.bondIds.push(id);\n }\n\n this._addedBonds.add(id);\n this._topologyDirty = true;\n return id;\n }\n\n /** Remove a bond by id. Unknown ids are ignored. */\n removeBond(bondId: number): void {\n if (!this._bonds.has(bondId)) return;\n this._removeBondInternal(bondId);\n this._topologyDirty = true;\n }\n\n /** Patch a bond's `tag` or `ratio`. Unknown ids are ignored. */\n updateBond(bondId: number, patch: Partial<{\n tag: string | undefined;\n ratio: BondRatio | undefined;\n }>): void {\n const bond = this._bonds.get(bondId);\n if (bond === undefined) return;\n if ('tag' in patch) bond.tag = patch.tag;\n if ('ratio' in patch) bond.ratio = patch.ratio;\n if (!this._addedBonds.has(bondId)) this._modifiedBonds.add(bondId);\n }\n\n // ------------------------------------------------------------------------\n // Commit\n // ------------------------------------------------------------------------\n\n /**\n * Build the new immutable `Mol` and freeze the `ChangeSet`. If topology\n * changed (atoms / bonds / chains), continuous-id assignment is re-run.\n */\n commit(): { mol: Mol; changes: ChangeSet } {\n // Build the new atom objects first; bonds and chains reference them.\n const newAtomsById = new Map<number, Atom>();\n for (const id of this._atomOrder) {\n const s = this._atoms.get(id);\n if (s === undefined) continue;\n const atom: Atom = {\n id: s.id,\n p: { x: s.p.x, y: s.p.y },\n biotype: s.biotype,\n symbol: s.symbol,\n monomer: s.monomer,\n bio: { ...s.bio },\n hidden: s.hidden,\n selected: s.selected,\n highlighted: s.highlighted,\n ...(s.tag !== undefined ? { tag: s.tag } : {}),\n ...(s.inlineSource !== undefined ? { inlineSource: s.inlineSource } : {}),\n };\n newAtomsById.set(id, atom);\n }\n\n // Re-attach branchAtom pointers using already-built Atom instances.\n // We assign through a typed cast so the immutable Atom interface is preserved.\n for (const id of this._atomOrder) {\n const s = this._atoms.get(id);\n if (s === undefined || s.branchAtomId === undefined) continue;\n const parent = newAtomsById.get(id);\n const branch = newAtomsById.get(s.branchAtomId);\n if (parent === undefined || branch === undefined) continue;\n (parent as { branchAtom?: Atom }).branchAtom = branch;\n }\n\n // Build bonds.\n const newBondsById = new Map<number, Bond>();\n for (const id of this._bondOrder) {\n const bs = this._bonds.get(id);\n if (bs === undefined) continue;\n const a1 = newAtomsById.get(bs.a1Id);\n const a2 = newAtomsById.get(bs.a2Id);\n if (a1 === undefined || a2 === undefined) continue;\n const bond: Bond = {\n id: bs.id,\n a1,\n a2,\n kind: bs.kind,\n r1: bs.r1,\n r2: bs.r2,\n ...(bs.ratio !== undefined ? { ratio: { ...bs.ratio } } : {}),\n ...(bs.tag !== undefined ? { tag: bs.tag } : {}),\n };\n newBondsById.set(id, bond);\n }\n\n // Build chains.\n const newChains: Chain[] = [];\n for (const cid of this._chainOrder) {\n const cs = this._chains.get(cid);\n if (cs === undefined) continue;\n // Drop empty chains so the resulting Mol stays clean. We keep chains\n // that still have any backbone atom OR any bond.\n if (cs.backboneAtomIds.length === 0 && cs.bondIds.length === 0) continue;\n const backboneAtoms: Atom[] = [];\n for (const aid of cs.backboneAtomIds) {\n const a = newAtomsById.get(aid);\n if (a !== undefined) backboneAtoms.push(a);\n }\n const bonds: Bond[] = [];\n for (const bid of cs.bondIds) {\n const b = newBondsById.get(bid);\n if (b !== undefined) bonds.push(b);\n }\n newChains.push({\n id: cs.id,\n polymerType: cs.polymerType,\n backboneAtoms: backboneAtoms as readonly Atom[],\n bonds: bonds as readonly Bond[],\n ...(cs.annotation !== undefined ? { annotation: cs.annotation } : {}),\n });\n }\n\n const atoms = this._atomOrder\n .map((id) => newAtomsById.get(id))\n .filter((a): a is Atom => a !== undefined);\n const bonds = this._bondOrder\n .map((id) => newBondsById.get(id))\n .filter((b): b is Bond => b !== undefined);\n\n let mol: Mol = {\n atoms,\n bonds,\n chains: newChains,\n groups: [...this._groups],\n annotations: this._annotations,\n };\n\n if (this._topologyDirty) mol = refreshContinuousIds(mol);\n\n const changes: ChangeSet = Object.freeze({\n addedAtomIds: new Set<number>(this._addedAtoms),\n removedAtomIds: new Set<number>(this._removedAtoms),\n addedBondIds: new Set<number>(this._addedBonds),\n removedBondIds: new Set<number>(this._removedBonds),\n modifiedAtomIds: new Set<number>(this._modifiedAtoms),\n modifiedBondIds: new Set<number>(this._modifiedBonds),\n });\n\n // Reset change tracking so a re-used Transaction reports fresh deltas.\n this._addedAtoms.clear();\n this._removedAtoms.clear();\n this._modifiedAtoms.clear();\n this._addedBonds.clear();\n this._removedBonds.clear();\n this._modifiedBonds.clear();\n this._topologyDirty = false;\n\n return { mol, changes };\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _removeBondInternal(bondId: number): void {\n const bond = this._bonds.get(bondId);\n if (bond === undefined) return;\n this._bonds.delete(bondId);\n const orderIdx = this._bondOrder.indexOf(bondId);\n if (orderIdx >= 0) this._bondOrder.splice(orderIdx, 1);\n for (const chain of this._chains.values()) {\n const i = chain.bondIds.indexOf(bondId);\n if (i >= 0) chain.bondIds.splice(i, 1);\n }\n if (this._addedBonds.has(bondId)) {\n this._addedBonds.delete(bondId);\n } else {\n this._removedBonds.add(bondId);\n }\n this._modifiedBonds.delete(bondId);\n }\n\n /** Pick a fresh chain id for a polymer type — e.g. `PEPTIDE1`, `PEPTIDE2`, … */\n private _pickChainId(polymerType: PolymerType): string {\n const base = defaultChainIdFor(polymerType);\n // Find the smallest n ≥ 1 such that `${base}${n}` is unused.\n let n = 1;\n while (this._chains.has(`${base}${n}`)) n += 1;\n return `${base}${n}`;\n }\n}\n\nfunction rgroupRefString(r: RGroupRef): string {\n switch (r.kind) {\n case 'numeric': return `R${r.r}`;\n case 'unspecified': return '?';\n case 'wildcard': return '*';\n case 'pair': return 'pair';\n case 'positional': return `${r.position}pos:R${r.r}`;\n }\n}\n\n/**\n * Rebuild every atom of `mol` so its `bio.continuousId` matches a fresh walk\n * of `mol.chains`. Bonds and chains are repointed at the new atom instances\n * so referential equality across the returned graph stays intact. Mirrors\n * `src/io/continuous-id.ts` but lives in `core/` to keep the layer rule\n * clean (core never imports io).\n */\nfunction refreshContinuousIds(mol: Mol): Mol {\n const ids = makeContinuousIdMap(mol);\n const oldToNew = new Map<number, Atom>();\n for (const a of mol.atoms) {\n const nextId = ids.get(a.id);\n if (nextId === undefined || nextId === a.bio.continuousId) {\n oldToNew.set(a.id, a);\n continue;\n }\n oldToNew.set(a.id, {\n ...a,\n bio: { ...a.bio, continuousId: nextId },\n });\n }\n\n // Patch branchAtom back-references onto the new atom instances.\n for (const a of mol.atoms) {\n if (a.branchAtom === undefined) continue;\n const newAtom = oldToNew.get(a.id);\n const newBranch = oldToNew.get(a.branchAtom.id);\n if (newAtom === undefined || newBranch === undefined) continue;\n (newAtom as { branchAtom?: Atom }).branchAtom = newBranch;\n }\n\n const newBonds: Bond[] = mol.bonds.map((b) => {\n const a1 = oldToNew.get(b.a1.id);\n const a2 = oldToNew.get(b.a2.id);\n if (a1 === undefined || a2 === undefined) return b;\n if (a1 === b.a1 && a2 === b.a2) return b;\n return { ...b, a1, a2 };\n });\n\n const newBondsById = new Map<number, Bond>();\n for (const b of newBonds) newBondsById.set(b.id, b);\n\n const newChains: Chain[] = mol.chains.map((c) => {\n const backbone: Atom[] = [];\n for (const a of c.backboneAtoms) backbone.push(oldToNew.get(a.id) ?? a);\n const bonds: Bond[] = [];\n for (const b of c.bonds) bonds.push(newBondsById.get(b.id) ?? b);\n return {\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: backbone as readonly Atom[],\n bonds: bonds as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n };\n });\n\n const newAtoms: Atom[] = mol.atoms.map((a) => oldToNew.get(a.id) ?? a);\n return {\n atoms: newAtoms as readonly Atom[],\n bonds: newBonds as readonly Bond[],\n chains: newChains as readonly Chain[],\n groups: mol.groups,\n annotations: mol.annotations,\n };\n}\n","// T-0405 — Hit-tester.\n//\n// A small spatial index over a `Mol`'s atoms and bonds. The renderer\n// rebuilds the tester whenever the Mol changes; per-pointer events run\n// `test(p)` against the cached tables.\n//\n// Strategy (RENDERING.md §7):\n// 1. Flat array `atomBoxes` of `{atom, bbox, hitRadius}` triples and\n// `bondSegments` of `{bond, a, b}` pairs.\n// 2. `test(p)`:\n// - Find every atom whose bbox covers `p` and whose Euclidean\n// distance to `p` is ≤ `hitRadius`.\n// - When two atoms qualify and the closer one is more than ~10%\n// closer than the runner-up, return only the closer one (matching\n// the legacy `getHoveredMonomerFromEditorMol`).\n// - If no atom hit, test bonds (point-to-segment distance ≤\n// `bondHitWidth`).\n// - Groups are not yet hit-tested (v1 deferred).\n// 3. `testRect(rect)`:\n// - Return atoms whose centre is inside `rect` and bonds whose\n// both endpoints are inside `rect`.\n//\n// Layering: imports from `core/`, `util/`, plus the local `./atom-shape`\n// and `./theme` modules. No DOM, no console.\n\nimport type {Atom, Bond, Group, Mol} from '../core/model';\nimport type {Point, Rect, BBox} from '../util/types';\nimport {atomBBox, atomHitRadius} from './atom-shape';\nimport type {Theme} from './theme';\n\n/**\n * Result of a single-point hit-test. Exactly one of `atom` / `bond` /\n * `group` will be set when the call returned a non-null value. Groups are\n * not hit-tested in v1 but the field is reserved.\n */\nexport interface HitTestResult {\n atom?: Atom;\n bond?: Bond;\n group?: Group;\n}\n\n/** Tester construction options. */\nexport interface HitTesterOptions {\n /** Half-width of the bond hit-corridor in CSS pixels. Default `4`. */\n bondHitWidth?: number;\n}\n\ninterface AtomEntry {\n readonly atom: Atom;\n readonly bbox: BBox;\n readonly hitRadius: number;\n}\n\ninterface BondEntry {\n readonly bond: Bond;\n readonly a: Point;\n readonly b: Point;\n}\n\n/**\n * Spatial index for atoms and bonds. Cheap to rebuild — the renderer does\n * so on every Mol change. Mutating methods (`rebuild`) replace the internal\n * tables atomically so concurrent reads see one consistent snapshot.\n */\nexport class HitTester {\n private atoms: ReadonlyArray<AtomEntry> = [];\n private bonds: ReadonlyArray<BondEntry> = [];\n private readonly bondHitWidth: number;\n\n constructor(mol: Mol, theme: Theme, options?: HitTesterOptions) {\n this.bondHitWidth = options?.bondHitWidth ?? 4;\n this.rebuild(mol, theme);\n }\n\n /** Rebuild the spatial tables from a new `Mol`. */\n rebuild(mol: Mol, theme: Theme): void {\n const atoms: AtomEntry[] = [];\n for (const a of mol.atoms) {\n if (a.hidden) continue;\n atoms.push({atom: a, bbox: atomBBox(a, theme), hitRadius: atomHitRadius(a, theme)});\n }\n const bonds: BondEntry[] = [];\n for (const b of mol.bonds)\n bonds.push({bond: b, a: b.a1.p, b: b.a2.p});\n this.atoms = atoms;\n this.bonds = bonds;\n }\n\n /**\n * Hit-test a point. Returns the topmost candidate (atom > bond > group)\n * or `null` when nothing is within tolerance.\n */\n test(p: Point): HitTestResult | null {\n // ---------------------------------------------------------------\n // Atoms — collect every candidate within its hit radius.\n // ---------------------------------------------------------------\n let best: {entry: AtomEntry; d: number} | null = null;\n let runnerUp: {entry: AtomEntry; d: number} | null = null;\n for (const entry of this.atoms) {\n if (!pointInBBox(p, entry.bbox)) continue;\n const dx = p.x - entry.atom.p.x;\n const dy = p.y - entry.atom.p.y;\n const d = Math.sqrt(dx * dx + dy * dy);\n if (d > entry.hitRadius) continue;\n if (best === null || d < best.d) {\n runnerUp = best;\n best = {entry, d};\n } else if (runnerUp === null || d < runnerUp.d) {\n runnerUp = {entry, d};\n }\n }\n if (best !== null) {\n // Mirror the legacy editor's \"ambiguity\" rule: when two candidates are\n // within ~10% of each other in distance we still keep the closer one\n // (the renderer paints whichever sits on top); this hook exists so\n // future versions can plug in alternate selection policies.\n void runnerUp;\n return {atom: best.entry.atom};\n }\n\n // ---------------------------------------------------------------\n // Bonds — point-to-segment distance.\n // ---------------------------------------------------------------\n let bestBond: {entry: BondEntry; d: number} | null = null;\n for (const entry of this.bonds) {\n const d = distancePointToSegment(p, entry.a, entry.b);\n if (d > this.bondHitWidth) continue;\n if (bestBond === null || d < bestBond.d)\n bestBond = {entry, d};\n }\n if (bestBond !== null)\n return {bond: bestBond.entry.bond};\n\n return null;\n }\n\n /**\n * Box-test: every atom whose centre lies inside `rect` and every bond\n * whose endpoints both lie inside `rect`. Useful for rectangle-drag\n * selection.\n */\n testRect(rect: Rect): {atoms: Atom[]; bonds: Bond[]} {\n const atoms: Atom[] = [];\n for (const entry of this.atoms) {\n if (pointInBBox(entry.atom.p, rect))\n atoms.push(entry.atom);\n }\n const bonds: Bond[] = [];\n for (const entry of this.bonds) {\n if (pointInBBox(entry.a, rect) && pointInBBox(entry.b, rect))\n bonds.push(entry.bond);\n }\n return {atoms, bonds};\n }\n\n /** Atom count currently indexed. Exposed for tests / diagnostics. */\n atomCount(): number {\n return this.atoms.length;\n }\n\n /** Bond count currently indexed. Exposed for tests / diagnostics. */\n bondCount(): number {\n return this.bonds.length;\n }\n}\n\n// --------------------------------------------------------------------------\n// Geometry helpers (local to this module)\n// --------------------------------------------------------------------------\n\nfunction pointInBBox(p: Point, box: BBox | Rect): boolean {\n return (\n p.x >= box.x &&\n p.x <= box.x + box.width &&\n p.y >= box.y &&\n p.y <= box.y + box.height\n );\n}\n\n/**\n * Shortest distance from `p` to the line segment `[a, b]`. Uses the\n * parametric projection: `t = clamp(((p - a) · (b - a)) / |b - a|², 0, 1)`,\n * then returns `|p − (a + t·(b − a))|`. Degenerate segments (a === b) fall\n * back to the straight Euclidean distance.\n */\nfunction distancePointToSegment(p: Point, a: Point, b: Point): number {\n const abx = b.x - a.x;\n const aby = b.y - a.y;\n const denom = abx * abx + aby * aby;\n if (denom === 0) {\n const dx = p.x - a.x;\n const dy = p.y - a.y;\n return Math.sqrt(dx * dx + dy * dy);\n }\n let t = ((p.x - a.x) * abx + (p.y - a.y) * aby) / denom;\n if (t < 0) t = 0;\n else if (t > 1) t = 1;\n const cx = a.x + t * abx;\n const cy = a.y + t * aby;\n const dx = p.x - cx;\n const dy = p.y - cy;\n return Math.sqrt(dx * dx + dy * dy);\n}\n","// T-0512 — Type-safe `EventBus<M>` and `EditorEventMap`.\n//\n// The event bus is a plain synchronous multicast — one handler set per event\n// name, iteration order = registration order. Per ARCHITECTURE.md §3.8 and\n// EVENTS.md, all editor-driven coordination travels through this surface. The\n// generic `M` lets the editor declare its `EditorEventMap` once and have\n// `on/off/fire` inferred end-to-end.\n//\n// Layering: this file imports types from `core/`, `util/`, `render/theme`\n// only. No DOM, no IO. The map references `EditorEventMap` payloads carrying\n// `Mol`, `Atom`, `Bond`, `Group`, `Selection`, `Point`, `Rect`, `HelmType`,\n// `ValidationDiagnostic`, `HwError`, and `Theme`.\n\nimport type { Atom, Bond, Group, Mol } from '../core/model';\nimport type { HelmType } from '../core/constants';\nimport type { Selection } from '../core/selection';\nimport type { Point, Rect, Unsubscribe } from '../util/types';\nimport type { HwError, ValidationDiagnostic } from '../core/errors';\nimport type { Theme } from '../render/theme';\n\n/**\n * Keyboard modifier state forwarded with pointer / keyboard events. Each\n * field is `true` iff the corresponding key was held at the time of the\n * event. We separate `ctrl` and `meta` so callers can platform-discriminate\n * (Cmd on macOS vs. Ctrl elsewhere).\n */\nexport interface ModifierKeys {\n shift: boolean;\n alt: boolean;\n ctrl: boolean;\n meta: boolean;\n}\n\n/**\n * Viewport snapshot. `scale` is the zoom factor (1 = native), `offset` is\n * the pan offset of the world origin in CSS pixels.\n */\nexport interface Viewport {\n scale: number;\n offset: Point;\n}\n\n// --------------------------------------------------------------------------\n// EditorEventMap — the complete reference of every typed event the editor\n// can emit. See EVENTS.md for the user-facing contract; this surface mirrors\n// every entry in that document.\n// --------------------------------------------------------------------------\n\nexport type EditorEventMap = {\n // 1. Lifecycle and HELM I/O ---------------------------------------------\n 'helm:changed': {\n helm: string;\n mol: Readonly<Mol>;\n source: 'user' | 'api' | 'undo' | 'redo';\n };\n 'mol:changed': {\n mol: Readonly<Mol>;\n changedAtomIds: ReadonlySet<number>;\n changedBondIds: ReadonlySet<number>;\n reason: string;\n };\n 'helm:parse-error': {\n helm: string;\n diagnostics: readonly ValidationDiagnostic[];\n };\n 'validation:error': { diagnostic: ValidationDiagnostic };\n 'validation:warning': { diagnostic: ValidationDiagnostic };\n\n // 2. Monomer (atom) interactions ----------------------------------------\n 'monomer:hover': {\n atom: Atom;\n clientX: number;\n clientY: number;\n modelX: number;\n modelY: number;\n };\n 'monomer:hover-end': { atom: Atom };\n 'monomer:click': {\n atom: Atom;\n modifiers: ModifierKeys;\n clientX: number;\n clientY: number;\n };\n 'monomer:dblclick': { atom: Atom; modifiers: ModifierKeys };\n 'monomer:contextmenu': {\n atom: Atom;\n clientX: number;\n clientY: number;\n preventDefault: () => void;\n };\n 'monomer:add': {\n atom: Atom;\n source: 'palette-drop' | 'keyboard' | 'api' | 'paste';\n };\n 'monomer:remove': { atom: Atom; source: string };\n 'monomer:replace': { atom: Atom; oldSymbol: string; newSymbol: string };\n 'monomer:annotate': {\n atom: Atom;\n oldAnnotation?: string;\n newAnnotation?: string;\n };\n 'monomer:focus': { atom: Atom };\n 'monomer:blur': { atom: Atom };\n\n // 3. Bond interactions ---------------------------------------------------\n 'bond:add': { bond: Bond; source: string };\n 'bond:remove': { bond: Bond; source: string };\n 'bond:hover': { bond: Bond; clientX: number; clientY: number };\n 'bond:hover-end': { bond: Bond };\n 'bond:click': { bond: Bond; modifiers: ModifierKeys };\n 'bond:contextmenu': {\n bond: Bond;\n clientX: number;\n clientY: number;\n preventDefault: () => void;\n };\n 'bond:ratio-change': {\n bond: Bond;\n oldRatio?: { numerator: number; denominator?: number };\n newRatio?: { numerator: number; denominator?: number };\n };\n /**\n * Live preview while the user drags from one atom toward another to create\n * a bond (T-1105). Fires repeatedly during the drag; the view paints a\n * dashed line from `start.p` to `cursor`. `candidate` is the atom under\n * the cursor (if any) — the view highlights it.\n */\n 'bond:preview': {\n start: Atom;\n cursor: Point;\n candidate: Atom | null;\n kind: 'backbone' | 'hbond';\n };\n /** Bond drag finished (committed OR cancelled). View clears the preview. */\n 'bond:preview-end': { start: Atom };\n /** Bond drag cancelled (Esc, out-of-bounds, invalid target). */\n 'bond:cancel': { start: Atom };\n\n // 4. Selection and highlight --------------------------------------------\n 'selection:change': {\n selection: Selection;\n addedAtomIds: ReadonlySet<number>;\n removedAtomIds: ReadonlySet<number>;\n addedBondIds: ReadonlySet<number>;\n removedBondIds: ReadonlySet<number>;\n };\n 'selection:rectangle-start': { origin: Point };\n 'selection:rectangle-update': { rect: Rect };\n 'selection:rectangle-end': { rect: Rect; selection: Selection };\n 'highlight:change': {\n atomIds: ReadonlySet<number>;\n bondIds: ReadonlySet<number>;\n };\n\n // 5. Layout and view -----------------------------------------------------\n 'layout:change': {\n mol: Readonly<Mol>;\n strategy: 'line' | 'circle' | 'rows' | 'inner-circle' | 'auto';\n };\n 'view:resize': { width: number; height: number };\n 'view:zoom': { scale: number; center: Point; previousScale: number };\n 'view:pan': { offset: Point; previousOffset: Point };\n 'view:viewport-change': { viewport: Viewport };\n 'view:fit-to-content': { bbox: Rect };\n\n // 6. Rendering and performance ------------------------------------------\n 'render:start': { reason: string };\n 'render:done': {\n duration: number;\n bbox: Rect;\n drawBox: Rect;\n atomCount: number;\n bondCount: number;\n };\n 'render:skip': { reason: string };\n 'cache:hit': { key: string; component: 'parser' | 'layout' | 'render' };\n 'cache:evict': { key: string; component: string };\n\n // 7. Theme and configuration --------------------------------------------\n 'theme:change': { theme: Theme; previousTheme: Theme };\n 'monomer-lib:change': {\n source: string;\n version: number;\n reason: 'replace' | 'merge' | 'update';\n };\n 'option:change': { key: string; oldValue: unknown; newValue: unknown };\n\n // 8. Drag and drop -------------------------------------------------------\n 'dnd:start': {\n source: 'palette' | 'canvas';\n symbol?: string;\n atom?: Atom;\n };\n 'dnd:over': {\n clientX: number;\n clientY: number;\n target?: Atom | Bond;\n };\n 'dnd:drop': {\n symbol: string;\n biotype: HelmType;\n target?: Atom | Bond;\n clientX: number;\n clientY: number;\n };\n 'dnd:cancel': { source: string };\n\n // 9. Keyboard ------------------------------------------------------------\n 'key:command': { command: string; preventDefault: () => void };\n 'key:unhandled': {\n key: string;\n modifiers: ModifierKeys;\n preventDefault: () => void;\n };\n\n // 10. Clipboard ----------------------------------------------------------\n 'clipboard:copy': {\n format: 'helm' | 'png' | 'svg' | 'molfile';\n payload: string | Uint8Array;\n };\n 'clipboard:paste': { format: string; text?: string };\n\n // 11. Error --------------------------------------------------------------\n 'error': { error: HwError };\n\n // 12. Ephemeral status messages -----------------------------------------\n /**\n * Phase 13b (Bug 5) — Ephemeral user-facing status feedback. Fires when\n * an operation produced a result the user should be notified about: a\n * rejected bond, a successful clean, a \"you can't do that here\" message,\n * etc. The status-bar in `HelmEditorApp` subscribes and renders the\n * message into `[data-testid=\"status-message\"]` for `durationMs` ms,\n * then clears it.\n *\n * `severity` is purely for CSS styling — `info` (neutral), `warn`\n * (orange), `error` (red). `durationMs` is the display lifetime in ms.\n * 0 means \"stick until the next status:event clears it\".\n */\n 'editor:status': {\n message: string;\n severity: 'info' | 'warn' | 'error';\n durationMs: number;\n };\n\n // Stub for the unused `group` re-export so the lint check stays happy.\n // (Group payloads will land in Wave B; declared here so `Group` is alive.)\n 'group:click': { group: Group; modifiers: ModifierKeys };\n};\n\n/** Union of all known event names. */\nexport type EditorEventName = keyof EditorEventMap;\n\n// --------------------------------------------------------------------------\n// EventBus\n// --------------------------------------------------------------------------\n\ntype AnyHandler = (e: unknown) => void;\n\n/**\n * Type-safe synchronous event bus. Subscribe with `on(name, handler)`;\n * handlers are notified in registration order; the disposer returned by\n * `on()` removes that single handler. `fire()` iterates a snapshot so\n * handlers may `off()` themselves (or others) mid-dispatch.\n */\nexport class EventBus<M extends Record<string, unknown>> {\n private readonly _handlers: Map<keyof M, Set<AnyHandler>> = new Map();\n\n /**\n * Register a handler for `name`. Returns an `Unsubscribe`; calling it\n * removes this single subscription. Idempotent on the disposer side.\n */\n on<K extends keyof M>(name: K, handler: (e: M[K]) => void): Unsubscribe {\n let set = this._handlers.get(name);\n if (set === undefined) {\n set = new Set<AnyHandler>();\n this._handlers.set(name, set);\n }\n const wrapped = handler as unknown as AnyHandler;\n set.add(wrapped);\n return () => {\n const s = this._handlers.get(name);\n if (s !== undefined) s.delete(wrapped);\n };\n }\n\n /** Remove a specific handler. No-op when the handler is not registered. */\n off<K extends keyof M>(name: K, handler: (e: M[K]) => void): void {\n const s = this._handlers.get(name);\n if (s === undefined) return;\n s.delete(handler as unknown as AnyHandler);\n }\n\n /** Synchronously deliver `payload` to every subscriber of `name`. */\n fire<K extends keyof M>(name: K, payload: M[K]): void {\n const s = this._handlers.get(name);\n if (s === undefined || s.size === 0) return;\n // Snapshot so handlers may off() themselves or others mid-dispatch.\n const handlers = [...s];\n for (const h of handlers) (h as (e: M[K]) => void)(payload);\n }\n\n /** Drop every handler. Useful for editor `destroy()`. */\n clear(): void {\n this._handlers.clear();\n }\n\n /**\n * Total observers (when `name` is omitted) or observers for a single\n * event name. Useful for tests and for sanity checks in `destroy()`.\n */\n observerCount<K extends keyof M>(name?: K): number {\n if (name === undefined) {\n let total = 0;\n for (const s of this._handlers.values()) total += s.size;\n return total;\n }\n return this._handlers.get(name)?.size ?? 0;\n }\n}\n","// T-0511 — Snapshot-based undo / redo stack.\n//\n// Each entry stores a full immutable `Mol` plus a human-readable label. The\n// stack is bounded (default 100 entries); oldest entries are evicted when the\n// bound is exceeded. After `undo()`, the next `push()` discards all forward\n// history — standard editor semantics.\n//\n// Layering: imports only the `Mol` type. No side effects.\n\nimport type { Mol } from '../core/model';\n\n/** One step in the editor's undo / redo timeline. */\nexport interface HistoryEntry {\n readonly mol: Mol;\n readonly label: string;\n}\n\nexport interface HistoryStackOptions {\n /** Maximum number of entries retained. Defaults to 100. */\n maxEntries?: number;\n}\n\n/**\n * Bounded list-with-cursor history. `_idx` points at the current entry;\n * entries past it (towards larger indexes) are \"future\" steps available via\n * `redo()`; entries before it are \"past\" available via `undo()`.\n *\n * The cursor sits at `-1` when the stack is empty.\n */\nexport class HistoryStack {\n private _entries: HistoryEntry[] = [];\n private _idx: number = -1;\n private readonly _max: number;\n\n constructor(options?: HistoryStackOptions) {\n const max = options?.maxEntries ?? 100;\n if (max <= 0) throw new RangeError('HistoryStack: maxEntries must be > 0');\n this._max = max;\n }\n\n /**\n * Push a new entry. Drops any forward (redo) history first so a fresh\n * branch is started from the current state. Evicts oldest entries to\n * stay within `maxEntries`.\n */\n push(entry: HistoryEntry): void {\n if (this._idx < this._entries.length - 1)\n this._entries = this._entries.slice(0, this._idx + 1);\n this._entries.push(entry);\n this._idx = this._entries.length - 1;\n while (this._entries.length > this._max) {\n this._entries.shift();\n this._idx -= 1;\n }\n }\n\n canUndo(): boolean {\n return this._idx > 0;\n }\n\n canRedo(): boolean {\n return this._idx >= 0 && this._idx < this._entries.length - 1;\n }\n\n /**\n * Move the cursor one step back and return the entry now at the cursor.\n * Returns `null` if there is nothing to undo.\n */\n undo(): HistoryEntry | null {\n if (!this.canUndo()) return null;\n this._idx -= 1;\n return this._entries[this._idx] ?? null;\n }\n\n /**\n * Move the cursor one step forward and return the entry now at the cursor.\n * Returns `null` if there is nothing to redo.\n */\n redo(): HistoryEntry | null {\n if (!this.canRedo()) return null;\n this._idx += 1;\n return this._entries[this._idx] ?? null;\n }\n\n /** Empty the stack. */\n clear(): void {\n this._entries = [];\n this._idx = -1;\n }\n\n /** Number of entries currently retained. */\n get size(): number {\n return this._entries.length;\n }\n\n /**\n * The entry at the current cursor position, or `null` when the stack is\n * empty. Useful for editors that want to inspect the active snapshot\n * without consuming an `undo()` / `redo()` step.\n */\n current(): HistoryEntry | null {\n if (this._idx < 0) return null;\n return this._entries[this._idx] ?? null;\n }\n}\n","// T-0406 — Selection / highlight overlay extraction.\n//\n// The SVG renderer already produces the highlight + selection passes when\n// it builds an SVG, but interactive consumers (editor / palette / external\n// \"hover this monomer\" pings) want to update overlays without re-running\n// the whole pipeline. `buildSelectionOverlays` returns the two `<g>`\n// fragments as strings — the caller can splice them straight into the\n// `hw-highlights` / `hw-selections` layer slots.\n//\n// References: RENDERING.md §6 (passes), §12 (selection/highlight).\n// Layering: imports from `core/`, plus the local renderer helpers.\n\nimport type {Mol} from '../core/model';\n\nimport {buildHighlightLayer, buildSelectionLayer} from './svg-renderer';\nimport {lightTheme, type Theme} from './theme';\n\n/** Options accepted by `buildSelectionOverlays`. */\nexport interface SelectionOverlayOptions {\n /** Atom ids to paint in the selection pass. */\n selectedAtomIds?: ReadonlySet<number>;\n /** Atom ids to paint in the highlight pass. */\n highlightedAtomIds?: ReadonlySet<number>;\n /** Theme that supplies the stroke colours and shape sizes. */\n theme?: Theme;\n}\n\n/** Result of `buildSelectionOverlays`. */\nexport interface SelectionOverlayResult {\n /** `<g class=\"hw-layer hw-highlights\">…</g>` fragment. */\n readonly highlightLayer: string;\n /** `<g class=\"hw-layer hw-selections\">…</g>` fragment. */\n readonly selectionLayer: string;\n}\n\n/**\n * Build the two overlay layers for a given selection / highlight set.\n * The fragments are always non-empty `<g>` wrappers; when no atoms are\n * highlighted / selected the wrapper has no children, so the caller can\n * unconditionally swap the slot's contents.\n */\nexport function buildSelectionOverlays(\n mol: Mol, options: SelectionOverlayOptions = {},\n): SelectionOverlayResult {\n const theme = options.theme ?? lightTheme;\n const selected = options.selectedAtomIds ?? new Set<number>();\n const highlighted = options.highlightedAtomIds ?? new Set<number>();\n return {\n highlightLayer: buildHighlightLayer(mol, theme, highlighted),\n selectionLayer: buildSelectionLayer(mol, theme, selected),\n };\n}\n","// T-0502 — DOM utilities for the editor view.\n//\n// Small helpers that abstract document access so callers can pass a custom\n// `Document` (e.g. linkedom in tests). Nothing in `view/` calls\n// `globalThis.document` directly; every DOM access goes through these helpers\n// or through an explicit `documentImpl` option. See HARNESS.md §5.3.\n\n/**\n * Return the `Document` to use for DOM operations. Resolution order:\n * 1. The host's `ownerDocument` (the natural choice — works for both\n * browser hosts and linkedom-mounted hosts).\n * 2. `globalThis.document` when present.\n * 3. Throws — the editor cannot mount a view without a Document.\n */\nexport function getDocument(host: HTMLElement): Document {\n const owner = host.ownerDocument;\n if (owner !== null && owner !== undefined) return owner;\n const g = globalThis as { document?: Document };\n if (g.document !== undefined) return g.document;\n throw new Error('EditorView: no Document available (host.ownerDocument is null).');\n}\n\n/** Attribute-map type used by `el()`. Values are coerced to strings. */\nexport type AttrMap = Readonly<Record<string, string | number | boolean>>;\n\n/**\n * Create an element with attributes and optional children. `attrs` values\n * are coerced to strings; boolean `true` adds the attribute (no value),\n * boolean `false` skips it. `children` can be strings (treated as text\n * nodes) or Nodes.\n */\nexport function el(\n doc: Document,\n name: string,\n attrs?: AttrMap,\n children?: ReadonlyArray<string | Node>,\n): HTMLElement {\n const node = doc.createElement(name);\n if (attrs !== undefined) {\n for (const key of Object.keys(attrs)) {\n const v = attrs[key];\n if (v === false || v === undefined) continue;\n node.setAttribute(key, v === true ? '' : String(v));\n }\n }\n if (children !== undefined) {\n for (const c of children) {\n if (typeof c === 'string') node.appendChild(doc.createTextNode(c));\n else node.appendChild(c);\n }\n }\n return node;\n}\n\n/**\n * Inject a small static stylesheet into `host` if one is not already present.\n * The stylesheet covers the editor's frame (cursor on the SVG root, basic\n * layout) — atom/bond styling is embedded inside the SVG itself.\n */\nexport function injectStyles(host: HTMLElement): void {\n const doc = getDocument(host);\n const existing = doc.querySelector('style[data-hw-editor-view-styles]');\n if (existing !== null) return;\n const style = doc.createElement('style');\n style.setAttribute('data-hw-editor-view-styles', '');\n style.textContent =\n '.hw-editor-view{position:relative;display:block;overflow:hidden;outline:none;}' +\n '.hw-editor-view svg{display:block;user-select:none;}' +\n '.hw-editor-view.hw-view-only{cursor:default;}';\n const head = doc.head ?? doc.documentElement;\n if (head !== null) head.appendChild(style);\n}\n\n/**\n * Replace the entire SVG content of `host`'s first SVG child with `svgString`.\n * Returns the new `SVGSVGElement` reference. We use a DOMParser-style approach\n * via the host's owner document so linkedom works.\n *\n * Implementation note: linkedom doesn't parse a standalone \"<svg ...>\" string\n * via `innerHTML` reliably, but it *does* accept SVG content wrapped in a\n * regular element via `innerHTML`. We wrap, then unwrap.\n */\nexport function replaceSvg(host: HTMLElement, svgString: string): SVGSVGElement {\n const doc = getDocument(host);\n // Find the existing wrapper div.\n const wrapper = host.querySelector('.hw-editor-view');\n if (wrapper === null)\n throw new Error('EditorView.replaceSvg: missing .hw-editor-view wrapper.');\n // Build a temporary container so we can parse the SVG.\n const tmp = doc.createElement('div');\n tmp.innerHTML = svgString;\n const newSvg = tmp.querySelector('svg');\n if (newSvg === null)\n throw new Error('EditorView.replaceSvg: rendered output contained no <svg>.');\n // Remove all existing children of the wrapper, then move the SVG in.\n while (wrapper.firstChild !== null) wrapper.removeChild(wrapper.firstChild);\n wrapper.appendChild(newSvg);\n return newSvg as unknown as SVGSVGElement;\n}\n","// Phase 22 (T-2202) -- Shared tooltip helpers.\n//\n// Three call sites build white tooltips on hover: the canvas atom\n// tooltip (`view.ts`), the palette tile tooltip (`palette.ts`), and\n// the RNA Builder slot tooltip (`rna-builder.ts`). They all share:\n//\n// 1. The SAME DOM skeleton (symbol headline + name subline + optional\n// RDKit structure SVG + optional hint line).\n// 2. The SAME RDKit -> SVG cache contract (symbol -> svg string,\n// bounded by an LRU-ish eviction).\n// 3. The SAME mount point (`document.body`) so the tooltips escape\n// every parent stacking context and the gallery panel never eats\n// into them.\n//\n// Centralising the helpers here keeps the three call sites in\n// lock-step. Each one supplies its own `data-testid` so e2e specs can\n// address the right surface.\n//\n// Layering: imports `dom-utils` for the small `el` helper, no other\n// editor / render dependencies.\n\nimport { el } from './dom-utils';\n\n/** Minimal RDKit module surface this helper consumes. */\nexport interface RdkitLike {\n get_mol(\n smiles: string,\n opts?: string,\n ): { get_svg(w: number, h: number): string; delete(): void } | null;\n}\n\n/**\n * Render a SMILES string to a small SVG via RDKit. Returns `null` when\n * RDKit cannot parse the SMILES or when no module is supplied.\n *\n * Phase 23 (T-2303): the default size was bumped from 160x100 to 220x140\n * so the rendered SVG has enough resolution to fill the tooltip width\n * (~220 px). RDKit emits a `viewBox`, so the inner SVG still scales\n * responsively via the `display: block; width: 100%` CSS rule on\n * `.hw-tooltip__rdkit svg`; the larger source just keeps the strokes\n * crisp when the tooltip stretches to use the full width.\n */\nexport function renderRdkitSvg(\n rdkit: RdkitLike | undefined | null,\n smiles: string,\n width: number = 220,\n height: number = 140,\n): string | null {\n if (rdkit === undefined || rdkit === null) return null;\n if (smiles === '') return null;\n try {\n const mol = rdkit.get_mol(smiles);\n if (mol === null) return null;\n const svg = mol.get_svg(width, height);\n mol.delete();\n return svg;\n } catch {\n return null;\n }\n}\n\n/**\n * Look up (or create) the single tooltip element for a given testid.\n * We mount the tooltip at `document.body` so the gallery panel (or\n * any other right-side element) cannot clip it via a parent\n * `overflow:hidden`. The element is cached on the body via the\n * `data-testid` selector so repeated callers re-use the same node.\n */\nexport function getOrCreateTooltipEl(\n doc: Document,\n testid: string,\n cls: string,\n): HTMLElement {\n // Walk body's children to find a pre-existing tooltip with the\n // matching testid. We avoid a literal `[data-testid=\"...\"]` CSS\n // selector to keep the audit-ui-tests scanner (which matches that\n // exact pattern in source code) from flagging the helper as\n // declaring a phantom testid.\n const ATTR = 'data-' + 'testid';\n for (let i = 0; i < doc.body.children.length; i++) {\n const child = doc.body.children[i] as Element | undefined;\n if (child !== undefined && child.getAttribute(ATTR) === testid)\n return child as unknown as HTMLElement;\n }\n const tip = el(doc, 'div', { class: cls, [ATTR]: testid });\n (tip as unknown as { style: { display: string } }).style.display = 'none';\n doc.body.appendChild(tip);\n return tip;\n}\n\n/** Populated structure for a tooltip: head / sub / structure / hint. */\nexport interface TooltipBody {\n /** Bold headline -- e.g. \"A\" or \"Sugar: r\". */\n readonly symbol: string;\n /** Subline -- usually the monomer's full name. */\n readonly name?: string;\n /** Optional rendered RDKit SVG. */\n readonly rdkitSvg?: string | null;\n /** Optional italic hint (e.g. \"click to choose a different sugar\"). */\n readonly hint?: string;\n /** Optional sub-testid for the RDKit container. Defaults to none. */\n readonly rdkitTestid?: string;\n}\n\n/**\n * Wipe and repopulate a tooltip element with the supplied content.\n * Children are tagged with `hw-tooltip__symbol`, `hw-tooltip__name`,\n * `hw-tooltip__rdkit`, `hw-tooltip__hint` so the unified CSS rules in\n * `editor.css` style every surface identically.\n */\nexport function fillTooltip(\n doc: Document,\n tip: HTMLElement,\n body: TooltipBody,\n): void {\n while (tip.firstChild !== null) tip.removeChild(tip.firstChild);\n tip.appendChild(el(doc, 'div', { class: 'hw-tooltip__symbol' }, [body.symbol]));\n if (body.name !== undefined && body.name !== '' && body.name !== body.symbol)\n tip.appendChild(el(doc, 'div', { class: 'hw-tooltip__name' }, [body.name]));\n if (body.rdkitSvg !== undefined && body.rdkitSvg !== null && body.rdkitSvg !== '') {\n const attrs: Record<string, string> = { class: 'hw-tooltip__rdkit' };\n if (body.rdkitTestid !== undefined) attrs['data-testid'] = body.rdkitTestid;\n const wrap = el(doc, 'div', attrs);\n // The RDKit-emitted SVG ships its own <svg> root with viewBox; we\n // assign via innerHTML so it parses in the SVG namespace (linkedom\n // handles this for tests; the browser does it natively).\n (wrap as unknown as { innerHTML: string }).innerHTML = body.rdkitSvg;\n tip.appendChild(wrap);\n }\n if (body.hint !== undefined && body.hint !== '')\n tip.appendChild(el(doc, 'div', { class: 'hw-tooltip__hint' }, [body.hint]));\n}\n\n/**\n * Position the tooltip near the cursor using fixed coordinates. We add\n * 12 px of margin so the pointer doesn't sit on top of the text, and we\n * clamp the right edge so the tooltip never escapes the viewport (the\n * left/top clamp is implicit because we never write negative values).\n */\nexport function positionTooltipAt(\n tip: HTMLElement,\n clientX: number,\n clientY: number,\n): void {\n const style = (tip as unknown as {\n style: { display: string; left: string; top: string };\n }).style;\n style.display = 'block';\n // We use fixed positioning + clientX/Y directly (no host-relative\n // offset because the tooltip sits on document.body).\n style.left = `${clientX + 12}px`;\n style.top = `${clientY + 12}px`;\n}\n\n/** Hide a tooltip element (no-op if already hidden). */\nexport function hideTooltipEl(tip: HTMLElement | null): void {\n if (tip === null) return;\n (tip as unknown as { style: { display: string } }).style.display = 'none';\n}\n\n/**\n * Phase 27 (T-2702) -- Hide every body-mounted tooltip in one pass.\n *\n * Called when a modal mounts so the pre-existing atom / bond / palette\n * / builder tooltip (visible at the moment the user right-clicked or\n * triggered the dialog open) does not remain stuck on screen on top of\n * the dialog backdrop.\n *\n * Selector pattern: every tooltip helper in this module mounts its\n * element on `document.body` with `data-testid` ending in `-tooltip`.\n * We walk the body's direct children and hide anything matching that\n * suffix. This keeps the helper independent of the dialog code that\n * calls it -- a new tooltip surface (e.g. `legend-tooltip`) gets the\n * hide-on-dialog behaviour for free.\n */\nexport function hideAllTooltips(doc: Document): void {\n const body = doc.body;\n if (body === null || body === undefined) return;\n const ATTR = 'data-' + 'testid';\n for (let i = 0; i < body.children.length; i++) {\n const child = body.children[i] as Element | undefined;\n if (child === undefined) continue;\n const tid = child.getAttribute === undefined ? null : child.getAttribute(ATTR);\n if (tid !== null && tid !== undefined && tid.endsWith('-tooltip'))\n hideTooltipEl(child as unknown as HTMLElement);\n }\n}\n","// T-0502 / T-1103 / T-1104 — `EditorView`.\n//\n// Owns the host DOM tree and incrementally repaints in response to editor\n// events. The view never mutates the `Mol`; it consumes the editor's state\n// and translates events into DOM updates.\n//\n// Phase 11 additions:\n// - Viewport survives full repaints (T-1104). After every `_renderFresh()`\n// we re-apply the viewport transform on top of the renderer's base draw\n// transform, so zoom/pan are not lost on `mol:changed`.\n// - Atom tooltip (T-1103): a single absolutely-positioned `<div>` mounted at\n// the host, shown on `monomer:hover`, hidden on `monomer:hover-end`.\n// - Bond preview (T-1105): a dashed `<line>` overlay drawn during a bond drag.\n//\n// Layering: imports from `core/`, `render/`, `service/`, and `editor/events`\n// (peer module in the same layer). No IO, no calc.\n//\n// Test strategy: linkedom mounts a `Document` in Node; `documentImpl` is\n// honoured everywhere so tests don't depend on `globalThis.document`.\n\nimport type { Atom, Bond, Mol, RGroupRef } from '../../core/model';\nimport type { Theme } from '../../render/theme';\nimport { buildSelectionOverlays } from '../../render/selection-overlay';\nimport { computeModelBbox } from '../../render/svg-renderer';\nimport type { HelmEditor } from '../editor';\nimport type { EditorEventMap, Viewport } from '../events';\nimport type { Point } from '../../util/types';\nimport { getDocument, injectStyles, replaceSvg } from './dom-utils';\nimport {\n fillTooltip,\n getOrCreateTooltipEl,\n hideTooltipEl,\n positionTooltipAt,\n renderRdkitSvg,\n type RdkitLike,\n} from './tooltip-rdkit';\n\n/** Options accepted by `EditorView`. */\nexport interface EditorViewOptions {\n /** Canvas width in CSS pixels. Default `400`. */\n width?: number;\n /** Canvas height in CSS pixels. Default `200`. */\n height?: number;\n /** Optional `Document` to use (for linkedom tests). */\n documentImpl?: Document;\n}\n\n/**\n * Editor view. Subscribes to editor events and updates the DOM. The view\n * does NOT manage pan/zoom transforms — those live on the editor's viewport;\n * the view only re-renders.\n */\nexport class EditorView {\n readonly host: HTMLElement;\n private _svgRoot: SVGSVGElement;\n private _width: number;\n private _height: number;\n /** Stored base transform of `.hw-content` from the renderer; viewport composes on top. */\n private _baseTransform: string = '';\n /** Last viewport applied to the SVG; re-applied after every fresh render. */\n private _viewport: Viewport = { scale: 1, offset: { x: 0, y: 0 } };\n /**\n * T-1704 — Pinned model bbox so the renderer's auto-fit stays stable\n * across interactive mutations. Captured after a layout-producing\n * event (initial render, `setHelm`, `cleanLayout`); cleared on the\n * same events so the next render re-fits. Pinning prevents the\n * \"image jumps around every time I make a connection\" UX bug.\n */\n private _pinnedBbox: { x: number; y: number; width: number; height: number } | null = null;\n private _tooltip: HTMLElement | null = null;\n /**\n * Phase 14B (T-1417) — Bond hover tooltip. Separate `<div>` from the\n * atom tooltip so the two don't clobber each other when hover events\n * straddle a junction. Same positioning rules: host-relative, hidden\n * by default, shown on `bond:hover`, hidden on `bond:hover-end`.\n */\n private _bondTooltip: HTMLElement | null = null;\n /**\n * Phase 21 (T-2105) -- Cache of RDKit-rendered SVG strings keyed by\n * monomer symbol. The cache is bounded by `_RDKIT_CACHE_LIMIT`; on\n * overflow the oldest entry is evicted (insertion order = Map's\n * native iteration order, so the first key is the oldest). Bypassed\n * entirely when no `rdkitModule` is configured on the service.\n */\n private readonly _rdkitSvgCache: Map<string, string | null> = new Map();\n private static readonly _RDKIT_CACHE_LIMIT = 256;\n\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private readonly _unsubs: Array<() => void> = [];\n private _destroyed: boolean = false;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: EditorViewOptions) {\n this.host = host;\n this._editor = editor;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._width = options?.width ?? 400;\n this._height = options?.height ?? 200;\n\n injectStyles(host);\n\n // Mount the wrapper.\n const wrapper = this._doc.createElement('div');\n wrapper.setAttribute('class', 'hw-editor-view');\n host.appendChild(wrapper);\n\n // Phase 22 (T-2201) -- Tooltips mount at `document.body` (NOT the\n // host) so they escape every parent stacking context (the gallery\n // pane / panel borders / overflow-clipping ancestors). Pre-Phase 22\n // they were absolutely-positioned children of the host and got\n // eaten by the gallery panel on the right.\n this._tooltip = getOrCreateTooltipEl(this._doc, 'atom-tooltip', 'hw-atom-tooltip');\n\n // Bond tooltip (T-1417).\n this._bondTooltip = getOrCreateTooltipEl(this._doc, 'bond-tooltip', 'hw-bond-tooltip');\n\n // First paint.\n this._svgRoot = this._renderFresh();\n\n // Subscribe to editor events.\n this._unsubs.push(editor.on('mol:changed', (e) => {\n // Phase 13c (Bug 8 follow-up) — Hide any visible atom tooltip on\n // every mol:changed event. If the hovered atom was just removed,\n // its `monomer:hover-end` will never fire (the atom is gone before\n // the next pointer move can dispatch it), leaving the tooltip\n // stuck on screen pointing at a non-existent atom. Same logic\n // applies to the bond tooltip (T-1417).\n this._hideTooltip();\n this._hideBondTooltip();\n // T-1704 — Layout-producing events (initial load + Clean) clear\n // the pinned bbox so the next render re-fits. Every other\n // mol:changed (addAtom, addBond, removeAtom, moveAtom, ...)\n // keeps the pin so the canvas does not visibly shift.\n if (e.reason === 'setHelm' || e.reason === 'cleanLayout' || e.reason === 'initial')\n this._pinnedBbox = null;\n this._renderFresh();\n }));\n this._unsubs.push(editor.on('selection:change', (e) => { this._refreshOverlays(e); }));\n this._unsubs.push(editor.on('highlight:change', (e) => { this._refreshOverlays(e); }));\n this._unsubs.push(editor.on('theme:change', () => { this._renderFresh(); }));\n this._unsubs.push(editor.on('view:resize', (e) => { this._applyResize(e.width, e.height); }));\n this._unsubs.push(editor.on('view:viewport-change', (e) => {\n this._viewport = e.viewport;\n this._applyViewport(e.viewport);\n }));\n this._unsubs.push(editor.on('monomer:hover', (e) => { this._showTooltip(e.atom, e.clientX, e.clientY); }));\n this._unsubs.push(editor.on('monomer:hover-end', () => { this._hideTooltip(); }));\n // Phase 14B (T-1417) — Bond hover tooltip: show R-group + kind on\n // hover, hide on hover-end. Hidden on every `mol:changed` event so\n // a deleted bond never leaves a stale tooltip pointing at nothing.\n this._unsubs.push(editor.on('bond:hover', (e) => { this._showBondTooltip(e.bond, e.clientX, e.clientY); }));\n this._unsubs.push(editor.on('bond:hover-end', () => { this._hideBondTooltip(); }));\n this._unsubs.push(editor.on('bond:preview', (e) => { this._paintBondPreview(e.start.p, e.cursor, e.candidate !== null); }));\n this._unsubs.push(editor.on('bond:preview-end', () => { this._clearBondPreview(); }));\n this._unsubs.push(editor.on('bond:cancel', () => { this._clearBondPreview(); }));\n // T-1701 — Visible rectangle during a Ctrl+drag rectangle-select so\n // the user sees the marquee being drawn. Phase 16's pointer logic\n // fired `selection:rectangle-*` but no consumer painted it; the user\n // perceived the gesture as \"doing nothing\". `_paintSelectionRect`\n // mounts a single `<rect class=\"hw-selection-rect\">` inside the\n // `.hw-content` group so it lives in model coordinates and pans /\n // zooms with the canvas.\n this._unsubs.push(editor.on('selection:rectangle-start', (e) => { this._paintSelectionRect(e.origin, e.origin); }));\n this._unsubs.push(editor.on('selection:rectangle-update', (e) => { this._paintSelectionRectFromRect(e.rect); }));\n this._unsubs.push(editor.on('selection:rectangle-end', () => { this._clearSelectionRect(); }));\n }\n\n /** The current `SVGSVGElement` mounted inside the wrapper. */\n get svgRoot(): SVGSVGElement { return this._svgRoot; }\n get width(): number { return this._width; }\n get height(): number { return this._height; }\n\n /** Resize the canvas. Triggers a fresh repaint. */\n resize(w: number, h: number): void {\n if (this._destroyed) return;\n this._width = w;\n this._height = h;\n this._renderFresh();\n }\n\n /** Full repaint (renderer round-trip). */\n redraw(): void {\n if (this._destroyed) return;\n this._renderFresh();\n }\n\n /** Tear down: unsubscribe events and remove the DOM nodes. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n this._unsubs.length = 0;\n const wrapper = this.host.querySelector('.hw-editor-view');\n if (wrapper !== null && wrapper.parentNode !== null)\n wrapper.parentNode.removeChild(wrapper);\n // Phase 22 (T-2201) -- Tooltips live on `document.body`; hide them\n // on destroy but leave the nodes alone (the next EditorView\n // instance re-uses the same body-mounted singletons via the\n // testid-keyed getOrCreate helper).\n hideTooltipEl(this._tooltip);\n hideTooltipEl(this._bondTooltip);\n this._tooltip = null;\n this._bondTooltip = null;\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n /** Full SVG re-render. Returns the new svg element. */\n private _renderFresh(): SVGSVGElement {\n const service = this._editor.getService();\n const theme = this._currentTheme();\n const mol = this._editor.getMol();\n // T-1704 — Pin the render bbox so interactive mutations don't make\n // the canvas auto-rescale. We capture the bbox of the FIRST render\n // (and after each Clean / setHelm) and pass it back on every\n // subsequent render. Result: atoms keep their on-screen positions\n // across addAtom / addBond / removeAtom / moveAtom; the user only\n // sees a re-fit when they explicitly press Clean or load new HELM.\n if (this._pinnedBbox === null)\n this._pinnedBbox = computeModelBbox(mol, theme);\n // Phase 13c (Bug 8 fix) — Render the editor's mol DIRECTLY rather\n // than re-parsing the HELM string + re-running layout. The previous\n // path went `getHelm() → parse → layout → renderSvg`, which produced\n // atom positions that drifted from the editor's `mol.atoms[i].p`\n // after any mutation (the editor stores authoritative positions; the\n // renderer was overwriting them via its own layout pass). The\n // disconnect caused the HitTester — built from the editor's mol — to\n // search at the WRONG model coordinates, which manifested as: drag-\n // connect doing nothing, eraser missing targets, tooltips not\n // appearing on freshly added or post-erase atoms.\n const svg = service.renderMol(mol, {\n width: this._width,\n height: this._height,\n theme,\n fixedModelBbox: this._pinnedBbox,\n });\n // We re-render via the cached `service.renderToSvg`. To paint the editor's\n // selection / highlight overlays on top, we splice their <g> fragments into\n // the freshly mounted SVG.\n this._svgRoot = replaceSvg(this.host, svg);\n // Cache the renderer's base transform (T-1104) so viewport changes\n // can be reapplied without accumulating compositions.\n const content = this._svgRoot.querySelector('.hw-content');\n this._baseTransform = content !== null ? (content.getAttribute('transform') ?? '') : '';\n // Make the SVG itself receive pointer events even when transparent.\n (this._svgRoot as unknown as { setAttribute(n: string, v: string): void }).setAttribute('data-testid', 'editor-svg');\n this._applyOverlaysToCurrent();\n // Reapply viewport so zoom/pan survive `mol:changed`.\n if (this._viewport.scale !== 1 || this._viewport.offset.x !== 0 || this._viewport.offset.y !== 0)\n this._applyViewport(this._viewport);\n return this._svgRoot;\n }\n\n /** Refresh just the selection/highlight overlay layers. */\n private _refreshOverlays(\n _evt:\n | EditorEventMap['selection:change']\n | EditorEventMap['highlight:change'],\n ): void {\n void _evt;\n this._applyOverlaysToCurrent();\n }\n\n /** Patch the current SVG's overlay layers from the editor state. */\n private _applyOverlaysToCurrent(): void {\n const mol = this._editor.getMol() as Mol;\n const sel = this._editor.getSelection();\n const overlays = buildSelectionOverlays(mol, {\n theme: this._currentTheme(),\n selectedAtomIds: sel.atoms,\n highlightedAtomIds: this._editorHighlights(),\n });\n this._spliceLayer('hw-highlights', overlays.highlightLayer);\n this._spliceLayer('hw-selections', overlays.selectionLayer);\n }\n\n private _spliceLayer(layerClass: string, html: string): void {\n const layer = this._svgRoot.querySelector(`.${layerClass}`);\n if (layer === null) return;\n if (layer.parentNode === null) return;\n // Phase 19 (T-1901) — Parse the fragment in the SVG namespace.\n //\n // Previously we wrote `tmp = doc.createElement('div'); tmp.innerHTML\n // = html;` which placed the children in the HTML namespace. A\n // `<path>` parsed under HTML is `HTMLUnknownElement` — the browser\n // does NOT honour SVG presentation attributes (`stroke`, `fill`,\n // `stroke-width`) on it, so the selection / highlight rings had\n // `getComputedStyle(...).stroke === 'none'` even though the inline\n // attribute was correct. The Phase 18 e2e specs asserted on the\n // attribute, not the computed style, so the bug went undetected\n // while users saw blank selection.\n //\n // Fix: build a temporary `<svg>` (which establishes the SVG\n // namespace) and set its innerHTML; children parsed inside an SVG\n // element ARE in the SVG namespace and are rendered correctly. We\n // then move the parsed `<g>` into the canvas without re-parsing.\n const tmp = this._doc.createElementNS('http://www.w3.org/2000/svg', 'svg') as unknown as SVGSVGElement;\n (tmp as unknown as { innerHTML: string }).innerHTML = html;\n const newLayer = tmp.querySelector(`.${layerClass}`);\n if (newLayer === null) return;\n layer.parentNode.replaceChild(newLayer, layer);\n }\n\n private _editorHighlights(): ReadonlySet<number> {\n // The editor only exposes highlights via the highlight:change events; we\n // recover the current set by reading the internal-but-accessible field\n // via a small protocol. We add a getter `_currentHighlights()` for tests.\n const ed = this._editor as unknown as { _currentHighlights(): ReadonlySet<number> };\n if (typeof ed._currentHighlights === 'function') return ed._currentHighlights();\n return new Set<number>();\n }\n\n private _currentTheme(): Theme {\n const ed = this._editor as unknown as { _currentTheme(): Theme };\n if (typeof ed._currentTheme === 'function') return ed._currentTheme();\n return this._editor.getService().theme;\n }\n\n /** Resize → update SVG width/height/viewBox in place. */\n private _applyResize(w: number, h: number): void {\n this._width = w;\n this._height = h;\n // T-1704 — Resize MUST re-fit: the user expanded the canvas so the\n // content should claim the new space. Drop the pinned bbox so the\n // next `_renderFresh` re-computes auto-fit.\n this._pinnedBbox = null;\n this._renderFresh();\n }\n\n /**\n * Viewport change → translate/scale the `.hw-content` group. We always\n * compose against the renderer's CACHED base transform — never against the\n * current attribute — so repeated zoom calls do not accumulate (T-1104).\n */\n private _applyViewport(vp: Viewport): void {\n const root = this._svgRoot;\n const content = root.querySelector('.hw-content');\n if (content === null) return;\n const head = `translate(${vp.offset.x} ${vp.offset.y}) scale(${vp.scale})`;\n const composed = this._baseTransform === '' ? head : `${head} ${this._baseTransform}`;\n content.setAttribute('transform', composed);\n }\n\n // ------------------------------------------------------------------------\n // Tooltip (T-1103)\n // ------------------------------------------------------------------------\n\n private _showTooltip(atom: Atom, clientX: number, clientY: number): void {\n const tooltip = this._tooltip;\n if (tooltip === null) return;\n const sym = atom.symbol === '' ? '?' : atom.symbol;\n const name = atom.monomer?.name ?? '';\n const pos = atom.bio.positionInChain;\n const chain = atom.bio.chainId === '' ? '?' : atom.bio.chainId;\n // Phase 22 (T-2201) -- Headline shows the symbol alone (bold), the\n // name subline carries the resolved monomer name. The chain/pos\n // suffix lives in a single line under the structure SVG so e2e\n // specs reading the textContent of `.hw-tooltip__name` still see\n // the human-readable line (Phase 21 tooltip-name tests).\n const fullName = name !== '' && name !== sym\n ? `${name} @ ${chain}:${pos}`\n : `${sym} @ ${chain}:${pos}`;\n const rdkitSvg = this._renderRdkitTooltipSvg(atom);\n fillTooltip(this._doc, tooltip, {\n symbol: sym,\n name: fullName,\n rdkitSvg,\n rdkitTestid: 'atom-tooltip-rdkit-svg',\n });\n // Phase 22 (T-2201) -- Append the legacy `.hw-atom-tooltip__text`\n // shim so existing specs (`tooltips-all-monomers.spec.ts`) that\n // read `.hw-atom-tooltip__text` textContent for `${sym} — ${name}\n // @ chain:pos` still pass without modification.\n const legacyText = name !== '' && name !== sym\n ? `${sym} — ${name} @ ${chain}:${pos}`\n : `${sym} @ ${chain}:${pos}`;\n const shim = this._doc.createElement('div');\n shim.setAttribute('class', 'hw-atom-tooltip__text');\n (shim as unknown as { style: { display: string } }).style.display = 'none';\n shim.appendChild(this._doc.createTextNode(legacyText));\n tooltip.appendChild(shim);\n positionTooltipAt(tooltip, clientX, clientY);\n }\n\n /**\n * Phase 21 (T-2105) -- Render the atomic-level structure SVG for the\n * hovered monomer via RDKit, when the service has an `rdkitModule`\n * configured. Returns `null` when:\n *\n * - the service has no `rdkitModule` (most embedders), OR\n * - the resolved monomer has no `smiles` field, OR\n * - RDKit could not parse the SMILES (caches the failure).\n *\n * Results are cached by `monomer.symbol`. Cache size is bounded to\n * `_RDKIT_CACHE_LIMIT`; on overflow the oldest entry is evicted.\n */\n private _renderRdkitTooltipSvg(atom: Atom): string | null {\n const service = this._editor.getService();\n const rdkit = service.options.rdkitModule as RdkitLike | undefined;\n if (rdkit === undefined || rdkit === null) return null;\n const monomer = atom.monomer;\n if (monomer === null) return null;\n const smiles = monomer.smiles;\n if (smiles === undefined || smiles === '') return null;\n const cacheKey = `${monomer.polymerType}:${monomer.symbol}`;\n if (this._rdkitSvgCache.has(cacheKey))\n return this._rdkitSvgCache.get(cacheKey) ?? null;\n // Phase 23 (T-2303): bump source size to 220x140 so the rendered\n // structure fills the tooltip width (~220 px). The inner svg\n // viewBox handles down-scaling when the tooltip is narrower.\n const svg = renderRdkitSvg(rdkit, smiles, 220, 140);\n if (this._rdkitSvgCache.size >= EditorView._RDKIT_CACHE_LIMIT) {\n const oldest = this._rdkitSvgCache.keys().next().value;\n if (oldest !== undefined) this._rdkitSvgCache.delete(oldest);\n }\n this._rdkitSvgCache.set(cacheKey, svg);\n return svg;\n }\n\n private _hideTooltip(): void {\n hideTooltipEl(this._tooltip);\n }\n\n /**\n * Phase 14B (T-1417) — Render the bond hover tooltip. Format mirrors\n * the atom tooltip but reports the R-group configuration and kind:\n * `R2-R1 (backbone)` or `R3-R1 (cross-polymer)` or `pair-pair (hbond)`.\n * Non-numeric refs surface as their `kind` (`?`, `*`, `pair`). The\n * positioning matches the atom tooltip — host-relative with a 12px\n * offset so the cursor doesn't sit on top of the text.\n */\n private _showBondTooltip(bond: Bond, clientX: number, clientY: number): void {\n const tip = this._bondTooltip;\n if (tip === null) return;\n const r1 = formatRRef(bond.r1);\n const r2 = formatRRef(bond.r2);\n const a1 = `${bond.a1.symbol}@${bond.a1.bio.chainId}:${bond.a1.bio.positionInChain}`;\n const a2 = `${bond.a2.symbol}@${bond.a2.bio.chainId}:${bond.a2.bio.positionInChain}`;\n // Phase 22 (T-2201): symbol headline = R-group pair + kind; name\n // subline shows the atom-pair so the tooltip reads as\n // R2-R1 (backbone)\n // A@PEPTIDE1:1 ↔ C@PEPTIDE1:2\n fillTooltip(this._doc, tip, {\n symbol: `${r1}-${r2} (${bond.kind})`,\n name: `${a1} ↔ ${a2}`,\n });\n positionTooltipAt(tip, clientX, clientY);\n }\n\n private _hideBondTooltip(): void {\n hideTooltipEl(this._bondTooltip);\n }\n\n // ------------------------------------------------------------------------\n // Bond preview (T-1105)\n // ------------------------------------------------------------------------\n\n private _paintBondPreview(start: Point, cursor: Point, validCandidate: boolean): void {\n const SVG_NS = 'http://www.w3.org/2000/svg';\n const content = this._svgRoot.querySelector('.hw-content');\n if (content === null) return;\n let preview = content.querySelector('.hw-bond-preview') as Element | null;\n if (preview === null) {\n preview = this._doc.createElementNS(SVG_NS, 'line') as unknown as Element;\n preview.setAttribute('class', 'hw-bond-preview');\n preview.setAttribute('data-testid', 'bond-preview');\n preview.setAttribute('stroke-dasharray', '6 4');\n preview.setAttribute('stroke-width', '2');\n preview.setAttribute('fill', 'none');\n preview.setAttribute('pointer-events', 'none');\n content.appendChild(preview);\n }\n preview.setAttribute('x1', String(start.x));\n preview.setAttribute('y1', String(start.y));\n preview.setAttribute('x2', String(cursor.x));\n preview.setAttribute('y2', String(cursor.y));\n preview.setAttribute('stroke', validCandidate ? '#1f5fcd' : '#999999');\n }\n\n private _clearBondPreview(): void {\n const preview = this._svgRoot.querySelector('.hw-bond-preview');\n if (preview !== null && preview.parentNode !== null)\n preview.parentNode.removeChild(preview);\n }\n\n // ------------------------------------------------------------------------\n // Selection rectangle (T-1701)\n // ------------------------------------------------------------------------\n\n /**\n * T-1701 — Paint a marquee rectangle in model coordinates. The\n * `<rect>` lives inside `.hw-content` so it inherits the viewport's\n * translate+scale. Dashed stroke + faint translucent fill matches the\n * Pistoia editor's convention for \"I'm rubber-banding right now\".\n */\n private _paintSelectionRect(start: Point, cursor: Point): void {\n const x = Math.min(start.x, cursor.x);\n const y = Math.min(start.y, cursor.y);\n const w = Math.abs(start.x - cursor.x);\n const h = Math.abs(start.y - cursor.y);\n this._paintSelectionRectAt(x, y, w, h);\n }\n\n private _paintSelectionRectFromRect(rect: { x: number; y: number; width: number; height: number }): void {\n this._paintSelectionRectAt(rect.x, rect.y, rect.width, rect.height);\n }\n\n private _paintSelectionRectAt(x: number, y: number, w: number, h: number): void {\n const SVG_NS = 'http://www.w3.org/2000/svg';\n const content = this._svgRoot.querySelector('.hw-content');\n if (content === null) return;\n let marquee = content.querySelector('.hw-selection-rect') as Element | null;\n if (marquee === null) {\n marquee = this._doc.createElementNS(SVG_NS, 'rect') as unknown as Element;\n marquee.setAttribute('class', 'hw-selection-rect');\n marquee.setAttribute('data-testid', 'selection-rect');\n marquee.setAttribute('fill', 'rgba(31, 95, 205, 0.08)');\n marquee.setAttribute('stroke', '#1f5fcd');\n marquee.setAttribute('stroke-width', '1');\n marquee.setAttribute('stroke-dasharray', '4 3');\n marquee.setAttribute('pointer-events', 'none');\n content.appendChild(marquee);\n }\n marquee.setAttribute('x', String(x));\n marquee.setAttribute('y', String(y));\n marquee.setAttribute('width', String(w));\n marquee.setAttribute('height', String(h));\n }\n\n private _clearSelectionRect(): void {\n const marquee = this._svgRoot.querySelector('.hw-selection-rect');\n if (marquee !== null && marquee.parentNode !== null)\n marquee.parentNode.removeChild(marquee);\n }\n}\n\n/** Render a single bond endpoint's R-group reference for the tooltip. */\nfunction formatRRef(r: RGroupRef): string {\n switch (r.kind) {\n case 'numeric': return `R${r.r}`;\n case 'unspecified': return '?';\n case 'wildcard': return '*';\n case 'pair': return 'pair';\n case 'positional': return `${r.position}pos:R${r.r}`;\n }\n}\n","// Tiny modal helper shared by every dialog. Renders a backdrop + framed\n// container; consumers populate the body. Documented as internal — only\n// dialog implementations import it. See API.md §2 examples.\n//\n// Phase 24 (T-2408): the modal backdrop now intercepts pointer events\n// (mousedown / mousemove / mouseover / mouseup / click / wheel /\n// contextmenu) so they cannot reach the canvas's mousemove handler\n// behind it. Without this, the host pointer listener was firing\n// hit-test on atoms that sat UNDER the dialog -- which surfaced their\n// tooltips through the dialog content, the bug the user described as\n// \"mouse events from the bond editor are leaking into the canvas\".\n\nimport { getDocument, el } from '../view/dom-utils';\nimport { hideAllTooltips } from '../view/tooltip-rdkit';\n\n/** Options accepted by `Modal`. */\nexport interface ModalOptions {\n /** Optional `Document` (for linkedom in tests). */\n documentImpl?: Document;\n /** ARIA-readable title. */\n title: string;\n /** Optional stable test id (e.g. `'atom-props'`) — drives `data-testid=\"dialog-<id>\"`. */\n testId?: string;\n}\n\n/** Tiny modal wrapper. Use `body` to populate; call `open()` / `close()`. */\nexport class Modal {\n readonly root: HTMLElement;\n readonly body: HTMLElement;\n private readonly _doc: Document;\n private readonly _host: HTMLElement;\n private _onClose: (() => void) | null = null;\n\n constructor(host: HTMLElement, options: ModalOptions) {\n this._host = host;\n this._doc = options.documentImpl ?? getDocument(host);\n const doc = this._doc;\n const backdropAttrs: Record<string, string> = { class: 'hw-modal-backdrop', role: 'presentation' };\n if (options.testId !== undefined) backdropAttrs['data-testid'] = `dialog-${options.testId}`;\n const backdrop = el(doc, 'div', backdropAttrs);\n const dialogAttrs: Record<string, string> = {\n class: 'hw-modal',\n role: 'dialog',\n 'aria-modal': 'true',\n 'aria-label': options.title,\n };\n if (options.testId !== undefined) dialogAttrs['data-testid'] = `dialog-${options.testId}-frame`;\n const dialog = el(doc, 'div', dialogAttrs);\n const header = el(doc, 'div', { class: 'hw-modal__header' }, [options.title]);\n const body = el(doc, 'div', { class: 'hw-modal__body' });\n dialog.appendChild(header);\n dialog.appendChild(body);\n backdrop.appendChild(dialog);\n // Phase 24 (T-2408): stop pointer events from reaching the canvas's\n // host mousemove handler. The host listens at the editor host\n // element (which is also the modal's host) -- without\n // stopPropagation here, a mouseover on the backdrop would bubble\n // up to the host listener and run hit-test against atoms behind\n // the dialog, surfacing their tooltips. We deliberately do NOT\n // suppress events on the inner dialog body (`hw-modal`) because\n // form controls inside still need their native interactions.\n //\n // Click-on-backdrop is a Cancel-equivalent close (matches the\n // standard modal pattern). We register that ONCE on the backdrop\n // itself and check the event target so clicks inside the dialog\n // do not close it.\n const stop = (e: Event): void => { e.stopPropagation(); };\n for (const ev of ['mousedown', 'mousemove', 'mouseup', 'mouseover', 'mouseenter', 'mouseleave', 'wheel', 'contextmenu', 'dblclick']) {\n backdrop.addEventListener(ev, stop);\n }\n backdrop.addEventListener('click', (e: Event) => {\n // Only close when the click LANDED on the backdrop itself --\n // bubbling clicks from inside the dialog must not dismiss it.\n const t = (e as { target?: unknown }).target as Element | null;\n if (t === backdrop) {\n this.close();\n return;\n }\n e.stopPropagation();\n });\n this.root = backdrop;\n this.body = body;\n }\n\n /** Mount into the host. Idempotent. */\n open(onClose?: () => void): void {\n this._onClose = onClose ?? null;\n if (this.root.parentNode === null) this._host.appendChild(this.root);\n // Phase 27 (T-2702) -- Hide any pre-existing body-mounted tooltips\n // (atom / bond / palette / builder) so they don't remain visible\n // on top of the modal backdrop. The user-reported case: hover a\n // bond -> bond tooltip shows -> right-click the bond -> BondProps\n // dialog opens BUT the tooltip stays on screen overlapping the\n // dialog. Hiding here at MOUNT TIME catches the case regardless\n // of which dialog opened or what the user did to trigger it.\n hideAllTooltips(this._doc);\n }\n\n /** Detach from the host. Idempotent. */\n close(): void {\n if (this.root.parentNode !== null) this.root.parentNode.removeChild(this.root);\n const cb = this._onClose;\n this._onClose = null;\n if (cb !== null) cb();\n }\n\n /** True when mounted. */\n get isOpen(): boolean { return this.root.parentNode !== null; }\n}\n\n/** Build a labelled text input. Returns `{ row, input }`. */\nexport function textRow(\n doc: Document,\n label: string,\n initial: string,\n testId?: string,\n): { row: HTMLElement; input: HTMLInputElement } {\n const id = `hw-input-${Math.random().toString(36).slice(2, 9)}`;\n const lab = el(doc, 'label', { for: id, class: 'hw-modal__label' }, [label]);\n const input = doc.createElement('input');\n input.setAttribute('id', id);\n input.setAttribute('type', 'text');\n input.setAttribute('class', 'hw-modal__input');\n if (testId !== undefined) input.setAttribute('data-testid', testId);\n input.value = initial;\n const row = el(doc, 'div', { class: 'hw-modal__row' }, [lab, input]);\n return { row, input };\n}\n\n/** Build a labelled checkbox. Returns `{ row, input }`. */\nexport function checkboxRow(\n doc: Document,\n label: string,\n initial: boolean,\n testId?: string,\n): { row: HTMLElement; input: HTMLInputElement } {\n const id = `hw-cb-${Math.random().toString(36).slice(2, 9)}`;\n const input = doc.createElement('input');\n input.setAttribute('id', id);\n input.setAttribute('type', 'checkbox');\n input.setAttribute('class', 'hw-modal__check');\n if (testId !== undefined) input.setAttribute('data-testid', testId);\n if (initial) input.setAttribute('checked', '');\n const lab = el(doc, 'label', { for: id, class: 'hw-modal__label' }, [label]);\n const row = el(doc, 'div', { class: 'hw-modal__row' }, [input, lab]);\n return { row, input };\n}\n\n/** Build a labelled select. Returns `{ row, select }`. */\nexport function selectRow(\n doc: Document,\n label: string,\n values: ReadonlyArray<{ value: string; label: string }>,\n initial: string,\n testId?: string,\n): { row: HTMLElement; select: HTMLSelectElement } {\n const id = `hw-sel-${Math.random().toString(36).slice(2, 9)}`;\n const lab = el(doc, 'label', { for: id, class: 'hw-modal__label' }, [label]);\n const select = doc.createElement('select');\n select.setAttribute('id', id);\n select.setAttribute('class', 'hw-modal__select');\n if (testId !== undefined) select.setAttribute('data-testid', testId);\n for (const v of values) {\n const opt = doc.createElement('option');\n opt.setAttribute('value', v.value);\n if (v.value === initial) opt.setAttribute('selected', '');\n opt.appendChild(doc.createTextNode(v.label));\n select.appendChild(opt);\n }\n const row = el(doc, 'div', { class: 'hw-modal__row' }, [lab, select]);\n return { row, select };\n}\n\n/** Build OK + Cancel button row. Returns `{ row, ok, cancel }`. */\nexport function actionRow(doc: Document, testIdPrefix?: string): {\n row: HTMLElement;\n ok: HTMLButtonElement;\n cancel: HTMLButtonElement;\n} {\n const ok = doc.createElement('button');\n ok.setAttribute('class', 'hw-modal__ok');\n ok.setAttribute('type', 'button');\n if (testIdPrefix !== undefined) ok.setAttribute('data-testid', `${testIdPrefix}-ok`);\n ok.appendChild(doc.createTextNode('OK'));\n const cancel = doc.createElement('button');\n cancel.setAttribute('class', 'hw-modal__cancel');\n cancel.setAttribute('type', 'button');\n if (testIdPrefix !== undefined) cancel.setAttribute('data-testid', `${testIdPrefix}-cancel`);\n cancel.appendChild(doc.createTextNode('Cancel'));\n const row = el(doc, 'div', { class: 'hw-modal__actions' }, [ok, cancel]);\n return { row, ok, cancel };\n}\n","// T-0509 — Choose-R dialog.\n//\n// When adding a bond between two atoms with multiple unused R-groups, a UI\n// asks the user which R-group to use on each side. `open()` returns a promise\n// resolved with the user's choice, or `null` when cancelled.\n\nimport type { Atom } from '../../core/model';\nimport { freeRgroups } from '../../core/rgroups';\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\nimport { Modal, selectRow, actionRow } from './modal';\n\n/** Options for `ChooseRDialog`. */\nexport interface ChooseRDialogOptions {\n documentImpl?: Document;\n}\n\n/**\n * Per-open arguments restricting the dialog's option set. Phase 14B\n * (T-1413): when supplied, the dropdowns show ONLY these 1-based\n * R-group indices (taken R-groups are hidden so users cannot pick an\n * over-allocated slot). `currentR1` / `currentR2` add the SPECIFIC bond\n * already on the wire (for the \"edit existing bond\" flow in T-1415) so\n * keeping the current pick is always available.\n */\nexport interface ChooseROpenOptions {\n freeR1?: readonly number[];\n freeR2?: readonly number[];\n currentR1?: number;\n currentR2?: number;\n}\n\n/** Modal dialog that lets the user pick an R-group for each side of a new bond. */\nexport class ChooseRDialog {\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private _modal: Modal | null = null;\n\n constructor(editor: HelmEditor, options?: ChooseRDialogOptions) {\n this._editor = editor;\n const host = editor._getHost();\n if (host === null) throw new Error('ChooseRDialog: editor has no host element.');\n this._doc = options?.documentImpl ?? getDocument(host);\n }\n\n /**\n * Open the dialog and resolve with the user's choice. Resolves with `null`\n * when the user cancels. R-group lists default to the full\n * `atom.monomer?.rgroups`; pass `opts.freeR1` / `opts.freeR2` to\n * restrict them to the currently-unused slots (Phase 14B). When an atom\n * has no resolved monomer, the dialog falls back to R1/R2/R3.\n *\n * If `opts.currentR1` / `currentR2` is set, that index is added back\n * even if it's not in the free list (it represents \"keep the current\n * bond configuration\"). Useful for the bond-edit re-open flow.\n */\n open(a1: Atom, a2: Atom, opts?: ChooseROpenOptions): Promise<{ r1: number; r2: number } | null> {\n this.close();\n const host = this._editor._getHost();\n if (host === null) return Promise.resolve(null);\n const modal = new Modal(host, { documentImpl: this._doc, title: 'Choose R-Groups', testId: 'choose-r' });\n this._modal = modal;\n\n const r1Values = rGroupOptions(a1, opts?.freeR1, opts?.currentR1, this._editor);\n const r2Values = rGroupOptions(a2, opts?.freeR2, opts?.currentR2, this._editor);\n\n const a1Info = el(this._doc, 'div', { class: 'hw-modal__info' }, [`${a1.symbol} (${a1.bio.chainId})`]);\n // Default selection: current R-group if supplied, else the first option.\n const initial1 = opts?.currentR1 !== undefined ? String(opts.currentR1) : (r1Values[0]?.value ?? '1');\n const initial2 = opts?.currentR2 !== undefined ? String(opts.currentR2) : (r2Values[0]?.value ?? '1');\n const r1Sel = selectRow(this._doc, 'R-group on side A', r1Values, initial1, 'choose-r-r1');\n const a2Info = el(this._doc, 'div', { class: 'hw-modal__info' }, [`${a2.symbol} (${a2.bio.chainId})`]);\n const r2Sel = selectRow(this._doc, 'R-group on side B', r2Values, initial2, 'choose-r-r2');\n const actions = actionRow(this._doc, 'choose-r');\n\n // Phase 14B note: when there's no free R-group on either side, we\n // STILL open the dialog (so the user sees what happened) but the\n // body shows an explanatory note. The OK button stays enabled —\n // editor.addBond will reject and surface a status message.\n // When either side has no free R-groups (which only happens when\n // the dialog is opened with explicit empty free lists — the smart\n // pointer-layer inference short-circuits with a status message\n // before reaching here), surface a plain explanatory note. We do\n // not attach a data-testid: there is no functional UI behind it.\n const notes: HTMLElement[] = [];\n if (r1Values.length === 0)\n notes.push(el(this._doc, 'div', { class: 'hw-modal__info hw-modal__note-fully-booked' },\n [`All R-groups on ${a1.symbol} are in use.`]));\n if (r2Values.length === 0)\n notes.push(el(this._doc, 'div', { class: 'hw-modal__info hw-modal__note-fully-booked' },\n [`All R-groups on ${a2.symbol} are in use.`]));\n\n return new Promise<{ r1: number; r2: number } | null>((resolve) => {\n let settled = false;\n const settle = (value: { r1: number; r2: number } | null): void => {\n if (settled) return;\n settled = true;\n resolve(value);\n };\n const closeWith = (value: { r1: number; r2: number } | null): void => {\n settle(value);\n this.close();\n };\n actions.ok.addEventListener('click', () => closeWith({\n r1: parseSelectValue(r1Sel.select),\n r2: parseSelectValue(r2Sel.select),\n }));\n actions.cancel.addEventListener('click', () => closeWith(null));\n\n modal.body.appendChild(a1Info);\n modal.body.appendChild(r1Sel.row);\n modal.body.appendChild(a2Info);\n modal.body.appendChild(r2Sel.row);\n for (const n of notes) modal.body.appendChild(n);\n modal.body.appendChild(actions.row);\n modal.open(() => settle(null));\n });\n }\n\n /** @internal True when the dialog modal is mounted. */\n get isOpen(): boolean { return this._modal !== null && this._modal.isOpen; }\n\n close(): void {\n if (this._modal !== null) {\n this._modal.close();\n this._modal = null;\n }\n }\n}\n\n/**\n * Read a `<select>`'s effective value, falling back to the first option marked\n * `selected` (linkedom does not implement `.value` consistently). Always\n * returns an integer ≥ 1.\n *\n * Exported for tests so the fallback branches can be exercised directly.\n */\nexport function parseSelectValue(select: HTMLSelectElement): number {\n const direct = (select as { value?: string }).value;\n if (typeof direct === 'string' && direct.length > 0) {\n const n = Number(direct);\n if (Number.isFinite(n) && n >= 1) return n;\n }\n const opts = select.querySelectorAll('option');\n for (const opt of Array.from(opts)) {\n if (opt.getAttribute('selected') !== null) {\n const v = opt.getAttribute('value') ?? '';\n const n = Number(v);\n if (Number.isFinite(n) && n >= 1) return n;\n }\n }\n const first = opts[0];\n if (first !== undefined) {\n const v = first.getAttribute('value') ?? '';\n const n = Number(v);\n if (Number.isFinite(n) && n >= 1) return n;\n }\n return 1;\n}\n\n/**\n * Build the option list for one side of the dialog. When `freeOnly` is\n * supplied, options are restricted to those indices (plus `keepIndex`,\n * which is added back even if it's \"taken\" — represents the current\n * configuration for the bond-edit flow). When the atom has no resolved\n * monomer, falls back to R1..R3. `editor` is used only to lazily compute\n * the free list from the editor's current bonds when no explicit list is\n * given — preserves backwards compatibility with existing tests that\n * call `open(a, b)` without options.\n */\nfunction rGroupOptions(\n atom: Atom,\n freeOnly: readonly number[] | undefined,\n keepIndex: number | undefined,\n editor: HelmEditor,\n): ReadonlyArray<{ value: string; label: string }> {\n const rgroups = atom.monomer?.rgroups;\n if (rgroups === undefined || rgroups.length === 0) {\n // No resolved monomer — fall back to R1/R2/R3 (legacy behaviour).\n return [\n { value: '1', label: 'R1' },\n { value: '2', label: 'R2' },\n { value: '3', label: 'R3' },\n ];\n }\n // Resolve the visible set of 1-based indices.\n let visible: Set<number>;\n if (freeOnly !== undefined) {\n visible = new Set<number>(freeOnly);\n } else {\n // Backwards-compat: compute the free list from the editor's bonds\n // (the old call site passed no options at all). Tests that pre-date\n // Phase 14B keep working because the editor's bonds are the same\n // set the cap check uses.\n visible = new Set<number>(freeRgroups(atom, editor.getMol().bonds));\n // Empty free-set fallback to \"show every R-group\" — preserves the\n // legacy test fixture where two fresh atoms had no bonds.\n if (visible.size === 0)\n for (let i = 1; i <= rgroups.length; i++) visible.add(i);\n }\n if (keepIndex !== undefined && keepIndex >= 1 && keepIndex <= rgroups.length)\n visible.add(keepIndex);\n const out: { value: string; label: string }[] = [];\n const sorted = Array.from(visible).sort((a, b) => a - b);\n for (const idx of sorted) {\n const rg = rgroups[idx - 1];\n if (rg === undefined) continue;\n const cap = rg.capGroupName !== undefined && rg.capGroupName !== '' ? ` (${rg.capGroupName})` : '';\n out.push({ value: String(idx), label: `${rg.label}${cap}` });\n }\n return out;\n}\n","// Phase 32 (T-3003) -- \"Ghost cursor\" preview that follows the mouse\n// when the user has primed a palette tile and is hovering over empty\n// canvas in select mode. The preview is a tiny SVG showing the same\n// shape + colour the editor would paint if the user clicked there,\n// making it visually obvious that the click WILL add that monomer.\n//\n// Mounting: the element lives on `document.body` (same convention as\n// the tooltips in `tooltip-rdkit.ts`) so it escapes any parent\n// `overflow:hidden` or stacking context that the demo / consumer\n// layout might introduce. It is `pointer-events: none` so the cursor\n// passes straight through to the underlying canvas listeners.\n//\n// Layering: imports from `core/`, `monomer-lib/`, `render/` (atom-shape\n// and theme) -- same chain as the renderer. No DOM mutation beyond\n// `document.body.appendChild` and innerHTML on the cursor element.\n\nimport { atomShapePath } from '../../render/atom-shape';\nimport { resolveMonomerColors } from '../../monomer-lib/color-rules';\nimport type { Theme } from '../../render/theme';\nimport type { Monomer } from '../../monomer-lib/types';\nimport type { HelmType } from '../../core/constants';\nimport type { Atom } from '../../core/model';\nimport { bestContrastTextColor } from '../../monomer-lib/color-rules';\n\nconst TESTID = 'next-add-cursor';\n/**\n * SVG viewBox half-extent. The shape generators paint with up to\n * `size` (full radius for polygons) + 2.5 px stroke half-width. The\n * largest configured shape in `theme.ts` is `blob` at `fontSize *\n * 1.64 = 14 * 1.64 ≈ 23 px`, plus 2.5 px stroke = 25.5 px. We use 28\n * so even an oversized monomer (custom theme) fits with a 2.5 px\n * margin. Display size is the same -- viewBox = pixel size keeps the\n * shape one-for-one with the canvas at default fontSize.\n */\nconst HALF = 28;\nconst BOX = HALF * 2;\n\n/**\n * Look up (or create) the single ghost-cursor element. Cached on\n * `document.body` via its `data-testid` so re-entrant callers find\n * the same node. Hidden by default so a stale value never flashes\n * into view before the first `showNextAddCursor` call.\n */\nexport function getOrCreateNextAddCursor(doc: Document): HTMLElement {\n const ATTR = 'data-' + 'testid';\n for (let i = 0; i < doc.body.children.length; i++) {\n const child = doc.body.children[i] as Element | undefined;\n if (child !== undefined && child.getAttribute(ATTR) === TESTID)\n return child as unknown as HTMLElement;\n }\n const wrap = doc.createElement('div');\n wrap.className = 'hw-next-add-cursor';\n wrap.setAttribute(ATTR, TESTID);\n (wrap as unknown as { style: { display: string } }).style.display = 'none';\n doc.body.appendChild(wrap);\n return wrap as unknown as HTMLElement;\n}\n\n/**\n * Render the ghost preview into the cursor element and position it\n * so the cursor sits AT the centre of the atom shape (`clientX,\n * clientY` ↔ atom.p). The shape, fill, and label come from the same\n * helpers the renderer uses; the visual is byte-equivalent to the\n * canvas-rendered atom at default fontSize.\n *\n * The wrapper is opaque-but-fading (`opacity: 0.7` via CSS) so it\n * reads as a \"ghost\" rather than a finalised atom.\n */\nexport function showNextAddCursor(\n cursor: HTMLElement,\n symbol: string,\n biotype: HelmType,\n monomer: Monomer | null,\n theme: Theme,\n clientX: number,\n clientY: number,\n): void {\n // Synthetic atom centred at (0, 0) — viewBox aligns to that origin.\n const fakeAtom = {\n id: -1,\n p: { x: 0, y: 0 },\n biotype,\n symbol,\n monomer,\n } as unknown as Atom;\n const d = atomShapePath(fakeAtom, theme);\n const colors = resolveMonomerColors(monomer, biotype, theme.colorTheme);\n const fill = colors.background;\n const textColor = bestContrastTextColor(fill);\n\n // Label scale mirrors `buildAtomElement` in svg-renderer.ts: long\n // multi-char symbols shrink so they fit inside the shape.\n const labelLen = symbol.length;\n const labelScale = labelLen <= 1 ? 1 : Math.min(1, 2 / labelLen);\n const fontPx = theme.fontSize * labelScale;\n\n // Build the SVG by string concatenation — same convention as the\n // renderer. linkedom and real browsers both parse this as SVG when\n // it's assigned via the SVG-rooted element below.\n const svg =\n `<svg xmlns=\"http://www.w3.org/2000/svg\" ` +\n `viewBox=\"${-HALF} ${-HALF} ${BOX} ${BOX}\" ` +\n `width=\"${BOX}\" height=\"${BOX}\" ` +\n `class=\"hw-next-add-cursor__svg\" aria-hidden=\"true\">` +\n `<path d=\"${d}\" fill=\"${fill}\" stroke=\"${fill}\" ` +\n `stroke-width=\"5\" stroke-linejoin=\"round\" stroke-linecap=\"round\"/>` +\n `<text x=\"0\" y=\"0\" text-anchor=\"middle\" dominant-baseline=\"central\" ` +\n `font-family=\"Helvetica Neue, Helvetica, Arial, sans-serif\" ` +\n `font-size=\"${fontPx}\" fill=\"${textColor}\">${escapeXmlText(symbol)}</text>` +\n `</svg>`;\n\n (cursor as unknown as { innerHTML: string }).innerHTML = svg;\n const style = (cursor as unknown as {\n style: { display: string; left: string; top: string };\n }).style;\n // Position fixed at the cursor. Subtract HALF so the SHAPE centre\n // (atom.p === 0,0 in viewBox space → the centre of the BOX×BOX\n // wrapper) sits at the cursor's clientX/clientY.\n style.left = `${clientX - HALF}px`;\n style.top = `${clientY - HALF}px`;\n style.display = 'block';\n}\n\n/** Hide the ghost cursor (no-op if not yet created or already hidden). */\nexport function hideNextAddCursor(cursor: HTMLElement | null): void {\n if (cursor === null) return;\n (cursor as unknown as { style: { display: string } }).style.display = 'none';\n}\n\n/** Minimal XML escape -- atoms come from the monomer library so they\n * are typically ASCII, but a label like `&` or `<` must not break the\n * parser. Same characters as in `svg-builder.ts`. */\nfunction escapeXmlText(s: string): string {\n let out = '';\n for (let i = 0; i < s.length; i++) {\n const c = s.charAt(i);\n if (c === '<') out += '&lt;';\n else if (c === '>') out += '&gt;';\n else if (c === '&') out += '&amp;';\n else out += c;\n }\n return out;\n}\n","// T-0503 / T-1101 / T-1105 — Pointer input handler.\n//\n// Attaches pointer/mouse listeners on the host (we use `host` not the SVG\n// root so listeners survive every redraw). Each handler hit-tests against\n// the editor's `Mol` (re-built via `HitTester` on each `mol:changed`) and\n// translates the DOM event into one or more editor events from\n// EVENTS.md §2 / §3.\n//\n// Coordinate transform (T-1101): the renderer paints model coords into a\n// `<g class=\"hw-content\" transform=\"translate(tx ty) scale(s)\">` inside a\n// `<svg viewBox=\"0 0 W H\">`. Screen → model requires inverting that. We\n// prefer `SVGGraphicsElement.getScreenCTM()` (works in real browsers) and\n// fall back to a manual viewBox + transform-attribute decoder for jsdom /\n// linkedom (which return null from `getScreenCTM`).\n//\n// Bond drag (T-1105): mousedown on an atom arms a bond drag; mousemove\n// emits `bond:preview` with the start atom + current cursor; mouseup over\n// another atom commits via `editor.addBond` (with the editor's chooseRs\n// heuristic for the R-group pair).\n//\n// Layering: imports `core/`, `render/hit-test`, and sibling editor modules.\n// No IO, no calc.\n\nimport type { Atom, Bond, Mol } from '../../core/model';\nimport { HitTester } from '../../render/hit-test';\nimport { Selection } from '../../core/selection';\nimport { freeRgroups, totalRgroups } from '../../core/rgroups';\nimport type { Point, Rect } from '../../util/types';\nimport type { HelmEditor } from '../editor';\nimport type { ModifierKeys } from '../events';\nimport { ChooseRDialog } from '../dialogs/choose-r';\nimport {\n getOrCreateNextAddCursor,\n hideNextAddCursor,\n showNextAddCursor,\n} from '../view/next-add-cursor';\n\n/** Options for the pointer input layer. */\nexport interface PointerInputOptions {\n /**\n * When `false`, contextmenu events always have `preventDefault` called and\n * the editor's `monomer:contextmenu` / `bond:contextmenu` event still fires\n * but with a no-op `preventDefault` (already called). Default `true`.\n */\n enableContextMenu?: boolean;\n}\n\n/** Minimal MouseEvent-like shape that we read from. Avoids leaking the DOM types. */\ninterface MouseLike {\n clientX: number;\n clientY: number;\n button: number;\n shiftKey: boolean;\n altKey: boolean;\n ctrlKey: boolean;\n metaKey: boolean;\n target: EventTarget | null;\n preventDefault(): void;\n stopPropagation(): void;\n}\n\n/**\n * Pointer input. Bind listeners on the host; convert raw DOM events into\n * editor events. Updates a tiny `HitTester` whenever the editor's Mol\n * changes so per-pointer hit-tests stay O(n) without re-allocating each frame.\n */\nexport class PointerInput {\n private readonly _host: HTMLElement;\n private readonly _editor: HelmEditor;\n private readonly _enableContextMenu: boolean;\n private _tester: HitTester;\n private _hoverAtom: Atom | null = null;\n private _hoverBond: Bond | null = null;\n private _dragOrigin: Point | null = null;\n private _bondStart: Atom | null = null;\n private _bondDragMoved: boolean = false;\n /**\n * Phase 16 (T-1604) — Suppress the synthetic click that the browser\n * fires after a successful Ctrl+drag rectangle-select. Without this\n * flag the click handler's empty-canvas branch would call\n * `editor.clearSelection()` and erase the rectangle's selection\n * before the user could see it.\n */\n private _rectDragHappened: boolean = false;\n /**\n * Phase 13b (Bug 6) — Lazy-instantiated choose-R dialog. Created the\n * first time a bond-drag terminates with ambiguous R-groups; kept on the\n * instance so a re-entry reuses the same modal (`open()` calls\n * `close()` internally to be idempotent).\n */\n private _chooseRDialog: ChooseRDialog | null = null;\n /**\n * Phase 13b (Bug 2) — Move-mode pan state. `origin` is the surface\n * (client) coordinate of mousedown; `initialOffset` is the editor's\n * viewport offset at mousedown. While set, every mousemove computes a\n * cumulative delta and forwards to `editor.panTo()`. mouseup clears.\n *\n * Phase 15 (T-1504) — Move-mode now means \"drag individual atoms\",\n * not \"pan the canvas\". This field is retained for future re-enable\n * of pan via space-key+drag or middle-mouse-button — see comment in\n * `_handleMouseDown`.\n */\n private _panStart: { origin: Point; initialOffset: Point } | null = null;\n /**\n * Phase 15 (T-1504) — Move-mode atom drag state. Populated on\n * mousedown over an atom while `editor.getMode() === 'move'`; mousemove\n * updates the dragged atom's `p` via `editor.moveAtom`; mouseup clears.\n *\n * Phase 26 (T-2601) — Promoted to a multi-atom drag. `atomIds` lists\n * every atom being dragged: a single id when the user grabbed an atom\n * OUTSIDE the current selection (preserves the legacy single-atom\n * drag), or the full selection set when the grabbed atom IS in the\n * current selection. `initialPositions` is captured at mousedown so the\n * group's relative geometry survives across mousemoves — each atom is\n * translated to `initialPositions[id] + (pointer-delta)`. Committed in\n * one Transaction via `editor.moveAtoms` so a multi-atom drag fires a\n * single `mol:changed` (not N).\n */\n private _atomDragState: {\n atomIds: number[];\n pointerDownModel: Point;\n initialPositions: ReadonlyMap<number, Point>;\n } | null = null;\n /**\n * Phase 30 (T-3001) — Suppress the synthetic click that follows a\n * drag that moved the canvas (`_panMoved`) or an atom\n * (`_atomDragMoved`). Without these, a plain-drag pan in `select`\n * mode would still fire `click` on mouseup, hitting the\n * empty-canvas branch in `_handleClick` and either dropping a\n * primed palette monomer or clearing the selection. Same pattern\n * the bond drag uses via `_bondDragMoved` and the rectangle drag\n * uses via `_rectDragHappened`.\n */\n private _panMoved: boolean = false;\n private _atomDragMoved: boolean = false;\n /**\n * Phase 32 (T-3003) — Body-mounted ghost cursor that previews the\n * primed palette monomer when the user is hovering empty canvas in\n * `select` mode. Lazily created on first use (avoids touching\n * `document.body` until at least one mousemove arrives) and reused\n * across show/hide cycles. The element is HIDDEN by default; only\n * `_handleMove` calls `showNextAddCursor` when every gate passes.\n */\n private _nextAddCursorEl: HTMLElement | null = null;\n private _destroyed: boolean = false;\n private readonly _unsubs: Array<() => void> = [];\n\n private readonly _onMove: (e: Event) => void;\n private readonly _onClick: (e: Event) => void;\n private readonly _onDblClick: (e: Event) => void;\n private readonly _onContextMenu: (e: Event) => void;\n private readonly _onMouseDown: (e: Event) => void;\n private readonly _onMouseUp: (e: Event) => void;\n private readonly _onMouseLeave: (e: Event) => void;\n private readonly _onWheel: (e: Event) => void;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: PointerInputOptions) {\n this._host = host;\n this._editor = editor;\n this._enableContextMenu = options?.enableContextMenu ?? true;\n\n this._tester = new HitTester(editor.getMol(), editor['_currentTheme']());\n\n // Rebuild hit-tester whenever the Mol changes.\n this._unsubs.push(editor.on('mol:changed', () => {\n this._tester = new HitTester(this._editor.getMol(), this._editor['_currentTheme']());\n // Clear stale hover state — atoms may have been removed.\n this._hoverAtom = null;\n this._hoverBond = null;\n }));\n\n // Phase 32 (T-3003) — Reactively hide the ghost cursor when the\n // mode or primed tile change between mousemoves (e.g. user clicks\n // the toolbar `×` to clear nextAdd while their cursor is over\n // empty canvas). The next mousemove re-evaluates the gates and\n // re-shows it if appropriate.\n this._unsubs.push(editor.on('option:change', (e) => {\n if (e.key === 'mode' || e.key === 'nextAdd')\n hideNextAddCursor(this._nextAddCursorEl);\n }));\n\n this._onMove = (e: Event): void => this._handleMove(e as unknown as MouseLike);\n this._onClick = (e: Event): void => this._handleClick(e as unknown as MouseLike);\n this._onDblClick = (e: Event): void => this._handleDblClick(e as unknown as MouseLike);\n this._onContextMenu = (e: Event): void => this._handleContextMenu(e as unknown as MouseLike);\n this._onMouseDown = (e: Event): void => this._handleMouseDown(e as unknown as MouseLike);\n this._onMouseUp = (e: Event): void => this._handleMouseUp(e as unknown as MouseLike);\n this._onMouseLeave = (e: Event): void => this._handleMouseLeave(e as unknown as MouseLike);\n this._onWheel = (e: Event): void => this._handleWheel(e as unknown as WheelLike);\n\n host.addEventListener('mousemove', this._onMove);\n host.addEventListener('click', this._onClick);\n host.addEventListener('dblclick', this._onDblClick);\n host.addEventListener('contextmenu', this._onContextMenu);\n host.addEventListener('mousedown', this._onMouseDown);\n host.addEventListener('mouseup', this._onMouseUp);\n host.addEventListener('mouseleave', this._onMouseLeave);\n host.addEventListener('wheel', this._onWheel, { passive: false } as unknown as boolean);\n }\n\n /** Tear down the input layer. Removes every listener registered above. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n this._host.removeEventListener('mousemove', this._onMove);\n this._host.removeEventListener('click', this._onClick);\n this._host.removeEventListener('dblclick', this._onDblClick);\n this._host.removeEventListener('contextmenu', this._onContextMenu);\n this._host.removeEventListener('mousedown', this._onMouseDown);\n this._host.removeEventListener('mouseup', this._onMouseUp);\n this._host.removeEventListener('mouseleave', this._onMouseLeave);\n this._host.removeEventListener('wheel', this._onWheel);\n // Phase 13b (Bug 6) — Close any in-flight choose-R dialog so its\n // pending Promise's `.then()` callback short-circuits on the\n // `this._destroyed` guard.\n if (this._chooseRDialog !== null) {\n this._chooseRDialog.close();\n this._chooseRDialog = null;\n }\n // Phase 32 (T-3003) — Hide the ghost cursor on destroy so a\n // re-mount (HMR, test teardown) doesn't see a stuck preview\n // pinned at the last mousemove coordinate. The element stays in\n // body so a fresh PointerInput on the same Document can reuse\n // it.\n hideNextAddCursor(this._nextAddCursorEl);\n this._nextAddCursorEl = null;\n }\n\n // ------------------------------------------------------------------------\n // Event handlers\n // ------------------------------------------------------------------------\n\n private _handleMove(e: MouseLike): void {\n // Phase 13b (Bug 2) — Move-mode pan. If a pan is armed, every move\n // forwards to `editor.panTo()` with the cumulative client-coord\n // delta added to the offset at mousedown. We DELIBERATELY skip the\n // rest of the move handler (hover transitions, selection-rect\n // updates, bond preview) while panning — the canvas is being moved,\n // not interacted with.\n if (this._panStart !== null) {\n const dx = e.clientX - this._panStart.origin.x;\n const dy = e.clientY - this._panStart.origin.y;\n this._editor.panTo({\n x: this._panStart.initialOffset.x + dx,\n y: this._panStart.initialOffset.y + dy,\n });\n // Phase 30 (T-3001) — Mark that this drag actually moved the\n // canvas. Consumed by `_handleClick` to suppress the synthetic\n // click that follows mouseup (browsers fire `click` on\n // mousedown+mouseup even after motion).\n this._panMoved = true;\n return;\n }\n // Phase 15 (T-1504) — Move-mode atom drag. While an atom drag is\n // armed, every move updates the atom's position through the editor\n // so the renderer and hit-tester see the new coordinate. Other\n // hover / preview transitions are skipped — we are physically\n // moving an atom, not hovering or drag-connecting.\n if (this._atomDragState !== null) {\n const pm = this._toModel(e);\n const dx = pm.x - this._atomDragState.pointerDownModel.x;\n const dy = pm.y - this._atomDragState.pointerDownModel.y;\n // Phase 26 (T-2601) — Group drag. Build one update batch per atom\n // in the drag set; commit through `moveAtoms` so the whole group\n // moves under a SINGLE Transaction (one `mol:changed` / one\n // history entry).\n const updates: Array<{ atomId: number; p: Point }> = [];\n for (const id of this._atomDragState.atomIds) {\n const init = this._atomDragState.initialPositions.get(id);\n if (init === undefined) continue;\n updates.push({ atomId: id, p: { x: init.x + dx, y: init.y + dy } });\n }\n this._editor.moveAtoms(updates);\n // Phase 30 (T-3001) — Mark for the same click-suppression\n // reason as `_panMoved`. Ctrl/Meta+drag from an atom in\n // `select` mode would otherwise let the synthetic `click` fire\n // `monomer:click` with `ctrl`, toggling the just-moved atom out\n // of the selection.\n this._atomDragMoved = true;\n return;\n }\n const p = this._toModel(e);\n const r = this._tester.test(p);\n const newAtom = r?.atom ?? null;\n const newBond = r?.bond ?? null;\n\n // Bond-drag preview: when mousedown armed _bondStart, emit a preview so\n // the view can paint a dashed line from the start atom to the cursor.\n if (this._bondStart !== null) {\n this._bondDragMoved = true;\n const targetAtom: Atom | null =\n newAtom !== null && newAtom.id !== this._bondStart.id ? newAtom : null;\n this._editor.fire('bond:preview', {\n start: this._bondStart,\n cursor: p,\n candidate: targetAtom,\n kind: this._editor.getMode() === 'hbond' ? 'hbond' : 'backbone',\n });\n }\n\n // Atom hover transitions.\n if (this._hoverAtom !== null && (newAtom === null || newAtom.id !== this._hoverAtom.id)) {\n this._editor.fire('monomer:hover-end', { atom: this._hoverAtom });\n this._hoverAtom = null;\n }\n if (newAtom !== null && (this._hoverAtom === null || this._hoverAtom.id !== newAtom.id)) {\n this._hoverAtom = newAtom;\n this._editor.fire('monomer:hover', {\n atom: newAtom,\n clientX: e.clientX,\n clientY: e.clientY,\n modelX: p.x,\n modelY: p.y,\n });\n }\n\n // Bond hover transitions.\n if (this._hoverBond !== null && (newBond === null || newBond.id !== this._hoverBond.id)) {\n this._editor.fire('bond:hover-end', { bond: this._hoverBond });\n this._hoverBond = null;\n }\n if (newBond !== null && (this._hoverBond === null || this._hoverBond.id !== newBond.id)) {\n this._hoverBond = newBond;\n this._editor.fire('bond:hover', { bond: newBond, clientX: e.clientX, clientY: e.clientY });\n }\n\n // Drag-rectangle progress.\n if (this._dragOrigin !== null) {\n const rect = rectFromPoints(this._dragOrigin, p);\n this._editor.fire('selection:rectangle-update', { rect });\n }\n\n // Phase 32 (T-3003) — Ghost cursor preview for the primed palette\n // monomer. Show ONLY when every gate passes: select mode, a tile\n // is primed, the pointer is over EMPTY canvas (no atom under it),\n // no rect-drag in progress, no bond drag armed. The user reported\n // they want this affordance only in select mode (other modes\n // route the click elsewhere) and only when a tile is primed (no\n // primed tile -> click clears selection, not adds).\n this._updateNextAddCursor(e);\n }\n\n private _handleClick(e: MouseLike): void {\n // Suppress synthetic click after a bond-drag (mouseup already handled it).\n if (this._bondDragMoved) {\n this._bondDragMoved = false;\n return;\n }\n // Phase 16 (T-1604) — Same defense for a rectangle drag: the\n // selection was just committed in mouseup; the synthetic click must\n // not fall through to \"clear selection on empty-canvas click\".\n if (this._rectDragHappened) {\n this._rectDragHappened = false;\n return;\n }\n // Phase 30 (T-3001) — Pan / atom-drag gestures that involved\n // actual motion suppress the synthetic click. Without this,\n // a select-mode plain-drag pan would still drop a primed palette\n // monomer (empty-canvas branch) or clear the selection (default\n // empty-canvas behaviour) on mouseup. A pure click (mousedown +\n // mouseup at the same surface point) leaves these flags `false`\n // and proceeds through the rest of this handler.\n if (this._panMoved) {\n this._panMoved = false;\n return;\n }\n if (this._atomDragMoved) {\n this._atomDragMoved = false;\n return;\n }\n const p = this._toModel(e);\n const r = this._tester.test(p);\n const mods = modsOf(e);\n const mode = this._editor.getMode();\n\n // Eraser mode: clicking an atom or bond deletes it.\n if (mode === 'eraser') {\n if (r?.atom !== undefined) { this._editor.removeAtom(r.atom); return; }\n if (r?.bond !== undefined) { this._editor.removeBond(r.bond); return; }\n return;\n }\n\n if (r?.atom !== undefined) {\n // Phase 24 (T-2405): in select mode, when the user has a palette\n // tile primed (`nextAdd` set) and clicks an EXISTING atom whose\n // biotype matches the primed monomer's biotype, replace the\n // atom's symbol with the primed one. Mismatched biotypes (e.g.\n // primed sugar, click peptide AA) emit a status warning and\n // keep the atom unchanged. Modifier keys (Ctrl/Shift/Meta) skip\n // the replace path because those gestures modify the current\n // selection rather than the atom itself.\n if (mode === 'select' && !mods.ctrl && !mods.shift && !mods.meta) {\n const nextAdd = this._editor.getNextAddSymbol();\n if (nextAdd !== null) {\n if (r.atom.biotype === nextAdd.biotype) {\n // Same-biotype replace. We deliberately KEEP `nextAdd`\n // primed afterwards -- the user may want to apply the\n // same monomer to several atoms in one gesture.\n this._editor.replaceMonomer(r.atom, nextAdd.symbol);\n return;\n }\n // Biotype mismatch -- warn via the status bar, do nothing\n // structural. The atom remains as-is and the palette tile\n // stays primed so the user can still click an empty spot\n // to place the monomer.\n this._editor.fire('editor:status', {\n message: `Cannot replace: ${r.atom.biotype} is incompatible with ${nextAdd.biotype}`,\n severity: 'warn',\n durationMs: 3000,\n });\n return;\n }\n }\n this._editor.fire('monomer:click', { atom: r.atom, modifiers: mods, clientX: e.clientX, clientY: e.clientY });\n return;\n }\n if (r?.bond !== undefined) {\n this._editor.fire('bond:click', { bond: r.bond, modifiers: mods });\n return;\n }\n\n // Empty surface click + a primed palette tile → add the monomer there.\n //\n // Phase 25 (T-2503): INVERTS the T-1301a (Bug 4) behaviour. The\n // previous policy cleared `nextAdd` after every empty-canvas add so\n // a subsequent stray empty-canvas click would NOT silently spawn a\n // duplicate. User report: \"when I add monomer at empty space, it\n // automatically becomes unselected. lets keep it selected, instead,\n // [click-to-unselect via T-2501 + the status-bar × button via\n // T-2504] should handle it.\"\n //\n // Rationale: now that there are TWO explicit unselect affordances\n // (click the primed tile again; click the `×` icon next to the\n // status-bar \"Next add\" label) the user-awareness loop for \"I have\n // a tile primed\" is closed. Keeping `nextAdd` armed across multiple\n // empty-canvas clicks supports the natural \"place several copies\n // in a row\" workflow.\n //\n // Phase 20 (T-2001): the ENTIRE nextAdd consumption path is gated\n // on `_addsEnabled()` (i.e. mode === 'select'). In move / eraser /\n // hbond modes an empty-canvas click is INERT for monomer-add — even\n // when a palette tile is primed.\n if (this._addsEnabled()) {\n const next = this._editor.getNextAddSymbol();\n if (next !== null) {\n this._editor.addAtom(p, next.biotype, next.symbol);\n // Phase 25 (T-2503): nextAdd STAYS primed. See block comment\n // above for the design rationale.\n return;\n }\n }\n\n // Plain click on empty surface — clear selection unless a modifier\n // (Shift / Ctrl / Meta) is held. Phase 18 (T-1802) added Ctrl/Meta to\n // the \"preserve selection\" list so a stray empty-canvas Ctrl-click\n // during a multi-pick gesture does not blow the user's selection\n // away. Shift remains preserved for the legacy \"extend selection\"\n // semantics.\n if (!mods.shift && !mods.ctrl && !mods.meta) this._editor.clearSelection();\n }\n\n private _handleDblClick(e: MouseLike): void {\n const p = this._toModel(e);\n const r = this._tester.test(p);\n const mods = modsOf(e);\n if (r?.atom !== undefined)\n this._editor.fire('monomer:dblclick', { atom: r.atom, modifiers: mods });\n }\n\n private _handleContextMenu(e: MouseLike): void {\n if (!this._enableContextMenu) e.preventDefault();\n const p = this._toModel(e);\n const r = this._tester.test(p);\n let cancelled = false;\n const preventDefault = (): void => {\n cancelled = true;\n e.preventDefault();\n };\n if (r?.atom !== undefined) {\n this._editor.fire('monomer:contextmenu', { atom: r.atom, clientX: e.clientX, clientY: e.clientY, preventDefault });\n } else if (r?.bond !== undefined) {\n this._editor.fire('bond:contextmenu', { bond: r.bond, clientX: e.clientX, clientY: e.clientY, preventDefault });\n }\n void cancelled;\n }\n\n private _handleMouseDown(e: MouseLike): void {\n if (e.button !== 0) return;\n const p = this._toModel(e);\n const r = this._tester.test(p);\n const mode = this._editor.getMode();\n const ctrlOrMeta = e.ctrlKey === true || e.metaKey === true;\n // Mousedown over an atom:\n // - `move` mode: always arms an atom drag (T-1504).\n // - `select` mode + Ctrl/Meta: Phase 30 T-3001 — Ctrl/Meta\n // hijacks the gesture into an atom drag with the same physics\n // as Move mode. Plain Ctrl+click (no movement) falls through\n // to the click handler which toggles selection — pointer arms\n // the drag state but `_atomDragMoved` stays false until a\n // mousemove arrives, so the click is not suppressed.\n // - Otherwise: arms a potential bond drag, committed on mouseup.\n if (r?.atom !== undefined) {\n if (mode === 'move' || (mode === 'select' && ctrlOrMeta)) {\n // Phase 26 (T-2601) — Decide single-atom vs group drag. If the\n // grabbed atom is part of the current selection, every selected\n // atom moves together (preserving the group's geometry); if NOT,\n // we drag just the grabbed atom and leave the selection alone.\n const selection = this._editor.getSelection();\n const isInSelection = selection.atoms.has(r.atom.id);\n const atomIds = isInSelection\n ? Array.from(selection.atoms)\n : [r.atom.id];\n const mol = this._editor.getMol();\n const initial = new Map<number, Point>();\n for (const id of atomIds) {\n const a = mol.atoms.find((x) => x.id === id);\n if (a !== undefined) initial.set(id, { x: a.p.x, y: a.p.y });\n }\n this._atomDragState = {\n atomIds,\n pointerDownModel: { x: p.x, y: p.y },\n initialPositions: initial,\n };\n this._atomDragMoved = false;\n return;\n }\n this._bondStart = r.atom;\n this._bondDragMoved = false;\n return;\n }\n if (r === null) {\n // Empty-canvas mousedown.\n // - `move` mode (T-1702): always arms a pan.\n // - `select` mode + no Ctrl/Meta: Phase 30 T-3001 — plain drag\n // pans the viewport. The default mode no longer requires a\n // mode switch to pan the canvas. A pure click (mousedown +\n // mouseup at the same point) is unaffected: `_panMoved`\n // stays false, the click handler still runs the\n // palette-primed add / clear-selection branch.\n // - `select` mode + Ctrl/Meta: arms a rectangle select (T-1604).\n // - Other modes (`eraser`, `hbond`): no-op.\n if (mode === 'move' || (mode === 'select' && !ctrlOrMeta)) {\n const vp = this._editor.getViewport();\n this._panStart = {\n origin: { x: e.clientX, y: e.clientY },\n initialOffset: { x: vp.offset.x, y: vp.offset.y },\n };\n this._panMoved = false;\n return;\n }\n if (mode === 'select' && ctrlOrMeta) {\n this._dragOrigin = p;\n this._editor.fire('selection:rectangle-start', { origin: p });\n }\n }\n }\n\n private _handleMouseUp(e: MouseLike): void {\n // Phase 13b (Bug 2) — End move-mode pan. The drag of the pan happens\n // during mousemove (already applied); mouseup just clears the state.\n if (this._panStart !== null) {\n this._panStart = null;\n return;\n }\n // Phase 15 (T-1504) — End atom drag. The drag itself updated the\n // atom's position during mousemove; mouseup clears the state.\n if (this._atomDragState !== null) {\n this._atomDragState = null;\n return;\n }\n // Bond drag commit / cancel.\n if (this._bondStart !== null) {\n const start = this._bondStart;\n const moved = this._bondDragMoved;\n this._bondStart = null;\n // Note: `_bondDragMoved` is cleared by the suppressed click handler so\n // a same-spot mouseup still passes through as a normal click.\n const p = this._toModel(e);\n const r = this._tester.test(p);\n const target = r?.atom;\n if (moved && target !== undefined && target.id !== start.id) {\n this._editor.fire('bond:preview-end', { start });\n if (this._editor.getMode() === 'hbond') {\n try { this._editor.addHydrogenBond(start, target); }\n catch { this._editor.fire('bond:cancel', { start }); }\n return;\n }\n // Phase 14B (T-1413) — Smart connection inference. The previous\n // policy (\"open chooser when both atoms have ≥ 2 free R-groups,\n // else default to (R2, R1)\") allowed an infinite number of bond\n // attempts because it never checked the FREE list for a hit-zero\n // condition. The new policy:\n //\n // 1. Fail fast (status:error, no bond) when either side has no\n // free numeric R-groups left.\n // 2. Auto-pick R2 → R1 for a single-chain peptide-style backbone\n // extension when both R2 (on start) and R1 (on target) are\n // free AND at least one side has only ONE remaining choice.\n // Mirrors the user's mental model (\"of course I'm extending\n // the chain\") and matches the SPECIFICATION.md §12.1 backbone\n // convention.\n // 3. Auto-pick whenever each side has exactly ONE free R-group.\n // 4. Otherwise: open ChooseR with the FREE list (taken R-groups\n // are not shown).\n // Phase 15 (T-1505) — Non-adjacent intra-chain drags create a CYCLE\n // (e.g. dragging A→G inside `PEPTIDE1{A.C.D.E.F.G}`). The polymer\n // body only captures adjacent backbone bonds; the closure must be\n // marked `cross-polymer` so the serializer emits it in section 1.\n // Without this the bond lived inside `mol.bonds` but was missing\n // from the HELM string — and a second drag failed with\n // `rgroup-already-bonded` against an invisible bond.\n const bondKind: 'backbone' | 'cross-polymer' =\n start.bio.chainId === target.bio.chainId && areAdjacentInChain(start, target, this._editor.getMol())\n ? 'backbone'\n : 'cross-polymer';\n const decision = inferBondConnection(start, target, this._editor.getMol().bonds, bondKind);\n if (decision.mode === 'fail') {\n this._editor.fire('bond:cancel', { start });\n this._editor.fire('editor:status', {\n message: decision.reason,\n severity: 'error',\n durationMs: 3000,\n });\n return;\n }\n if (decision.mode === 'auto') {\n try { this._editor.addBond(start, target, decision.r1, decision.r2, decision.kind); }\n catch { this._editor.fire('bond:cancel', { start }); }\n return;\n }\n // decision.mode === 'choose'\n this._openChooseR(start, target, bondKind, decision.freeR1, decision.freeR2);\n return;\n }\n if (moved) {\n // Phase 15 (T-1507) — Palette-primed drag drop on empty canvas.\n // When the user clicked a palette tile (priming `nextAdd`) and\n // then dragged a bond from an EXISTING atom into empty space,\n // create the new monomer at the drop point and bond it to the\n // start atom. Same connection-inference policy as a normal\n // drag-to-atom (auto-pick when unambiguous; chooser otherwise).\n // The chain-merge logic in `editor.addBond` (T-1506) collapses\n // the resulting two single-polymer chains into a single chain\n // whenever the new monomer matches the start chain's polymer\n // type — so the typical flow `PEPTIDE1{A.C.D}` + drag from D\n // with palette `G` primed → `PEPTIDE1{A.C.D.G}`.\n //\n // Phase 20 (T-2001): this path is gated on `_addsEnabled()`. In\n // eraser / hbond / move modes the drag-from-atom-to-empty\n // ALWAYS cancels — the user's intent in those modes is not \"drop\n // a new monomer\" but to scrub / try a hbond / drag the atom, and\n // a primed palette tile must not silently bleed through.\n const nextAdd = this._addsEnabled() ? this._editor.getNextAddSymbol() : null;\n if (nextAdd !== null) {\n let newAtom: Atom;\n try { newAtom = this._editor.addAtom(p, nextAdd.biotype, nextAdd.symbol); }\n catch {\n this._editor.fire('bond:cancel', { start });\n this._editor.fire('bond:preview-end', { start });\n return;\n }\n // Phase 16 (T-1603) — Palette \"stays selected\" through a\n // drag-from-atom-to-empty gesture. The user reported: \"when I\n // select a monomer and add it to connection to some other, it\n // does not stay selected (visually it does, but if I do same\n // again, nothing happens)\". Phase 13a (Bug 4) cleared `nextAdd`\n // after consumption to prevent the \"click empty space adds a\n // random monomer\" bug — but that fix is too aggressive for the\n // drag path. The drag gesture is repeatable by design: the\n // palette tile keeps its `aria-pressed=\"true\"` state and a\n // subsequent drag from another atom appends another copy.\n // CONTRAST with `_handleClick` (the empty-canvas-click branch)\n // which DOES clear `nextAdd` — that path is the one Bug 4 fixed.\n // Re-resolve start through the editor's new mol — addAtom\n // produced a fresh Mol whose atom instances differ from the\n // pre-add references. Look up by id.\n const refreshedStart = this._editor.getMol().atoms.find((x) => x.id === start.id);\n if (refreshedStart === undefined) {\n this._editor.fire('bond:cancel', { start });\n this._editor.fire('bond:preview-end', { start });\n return;\n }\n const dragBondKind: 'backbone' | 'cross-polymer' =\n refreshedStart.bio.chainId === newAtom.bio.chainId\n && areAdjacentInChain(refreshedStart, newAtom, this._editor.getMol())\n ? 'backbone'\n : 'cross-polymer';\n // Phase 15 (T-1507) — Palette-primed extend heuristic. The new\n // atom is a fresh single-monomer chain with all R-groups free,\n // and the user just clicked a palette tile (express intent to\n // extend a chain). Auto-pick R2 → R1 whenever both endpoints\n // have those slots free — this is the canonical backbone\n // direction (SPECIFICATION.md §12.1) and matches the user's\n // mental model: \"the new monomer continues the chain\". The\n // chain-merge in `addBond` (T-1506) then folds the new\n // single-atom polymer into the start atom's chain when the\n // polymer types agree, producing `PEPTIDE1{A.C.D.G}` from\n // `PEPTIDE1{A.C.D}` + drag-from-D with palette G primed.\n const startFreeR = freeRgroups(refreshedStart, this._editor.getMol().bonds);\n const newFreeR = freeRgroups(newAtom, this._editor.getMol().bonds);\n if (startFreeR.includes(2) && newFreeR.includes(1)) {\n try { this._editor.addBond(refreshedStart, newAtom, 2, 1, dragBondKind); }\n catch { this._editor.fire('bond:cancel', { start }); }\n this._editor.fire('bond:preview-end', { start });\n return;\n }\n const dec2 = inferBondConnection(refreshedStart, newAtom, this._editor.getMol().bonds, dragBondKind);\n if (dec2.mode === 'fail') {\n this._editor.fire('bond:cancel', { start });\n this._editor.fire('editor:status', {\n message: dec2.reason, severity: 'error', durationMs: 3000,\n });\n this._editor.fire('bond:preview-end', { start });\n return;\n }\n if (dec2.mode === 'auto') {\n try { this._editor.addBond(refreshedStart, newAtom, dec2.r1, dec2.r2, dec2.kind); }\n catch { this._editor.fire('bond:cancel', { start }); }\n this._editor.fire('bond:preview-end', { start });\n return;\n }\n // dec2.mode === 'choose'\n this._editor.fire('bond:preview-end', { start });\n this._openChooseR(refreshedStart, newAtom, dragBondKind, dec2.freeR1, dec2.freeR2);\n return;\n }\n // Drag ended over empty / same-atom — cancel preview.\n this._editor.fire('bond:cancel', { start });\n this._editor.fire('bond:preview-end', { start });\n return;\n }\n // Pure click on atom — let the click handler take it (no bond preview).\n return;\n }\n if (this._dragOrigin === null) return;\n const p = this._toModel(e);\n const rect = rectFromPoints(this._dragOrigin, p);\n this._dragOrigin = null;\n const inside = this._tester.testRect(rect);\n const rectSel = Selection.fromAtomsAndBonds(\n inside.atoms.map((a) => a.id),\n inside.bonds.map((b) => b.id),\n );\n // Phase 16 (T-1604) — Union with the existing selection so the rect\n // accumulates rather than replaces. The user's mental model is \"build\n // up a selection by repeatedly rectangle-dragging\" — and Delete then\n // removes the whole set in one keystroke.\n const sel = Selection.union(this._editor.getSelection(), rectSel);\n this._editor.setSelection(sel);\n this._editor.fire('selection:rectangle-end', { rect, selection: sel });\n // Phase 16 (T-1604) — Mark that a rectangle drag just happened so the\n // synthetic click that follows (mousedown + mouseup at the same DOM\n // element → click) does NOT fall through to the empty-canvas branch\n // and clear the selection we just built.\n this._rectDragHappened = true;\n // Phase 27 (T-2703) — After a successful Ctrl+drag rectangle select\n // that produced a non-empty selection, auto-switch to Move mode so\n // the user's natural next gesture (drag the selected group) just\n // works without an explicit mode click. We only flip when the\n // editor is currently in `select` mode -- a rectangle drag while\n // already in `move` / `eraser` / `hbond` mode keeps the user's\n // existing context. Empty rects (no atoms selected) leave the mode\n // alone: there's nothing to move, switching would be surprising.\n if (sel.atoms.size > 0 && this._editor.getMode() === 'select')\n this._editor.setMode('move');\n }\n\n private _handleMouseLeave(_e: MouseLike): void {\n if (this._hoverAtom !== null) {\n this._editor.fire('monomer:hover-end', { atom: this._hoverAtom });\n this._hoverAtom = null;\n }\n if (this._hoverBond !== null) {\n this._editor.fire('bond:hover-end', { bond: this._hoverBond });\n this._hoverBond = null;\n }\n if (this._bondStart !== null) {\n this._editor.fire('bond:cancel', { start: this._bondStart });\n this._editor.fire('bond:preview-end', { start: this._bondStart });\n this._bondStart = null;\n this._bondDragMoved = false;\n }\n this._dragOrigin = null;\n // Phase 13b (Bug 2) — Abort any in-progress pan if the cursor leaves\n // the host. Subsequent mousemoves outside the host don't reach us,\n // so without this the next re-entry would resume panning at a stale\n // origin and produce a visible jump.\n this._panStart = null;\n // Phase 15 (T-1504) — Same defence for the atom-drag state.\n this._atomDragState = null;\n // Phase 30 (T-3001) — Clear the click-suppression flags too;\n // no click will fire after a mouseleave-aborted drag and a stale\n // `true` would swallow the NEXT click instead.\n this._panMoved = false;\n this._atomDragMoved = false;\n // Phase 32 (T-3003) — Hide the ghost cursor when the pointer\n // leaves the canvas. The element stays mounted on body so the\n // next mouseenter+move can re-show it without re-creating.\n hideNextAddCursor(this._nextAddCursorEl);\n }\n\n /**\n * Phase 13b / 14B — Open the choose-R dialog for an ambiguous\n * cross-chain (or same-chain) bond drag. `freeR1` / `freeR2` are the\n * R-group indices on each endpoint that are still UNUSED — the dialog\n * shows only these (taken R-groups never appear so the user cannot\n * pick an over-allocated slot). The dialog resolves with `{r1, r2}` on\n * OK and `null` on Cancel/dismiss. Errors during the eventual\n * `addBond` surface as `bond:cancel` + the editor:status event that\n * `editor.addBond` itself fires.\n */\n private _openChooseR(\n start: Atom,\n target: Atom,\n bondKind: 'backbone' | 'cross-polymer',\n freeR1: readonly number[],\n freeR2: readonly number[],\n ): void {\n if (this._chooseRDialog === null)\n this._chooseRDialog = new ChooseRDialog(this._editor);\n const dialog = this._chooseRDialog;\n void dialog.open(start, target, { freeR1, freeR2 }).then((choice) => {\n if (this._destroyed) return;\n if (choice === null) {\n this._editor.fire('bond:cancel', { start });\n return;\n }\n try { this._editor.addBond(start, target, choice.r1, choice.r2, bondKind); }\n catch { this._editor.fire('bond:cancel', { start }); }\n });\n }\n\n /**\n * Phase 32 (T-3003) — Decide whether to show the ghost-cursor\n * preview at the current mouse position. The preview previews what\n * a left-click would add, so it shows exactly when the click would\n * SPAWN a new monomer:\n *\n * - mode === 'select' (other modes ignore palette adds — see\n * `_addsEnabled`).\n * - a tile is primed (`editor.getNextAddSymbol() !== null`).\n * - no atom under the cursor (an atom-under-cursor click goes\n * through the REPLACE branch in `_handleClick`, T-2405).\n * - no rect-drag, bond-drag, atom-drag, or pan in progress.\n *\n * The element is lazily created on first show. `hideNextAddCursor`\n * is a no-op on the initial null so calling it from `_handleMove`\n * before the first show is safe.\n */\n private _updateNextAddCursor(e: MouseLike): void {\n const next = this._editor.getNextAddSymbol();\n const mode = this._editor.getMode();\n const hoveringAtom = this._hoverAtom !== null;\n const dragging =\n this._bondStart !== null\n || this._dragOrigin !== null\n || this._panStart !== null\n || this._atomDragState !== null;\n const shouldShow =\n mode === 'select'\n && next !== null\n && !hoveringAtom\n && !dragging;\n if (!shouldShow) {\n if (this._nextAddCursorEl !== null) hideNextAddCursor(this._nextAddCursorEl);\n return;\n }\n const doc = this._host.ownerDocument;\n if (doc === null) return;\n if (this._nextAddCursorEl === null)\n this._nextAddCursorEl = getOrCreateNextAddCursor(doc);\n // Resolve the monomer's display fields from the editor's library\n // (so the ghost picks up `meta.colors`, custom fills, etc. -- the\n // SAME data the renderer consumes). `MonomerLib.getMonomer` keys\n // on `(polymerType, symbol)`, not `(biotype, symbol)`; we scan\n // the lib's polymer types and take the first match, mirroring\n // `palette.ts:_findMonomer`. A null monomer is fine -- the\n // renderer falls back to the error palette so the ghost stays\n // visible even when the symbol isn't in the active library.\n const lib = this._editor.getService().monomerLib;\n let monomer = null;\n for (const pt of lib.getPolymerTypes()) {\n const m = lib.getMonomer(pt, next.symbol);\n if (m !== null) { monomer = m; break; }\n }\n showNextAddCursor(\n this._nextAddCursorEl,\n next.symbol,\n next.biotype,\n monomer,\n this._editor['_currentTheme'](),\n e.clientX,\n e.clientY,\n );\n }\n\n /**\n * Phase 20 (T-2001) — Are add-monomer paths armed for the current mode?\n *\n * Returns `true` ONLY when the editor is in `'select'` mode. Every\n * code path that consumes `editor.getNextAddSymbol()` to create a new\n * atom (empty-canvas click; drag-from-atom-to-empty) gates on this\n * predicate. Modes `'move'`, `'eraser'`, and `'hbond'` are inert\n * w.r.t. palette-primed adds — a click on empty canvas, or a drag\n * from an existing atom onto empty canvas, must NOT spawn a monomer\n * even when a tile remains visually \"primed\" in the palette.\n *\n * Rationale: the user reported (Phase 20 bug 1) \"when I have monomer\n * selected and in move mode, when I release the mouse monomer gets\n * added\". The synthetic click that follows a pan-mouseup was hitting\n * the empty-canvas add branch.\n */\n private _addsEnabled(): boolean {\n return this._editor.getMode() === 'select';\n }\n\n /** Wheel + Ctrl: zoom in/out around the cursor. Plain wheel: pass through. */\n private _handleWheel(e: WheelLike): void {\n if (!e.ctrlKey && !e.metaKey) return;\n e.preventDefault();\n const factor = e.deltaY < 0 ? 1.1 : 1 / 1.1;\n const around = this._toModel({ clientX: e.clientX, clientY: e.clientY });\n this._editor.zoom(factor, around);\n }\n\n /**\n * Convert client coordinates to model coordinates by inverting the SVG's\n * draw transform (T-1101). Tries `getScreenCTM()` first (real browsers),\n * falls back to parsing the `.hw-content` group's `transform` attribute\n * and applying the inverse manually (jsdom / linkedom).\n *\n * The fallback assumes the SVG fills the host (the standard editor\n * layout — `.hw-editor-view > svg` with `display:block; width:100%`).\n */\n private _toModel(e: { clientX: number; clientY: number }): Point {\n const svg = this._host.querySelector('svg');\n const content = svg !== null ? svg.querySelector('.hw-content') : null;\n if (svg !== null && content !== null) {\n const fromCtm = tryCtmInverse(content as unknown as SVGGraphicsElement, e.clientX, e.clientY);\n if (fromCtm !== null) return fromCtm;\n // Fallback: manual decode for jsdom/linkedom.\n const rect = this._host.getBoundingClientRect();\n const sx = e.clientX - rect.left;\n const sy = e.clientY - rect.top;\n const decoded = decodeTranslateScale(content.getAttribute('transform') ?? '');\n if (decoded !== null) {\n return {\n x: (sx - decoded.tx) / (decoded.scale === 0 ? 1 : decoded.scale),\n y: (sy - decoded.ty) / (decoded.scale === 0 ? 1 : decoded.scale),\n };\n }\n // No transform on `.hw-content` — surface coord equals model coord.\n return { x: sx, y: sy };\n }\n // No SVG mounted yet (pre-render) — fall back to raw host-relative.\n const rect = this._host.getBoundingClientRect();\n return { x: e.clientX - rect.left, y: e.clientY - rect.top };\n }\n}\n\ninterface WheelLike {\n clientX: number;\n clientY: number;\n deltaY: number;\n ctrlKey: boolean;\n metaKey: boolean;\n preventDefault(): void;\n}\n\n/**\n * Phase 14B (T-1413) — Decide how to commit a bond drag between two atoms.\n *\n * - `fail`: at least one endpoint has zero free numeric R-groups. The\n * caller cancels the preview and surfaces a status-bar message.\n * - `auto`: the unique sensible R-group pair was inferable; the caller\n * skips the chooser and adds the bond directly.\n * - `choose`: the pair is ambiguous; open the choose-R dialog with the\n * free-only option lists.\n *\n * **Heuristic note (linear peptide extension)**: When the user drags from\n * an atom whose R2 (C-term) is free, onto another peptide-type atom whose\n * R1 (N-term) is free, AND at least one of the two atoms has only one\n * free slot, we auto-pick `R2 → R1` regardless of the cross-chain\n * boundary. This matches the \"obvious extension\" case the user described:\n * \"for peptides, R2 of last monomer connects to R1 of next monomer\". When\n * BOTH atoms still have > 1 free slot, we punt to the chooser — there's\n * genuine ambiguity about which side ought to bind.\n *\n * For atoms without a resolved monomer (totalRgroups === 0) we fall back\n * to `(2, 1)` as the canonical first guess — the editor's addBond cap\n * check accepts this because there's no monomer constraint to violate.\n */\nexport type InferBondDecision =\n | { mode: 'auto'; r1: number; r2: number; kind: 'backbone' | 'cross-polymer' }\n | { mode: 'choose'; freeR1: number[]; freeR2: number[] }\n | { mode: 'fail'; reason: string };\n\nexport function inferBondConnection(\n start: Atom,\n target: Atom,\n bonds: readonly Bond[],\n bondKind: 'backbone' | 'cross-polymer',\n): InferBondDecision {\n const startTotal = totalRgroups(start);\n const targetTotal = totalRgroups(target);\n\n // Unresolved monomer on either side → no cap to enforce; fall back to\n // the canonical (R2, R1) default. The editor.addBond guard agrees:\n // totalRgroups === 0 disables the cap.\n if (startTotal === 0 || targetTotal === 0)\n return { mode: 'auto', r1: 2, r2: 1, kind: bondKind };\n\n const startFree = freeRgroups(start, bonds);\n const targetFree = freeRgroups(target, bonds);\n\n if (startFree.length === 0)\n return { mode: 'fail', reason: `${start.symbol} has no free R-groups (max ${startTotal}).` };\n if (targetFree.length === 0)\n return { mode: 'fail', reason: `${target.symbol} has no free R-groups (max ${targetTotal}).` };\n\n // Linear peptide extension heuristic: R2-on-start + R1-on-target with\n // at least one side narrowed to a single option. Matches the user's\n // mental model of extending a chain.\n if (startFree.includes(2) && targetFree.includes(1)\n && (startFree.length === 1 || targetFree.length === 1))\n return { mode: 'auto', r1: 2, r2: 1, kind: bondKind };\n\n // Each side has exactly one free slot — unambiguous.\n if (startFree.length === 1 && targetFree.length === 1) {\n const r1 = startFree[0] as number;\n const r2 = targetFree[0] as number;\n return { mode: 'auto', r1, r2, kind: bondKind };\n }\n\n // Genuinely ambiguous — surface the chooser with FREE-ONLY options.\n return { mode: 'choose', freeR1: startFree, freeR2: targetFree };\n}\n\n/**\n * Invert the element's screen CTM and project `(clientX, clientY)` into the\n * element's local coordinate space. Returns null when CTM is unavailable or\n * not invertible (typical in headless DOMs).\n */\nfunction tryCtmInverse(el: SVGGraphicsElement, clientX: number, clientY: number): Point | null {\n const e = el as unknown as {\n getScreenCTM?: () => DOMMatrix | null;\n ownerSVGElement?: { createSVGPoint?: () => { x: number; y: number; matrixTransform(m: DOMMatrix): { x: number; y: number } } };\n };\n if (typeof e.getScreenCTM !== 'function') return null;\n const ctm = e.getScreenCTM();\n if (ctm === null) return null;\n let inv: DOMMatrix | null = null;\n try {\n const m = ctm as unknown as { inverse?: () => DOMMatrix };\n if (typeof m.inverse === 'function') inv = m.inverse();\n } catch {\n return null;\n }\n if (inv === null) return null;\n const svg = e.ownerSVGElement;\n if (svg !== null && svg !== undefined && typeof svg.createSVGPoint === 'function') {\n const p = svg.createSVGPoint();\n p.x = clientX;\n p.y = clientY;\n const r = p.matrixTransform(inv);\n return { x: r.x, y: r.y };\n }\n // Manual: apply the inverse matrix's a/b/c/d/e/f directly.\n const m = inv as unknown as { a: number; b: number; c: number; d: number; e: number; f: number };\n return {\n x: m.a * clientX + m.c * clientY + m.e,\n y: m.b * clientX + m.d * clientY + m.f,\n };\n}\n\n/**\n * Decode a `transform=\"translate(tx ty) scale(s)\"` attribute. Supports the\n * two shapes the renderer emits (with and without explicit scale arg) and\n * tolerates the viewport-prepended form `translate(0 0) scale(1) translate(...) scale(...)`\n * by composing left-to-right.\n */\nfunction decodeTranslateScale(transform: string): { tx: number; ty: number; scale: number } | null {\n if (transform === '') return null;\n // Compose: start with identity, multiply each translate/scale token in order.\n let tx = 0;\n let ty = 0;\n let scale = 1;\n const re = /(translate|scale)\\(([^)]+)\\)/g;\n let m: RegExpExecArray | null;\n let matched = false;\n while ((m = re.exec(transform)) !== null) {\n matched = true;\n const kind = m[1];\n const args = (m[2] ?? '').split(/[,\\s]+/).map((s) => Number(s)).filter((n) => Number.isFinite(n));\n if (kind === 'translate') {\n const dx = args[0] ?? 0;\n const dy = args[1] ?? 0;\n tx = tx + scale * dx;\n ty = ty + scale * dy;\n } else if (kind === 'scale') {\n const s = args[0] ?? 1;\n scale = scale * s;\n }\n }\n return matched ? { tx, ty, scale } : null;\n}\n\n/**\n * Phase 15 (T-1505) — Are `a` and `b` adjacent backbone atoms in the same\n * chain? Used by the pointer mouseup handler to decide between a `backbone`\n * (adjacent) and `cross-polymer` (non-adjacent, e.g. cyclic closure)\n * bond kind. Returns `false` when the atoms live in different chains or\n * the chain cannot be located.\n */\nexport function areAdjacentInChain(a: Atom, b: Atom, mol: Mol): boolean {\n if (a.bio.chainId !== b.bio.chainId) return false;\n const chain = mol.chains.find((c) => c.id === a.bio.chainId);\n if (chain === undefined) return false;\n let ia = -1;\n let ib = -1;\n for (let i = 0; i < chain.backboneAtoms.length; i++) {\n const at = chain.backboneAtoms[i]!;\n if (at.id === a.id) ia = i;\n if (at.id === b.id) ib = i;\n }\n if (ia < 0 || ib < 0) return false;\n return Math.abs(ia - ib) === 1;\n}\n\nfunction modsOf(e: MouseLike): ModifierKeys {\n return {\n shift: e.shiftKey === true,\n alt: e.altKey === true,\n ctrl: e.ctrlKey === true,\n meta: e.metaKey === true,\n };\n}\n\nfunction rectFromPoints(a: Point, b: Point): Rect {\n const x = Math.min(a.x, b.x);\n const y = Math.min(a.y, b.y);\n return { x, y, width: Math.abs(a.x - b.x), height: Math.abs(a.y - b.y) };\n}\n","// T-0504 — Keyboard input handler.\n//\n// Listens for keystrokes on the host (the host must be focusable, so we set\n// tabindex=\"0\" if not already set). Each handler fires `key:command` first\n// with a `preventDefault()` that suppresses internal handling; unmatched\n// keystrokes fire `key:unhandled`.\n//\n// See EVENTS.md §9 for the command list.\n\nimport type { HelmEditor } from '../editor';\nimport type { ModifierKeys } from '../events';\n\n/** Options for the keyboard input layer. */\nexport interface KeyboardInputOptions {\n enableKeyboard?: boolean;\n}\n\n/** Minimal KeyboardEvent shape we read from. */\ninterface KeyLike {\n key: string;\n shiftKey: boolean;\n altKey: boolean;\n ctrlKey: boolean;\n metaKey: boolean;\n preventDefault(): void;\n stopPropagation(): void;\n}\n\n/**\n * Keyboard input layer. Bind a single `keydown` listener on `host`; on each\n * stroke, classify it as a command, fire `key:command` (which any handler can\n * suppress by calling `preventDefault`), then run the internal action.\n */\nexport class KeyboardInput {\n private readonly _host: HTMLElement;\n private readonly _editor: HelmEditor;\n private readonly _enabled: boolean;\n private _destroyed: boolean = false;\n private readonly _onKey: (e: Event) => void;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: KeyboardInputOptions) {\n this._host = host;\n this._editor = editor;\n this._enabled = options?.enableKeyboard !== false;\n if (this._enabled && host.getAttribute('tabindex') === null)\n host.setAttribute('tabindex', '0');\n this._onKey = (e: Event): void => this._handleKey(e as unknown as KeyLike);\n host.addEventListener('keydown', this._onKey);\n }\n\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n this._host.removeEventListener('keydown', this._onKey);\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _handleKey(e: KeyLike): void {\n if (!this._enabled) return;\n const command = this._classify(e);\n const mods = modsOf(e);\n if (command === null) {\n this._editor.fire('key:unhandled', {\n key: e.key,\n modifiers: mods,\n preventDefault: () => e.preventDefault(),\n });\n return;\n }\n let suppressed = false;\n const preventDefault = (): void => {\n suppressed = true;\n e.preventDefault();\n };\n this._editor.fire('key:command', { command, preventDefault });\n if (suppressed) return;\n e.preventDefault();\n this._execute(command);\n }\n\n private _classify(e: KeyLike): string | null {\n const k = e.key;\n const cmd = e.ctrlKey || e.metaKey;\n if (k === 'Delete' || k === 'Backspace') return 'delete';\n if (cmd && (k === 'z' || k === 'Z') && !e.shiftKey) return 'undo';\n if (cmd && ((k === 'z' || k === 'Z') && e.shiftKey || k === 'y' || k === 'Y')) return 'redo';\n if (cmd && (k === 'a' || k === 'A')) return 'selectAll';\n // T-1107 — Route Ctrl/Cmd+C / +V / +X through the editor so the host can\n // observe `key:command` and the editor can fire `clipboard:copy` etc.\n if (cmd && (k === 'c' || k === 'C')) return 'copy';\n if (cmd && (k === 'v' || k === 'V')) return 'paste';\n if (cmd && (k === 'x' || k === 'X')) return 'cut';\n if (k === 'Escape') return 'clearSelection';\n if (k === '+' || k === '=') return 'zoomIn';\n if (k === '-' || k === '_') return 'zoomOut';\n if (k === '0') return 'fitToContent';\n if (k === 'ArrowUp') return 'nudgeUp';\n if (k === 'ArrowDown') return 'nudgeDown';\n if (k === 'ArrowLeft') return 'nudgeLeft';\n if (k === 'ArrowRight') return 'nudgeRight';\n return null;\n }\n\n private _execute(command: string): void {\n switch (command) {\n case 'delete':\n this._editor.deleteSelection();\n return;\n case 'undo':\n this._editor.undo();\n return;\n case 'redo':\n this._editor.redo();\n return;\n case 'selectAll':\n this._editor.selectAll();\n return;\n case 'clearSelection':\n this._editor.clearSelection();\n return;\n case 'zoomIn':\n this._editor.zoom(1.1);\n return;\n case 'zoomOut':\n this._editor.zoom(1 / 1.1);\n return;\n case 'fitToContent':\n this._editor.fitToContent();\n return;\n case 'nudgeUp':\n this._editor.nudgeSelection(0, -5);\n return;\n case 'nudgeDown':\n this._editor.nudgeSelection(0, 5);\n return;\n case 'nudgeLeft':\n this._editor.nudgeSelection(-5, 0);\n return;\n case 'nudgeRight':\n this._editor.nudgeSelection(5, 0);\n return;\n case 'copy': {\n // Fire `clipboard:copy` with the editor's serialized HELM so hosts\n // (and the test bridge) can observe a real keyboard-driven copy.\n const helm = this._editor.getHelm();\n this._editor.fire('clipboard:copy', { format: 'helm', payload: helm });\n return;\n }\n case 'cut': {\n const helm = this._editor.getHelm();\n this._editor.fire('clipboard:copy', { format: 'helm', payload: helm });\n this._editor.deleteSelection();\n return;\n }\n case 'paste':\n // Paste is host-driven (we don't synthesise a paste payload here).\n this._editor.fire('clipboard:paste', { format: 'helm' });\n return;\n default:\n return;\n }\n }\n}\n\nfunction modsOf(e: KeyLike): ModifierKeys {\n return {\n shift: e.shiftKey === true,\n alt: e.altKey === true,\n ctrl: e.ctrlKey === true,\n meta: e.metaKey === true,\n };\n}\n","// T-0505 / T-1102 — Drag-and-drop input handler.\n//\n// Real HTML5 DnD path:\n// 1. Palette tiles set `dataTransfer.setData('application/x-hwe-monomer', JSON)`\n// on `dragstart` (see palette.ts).\n// 2. The canvas/host calls `e.preventDefault()` on `dragover` so the\n// browser treats it as a drop zone and sets `dropEffect = 'copy'`.\n// 3. The `drop` handler reads `dataTransfer` and falls back to the\n// in-flight `_currentPaletteSymbol` (set via `startPaletteDrag`) for\n// programmatic callers / headless tests where the synthesized\n// `DataTransfer` may be missing data.\n//\n// We share `_toModel` with `PointerInput` (T-1101) so a drop on a real SVG\n// resolves to true model coords.\n\nimport type { Atom, Bond } from '../../core/model';\nimport type { HelmType } from '../../core/constants';\nimport { HitTester } from '../../render/hit-test';\nimport type { Point } from '../../util/types';\nimport type { HelmEditor } from '../editor';\n\n/** Mime type used by HWE palette tiles when initiating an HTML5 drag. */\nexport const HWE_DND_MIME = 'application/x-hwe-monomer';\n\n/** Minimal DragEvent-like shape we read from. */\ninterface DndLike {\n clientX: number;\n clientY: number;\n preventDefault(): void;\n stopPropagation(): void;\n dataTransfer: DataTransferLike | null;\n}\n\n/** Subset of `DataTransfer` we touch. */\ninterface DataTransferLike {\n dropEffect?: string;\n effectAllowed?: string;\n setData(type: string, data: string): void;\n getData(type: string): string;\n}\n\n/**\n * Drag-and-drop input. Listens to native DnD events on the host, plus exposes\n * `startPaletteDrag(symbol, biotype)` for programmatic callers. The two paths\n * converge in `_handleDrop`: whichever channel supplies a (symbol, biotype),\n * the drop commits the same way (replace target / addAtom on empty).\n */\nexport class DragDropInput {\n private readonly _host: HTMLElement;\n private readonly _editor: HelmEditor;\n private _tester: HitTester;\n private _currentPaletteSymbol: string | null = null;\n private _currentPaletteBiotype: HelmType | null = null;\n private _destroyed: boolean = false;\n private readonly _unsubs: Array<() => void> = [];\n\n private readonly _onDragOver: (e: Event) => void;\n private readonly _onDrop: (e: Event) => void;\n private readonly _onDragStart: (e: Event) => void;\n private readonly _onDragEnd: (e: Event) => void;\n private readonly _onDragEnter: (e: Event) => void;\n private readonly _onDragLeave: (e: Event) => void;\n\n constructor(host: HTMLElement, editor: HelmEditor) {\n this._host = host;\n this._editor = editor;\n this._tester = new HitTester(editor.getMol(), editor['_currentTheme']());\n\n this._unsubs.push(editor.on('mol:changed', () => {\n this._tester = new HitTester(this._editor.getMol(), this._editor['_currentTheme']());\n }));\n\n this._onDragOver = (e: Event): void => this._handleDragOver(e as unknown as DndLike);\n this._onDrop = (e: Event): void => this._handleDrop(e as unknown as DndLike);\n this._onDragStart = (e: Event): void => this._handleDragStart(e as unknown as DndLike);\n this._onDragEnd = (e: Event): void => this._handleDragEnd(e as unknown as DndLike);\n this._onDragEnter = (e: Event): void => this._handleDragEnter(e as unknown as DndLike);\n this._onDragLeave = (e: Event): void => this._handleDragLeave(e as unknown as DndLike);\n\n host.addEventListener('dragover', this._onDragOver);\n host.addEventListener('drop', this._onDrop);\n host.addEventListener('dragstart', this._onDragStart);\n host.addEventListener('dragend', this._onDragEnd);\n host.addEventListener('dragenter', this._onDragEnter);\n host.addEventListener('dragleave', this._onDragLeave);\n }\n\n /**\n * External entry point: kick off a drag from a palette tile (programmatic /\n * test path). The user-facing HTML5 path doesn't need this — palette tiles\n * call `setData(HWE_DND_MIME, JSON)` directly on `dragstart` (see\n * `palette.ts`). Calling this method is still useful when the host wants\n * to script a drop without going through a real `dragstart`.\n */\n startPaletteDrag(symbol: string, biotype: HelmType): void {\n this._currentPaletteSymbol = symbol;\n this._currentPaletteBiotype = biotype;\n this._editor.fire('dnd:start', { source: 'palette', symbol });\n }\n\n /** Cancel any in-flight palette drag. */\n cancelPaletteDrag(): void {\n if (this._currentPaletteSymbol === null) return;\n this._currentPaletteSymbol = null;\n this._currentPaletteBiotype = null;\n this._editor.fire('dnd:cancel', { source: 'palette' });\n }\n\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n this._host.removeEventListener('dragover', this._onDragOver);\n this._host.removeEventListener('drop', this._onDrop);\n this._host.removeEventListener('dragstart', this._onDragStart);\n this._host.removeEventListener('dragend', this._onDragEnd);\n this._host.removeEventListener('dragenter', this._onDragEnter);\n this._host.removeEventListener('dragleave', this._onDragLeave);\n }\n\n // ------------------------------------------------------------------------\n // Handlers\n // ------------------------------------------------------------------------\n\n private _activePaletteSymbol(e: DndLike): { symbol: string; biotype: HelmType } | null {\n if (this._currentPaletteSymbol !== null && this._currentPaletteBiotype !== null)\n return { symbol: this._currentPaletteSymbol, biotype: this._currentPaletteBiotype };\n // Try reading the HTML5 DataTransfer payload (set by palette.ts).\n const dt = e.dataTransfer;\n if (dt === null || dt === undefined) return null;\n try {\n const raw = typeof dt.getData === 'function' ? dt.getData(HWE_DND_MIME) : '';\n if (raw === '') return null;\n const parsed = JSON.parse(raw) as { symbol?: unknown; biotype?: unknown };\n if (typeof parsed.symbol !== 'string' || typeof parsed.biotype !== 'string') return null;\n return { symbol: parsed.symbol, biotype: parsed.biotype as HelmType };\n } catch {\n return null;\n }\n }\n\n private _handleDragEnter(e: DndLike): void {\n const active = this._activePaletteSymbol(e);\n if (active === null) return;\n e.preventDefault();\n if (e.dataTransfer !== null && e.dataTransfer !== undefined) {\n try { e.dataTransfer.dropEffect = 'copy'; } catch { /* read-only in some environments */ }\n }\n }\n\n private _handleDragLeave(_e: DndLike): void {\n // Visual leave handled by CSS via :hover on host; nothing to do here.\n }\n\n private _handleDragOver(e: DndLike): void {\n const active = this._activePaletteSymbol(e);\n if (active === null) return;\n e.preventDefault(); // mandatory to mark host as a valid drop target\n if (e.dataTransfer !== null && e.dataTransfer !== undefined) {\n try { e.dataTransfer.dropEffect = 'copy'; } catch { /* ignore */ }\n }\n const p = this._toModel(e);\n const r = this._tester.test(p);\n const target: Atom | Bond | undefined =\n r?.atom !== undefined ? r.atom : (r?.bond !== undefined ? r.bond : undefined);\n const payload: { clientX: number; clientY: number; target?: Atom | Bond } = {\n clientX: e.clientX,\n clientY: e.clientY,\n };\n if (target !== undefined) payload.target = target;\n this._editor.fire('dnd:over', payload);\n }\n\n private _handleDrop(e: DndLike): void {\n const active = this._activePaletteSymbol(e);\n if (active === null) return;\n e.preventDefault();\n const { symbol, biotype } = active;\n const p = this._toModel(e);\n const r = this._tester.test(p);\n const target: Atom | Bond | undefined =\n r?.atom !== undefined ? r.atom : (r?.bond !== undefined ? r.bond : undefined);\n const payload: { symbol: string; biotype: HelmType; target?: Atom | Bond; clientX: number; clientY: number } = {\n symbol,\n biotype,\n clientX: e.clientX,\n clientY: e.clientY,\n };\n if (target !== undefined) payload.target = target;\n this._editor.fire('dnd:drop', payload);\n\n if (r?.atom !== undefined) {\n this._editor.replaceMonomer(r.atom, symbol);\n } else {\n this._editor.addAtom(p, biotype, symbol);\n }\n\n this._currentPaletteSymbol = null;\n this._currentPaletteBiotype = null;\n }\n\n private _handleDragStart(_e: DndLike): void {\n this._editor.fire('dnd:start', { source: 'canvas' });\n }\n\n private _handleDragEnd(_e: DndLike): void {\n if (this._currentPaletteSymbol !== null) {\n this._currentPaletteSymbol = null;\n this._currentPaletteBiotype = null;\n this._editor.fire('dnd:cancel', { source: 'palette' });\n }\n }\n\n /**\n * Same model-coordinate transform as `PointerInput._toModel` (T-1101).\n * We duplicate (small, contained logic) rather than expose internals.\n */\n private _toModel(e: { clientX: number; clientY: number }): Point {\n const svg = this._host.querySelector('svg');\n const content = svg !== null ? svg.querySelector('.hw-content') : null;\n if (svg !== null && content !== null) {\n const fromCtm = tryCtmInverseDnd(content as unknown as SVGGraphicsElement, e.clientX, e.clientY);\n if (fromCtm !== null) return fromCtm;\n const rect = this._host.getBoundingClientRect();\n const sx = e.clientX - rect.left;\n const sy = e.clientY - rect.top;\n const decoded = decodeTranslateScaleDnd(content.getAttribute('transform') ?? '');\n if (decoded !== null) {\n return {\n x: (sx - decoded.tx) / (decoded.scale === 0 ? 1 : decoded.scale),\n y: (sy - decoded.ty) / (decoded.scale === 0 ? 1 : decoded.scale),\n };\n }\n return { x: sx, y: sy };\n }\n const rect = this._host.getBoundingClientRect();\n return { x: e.clientX - rect.left, y: e.clientY - rect.top };\n }\n}\n\nfunction tryCtmInverseDnd(el: SVGGraphicsElement, clientX: number, clientY: number): Point | null {\n const e = el as unknown as {\n getScreenCTM?: () => DOMMatrix | null;\n ownerSVGElement?: { createSVGPoint?: () => { x: number; y: number; matrixTransform(m: DOMMatrix): { x: number; y: number } } };\n };\n if (typeof e.getScreenCTM !== 'function') return null;\n const ctm = e.getScreenCTM();\n if (ctm === null) return null;\n let inv: DOMMatrix | null = null;\n try {\n const m = ctm as unknown as { inverse?: () => DOMMatrix };\n if (typeof m.inverse === 'function') inv = m.inverse();\n } catch {\n return null;\n }\n if (inv === null) return null;\n const svg = e.ownerSVGElement;\n if (svg !== null && svg !== undefined && typeof svg.createSVGPoint === 'function') {\n const p = svg.createSVGPoint();\n p.x = clientX;\n p.y = clientY;\n const r = p.matrixTransform(inv);\n return { x: r.x, y: r.y };\n }\n const m = inv as unknown as { a: number; b: number; c: number; d: number; e: number; f: number };\n return {\n x: m.a * clientX + m.c * clientY + m.e,\n y: m.b * clientX + m.d * clientY + m.f,\n };\n}\n\nfunction decodeTranslateScaleDnd(transform: string): { tx: number; ty: number; scale: number } | null {\n if (transform === '') return null;\n let tx = 0;\n let ty = 0;\n let scale = 1;\n const re = /(translate|scale)\\(([^)]+)\\)/g;\n let m: RegExpExecArray | null;\n let matched = false;\n while ((m = re.exec(transform)) !== null) {\n matched = true;\n const kind = m[1];\n const args = (m[2] ?? '').split(/[,\\s]+/).map((s) => Number(s)).filter((n) => Number.isFinite(n));\n if (kind === 'translate') {\n const dx = args[0] ?? 0;\n const dy = args[1] ?? 0;\n tx = tx + scale * dx;\n ty = ty + scale * dy;\n } else if (kind === 'scale') {\n const s = args[0] ?? 1;\n scale = scale * s;\n }\n }\n return matched ? { tx, ty, scale } : null;\n}\n","// T-0507 — Atom properties dialog.\n//\n// Renders a small modal with read-only position info and editable symbol /\n// annotation / hidden fields. OK commits via Transaction; Cancel detaches\n// without changes.\n\nimport type { Atom } from '../../core/model';\nimport { Transaction } from '../../core/transaction';\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\nimport { Modal, textRow, checkboxRow, actionRow } from './modal';\n\n/** Options for `AtomPropsDialog`. */\nexport interface AtomPropsDialogOptions {\n documentImpl?: Document;\n}\n\n/** Editable monomer-property dialog. */\nexport class AtomPropsDialog {\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private _modal: Modal | null = null;\n private _atom: Atom | null = null;\n\n constructor(editor: HelmEditor, options?: AtomPropsDialogOptions) {\n this._editor = editor;\n const host = editor._getHost();\n if (host === null) throw new Error('AtomPropsDialog: editor has no host element.');\n this._doc = options?.documentImpl ?? getDocument(host);\n }\n\n /** True when the dialog is currently mounted. */\n get isOpen(): boolean { return this._modal !== null && this._modal.isOpen; }\n\n /** Open the dialog for `atom`. */\n open(atom: Atom): void {\n this.close();\n this._atom = atom;\n const host = this._editor._getHost();\n if (host === null) return;\n const modal = new Modal(host, { documentImpl: this._doc, title: 'Monomer Properties', testId: 'atom-props' });\n this._modal = modal;\n\n const info = el(this._doc, 'div', { class: 'hw-modal__info' }, [\n `Position ${atom.bio.continuousId} in ${atom.bio.chainId}`,\n ]);\n const sym = textRow(this._doc, 'Symbol', atom.symbol, 'atom-props-symbol');\n const ann = textRow(this._doc, 'Annotation', atom.bio.annotation ?? '', 'atom-props-annotation');\n const hidden = checkboxRow(this._doc, 'Hidden', atom.hidden, 'atom-props-hidden');\n const actions = actionRow(this._doc, 'atom-props');\n\n actions.ok.addEventListener('click', () => this._commit(sym.input.value, ann.input.value, !!hidden.input.checked));\n actions.cancel.addEventListener('click', () => this.close());\n\n modal.body.appendChild(info);\n modal.body.appendChild(sym.row);\n modal.body.appendChild(ann.row);\n modal.body.appendChild(hidden.row);\n modal.body.appendChild(actions.row);\n modal.open();\n }\n\n /** Close the dialog. Idempotent. */\n close(): void {\n if (this._modal !== null) {\n this._modal.close();\n this._modal = null;\n }\n this._atom = null;\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _commit(symbol: string, annotation: string, hidden: boolean): void {\n const atom = this._atom;\n if (atom === null) { this.close(); return; }\n\n const trimmedSymbol = symbol.trim();\n const annotationChanged = (atom.bio.annotation ?? '') !== annotation;\n const hiddenChanged = atom.hidden !== hidden;\n const symbolChanged = trimmedSymbol.length > 0 && trimmedSymbol !== atom.symbol;\n\n if (symbolChanged) this._editor.replaceMonomer(atom, trimmedSymbol);\n if (annotationChanged || hiddenChanged) {\n // The Transaction.updateAtom patch doesn't support `bio.annotation` directly,\n // so we patch via tag-style helpers: hidden directly, annotation via a\n // small Mol mutation. The current Transaction surface supports `hidden`\n // and `tag`; we drop annotation to `tag` for now (a placeholder so the\n // change is recorded and the event fires).\n const tx = new Transaction(this._editor.getMol());\n const patch: { hidden?: boolean; tag?: string | undefined } = {};\n if (hiddenChanged) patch.hidden = hidden;\n if (annotationChanged) patch.tag = annotation === '' ? undefined : annotation;\n tx.updateAtom(atom.id, patch);\n const { mol } = tx.commit();\n this._editor.setMol(mol);\n if (annotationChanged) {\n const updated = mol.atoms.find((a) => a.id === atom.id);\n if (updated !== undefined) {\n const payload: {\n atom: Atom;\n oldAnnotation?: string;\n newAnnotation?: string;\n } = { atom: updated };\n if (atom.bio.annotation !== undefined) payload.oldAnnotation = atom.bio.annotation;\n if (annotation !== '') payload.newAnnotation = annotation;\n this._editor.fire('monomer:annotate', payload);\n }\n }\n }\n\n this.close();\n }\n}\n","// T-0508 — Bond properties dialog.\n//\n// Renders a small modal with the bond's kind (read-only) and R-group\n// pickers per endpoint. Phase 23 added an RDKit structures row. Phase\n// 24 (T-2407) removed the ratio numerator/denominator inputs AND the\n// annotation textbox -- the user reported those fields are unused and\n// clutter the dialog. OK commits via `editor.removeBond` +\n// `editor.addBond` (so the cap check re-runs against a clean mol);\n// Cancel detaches without changes.\n\nimport type { Bond, RGroupRef, Atom } from '../../core/model';\nimport { freeRgroups } from '../../core/rgroups';\nimport { HwError } from '../../core/errors';\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\nimport { renderRdkitSvg, type RdkitLike } from '../view/tooltip-rdkit';\nimport { Modal, selectRow, actionRow } from './modal';\n\n/** Options for `BondPropsDialog`. */\nexport interface BondPropsDialogOptions {\n documentImpl?: Document;\n}\n\n/** Editable bond-property dialog. */\nexport class BondPropsDialog {\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private _modal: Modal | null = null;\n private _bond: Bond | null = null;\n\n constructor(editor: HelmEditor, options?: BondPropsDialogOptions) {\n this._editor = editor;\n const host = editor._getHost();\n if (host === null) throw new Error('BondPropsDialog: editor has no host element.');\n this._doc = options?.documentImpl ?? getDocument(host);\n }\n\n get isOpen(): boolean { return this._modal !== null && this._modal.isOpen; }\n\n open(bond: Bond): void {\n this.close();\n this._bond = bond;\n const host = this._editor._getHost();\n if (host === null) return;\n const modal = new Modal(host, { documentImpl: this._doc, title: 'Bond Properties', testId: 'bond-props' });\n this._modal = modal;\n\n const info = el(this._doc, 'div', { class: 'hw-modal__info' }, [`Kind: ${bond.kind}`]);\n\n // Phase 23 (T-2304) -- User asked for both endpoint molecules to be\n // rendered in the bond editor when RDKit is available, so the user\n // can see the atomic structures while picking R-groups. We probe\n // `service.options.rdkitModule` (same pattern view.ts and palette\n // use) and silently skip the block when RDKit is absent so headless\n // tests / embedders without RDKit get the same dialog as before.\n const atomsRow = this._buildAtomsPreviewRow(bond);\n\n // Phase 14B (T-1415) — R-group editor rows. For numeric refs, show\n // a dropdown with the FREE R-groups on each endpoint plus the\n // current pick (so the user can keep it or switch to any free\n // slot). Non-numeric refs (`unspecified`/`wildcard`/`pair`) are\n // shown read-only — editing them would require a different UX (the\n // user would need to first convert them to numeric).\n const a1Numeric = bond.r1.kind === 'numeric';\n const a2Numeric = bond.r2.kind === 'numeric';\n const editable = a1Numeric && a2Numeric;\n const mol = this._editor.getMol();\n const bonds = mol.bonds;\n // Compute \"free + current\" option sets. The current R-group on\n // each side is always in the dropdown (it represents \"keep the\n // existing pick\") even though it's technically \"taken\" by this\n // very bond.\n const optsR1 = editable\n ? buildRSelectValues(bond.r1 as RGroupRef & { kind: 'numeric' }, bond.a1, bonds)\n : [];\n const optsR2 = editable\n ? buildRSelectValues(bond.r2 as RGroupRef & { kind: 'numeric' }, bond.a2, bonds)\n : [];\n\n let r1Sel: { row: HTMLElement; select: HTMLSelectElement } | null = null;\n let r2Sel: { row: HTMLElement; select: HTMLSelectElement } | null = null;\n if (editable) {\n const currentR1 = String((bond.r1 as RGroupRef & { kind: 'numeric' }).r);\n const currentR2 = String((bond.r2 as RGroupRef & { kind: 'numeric' }).r);\n r1Sel = selectRow(this._doc,\n `R-group on ${bond.a1.symbol} (${bond.a1.bio.chainId}:${bond.a1.bio.positionInChain})`,\n optsR1, currentR1, 'bond-props-r1');\n r2Sel = selectRow(this._doc,\n `R-group on ${bond.a2.symbol} (${bond.a2.bio.chainId}:${bond.a2.bio.positionInChain})`,\n optsR2, currentR2, 'bond-props-r2');\n }\n\n // Phase 24 (T-2407): the ratio + annotation rows that lived here\n // (numerator, denominator, annotation textbox) were dropped per\n // user report \"nobody uses ratio/annotation -- the structures and\n // R-groups are what matter for picking a bond\". The dialog now\n // shows only kind, the structure preview row, and the R-group\n // selectors.\n const actions = actionRow(this._doc, 'bond-props');\n\n actions.ok.addEventListener('click', () => {\n const newR1 = r1Sel !== null ? Number(parseSelectValueLocal(r1Sel.select, (bond.r1 as RGroupRef & { kind: 'numeric' }).r)) : null;\n const newR2 = r2Sel !== null ? Number(parseSelectValueLocal(r2Sel.select, (bond.r2 as RGroupRef & { kind: 'numeric' }).r)) : null;\n this._commit(newR1, newR2);\n });\n actions.cancel.addEventListener('click', () => this.close());\n\n modal.body.appendChild(info);\n if (atomsRow !== null) modal.body.appendChild(atomsRow);\n if (r1Sel !== null) modal.body.appendChild(r1Sel.row);\n if (r2Sel !== null) modal.body.appendChild(r2Sel.row);\n modal.body.appendChild(actions.row);\n modal.open();\n }\n\n /**\n * Phase 23 (T-2304) -- Render a row containing both endpoint atoms'\n * structures via RDKit. Returns `null` when neither endpoint has a\n * smiles string AND RDKit is unavailable so the dialog falls back to\n * its pre-Phase-23 layout. Each endpoint cell carries a stable\n * `data-testid` (`bond-props-atom-a1` / `bond-props-atom-a2`) plus an\n * inner `*-rdkit` testid for the structure SVG container, so e2e\n * specs can address them deterministically.\n */\n private _buildAtomsPreviewRow(bond: Bond): HTMLElement | null {\n const rdkit = this._rdkit();\n // We still render the labels / arrow row even without RDKit so the\n // dialog always shows the symbol -- name for each endpoint. The\n // SVG container stays empty when RDKit cannot resolve a structure.\n const cellA = this._buildAtomCell(bond.a1, rdkit, 'bond-props-atom-a1');\n const cellB = this._buildAtomCell(bond.a2, rdkit, 'bond-props-atom-a2');\n const arrow = el(this._doc, 'div', { class: 'hw-bond-props__bond-arrow' }, ['↔']);\n return el(this._doc, 'div', {\n class: 'hw-bond-props__atoms',\n 'data-testid': 'bond-props-atoms',\n }, [cellA, arrow, cellB]);\n }\n\n private _buildAtomCell(atom: Atom, rdkit: RdkitLike | null, testid: string): HTMLElement {\n const name = atom.monomer?.name ?? atom.symbol;\n const label = atom.symbol === name\n ? atom.symbol\n : `${atom.symbol} — ${name}`;\n const labelEl = el(this._doc, 'div', { class: 'hw-bond-props__atom-label' }, [label]);\n const svgAttrs: Record<string, string> = {\n class: 'hw-bond-props__atom-rdkit',\n 'data-testid': `${testid}-rdkit`,\n };\n const rdkitWrap = el(this._doc, 'div', svgAttrs);\n const smiles = atom.monomer?.smiles;\n if (rdkit !== null && smiles !== undefined && smiles !== '') {\n // 220x140 matches the tooltip default; the SVG carries its own\n // viewBox so the .hw-bond-props__atom-rdkit svg { width:100%;\n // height:100% } rule in editor.css down-scales it to the 180x120\n // cell.\n const svg = renderRdkitSvg(rdkit, smiles, 220, 140);\n if (svg !== null && svg !== '') {\n (rdkitWrap as unknown as { innerHTML: string }).innerHTML = svg;\n }\n }\n return el(this._doc, 'div', {\n class: 'hw-bond-props__atom',\n 'data-testid': testid,\n }, [labelEl, rdkitWrap]);\n }\n\n /**\n * Phase 23 (T-2304) -- Probe the host service for an optional RDKit\n * module. Mirrors the lookup pattern in palette.ts / rna-builder.ts so\n * a single `service.options.rdkitModule` setting flows to every\n * tooltip + dialog surface.\n */\n private _rdkit(): RdkitLike | null {\n const svc = this._editor.getService() as unknown as {\n options?: { rdkitModule?: unknown };\n };\n const mod = svc.options?.rdkitModule;\n return (mod === undefined || mod === null) ? null : (mod as RdkitLike);\n }\n\n close(): void {\n if (this._modal !== null) {\n this._modal.close();\n this._modal = null;\n }\n this._bond = null;\n }\n\n /**\n * Phase 24 (T-2407) -- Apply the user's R-group changes. Ratio /\n * annotation fields were removed; OK now only acts on the R-group\n * dropdowns. When no R-groups changed the OK is a no-op (close).\n */\n private _commit(newR1: number | null, newR2: number | null): void {\n const bond = this._bond;\n if (bond === null) { this.close(); return; }\n\n // Phase 14B (T-1415) — R-group re-assignment is a remove-then-add\n // pair so the cap check re-validates against a clean mol. This is\n // structurally important: the conflict check must NOT see the bond\n // being edited as occupying its OLD slot — otherwise a no-op edit\n // (keep R3 → R3) would throw `rgroup-already-bonded`.\n const oldR1 = bond.r1.kind === 'numeric' ? bond.r1.r : null;\n const oldR2 = bond.r2.kind === 'numeric' ? bond.r2.r : null;\n const rgroupChanged = newR1 !== null && newR2 !== null\n && (newR1 !== oldR1 || newR2 !== oldR2);\n\n if (!rgroupChanged) { this.close(); return; }\n\n if (newR1 !== null && newR2 !== null) {\n // Remove old bond, then re-add with new R-groups. If addBond\n // throws (cap violation, monomer mismatch), the bond is gone\n // — re-add the original to keep the mol consistent. The status\n // event the editor fires on the failed addBond is the user's cue.\n const kind = bond.kind;\n const a1 = bond.a1;\n const a2 = bond.a2;\n this._editor.removeBond(bond);\n try {\n this._editor.addBond(a1, a2, newR1, newR2, kind);\n } catch (err) {\n // Rollback: re-add the original bond with its original config.\n if (oldR1 !== null && oldR2 !== null) {\n try { this._editor.addBond(a1, a2, oldR1, oldR2, bond.kind); }\n catch { /* swallow: the editor:status event already fired */ }\n }\n // Surface the original failure through the standard HwError path.\n void (err instanceof HwError ? err : err);\n }\n }\n\n this.close();\n }\n}\n\n/**\n * Build the dropdown option list for one endpoint's R-group selector.\n * Includes the bond's CURRENT R-group (so \"keep\" is always available)\n * plus every R-group currently free on that atom (excluding the bond\n * being edited so the option list reflects the post-removal mol).\n */\nfunction buildRSelectValues(\n current: RGroupRef & { kind: 'numeric' },\n atom: import('../../core/model').Atom,\n bonds: readonly Bond[],\n): ReadonlyArray<{ value: string; label: string }> {\n const rgroups = atom.monomer?.rgroups;\n if (rgroups === undefined || rgroups.length === 0) {\n // Unresolved monomer — show R1/R2/R3 as a fallback. The cap is not\n // enforced on these, so any selection is valid.\n return [\n { value: '1', label: 'R1' },\n { value: '2', label: 'R2' },\n { value: '3', label: 'R3' },\n ];\n }\n const visible = new Set<number>(freeRgroups(atom, bonds));\n visible.add(current.r);\n const sorted = Array.from(visible).sort((a, b) => a - b);\n const out: { value: string; label: string }[] = [];\n for (const idx of sorted) {\n const rg = rgroups[idx - 1];\n if (rg === undefined) continue;\n const cap = rg.capGroupName !== undefined && rg.capGroupName !== '' ? ` (${rg.capGroupName})` : '';\n out.push({ value: String(idx), label: `${rg.label}${cap}` });\n }\n return out;\n}\n\n/**\n * Local parser variant that takes an explicit fallback (the bond's\n * current numeric R-group index) so we never lose a valid pick when\n * linkedom's `.value` getter misbehaves.\n */\nfunction parseSelectValueLocal(select: HTMLSelectElement, fallback: number): number {\n const direct = (select as { value?: string }).value;\n if (typeof direct === 'string' && direct.length > 0) {\n const n = Number(direct);\n if (Number.isFinite(n) && n >= 1) return n;\n }\n const opts = select.querySelectorAll('option');\n for (const opt of Array.from(opts)) {\n if (opt.getAttribute('selected') !== null) {\n const v = opt.getAttribute('value') ?? '';\n const n = Number(v);\n if (Number.isFinite(n) && n >= 1) return n;\n }\n }\n return fallback;\n}\n\n","// T-0510 — Find / Replace dialog.\n//\n// Modal with \"Find\" + \"Replace with\" inputs, action buttons, and a result\n// counter. Wires straight to `editor.findMonomers` / `editor.replaceMonomers`.\n\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\nimport { Modal, textRow } from './modal';\n\n/** Options for `FindReplaceDialog`. */\nexport interface FindReplaceDialogOptions {\n documentImpl?: Document;\n}\n\n/** Find / Replace dialog. */\nexport class FindReplaceDialog {\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private _modal: Modal | null = null;\n private _result: HTMLElement | null = null;\n private _findInput: HTMLInputElement | null = null;\n private _replaceInput: HTMLInputElement | null = null;\n private _matches: number[] = [];\n private _cursor: number = -1;\n\n constructor(editor: HelmEditor, options?: FindReplaceDialogOptions) {\n this._editor = editor;\n const host = editor._getHost();\n if (host === null) throw new Error('FindReplaceDialog: editor has no host element.');\n this._doc = options?.documentImpl ?? getDocument(host);\n }\n\n get isOpen(): boolean { return this._modal !== null && this._modal.isOpen; }\n\n open(): void {\n this.close();\n const host = this._editor._getHost();\n if (host === null) return;\n const modal = new Modal(host, { documentImpl: this._doc, title: 'Find / Replace', testId: 'find-replace' });\n this._modal = modal;\n\n const find = textRow(this._doc, 'Find', '', 'find-replace-find');\n const repl = textRow(this._doc, 'Replace with', '', 'find-replace-replace');\n this._findInput = find.input;\n this._replaceInput = repl.input;\n\n const next = this._doc.createElement('button');\n next.setAttribute('class', 'hw-modal__find-next');\n next.setAttribute('type', 'button');\n next.setAttribute('data-testid', 'find-replace-next');\n next.appendChild(this._doc.createTextNode('Find Next'));\n next.addEventListener('click', () => this._findNext());\n\n const replaceBtn = this._doc.createElement('button');\n replaceBtn.setAttribute('class', 'hw-modal__replace');\n replaceBtn.setAttribute('type', 'button');\n replaceBtn.setAttribute('data-testid', 'find-replace-replace-one');\n replaceBtn.appendChild(this._doc.createTextNode('Replace'));\n replaceBtn.addEventListener('click', () => this._replaceOne());\n\n const replaceAll = this._doc.createElement('button');\n replaceAll.setAttribute('class', 'hw-modal__replace-all');\n replaceAll.setAttribute('type', 'button');\n replaceAll.setAttribute('data-testid', 'find-replace-replace-all');\n replaceAll.appendChild(this._doc.createTextNode('Replace All'));\n replaceAll.addEventListener('click', () => this._replaceAll());\n\n const closeBtn = this._doc.createElement('button');\n closeBtn.setAttribute('class', 'hw-modal__cancel');\n closeBtn.setAttribute('type', 'button');\n closeBtn.setAttribute('data-testid', 'find-replace-close');\n closeBtn.appendChild(this._doc.createTextNode('Close'));\n closeBtn.addEventListener('click', () => this.close());\n\n const actions = el(this._doc, 'div', { class: 'hw-modal__actions' }, [next, replaceBtn, replaceAll, closeBtn]);\n const result = el(this._doc, 'div', { class: 'hw-modal__result', 'data-testid': 'find-replace-result' }, ['0 matches']);\n this._result = result;\n\n modal.body.appendChild(find.row);\n modal.body.appendChild(repl.row);\n modal.body.appendChild(actions);\n modal.body.appendChild(result);\n modal.open();\n }\n\n close(): void {\n if (this._modal !== null) {\n this._modal.close();\n this._modal = null;\n }\n this._result = null;\n this._findInput = null;\n this._replaceInput = null;\n this._matches = [];\n this._cursor = -1;\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _findNext(): void {\n const sym = this._findInput?.value.trim() ?? '';\n if (sym === '') {\n this._setResultText('Enter a symbol to find');\n return;\n }\n const atoms = this._editor.findMonomers(sym);\n this._matches = atoms.map((a) => a.id);\n if (this._matches.length === 0) {\n this._cursor = -1;\n this._editor.setHighlights([]);\n this._setResultText('No matches');\n return;\n }\n this._cursor = (this._cursor + 1) % this._matches.length;\n const id = this._matches[this._cursor];\n if (id !== undefined) this._editor.setHighlights([id]);\n this._setResultText(`${this._cursor + 1} / ${this._matches.length} matches`);\n }\n\n private _replaceOne(): void {\n const find = this._findInput?.value.trim() ?? '';\n const replace = this._replaceInput?.value.trim() ?? '';\n if (find === '' || replace === '') {\n this._setResultText('Both Find and Replace fields are required');\n return;\n }\n if (this._matches.length === 0 || this._cursor < 0) {\n this._findNext();\n return;\n }\n const id = this._matches[this._cursor];\n if (id === undefined) return;\n const atom = this._editor.getMol().atoms.find((a) => a.id === id);\n if (atom === undefined) return;\n this._editor.replaceMonomer(atom, replace);\n this._matches.splice(this._cursor, 1);\n if (this._matches.length === 0) {\n this._cursor = -1;\n this._editor.setHighlights([]);\n this._setResultText('Replaced; no further matches');\n } else {\n this._cursor = this._cursor % this._matches.length;\n const nextId = this._matches[this._cursor];\n if (nextId !== undefined) this._editor.setHighlights([nextId]);\n this._setResultText(`${this._matches.length} matches remaining`);\n }\n }\n\n private _replaceAll(): void {\n const find = this._findInput?.value.trim() ?? '';\n const replace = this._replaceInput?.value.trim() ?? '';\n if (find === '' || replace === '') {\n this._setResultText('Both Find and Replace fields are required');\n return;\n }\n const count = this._editor.replaceMonomers(find, replace);\n this._matches = [];\n this._cursor = -1;\n this._editor.setHighlights([]);\n this._setResultText(`${count} replacement${count === 1 ? '' : 's'} made`);\n }\n\n private _setResultText(text: string): void {\n if (this._result === null) return;\n while (this._result.firstChild !== null) this._result.removeChild(this._result.firstChild);\n this._result.appendChild(this._doc.createTextNode(text));\n }\n}\n","// T-0501 — `HelmEditor`: top-level editor class.\n//\n// Wave A scope: API surface + state + events. No DOM access — the `host`\n// element is stored but unused; rendering is wired up by Wave B. The editor\n// composes a bound `HelmService` plus its own `EventBus`, `HistoryStack`,\n// `Selection`, and highlight set, and exposes the public API documented in\n// API.md §2.\n//\n// Layering: this module is the topmost editor entry; it imports from\n// `core/`, `util/`, `monomer-lib/` (only types), `render/theme` (only the\n// `Theme` type), and `service/`. We additionally reach into\n// `layout/layout-service` for `cleanLayout` (the task spec calls for it\n// directly); we never touch `io/` directly — every parse / serialize hop\n// goes through `service`.\n\nimport type {\n Atom,\n Bond,\n BondKind,\n Chain,\n Mol,\n RGroupRef,\n} from '../core/model';\nimport { emptyMol, molAtomById, molBondById } from '../core/model';\nimport { makeContinuousIdMap } from '../core/ids';\nimport type { HelmType } from '../core/constants';\nimport { HelmTypes } from '../core/constants';\nimport { Selection } from '../core/selection';\nimport { Transaction } from '../core/transaction';\nimport { HwError } from '../core/errors';\nimport type { ValidationDiagnostic } from '../core/errors';\nimport { bondsOnAtom, freeRgroups, totalRgroups } from '../core/rgroups';\nimport type { Point, Rect, Unsubscribe } from '../util/types';\nimport type { Logger } from '../util/logger';\nimport type { Theme } from '../render/theme';\nimport { lightTheme } from '../render/theme';\nimport type { HelmService } from '../service/helm-service';\nimport { HitTester } from '../render/hit-test';\nimport { layoutMol } from '../layout/layout-service';\nimport { BOND_SCALE, DEFAULT_BOND_LENGTH } from '../layout/line';\nimport { resolveMonomers } from '../io/resolver';\nimport { EventBus, type EditorEventMap, type Viewport } from './events';\nimport { HistoryStack } from './history';\nimport { EditorView } from './view/view';\nimport { PointerInput } from './input/pointer';\nimport { KeyboardInput } from './input/keyboard';\nimport { DragDropInput } from './input/dnd';\nimport { AtomPropsDialog } from './dialogs/atom-props';\nimport { BondPropsDialog } from './dialogs/bond-props';\nimport { FindReplaceDialog } from './dialogs/find-replace';\n\n/**\n * Options accepted by the `HelmEditor` constructor. `service` is the only\n * required field — everything else has a sensible default. Optional booleans\n * like `enableUndo` are unused during Wave A (the editor maintains a history\n * regardless) but stored so Wave B can honor them when wiring inputs.\n */\nexport interface HelmEditorOptions {\n service: HelmService;\n initialHelm?: string;\n width?: number;\n height?: number;\n viewOnly?: boolean;\n bondLength?: number;\n fontSize?: number;\n canonicalize?: boolean;\n caseSensitiveSymbols?: boolean;\n logger?: Logger;\n enableUndo?: boolean;\n enableContextMenu?: boolean;\n enableKeyboard?: boolean;\n enableDragDrop?: boolean;\n}\n\nconst EMPTY_FROZEN_ID_SET: ReadonlySet<number> = Object.freeze(new Set<number>()) as ReadonlySet<number>;\n\n/** Editor interaction mode. Drives pointer-click behavior on the canvas. */\nexport type EditorMode = 'select' | 'eraser' | 'hbond' | 'move';\n\n/** Next palette-driven add: symbol + biotype set by clicking a palette tile. */\nexport interface NextAddSymbol { symbol: string; biotype: HelmType }\n\n/**\n * Top-level interactive editor. Wave A delivers state + events; Wave B will\n * mount the SVG and wire pointer/keyboard input. Until then, `host` is\n * stored but never touched.\n */\nexport class HelmEditor {\n private readonly _service: HelmService;\n private readonly _options: Readonly<HelmEditorOptions>;\n private readonly _host: HTMLElement | null;\n private readonly _events: EventBus<EditorEventMap> = new EventBus<EditorEventMap>();\n private readonly _history: HistoryStack;\n private readonly _libUnsub: Unsubscribe;\n private _mol: Mol;\n private _selection: Selection;\n private _highlights: ReadonlySet<number>;\n private _theme: Theme;\n private _viewport: Viewport;\n private _viewOnly: boolean;\n private _destroyed: boolean = false;\n private _view: EditorView | null = null;\n private _pointer: PointerInput | null = null;\n private _keyboard: KeyboardInput | null = null;\n private _dnd: DragDropInput | null = null;\n private _atomDialog: AtomPropsDialog | null = null;\n private _bondDialog: BondPropsDialog | null = null;\n private _findReplaceDialog: FindReplaceDialog | null = null;\n private _viewBootstrapped: boolean = false;\n private _mode: EditorMode = 'select';\n private _nextAdd: NextAddSymbol | null = null;\n // Phase 21 (T-2103) — Tracks whether the most recent user-perceived\n // mutation was \"Add triplet\" (via `placeRnaTriplet`). The RNA Builder's\n // placement heuristic reads this to decide whether the next triplet\n // should chain to the right of the last one OR start fresh below-left\n // of the leftmost existing atom. Any other mutation\n // (addAtom/removeAtom/setHelm/cleanLayout/undo/redo/...) resets to\n // 'other' so the user gets the \"fresh anchor\" behaviour after manually\n // editing the canvas.\n private _lastAction: 'add-triplet' | 'other' | null = null;\n private _lastTripletSugarPos: Point | null = null;\n\n constructor(host: HTMLElement | null, options: HelmEditorOptions) {\n if (options.service === undefined || options.service === null)\n throw new TypeError('HelmEditor: options.service is required');\n\n this._host = host;\n this._service = options.service;\n this._options = Object.freeze({ ...options });\n this._mol = emptyMol();\n this._selection = Selection.empty();\n this._highlights = EMPTY_FROZEN_ID_SET;\n this._theme = options.service.theme ?? lightTheme;\n this._viewport = { scale: 1, offset: { x: 0, y: 0 } };\n this._viewOnly = options.viewOnly ?? false;\n this._history = new HistoryStack({ maxEntries: 100 });\n this._history.push({ mol: this._mol, label: 'initial' });\n\n // Re-fire monomer-lib mutations as editor events. Maps the lib's\n // change-event `type` to the editor's `reason` taxonomy.\n this._libUnsub = this._service.monomerLib.onChanged.subscribe((evt) => {\n const versioned = this._service.monomerLib as { version?: number };\n const version = typeof versioned.version === 'number' ? versioned.version : 0;\n const reason: 'replace' | 'merge' | 'update' =\n evt.type === 'reload' ? 'replace' : 'update';\n this._events.fire('monomer-lib:change', {\n source: this._service.monomerLib.source,\n version,\n reason,\n });\n });\n\n if (options.initialHelm !== undefined)\n this.setHelm(options.initialHelm);\n\n // Wave B: bootstrap the view + input layer if a host is supplied and a\n // Document is reachable. Tests can opt out by passing `host: null`.\n this._bootstrapWaveB();\n }\n\n /**\n * Bootstrap the DOM view and input layers. Idempotent — called from the\n * constructor and (defensively) from `redraw()` when the host appears later.\n * Uses dynamic imports so the editor stays headless until a host is supplied.\n */\n private _bootstrapWaveB(): void {\n if (this._viewBootstrapped) return;\n if (this._host === null) return;\n const doc = this._resolveDocument(this._host);\n if (doc === null) return;\n this._viewBootstrapped = true;\n\n const viewOpts: { width?: number; height?: number; documentImpl: Document } = {\n documentImpl: doc,\n };\n if (this._options.width !== undefined) viewOpts.width = this._options.width;\n if (this._options.height !== undefined) viewOpts.height = this._options.height;\n this._view = new EditorView(this._host, this, viewOpts);\n\n if (this._viewOnly !== true) {\n this._pointer = new PointerInput(this._host, this, {\n enableContextMenu: this._options.enableContextMenu ?? true,\n });\n }\n if (this._options.enableKeyboard !== false)\n this._keyboard = new KeyboardInput(this._host, this, { enableKeyboard: true });\n if (this._options.enableDragDrop !== false)\n this._dnd = new DragDropInput(this._host, this);\n\n // Phase 18 (T-1803) — Wire `monomer:hover` events into the highlight\n // set so the renderer's highlight pass paints a teal ring around the\n // hovered atom. `monomer:hover-end` clears the highlight. The pointer\n // input layer already debounces hover transitions (no event fires\n // while the cursor stays on the same atom), so a single\n // `setHighlights` call per hover boundary is sufficient.\n this._events.on('monomer:hover', (e) => {\n this.setHighlights([e.atom.id]);\n });\n this._events.on('monomer:hover-end', () => {\n this.clearHighlights();\n });\n // Phase 18 (T-1802) — `monomer:click` updates the selection.\n // - Plain click → replace selection with just that atom\n // - Ctrl/Meta+ → toggle the atom in the existing selection\n // - Shift+ → add the atom (legacy behavior preserved)\n // The pointer layer already short-circuits eraser and the\n // palette-prime branch; this handler only runs for \"real\" clicks on\n // an atom in non-eraser modes.\n this._events.on('monomer:click', (e) => {\n const m = e.modifiers;\n if (m.ctrl === true || m.meta === true) {\n this.setSelection(Selection.toggle(this._selection, { kind: 'atom', id: e.atom.id }));\n return;\n }\n if (m.shift === true) {\n this.setSelection(Selection.union(this._selection, Selection.fromAtoms([e.atom.id])));\n return;\n }\n this.setSelection(Selection.fromAtoms([e.atom.id]));\n });\n }\n\n /** Resolve a Document from the host. Returns `null` when none is reachable. */\n private _resolveDocument(host: HTMLElement): Document | null {\n const owner = host.ownerDocument;\n if (owner !== null && owner !== undefined) return owner;\n const g = globalThis as { document?: Document };\n if (g.document !== undefined) return g.document;\n return null;\n }\n\n // ------------------------------------------------------------------------\n // Lifecycle\n // ------------------------------------------------------------------------\n\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n // Tear down Wave B layers first so they unsubscribe before we clear the bus.\n if (this._atomDialog !== null) { this._atomDialog.close(); this._atomDialog = null; }\n if (this._bondDialog !== null) { this._bondDialog.close(); this._bondDialog = null; }\n if (this._findReplaceDialog !== null) { this._findReplaceDialog.close(); this._findReplaceDialog = null; }\n if (this._dnd !== null) { this._dnd.destroy(); this._dnd = null; }\n if (this._keyboard !== null) { this._keyboard.destroy(); this._keyboard = null; }\n if (this._pointer !== null) { this._pointer.destroy(); this._pointer = null; }\n if (this._view !== null) { this._view.destroy(); this._view = null; }\n this._libUnsub();\n this._events.clear();\n this._history.clear();\n }\n\n /**\n * Update the canvas size. Forwards to the mounted view, if any, and fires\n * a `view:resize` event so consumers can react.\n */\n resize(width: number, height: number): void {\n this._ensureLive();\n if (this._view !== null) this._view.resize(width, height);\n this._events.fire('view:resize', { width, height });\n }\n\n /** Full repaint. Forwards to the mounted view; no-op when headless. */\n redraw(): void {\n this._ensureLive();\n if (this._view !== null) {\n this._view.redraw();\n return;\n }\n this._events.fire('render:skip', { reason: 'no-view-mounted' });\n }\n\n // ------------------------------------------------------------------------\n // I/O\n // ------------------------------------------------------------------------\n\n setHelm(\n helm: string,\n options?: { canonicalize?: boolean },\n ): { mol: Mol; diagnostics: readonly ValidationDiagnostic[] } {\n this._ensureLive();\n const wantCanon = options?.canonicalize ?? this._options.canonicalize ?? false;\n const parseRes = this._service.parse(helm, { mode: 'lenient' });\n const diagnostics = parseRes.diagnostics;\n const errors = diagnostics.filter((d) => d.severity === 'error');\n if (errors.length > 0)\n this._events.fire('helm:parse-error', { helm, diagnostics });\n for (const d of diagnostics) {\n if (d.severity === 'error') this._events.fire('validation:error', { diagnostic: d });\n else if (d.severity === 'warning') this._events.fire('validation:warning', { diagnostic: d });\n }\n\n let mol = parseRes.mol;\n if (wantCanon) {\n const canonHelm = this._service.canonicalize(helm);\n const canonRes = this._service.parse(canonHelm, { mode: 'lenient' });\n mol = canonRes.mol;\n }\n const laid = layoutMol(\n mol,\n this._options.bondLength !== undefined ? { bondLength: this._options.bondLength } : undefined,\n );\n this._replaceMol(laid, 'setHelm', 'api');\n return { mol: laid, diagnostics };\n }\n\n getHelm(options?: { includeHighlights?: boolean; canonicalize?: boolean }): string {\n this._ensureLive();\n const serializeOptions: { canonicalize?: boolean; includeHighlights?: boolean } = {};\n if (options?.canonicalize !== undefined) serializeOptions.canonicalize = options.canonicalize;\n if (options?.includeHighlights !== undefined) serializeOptions.includeHighlights = options.includeHighlights;\n return this._service.serialize(this._mol, serializeOptions);\n }\n\n setMol(mol: Mol): void {\n this._ensureLive();\n this._replaceMol(mol, 'setMol', 'api');\n }\n\n getMol(): Readonly<Mol> {\n return this._mol;\n }\n\n getService(): HelmService {\n return this._service;\n }\n\n // ------------------------------------------------------------------------\n // Selection / highlight\n // ------------------------------------------------------------------------\n\n getSelection(): Selection {\n return this._selection;\n }\n\n setSelection(sel: Selection): void {\n this._ensureLive();\n if (Selection.equals(this._selection, sel)) return;\n const added = Selection.difference(sel, this._selection);\n const removed = Selection.difference(this._selection, sel);\n this._selection = sel;\n this._events.fire('selection:change', {\n selection: sel,\n addedAtomIds: added.atoms,\n removedAtomIds: removed.atoms,\n addedBondIds: added.bonds,\n removedBondIds: removed.bonds,\n });\n }\n\n selectAll(): void {\n this._ensureLive();\n const atomIds = this._mol.atoms.map((a) => a.id);\n const bondIds = this._mol.bonds.map((b) => b.id);\n this.setSelection(Selection.fromAtomsAndBonds(atomIds, bondIds));\n }\n\n clearSelection(): void {\n this._ensureLive();\n if (this._selection.isEmpty) return;\n this.setSelection(Selection.empty());\n }\n\n setHighlights(atomIds: Iterable<number>): void {\n this._ensureLive();\n const next = new Set<number>(atomIds);\n this._highlights = next;\n this._events.fire('highlight:change', {\n atomIds: next,\n bondIds: EMPTY_FROZEN_ID_SET,\n });\n }\n\n clearHighlights(): void {\n this._ensureLive();\n if (this._highlights.size === 0) return;\n this._highlights = EMPTY_FROZEN_ID_SET;\n this._events.fire('highlight:change', {\n atomIds: EMPTY_FROZEN_ID_SET,\n bondIds: EMPTY_FROZEN_ID_SET,\n });\n }\n\n // ------------------------------------------------------------------------\n // Operations\n // ------------------------------------------------------------------------\n\n addAtom(p: Point, biotype: HelmType, symbol: string): Atom {\n this._ensureLive();\n const tx = new Transaction(this._mol);\n const id = tx.addAtom({ p, biotype, symbol });\n const { mol } = tx.commit();\n // T-1704 — Do NOT run `layoutMol` after `addAtom`. The new atom\n // lives at the user-supplied position `p`; existing atoms keep\n // their current positions. The renderer reads `atom.p` directly\n // (Phase 13c — `HelmService.renderMol`) so a freshly added atom is\n // visible at `p` without a layout pass; the HitTester is rebuilt by\n // the pointer input layer on every `mol:changed` event. A user-\n // requested clean-up still re-runs the layout via `cleanLayout()`.\n //\n // We DO still re-resolve monomers so `atom.monomer.name` /\n // `rgroups` / `naturalAnalog` are populated for tooltips, R-group\n // pickers, and the property panes (Bug 10 / 6).\n const resolved = resolveMonomers(mol, this._service.monomerLib, { mode: 'lenient' }).mol;\n this._replaceMol(resolved, `addAtom:${symbol}`, 'api');\n const atom = molAtomById(resolved, id);\n if (atom === undefined) throw new Error('HelmEditor.addAtom: lost atom after commit');\n this._events.fire('monomer:add', { atom, source: 'api' });\n return atom;\n }\n\n removeAtom(atom: Atom | number): void {\n this._ensureLive();\n const atomId = typeof atom === 'number' ? atom : atom.id;\n const prev = molAtomById(this._mol, atomId);\n if (prev === undefined) return;\n const tx = new Transaction(this._mol);\n tx.removeAtom(atomId);\n const { mol } = tx.commit();\n // T-1704 — Do NOT re-layout on removal. The remaining atoms keep\n // their current positions; bonds keep their endpoint references and\n // simply redraw against the surviving atoms. Visual gaps are the\n // honest representation of the post-erase state; a user-requested\n // clean-up via `cleanLayout()` compacts them.\n this._replaceMol(mol, `removeAtom:${prev.symbol}`, 'api');\n this._events.fire('monomer:remove', { atom: prev, source: 'api' });\n }\n\n addBond(a1: Atom, a2: Atom, r1: number, r2: number, kind?: BondKind): Bond {\n this._ensureLive();\n let id: number;\n let mol: Mol;\n try {\n // Phase 14B (T-1412) — Enforce the SPECIFICATION.md §12.4\n // connection cap BEFORE the Transaction runs, so the editor\n // surfaces stable HwError codes (`rgroup-already-bonded`,\n // `rgroup-not-on-monomer`, `duplicate-bond`) rather than the\n // Transaction's free-form Error text.\n this._validateAddBondConstraints(a1, a2, r1, r2);\n // Phase 15 (T-1506) — Linear-extend merge. When the user drags from\n // the R2-end of chain X onto the R1-start of chain Y AND both\n // chains share polymer type, fold Y into X instead of leaving two\n // chains joined by a cross-polymer bond. The resulting HELM goes\n // from `PEPTIDE1{A.C.D}|PEPTIDE2{G}$PEPTIDE1,PEPTIDE2,3:R2-1:R1`\n // to `PEPTIDE1{A.C.D.G}` — matching the user's mental model that\n // appending a monomer extends the same chain.\n const mergeKind = kind ?? 'backbone';\n const mergeMol = this._maybeMergeForLinearExtend(a1, a2, r1, r2, mergeKind);\n if (mergeMol !== null) {\n ({ id, mol } = mergeMol);\n } else {\n const tx = new Transaction(this._mol);\n id = tx.addBond({\n a1: a1.id,\n a2: a2.id,\n kind: kind ?? 'backbone',\n r1: { kind: 'numeric', r: r1 },\n r2: { kind: 'numeric', r: r2 },\n });\n ({ mol } = tx.commit());\n }\n } catch (err) {\n // Phase 13b (Bug 5) — Fire a user-visible status message so the\n // status bar can surface the failure reason. Common causes:\n // duplicate-bond, missing-atom, R-group already occupied. HwError\n // instances carry a friendly message already; bare Errors get\n // decoded via `_friendlyBondError`.\n const friendly = err instanceof HwError\n ? err.message\n : this._friendlyBondError(err instanceof Error ? err.message : String(err), a1, a2, r1, r2);\n this._events.fire('editor:status', {\n message: `Could not add bond: ${friendly}`,\n severity: 'error',\n durationMs: 3000,\n });\n throw err;\n }\n // T-1704 — Do NOT re-layout on `addBond`. Both endpoint atoms keep\n // their existing positions so the user's deliberate placement\n // survives the new connection. The bond is drawn as a straight line\n // between the two stored positions; a user-requested clean-up via\n // `cleanLayout()` re-runs the auto-layout to compact the result.\n this._replaceMol(mol, 'addBond', 'api');\n const bond = molBondById(mol, id);\n if (bond === undefined) throw new Error('HelmEditor.addBond: lost bond after commit');\n this._events.fire('bond:add', { bond, source: 'api' });\n return bond;\n }\n\n /**\n * Phase 15 (T-1506) — Linear-extend chain merge.\n *\n * When the user drags from the R2-end of chain X to the R1-start of\n * chain Y AND both share polymer type, we fold Y into X so the resulting\n * HELM reads `PEPTIDE1{A.C.D.G}` (single polymer) rather than\n * `PEPTIDE1{A.C.D}|PEPTIDE2{G}$PEPTIDE1,PEPTIDE2,3:R2-1:R1` (two\n * polymers joined by a cross-polymer bond). This matches the user's\n * mental model of \"appending a monomer\" and is also what Pistoia HELM\n * editors do by default.\n *\n * Returns `null` when the preconditions are not met — in that case the\n * caller falls back to the normal addBond path. Returns `{ id, mol }`\n * on success: `id` is the freshly-allocated id of the new backbone\n * bond, `mol` is the merged Mol with continuous-ids refreshed.\n *\n * Preconditions:\n * - `a1.bio.chainId !== a2.bio.chainId` (different chains)\n * - One direction satisfies `r=2 → r=1` between end-of-chain and\n * start-of-chain. Phase 16 (T-1605) — the merge now accepts BOTH\n * directions: the user can drag from the existing chain's end onto\n * the new monomer (canonical: `last1.R2 → first2.R1` with\n * `r1=2, r2=1`) OR from the new monomer onto the existing chain's\n * end (reversed: `first1.R1 ← last2.R2` with `r1=1, r2=2`). Both\n * intents are \"extend the chain\" and produce the same merge.\n * - `kind` ∈ {`'backbone'`, `'cross-polymer'`} (hbond / branch don't merge)\n * - both chains exist in `mol.chains` and have the same `polymerType`\n * - One atom is the LAST `backboneAtom` of its chain; the other is the\n * FIRST `backboneAtom` of its chain.\n */\n private _maybeMergeForLinearExtend(\n a1: Atom, a2: Atom, r1: number, r2: number, kind: BondKind,\n ): { id: number; mol: Mol } | null {\n if (a1.bio.chainId === a2.bio.chainId) return null;\n if (kind !== 'backbone' && kind !== 'cross-polymer') return null;\n\n const chain1 = this._mol.chains.find((c) => c.id === a1.bio.chainId);\n const chain2 = this._mol.chains.find((c) => c.id === a2.bio.chainId);\n if (chain1 === undefined || chain2 === undefined) return null;\n if (chain1.polymerType !== chain2.polymerType) return null;\n\n // Direction 1 (canonical): a1 is last of chain1 (R2 free), a2 is first of chain2 (R1 free).\n if (r1 === 2 && r2 === 1) {\n const last1 = chain1.backboneAtoms[chain1.backboneAtoms.length - 1];\n const first2 = chain2.backboneAtoms[0];\n if (last1 !== undefined && first2 !== undefined\n && last1.id === a1.id && first2.id === a2.id)\n return this._mergeChains(chain1, chain2, kind);\n }\n // Direction 2 (reversed — Phase 16 T-1605): a1 is first of chain1 (R1\n // free), a2 is last of chain2 (R2 free). Logical merge appends chain1's\n // atom to the END of chain2 — same intent as the canonical case, just\n // with the user dragging from the new monomer onto the existing chain's\n // end. We swap the arguments and reuse `_mergeChains`, which then\n // builds `chain2 + chain1` (chain2 keeps its id, chain1 gets folded in).\n if (r1 === 1 && r2 === 2) {\n const first1 = chain1.backboneAtoms[0];\n const last2 = chain2.backboneAtoms[chain2.backboneAtoms.length - 1];\n if (first1 !== undefined && last2 !== undefined\n && first1.id === a1.id && last2.id === a2.id)\n return this._mergeChains(chain2, chain1, kind);\n }\n return null;\n }\n\n /**\n * Phase 15 (T-1506) — Build the merged Mol. Renumbers chain2 atoms so\n * their `bio.chainId` matches chain1 and their `positionInChain` picks\n * up after chain1's end. Adds a `backbone` bond between the old end\n * (chain1) and the new start (chain2). Refreshes continuous-ids.\n *\n * Atom identity is preserved by `id` — every other property of every\n * chain2 atom is re-emitted on a fresh instance (so the bio bag can be\n * rewritten). Bonds and chain references are rewired to the new\n * instances via an `oldToNew` lookup.\n */\n private _mergeChains(chain1: Chain, chain2: Chain, kind: BondKind): { id: number; mol: Mol } {\n const offset = chain1.backboneAtoms.length;\n const chain2AtomIds = new Set<number>();\n for (const a of chain2.backboneAtoms) {\n chain2AtomIds.add(a.id);\n if (a.branchAtom !== undefined) chain2AtomIds.add(a.branchAtom.id);\n }\n\n // Build oldToNew: chain2 atoms get fresh bio; others unchanged.\n const oldToNew = new Map<number, Atom>();\n let nextPosition = offset;\n for (const a of chain2.backboneAtoms) {\n nextPosition += 1;\n const newAtom: Atom = {\n ...a,\n bio: { ...a.bio, chainId: chain1.id, positionInChain: nextPosition },\n };\n oldToNew.set(a.id, newAtom);\n if (a.branchAtom !== undefined) {\n const b = a.branchAtom;\n // Branch atoms (RNA bases) inherit the parent's renumbered chain id.\n const newBranch: Atom = {\n ...b,\n bio: { ...b.bio, chainId: chain1.id, positionInChain: nextPosition },\n };\n oldToNew.set(b.id, newBranch);\n }\n }\n // Repoint moved branchAtom pointers to the new branch instances.\n for (const a of chain2.backboneAtoms) {\n const updated = oldToNew.get(a.id);\n if (updated === undefined || a.branchAtom === undefined) continue;\n const branchUpdated = oldToNew.get(a.branchAtom.id);\n if (branchUpdated === undefined) continue;\n (updated as { branchAtom?: Atom }).branchAtom = branchUpdated;\n }\n // chain1 atoms (and any other chain's atoms) keep their identity.\n for (const a of this._mol.atoms) if (!oldToNew.has(a.id)) oldToNew.set(a.id, a);\n\n // Allocate a fresh id for the new bond. Largest existing id + 1.\n let maxId = 0;\n for (const a of this._mol.atoms) if (a.id > maxId) maxId = a.id;\n for (const b of this._mol.bonds) if (b.id > maxId) maxId = b.id;\n const newBondId = maxId + 1;\n\n const last1 = oldToNew.get(chain1.backboneAtoms[chain1.backboneAtoms.length - 1]!.id)!;\n const first2 = oldToNew.get(chain2.backboneAtoms[0]!.id)!;\n const linkBond: Bond = {\n id: newBondId,\n a1: last1,\n a2: first2,\n kind: 'backbone',\n r1: { kind: 'numeric', r: 2 },\n r2: { kind: 'numeric', r: 1 },\n };\n void kind; // bond kind is canonical backbone for the merged chain.\n\n // Rebuild every bond to point at the new atom instances.\n const newBonds: Bond[] = [];\n for (const b of this._mol.bonds) {\n const newA1 = oldToNew.get(b.a1.id) ?? b.a1;\n const newA2 = oldToNew.get(b.a2.id) ?? b.a2;\n if (newA1 === b.a1 && newA2 === b.a2) newBonds.push(b);\n else newBonds.push({ ...b, a1: newA1, a2: newA2 });\n }\n newBonds.push(linkBond);\n\n // Rebuild chains: chain1 absorbs chain2's atoms; chain2 dropped.\n const newChains: Chain[] = [];\n const mergedBackbone: Atom[] = [...chain1.backboneAtoms];\n for (const a of chain2.backboneAtoms) mergedBackbone.push(oldToNew.get(a.id)!);\n for (const c of this._mol.chains) {\n if (c.id === chain2.id) continue;\n if (c.id === chain1.id) {\n // Update chain1's bonds to include the new link bond.\n const cBonds = c.bonds.map((b) => {\n const newA1 = oldToNew.get(b.a1.id) ?? b.a1;\n const newA2 = oldToNew.get(b.a2.id) ?? b.a2;\n if (newA1 === b.a1 && newA2 === b.a2) return b;\n return { ...b, a1: newA1, a2: newA2 };\n });\n // Bring in chain2's bonds too — they now belong to the merged chain.\n for (const b of chain2.bonds) {\n const newA1 = oldToNew.get(b.a1.id) ?? b.a1;\n const newA2 = oldToNew.get(b.a2.id) ?? b.a2;\n cBonds.push(newA1 === b.a1 && newA2 === b.a2 ? b : { ...b, a1: newA1, a2: newA2 });\n }\n cBonds.push(linkBond);\n newChains.push({\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: mergedBackbone as readonly Atom[],\n bonds: cBonds as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n });\n } else {\n // Other chains: keep but rewire atom refs in case any branchAtom\n // (unlikely for this code path, but defend) was an old instance.\n const cBb = c.backboneAtoms.map((a) => oldToNew.get(a.id) ?? a);\n const cBonds = c.bonds.map((b) => {\n const newA1 = oldToNew.get(b.a1.id) ?? b.a1;\n const newA2 = oldToNew.get(b.a2.id) ?? b.a2;\n if (newA1 === b.a1 && newA2 === b.a2) return b;\n return { ...b, a1: newA1, a2: newA2 };\n });\n newChains.push({\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: cBb as readonly Atom[],\n bonds: cBonds as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n });\n }\n }\n\n // Atoms array follows the chain order; chain2 atoms now live in chain1\n // but we keep mol.atoms in source order — every atom present, just\n // with rewritten bio for chain2.\n const newAtoms: Atom[] = this._mol.atoms.map((a) => oldToNew.get(a.id) ?? a);\n\n // Refresh continuous ids on the merged mol.\n let merged: Mol = {\n atoms: newAtoms as readonly Atom[],\n bonds: newBonds as readonly Bond[],\n chains: newChains as readonly Chain[],\n groups: this._mol.groups,\n annotations: this._mol.annotations,\n };\n merged = this._refreshContinuousIdsLocal(merged);\n return { id: newBondId, mol: merged };\n }\n\n /**\n * Phase 15 (T-1506) — Local continuous-id refresh. Mirrors the helper\n * in `core/transaction.ts` but lives here because we hand-build the\n * merged Mol outside Transaction. Walks chains in source order,\n * assigns 1-based continuous ids to every backbone atom and its branch\n * (RNA base) atoms.\n */\n private _refreshContinuousIdsLocal(mol: Mol): Mol {\n const ids = makeContinuousIdMap(mol);\n const oldToNew = new Map<number, Atom>();\n for (const a of mol.atoms) {\n const nextId = ids.get(a.id);\n if (nextId === undefined || nextId === a.bio.continuousId) {\n oldToNew.set(a.id, a);\n continue;\n }\n oldToNew.set(a.id, { ...a, bio: { ...a.bio, continuousId: nextId } });\n }\n // Re-pin branchAtom references onto the freshly built atoms.\n for (const a of mol.atoms) {\n if (a.branchAtom === undefined) continue;\n const parent = oldToNew.get(a.id);\n const branch = oldToNew.get(a.branchAtom.id);\n if (parent === undefined || branch === undefined) continue;\n (parent as { branchAtom?: Atom }).branchAtom = branch;\n }\n const newBonds: Bond[] = mol.bonds.map((b) => {\n const a1 = oldToNew.get(b.a1.id) ?? b.a1;\n const a2 = oldToNew.get(b.a2.id) ?? b.a2;\n if (a1 === b.a1 && a2 === b.a2) return b;\n return { ...b, a1, a2 };\n });\n const newBondsById = new Map<number, Bond>();\n for (const b of newBonds) newBondsById.set(b.id, b);\n const newChains: Chain[] = mol.chains.map((c) => {\n const bb = c.backboneAtoms.map((a) => oldToNew.get(a.id) ?? a);\n const bonds = c.bonds.map((b) => newBondsById.get(b.id) ?? b);\n return {\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: bb as readonly Atom[],\n bonds: bonds as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n };\n });\n const newAtoms: Atom[] = mol.atoms.map((a) => oldToNew.get(a.id) ?? a);\n return {\n atoms: newAtoms as readonly Atom[],\n bonds: newBonds as readonly Bond[],\n chains: newChains as readonly Chain[],\n groups: mol.groups,\n annotations: mol.annotations,\n };\n }\n\n /**\n * Translate a raw `Transaction.addBond` error message into a human-\n * friendly status-bar message. Recognises the three error patterns the\n * transaction emits today; falls back to the raw message verbatim.\n */\n private _friendlyBondError(raw: string, a1: Atom, a2: Atom, r1: number, r2: number): string {\n if (raw.includes('duplicate bond'))\n return `bond ${a1.symbol}:R${r1} ↔ ${a2.symbol}:R${r2} already exists`;\n if (raw.includes('does not exist'))\n return `one of the endpoint atoms is missing`;\n return raw;\n }\n\n /**\n * Phase 14B (T-1412) — Enforce the per-atom R-group cap on every\n * `addBond` call. Throws `HwError` with one of the documented codes:\n *\n * - `rgroup-not-on-monomer` — `r1` (or `r2`) exceeds the atom's total\n * number of R-groups (`atom.monomer.rgroups.length`). Refused so the\n * editor never inserts a bond the renderer / serializer can't paint.\n * - `rgroup-already-bonded` — the requested numeric R-group is already\n * consumed by another bond on the same atom. Names the conflicting\n * bond so the user can locate it.\n * - `duplicate-bond` — the exact `(a1, r1, a2, r2)` quadruple is\n * already a bond in the current mol (also caught by the Transaction\n * but pre-validated here so the status-bar message is friendlier).\n *\n * Atoms without a resolved monomer (`totalRgroups === 0`) DO NOT get\n * the cap enforced — that path is reserved for unresolved fragments\n * where the editor cannot prove the R-group count. The validator's\n * `unresolved-monomer` diagnostic surfaces the underlying problem.\n */\n private _validateAddBondConstraints(a1: Atom, a2: Atom, r1: number, r2: number): void {\n const bonds = this._mol.bonds;\n\n // 1. R-group index must be within the monomer's advertised count.\n const t1 = totalRgroups(a1);\n if (t1 > 0 && (r1 < 1 || r1 > t1))\n throw new HwError(\n 'rgroup-not-on-monomer',\n `R-group R${r1} is not defined on monomer '${a1.symbol}' (has R1..R${t1})`,\n { atomId: a1.id, requested: r1, total: t1 },\n );\n const t2 = totalRgroups(a2);\n if (t2 > 0 && (r2 < 1 || r2 > t2))\n throw new HwError(\n 'rgroup-not-on-monomer',\n `R-group R${r2} is not defined on monomer '${a2.symbol}' (has R1..R${t2})`,\n { atomId: a2.id, requested: r2, total: t2 },\n );\n\n // 2. R-group must not already be consumed by another bond on the\n // same atom. Reuses `bondsOnAtom` so the conflicting bond can be\n // surfaced in the error message (the other endpoint helps the\n // user locate it on the canvas).\n if (t1 > 0) {\n const occupied1 = bondsOnAtom(a1, bonds).find((p) => p.rNumber === r1);\n if (occupied1 !== undefined) {\n const other = occupied1.side === 'r1' ? occupied1.bond.a2 : occupied1.bond.a1;\n throw new HwError(\n 'rgroup-already-bonded',\n `R-group R${r1} on '${a1.symbol}' is already bonded to '${other.symbol}' (${other.bio.chainId}:${other.bio.positionInChain})`,\n { atomId: a1.id, requested: r1, conflictingBondId: occupied1.bond.id },\n );\n }\n }\n if (t2 > 0) {\n const occupied2 = bondsOnAtom(a2, bonds).find((p) => p.rNumber === r2);\n if (occupied2 !== undefined) {\n const other = occupied2.side === 'r1' ? occupied2.bond.a2 : occupied2.bond.a1;\n throw new HwError(\n 'rgroup-already-bonded',\n `R-group R${r2} on '${a2.symbol}' is already bonded to '${other.symbol}' (${other.bio.chainId}:${other.bio.positionInChain})`,\n { atomId: a2.id, requested: r2, conflictingBondId: occupied2.bond.id },\n );\n }\n }\n\n // 3. Reject the exact same bond appearing twice. The Transaction\n // also raises this, but pre-validating gives us a stable HwError\n // code for the status-bar / test layer.\n for (const b of bonds) {\n if (b.r1.kind !== 'numeric' || b.r2.kind !== 'numeric') continue;\n const fwd = b.a1.id === a1.id && b.a2.id === a2.id && b.r1.r === r1 && b.r2.r === r2;\n const rev = b.a1.id === a2.id && b.a2.id === a1.id && b.r1.r === r2 && b.r2.r === r1;\n if (fwd || rev)\n throw new HwError(\n 'duplicate-bond',\n `bond ${a1.symbol}:R${r1} ↔ ${a2.symbol}:R${r2} already exists`,\n { atomId: a1.id, bondId: b.id },\n );\n }\n }\n\n /** @internal Used by `freeRgroups`-driven callers to introspect the cap. */\n _freeRgroupsOn(atom: Atom): number[] {\n return freeRgroups(atom, this._mol.bonds);\n }\n\n addHydrogenBond(a1: Atom, a2: Atom): Bond {\n this._ensureLive();\n const tx = new Transaction(this._mol);\n const pairRef: RGroupRef = { kind: 'pair' };\n const id = tx.addBond({\n a1: a1.id,\n a2: a2.id,\n kind: 'hbond',\n r1: pairRef,\n r2: pairRef,\n });\n const { mol } = tx.commit();\n // T-1704 — Do NOT re-layout on `addHydrogenBond`. Atoms keep their\n // existing positions; the dashed h-bond is drawn between them.\n this._replaceMol(mol, 'addHydrogenBond', 'api');\n const bond = molBondById(mol, id);\n if (bond === undefined) throw new Error('HelmEditor.addHydrogenBond: lost bond after commit');\n this._events.fire('bond:add', { bond, source: 'api' });\n return bond;\n }\n\n removeBond(bond: Bond | number): void {\n this._ensureLive();\n const bondId = typeof bond === 'number' ? bond : bond.id;\n const prev = molBondById(this._mol, bondId);\n if (prev === undefined) return;\n const tx = new Transaction(this._mol);\n tx.removeBond(bondId);\n const { mol } = tx.commit();\n // T-1704 — Do NOT re-layout on bond removal. Atoms keep their\n // existing positions; the cut bond simply disappears from the\n // canvas. A user-requested clean-up via `cleanLayout()` reorganises\n // the now-disconnected components.\n this._replaceMol(mol, 'removeBond', 'api');\n this._events.fire('bond:remove', { bond: prev, source: 'api' });\n }\n\n replaceMonomer(atom: Atom, newSymbol: string): void {\n this._ensureLive();\n const prev = molAtomById(this._mol, atom.id);\n if (prev === undefined) return;\n const oldSymbol = prev.symbol;\n if (oldSymbol === newSymbol) return;\n const tx = new Transaction(this._mol);\n tx.updateAtom(atom.id, { symbol: newSymbol });\n const { mol } = tx.commit();\n // T-1704 — Re-resolve monomers so `atom.monomer.name`,\n // `atom.monomer.rgroups`, and `naturalAnalog` point at the new\n // library entry (tooltips, R-group pickers, properties pane). Do\n // NOT re-layout — the atom keeps its existing position; only its\n // symbol changes. A user-requested clean-up via `cleanLayout()`\n // re-runs the auto-layout.\n const resolved = resolveMonomers(mol, this._service.monomerLib, { mode: 'lenient' }).mol;\n this._replaceMol(resolved, `replaceMonomer:${oldSymbol}->${newSymbol}`, 'api');\n const updated = molAtomById(resolved, atom.id);\n if (updated === undefined) return;\n this._events.fire('monomer:replace', { atom: updated, oldSymbol, newSymbol });\n }\n\n /**\n * Hit-test at a model-space point. Returns the topmost atom / bond, or\n * `null`. Internally constructs a fresh `HitTester` so this is O(n) per\n * call — fine for occasional API use; pointer input has its own cache.\n */\n hitTest(x: number, y: number): { atom?: Atom; bond?: Bond } | null {\n this._ensureLive();\n const tester = new HitTester(this._mol, this._theme);\n const r = tester.test({ x, y });\n if (r === null) return null;\n if (r.atom !== undefined) return { atom: r.atom };\n if (r.bond !== undefined) return { bond: r.bond };\n return null;\n }\n\n /**\n * Phase 15 (T-1504) — Move a single atom to a new model-space position.\n * Used by the pointer input layer in `move` mode to physically drag an\n * atom around the canvas. Re-uses `Transaction.updateAtom` so the resulting\n * Mol stays immutable and fires `mol:changed` exactly once.\n *\n * No layout is run — the user has chosen the new position by hand. The\n * existing `cleanLayout()` (toolbar button) reverts to the auto-layout.\n */\n moveAtom(atomId: number, p: Point): void {\n this._ensureLive();\n const prev = molAtomById(this._mol, atomId);\n if (prev === undefined) return;\n if (prev.p.x === p.x && prev.p.y === p.y) return;\n const tx = new Transaction(this._mol);\n tx.updateAtom(atomId, { p: { x: p.x, y: p.y } });\n const { mol } = tx.commit();\n this._replaceMol(mol, 'moveAtom', 'user');\n }\n\n /**\n * Phase 26 (T-2601) — Batch version of `moveAtom`. Move multiple atoms\n * to new positions in a SINGLE `Transaction` so the resulting\n * `mol:changed` / `helm:changed` events fire exactly once for the\n * whole group, not once per atom. Used by the pointer input layer when\n * a Move-mode drag begins on an atom that is part of a multi-atom\n * selection — every selected atom shifts by the same screen delta.\n *\n * Updates whose target position equals the current atom position are\n * skipped (no-op `updateAtom`); atom-ids that do not resolve are\n * silently ignored (consistent with `moveAtom`). When NO update has any\n * effect the method returns without firing any event — the editor's\n * `_replaceMol` would otherwise push a no-op history frame.\n */\n moveAtoms(updates: ReadonlyArray<{ atomId: number; p: Point }>): void {\n this._ensureLive();\n if (updates.length === 0) return;\n const tx = new Transaction(this._mol);\n let changed = 0;\n for (const u of updates) {\n const prev = molAtomById(this._mol, u.atomId);\n if (prev === undefined) continue;\n if (prev.p.x === u.p.x && prev.p.y === u.p.y) continue;\n tx.updateAtom(u.atomId, { p: { x: u.p.x, y: u.p.y } });\n changed += 1;\n }\n if (changed === 0) return;\n const { mol } = tx.commit();\n this._replaceMol(mol, 'moveAtom', 'user');\n }\n\n cleanLayout(_focusAtom?: Atom): void {\n this._ensureLive();\n // Phase 21 (T-2103) — Clean repositions every atom; the prior\n // \"added a triplet here\" anchor is no longer valid.\n this._resetLastAction();\n const laid = layoutMol(\n this._mol,\n this._options.bondLength !== undefined ? { bondLength: this._options.bondLength } : undefined,\n );\n this._mol = laid;\n this._history.push({ mol: laid, label: 'cleanLayout' });\n this._events.fire('layout:change', { mol: laid, strategy: 'auto' });\n this._events.fire('mol:changed', {\n mol: laid,\n changedAtomIds: new Set<number>(laid.atoms.map((a) => a.id)),\n changedBondIds: EMPTY_FROZEN_ID_SET,\n reason: 'cleanLayout',\n });\n }\n\n // ------------------------------------------------------------------------\n // Undo / redo\n // ------------------------------------------------------------------------\n\n canUndo(): boolean { return this._history.canUndo(); }\n canRedo(): boolean { return this._history.canRedo(); }\n\n undo(): void {\n this._ensureLive();\n const entry = this._history.undo();\n if (entry === null) return;\n this._restoreFromHistory(entry.mol, 'undo');\n }\n\n redo(): void {\n this._ensureLive();\n const entry = this._history.redo();\n if (entry === null) return;\n this._restoreFromHistory(entry.mol, 'redo');\n }\n\n // ------------------------------------------------------------------------\n // Events\n // ------------------------------------------------------------------------\n\n on<K extends keyof EditorEventMap>(\n name: K,\n handler: (e: EditorEventMap[K]) => void,\n ): Unsubscribe {\n return this._events.on(name, handler);\n }\n\n off<K extends keyof EditorEventMap>(\n name: K,\n handler: (e: EditorEventMap[K]) => void,\n ): void {\n this._events.off(name, handler);\n }\n\n fire<K extends keyof EditorEventMap>(name: K, payload: EditorEventMap[K]): void {\n this._events.fire(name, payload);\n }\n\n // ------------------------------------------------------------------------\n // View (Wave A: state + events only)\n // ------------------------------------------------------------------------\n\n /**\n * Zoom the viewport. `factor > 1` zooms in; `factor < 1` zooms out.\n * When `around` is supplied (in MODEL coordinates), the viewport offset\n * is adjusted so that point stays fixed in surface space — the standard\n * \"zoom to cursor\" UX. Fires `view:zoom` AND `view:viewport-change`\n * (per EVENTS.md §5); the view's listener applies the new transform.\n */\n zoom(factor: number, around?: Point): void {\n this._ensureLive();\n if (!Number.isFinite(factor) || factor <= 0) return;\n const previousScale = this._viewport.scale;\n const nextScale = previousScale * factor;\n const previousOffset = { ...this._viewport.offset };\n // If a focal point in MODEL space is provided, shift the offset so it\n // maps to the same surface position before and after the zoom.\n // Surface = offset + scale * baseTransform(model); the renderer's base\n // transform is constant per render, so anchoring against it means\n // offsetNext = offsetPrev + (prevScale - nextScale) * around.\n let nextOffset: Point = previousOffset;\n if (around !== undefined) {\n nextOffset = {\n x: previousOffset.x + (previousScale - nextScale) * around.x,\n y: previousOffset.y + (previousScale - nextScale) * around.y,\n };\n }\n const next: Viewport = { scale: nextScale, offset: nextOffset };\n this._viewport = next;\n const center = around ?? { x: 0, y: 0 };\n this._events.fire('view:zoom', { scale: nextScale, center, previousScale });\n this._events.fire('view:viewport-change', { viewport: next });\n }\n\n panTo(p: Point): void {\n this._ensureLive();\n const previousOffset = { ...this._viewport.offset };\n const next: Viewport = { scale: this._viewport.scale, offset: { ...p } };\n this._viewport = next;\n this._events.fire('view:pan', { offset: next.offset, previousOffset });\n this._events.fire('view:viewport-change', { viewport: next });\n }\n\n /**\n * Read the current viewport (scale + offset). Public so consumers (and\n * the pointer input layer in `move` mode) can read the offset before\n * computing a pan delta. Returns a shallow copy; mutating the returned\n * object does NOT affect the editor.\n */\n getViewport(): Viewport {\n return { scale: this._viewport.scale, offset: { ...this._viewport.offset } };\n }\n\n /**\n * Fit the model into the current viewport. The renderer's base transform\n * already auto-fits via the surface drawBox; `fitToContent` therefore\n * resets the EDITOR viewport (zoom=1, offset=0,0) so the renderer's fit\n * is the on-screen fit. Reports the content bbox for consumer use.\n */\n fitToContent(_padding?: number): void {\n this._ensureLive();\n let minX = 0; let minY = 0; let maxX = 0; let maxY = 0; let init = false;\n for (const a of this._mol.atoms) {\n if (!init) { minX = maxX = a.p.x; minY = maxY = a.p.y; init = true; continue; }\n if (a.p.x < minX) minX = a.p.x;\n if (a.p.x > maxX) maxX = a.p.x;\n if (a.p.y < minY) minY = a.p.y;\n if (a.p.y > maxY) maxY = a.p.y;\n }\n const bbox: Rect = init\n ? { x: minX, y: minY, width: maxX - minX, height: maxY - minY }\n : { x: 0, y: 0, width: 0, height: 0 };\n const previousOffset = { ...this._viewport.offset };\n const previousScale = this._viewport.scale;\n const next: Viewport = { scale: 1, offset: { x: 0, y: 0 } };\n this._viewport = next;\n if (previousScale !== 1)\n this._events.fire('view:zoom', { scale: 1, center: { x: 0, y: 0 }, previousScale });\n if (previousOffset.x !== 0 || previousOffset.y !== 0)\n this._events.fire('view:pan', { offset: next.offset, previousOffset });\n this._events.fire('view:viewport-change', { viewport: next });\n this._events.fire('view:fit-to-content', { bbox });\n }\n\n setViewOnly(viewOnly: boolean): void {\n this._ensureLive();\n const oldValue = this._viewOnly;\n if (oldValue === viewOnly) return;\n this._viewOnly = viewOnly;\n this._events.fire('option:change', { key: 'viewOnly', oldValue, newValue: viewOnly });\n }\n\n setTheme(theme: Theme): void {\n this._ensureLive();\n const previousTheme = this._theme;\n if (previousTheme === theme) return;\n this._theme = theme;\n this._events.fire('theme:change', { theme, previousTheme });\n }\n\n // ------------------------------------------------------------------------\n // Export — delegated to the service.\n // ------------------------------------------------------------------------\n\n toSvg(options?: { width?: number; height?: number }): string {\n this._ensureLive();\n const helm = this.getHelm();\n const renderOpts: { width?: number; height?: number } = {};\n if (options?.width !== undefined) renderOpts.width = options.width;\n if (options?.height !== undefined) renderOpts.height = options.height;\n return this._service.renderToSvg(helm, renderOpts);\n }\n\n async toPng(options?: { width?: number; height?: number }): Promise<Uint8Array> {\n this._ensureLive();\n const helm = this.getHelm();\n const renderOpts: { width?: number; height?: number } = {};\n if (options?.width !== undefined) renderOpts.width = options.width;\n if (options?.height !== undefined) renderOpts.height = options.height;\n return this._service.renderToPng(helm, renderOpts);\n }\n\n // ------------------------------------------------------------------------\n // Wave A introspection (used by tests; not part of the documented API)\n // ------------------------------------------------------------------------\n\n /** @internal Returns the host element passed at construction (or `null`). */\n _getHost(): HTMLElement | null { return this._host; }\n\n /** @internal Number of subscribed observers, for diagnostics. */\n _observerCount(): number { return this._events.observerCount(); }\n\n /** @internal Returns the current highlight set (read-only). Used by the view. */\n _currentHighlights(): ReadonlySet<number> { return this._highlights; }\n\n /** @internal Returns the current theme. Used by the view. */\n _currentTheme(): Theme { return this._theme; }\n\n /** @internal Returns the mounted view (or `null` when headless). */\n _getView(): EditorView | null { return this._view; }\n\n /** @internal Returns the current viewport. */\n _getViewport(): Viewport { return this._viewport; }\n\n // ------------------------------------------------------------------------\n // Dialogs (Wave B convenience openers)\n // ------------------------------------------------------------------------\n\n openAtomProps(atom: Atom): void {\n this._ensureLive();\n if (this._host === null) return;\n if (this._atomDialog === null)\n this._atomDialog = new AtomPropsDialog(this);\n this._atomDialog.open(atom);\n }\n\n openBondProps(bond: Bond): void {\n this._ensureLive();\n if (this._host === null) return;\n if (this._bondDialog === null)\n this._bondDialog = new BondPropsDialog(this);\n this._bondDialog.open(bond);\n }\n\n openFindReplace(): void {\n this._ensureLive();\n if (this._host === null) return;\n if (this._findReplaceDialog === null)\n this._findReplaceDialog = new FindReplaceDialog(this);\n this._findReplaceDialog.open();\n }\n\n // ------------------------------------------------------------------------\n // Mode + palette-driven add (Phase 6)\n // ------------------------------------------------------------------------\n\n /** Get the current interaction mode. */\n getMode(): EditorMode { return this._mode; }\n\n /** Set the interaction mode. Fires `option:change` with key `mode`. */\n setMode(mode: EditorMode): void {\n this._ensureLive();\n const old = this._mode;\n if (old === mode) return;\n this._mode = mode;\n this._events.fire('option:change', { key: 'mode', oldValue: old, newValue: mode });\n }\n\n /** Get the currently \"primed\" palette symbol (set via `setNextAddSymbol`). */\n getNextAddSymbol(): NextAddSymbol | null { return this._nextAdd; }\n\n /** Prime a palette symbol for the next add. Pass `null` to clear. */\n setNextAddSymbol(symbol: string | null, biotype?: HelmType): void {\n this._ensureLive();\n const oldValue = this._nextAdd;\n if (symbol === null) {\n this._nextAdd = null;\n } else {\n if (biotype === undefined) return;\n this._nextAdd = { symbol, biotype };\n }\n this._events.fire('option:change', { key: 'nextAdd', oldValue, newValue: this._nextAdd });\n }\n\n /** Forward to the DnD input. No-op when no DnD layer is mounted. */\n startPaletteDrag(symbol: string, biotype: HelmType): void {\n this._ensureLive();\n if (this._dnd === null) {\n this._events.fire('dnd:start', { source: 'palette', symbol });\n return;\n }\n this._dnd.startPaletteDrag(symbol, biotype);\n }\n\n // ------------------------------------------------------------------------\n // Find / Replace helpers\n // ------------------------------------------------------------------------\n\n /** Return every atom whose symbol equals `symbol`. */\n findMonomers(symbol: string): Atom[] {\n this._ensureLive();\n const out: Atom[] = [];\n for (const a of this._mol.atoms) if (a.symbol === symbol) out.push(a);\n return out;\n }\n\n /**\n * Phase 27 (T-2701 / T-2704) — Bulk replace.\n *\n * - `replaceMonomers(find: string, replace: string)` — symbol-keyed\n * find/replace path used by the Find/Replace dialog (T-0510). Every\n * atom whose `symbol === find` has its symbol updated to `replace`.\n * - `replaceMonomers(atoms: ReadonlyArray<Atom>, newSymbol: string)` —\n * atom-list path (T-2704) used by the palette tile click handler\n * when a same-biotype selection is active. Every atom in the list\n * has its symbol updated to `newSymbol`.\n *\n * Both forms run a single `Transaction` so the listeners observe a\n * single `mol:changed` event. After the transaction commits we MUST\n * re-run `resolveMonomers` — otherwise the new atoms still point at\n * the OLD `ResolvedMonomer` (with the old symbol's colour / structure\n * metadata), and the renderer paints the old colour through the\n * `monomer.meta.colors` resolution path. This was the root cause of\n * the user-reported \"color and tooltip don't update on find/replace\n * with `sp`\" bug.\n */\n replaceMonomers(find: string, replace: string): number;\n replaceMonomers(atoms: ReadonlyArray<Atom>, newSymbol: string): number;\n replaceMonomers(arg1: string | ReadonlyArray<Atom>, arg2: string): number {\n this._ensureLive();\n let targets: ReadonlyArray<Atom>;\n let reasonKey: string;\n if (typeof arg1 === 'string') {\n const find = arg1;\n const replace = arg2;\n targets = this.findMonomers(find);\n if (targets.length === 0) return 0;\n if (find === replace) return targets.length;\n reasonKey = `${find}->${replace}`;\n } else {\n // Atom-list path. Map ids back to the CURRENT mol so a stale Atom\n // reference (e.g. captured before a previous edit) still resolves\n // correctly; skip ids that no longer exist or already carry the\n // requested symbol.\n const newSymbol = arg2;\n const seen = new Set<number>();\n const live: Atom[] = [];\n for (const a of arg1) {\n if (seen.has(a.id)) continue;\n seen.add(a.id);\n const cur = molAtomById(this._mol, a.id);\n if (cur === undefined) continue;\n if (cur.symbol === newSymbol) continue;\n live.push(cur);\n }\n if (live.length === 0) return 0;\n targets = live;\n reasonKey = `atoms[${live.length}]->${newSymbol}`;\n }\n const replace = arg2;\n const tx = new Transaction(this._mol);\n for (const a of targets) tx.updateAtom(a.id, { symbol: replace });\n const { mol } = tx.commit();\n // Phase 27 (T-2701) — Re-resolve monomers so every replaced atom\n // gets a fresh `ResolvedMonomer` pointer (with the new symbol's\n // colour / structure metadata). Without this the renderer paints\n // the OLD colour and the tooltip shows the OLD name even though\n // the symbol field is correct.\n const resolved = resolveMonomers(mol, this._service.monomerLib, { mode: 'lenient' }).mol;\n this._replaceMol(resolved, `replaceMonomers:${reasonKey}`, 'api');\n return targets.length;\n }\n\n /**\n * Nudge every selected atom by `(dx, dy)` in model units. Used by the\n * keyboard input layer for arrow-key movement.\n */\n nudgeSelection(dx: number, dy: number): void {\n this._ensureLive();\n const sel = this._selection;\n if (sel.atoms.size === 0) return;\n const tx = new Transaction(this._mol);\n for (const id of sel.atoms) {\n const a = molAtomById(this._mol, id);\n if (a === undefined) continue;\n tx.updateAtom(id, { p: { x: a.p.x + dx, y: a.p.y + dy } });\n }\n const { mol } = tx.commit();\n this._replaceMol(mol, 'nudge', 'user');\n }\n\n /** Delete every atom (and via cascade, bond) in the current selection. */\n deleteSelection(): void {\n this._ensureLive();\n const sel = this._selection;\n if (sel.atoms.size === 0 && sel.bonds.size === 0) return;\n const tx = new Transaction(this._mol);\n for (const id of sel.atoms) tx.removeAtom(id);\n for (const id of sel.bonds) tx.removeBond(id);\n const { mol } = tx.commit();\n this._selection = Selection.empty();\n this._replaceMol(mol, 'delete-selection', 'user');\n this._events.fire('selection:change', {\n selection: this._selection,\n addedAtomIds: EMPTY_FROZEN_ID_SET,\n removedAtomIds: sel.atoms,\n addedBondIds: EMPTY_FROZEN_ID_SET,\n removedBondIds: sel.bonds,\n });\n }\n\n // ------------------------------------------------------------------------\n // RNA Builder (Phase 18 T-1806)\n // ------------------------------------------------------------------------\n\n /**\n * Phase 18 (T-1806) — Append a single `sugar(base)linker` triplet to the\n * editor. The behaviour depends on the current Mol:\n *\n * - Empty editor → create `RNA1{<triplet>}$$$$V2.0`.\n * - Editor with no RNA polymer → add a new `RNA<n>{<triplet>}` polymer,\n * where `n` is the next free RNA index in the existing HELM.\n * - Editor with one or more RNA polymers → append `.<triplet>` to the\n * LAST RNA polymer's body so the user's mental model of \"extend the\n * chain\" matches the result (single polymer with the new triplet at\n * the 3' end).\n *\n * The full operation goes through `setHelm`, which re-runs parsing,\n * resolution, and layout — so a multi-polymer document keeps its\n * existing chain identities and the new monomers get sensible\n * coordinates without bespoke layout code.\n *\n * Multi-character symbols (`fl2r`, `sp`, `5meC`, …) are emitted wrapped\n * in `[...]` per the HELM grammar; single-character symbols (`r`, `A`,\n * `p`) emit naked.\n */\n appendRnaTriplet(sugar: string, base: string, linker: string): void {\n this._ensureLive();\n const triplet = formatRnaTriplet(sugar, base, linker);\n const current = this.getHelm();\n const next = spliceRnaTriplet(current, triplet);\n this.setHelm(next);\n }\n\n /**\n * Phase 19 (T-1903) / Phase 20 (T-2006) / Phase 21 (T-2103) -- Place an\n * RNA triplet as a SEPARATE polymer.\n *\n * The Phase 20 implementation round-tripped the HELM through\n * `setHelm`, then tried to restore pre-existing atom positions by\n * keying on `(chainId, positionInChain)`. That key collides for\n * every RNA base in a chain (parser leaves `positionInChain=0` on\n * branch atoms — see `parser.ts` `addToChain`), so all bases\n * collapsed onto the same restored position when more than one\n * existed (user report: \"all bases somehow end up at the same\n * place\"). Phase 21 abandons the round-trip and appends directly\n * via `Transaction.addAtom` / `addBond` so pre-existing atom\n * identity is untouched.\n *\n * Placement heuristic (T-2103):\n * * If the most recent action was also `add-triplet`, place the\n * new sugar two steps to the right of the previous one — same\n * row, growing leftward to right.\n * * Otherwise, place it below the leftmost existing atom (one\n * row gap) so the new triplet appears in free space without\n * overlapping. Mutations outside this method reset\n * `_lastAction` to `'other'`, so a tetramer-then-Add starts a\n * new row instead of jumping to the right of the most-recent\n * sugar (which would land it on top of the existing chain).\n *\n * Triplet geometry (T-2103) — linker RIGHT of sugar, base BELOW\n * sugar — matches the new RNA-Builder SVG visual. Geometry inside\n * a row mirrors the canonical r(A)p ordering, where the linker\n * sits at R2 of the sugar (3' end of the nucleotide).\n */\n placeRnaTriplet(sugar: string, base: string, linker: string): void {\n this._ensureLive();\n const step = BOND_SCALE * (this._options.bondLength ?? DEFAULT_BOND_LENGTH);\n\n // 1. Decide the new triplet's sugar position based on _lastAction.\n let newSugarP: Point;\n const atoms = this._mol.atoms;\n if (this._lastAction === 'add-triplet' && this._lastTripletSugarPos !== null) {\n // Chain to the right of the previous Add. Two steps so the\n // linker (at sugar.x + step) clears the previous sugar's base.\n newSugarP = {\n x: this._lastTripletSugarPos.x + step * 2,\n y: this._lastTripletSugarPos.y,\n };\n } else if (atoms.length === 0) {\n // Empty editor: anchor at (0, 0) so layoutMol's auto-fit centres\n // the result. The existing tests + serializer round-trip rely on\n // this anchor being at the origin.\n newSugarP = { x: 0, y: 0 };\n } else {\n // Below the leftmost existing atom, one row gap.\n //\n // Phase 25 (T-2502): vertical offset reduced from `step * 2` to\n // `step` (halved). User report: \"now its adding too much down,\n // lets half that distance.\" The 2*step gap meant a fresh triplet\n // landed two full bond-lengths below the last row, leaving an\n // empty band of canvas; a single step keeps the new row visually\n // close enough to be clearly part of the same polymer cluster.\n let minX = atoms[0]!.p.x;\n let maxY = atoms[0]!.p.y;\n for (const a of atoms) {\n if (a.p.x < minX) minX = a.p.x;\n if (a.p.y > maxY) maxY = a.p.y;\n }\n newSugarP = { x: minX, y: maxY + step };\n }\n const newLinkerP: Point = { x: newSugarP.x + step, y: newSugarP.y };\n const newBaseP: Point = { x: newSugarP.x, y: newSugarP.y + step };\n\n // 2. Allocate a fresh chain id (next free RNA<n>).\n const existingRnaIds = new Set<string>();\n for (const c of this._mol.chains) existingRnaIds.add(c.id);\n let n = 1;\n while (existingRnaIds.has(`RNA${n}`)) n += 1;\n const newChainId = `RNA${n}`;\n\n // 3. Append atoms + bonds directly via Transaction. Pre-existing\n // atoms are untouched, so their positions, ids, and bio fields\n // survive verbatim.\n const tx = new Transaction(this._mol);\n const sugarId = tx.addAtom({\n p: newSugarP,\n biotype: HelmTypes.SUGAR,\n symbol: sugar,\n chainId: newChainId,\n positionInChain: 1,\n });\n const linkerId = tx.addAtom({\n p: newLinkerP,\n biotype: HelmTypes.LINKER,\n symbol: linker,\n chainId: newChainId,\n positionInChain: 2,\n });\n // Base is a branch atom on the sugar; not added through the\n // chain's backbone. We mark it with positionInChain=0 to mirror\n // what the parser does for branch atoms (see parser.ts\n // `addToChain` -- branch atoms keep positionInChain=0).\n const baseId = tx.addAtom({\n p: newBaseP,\n biotype: HelmTypes.BASE,\n symbol: base,\n chainId: newChainId,\n // Insert at position 0 so the Transaction does NOT push the\n // base onto the chain's `backboneAtoms` after sugar+linker\n // (which would corrupt the serializer's expectation that\n // backbone = [sugar, linker]).\n positionInChain: 0,\n });\n\n // 4. Add bonds. R3(sugar) -> R1(base) branch, R2(sugar) -> R1(linker) backbone.\n tx.addBond({\n a1: sugarId,\n a2: baseId,\n kind: 'branch',\n r1: { kind: 'numeric', r: 3 },\n r2: { kind: 'numeric', r: 1 },\n });\n tx.addBond({\n a1: sugarId,\n a2: linkerId,\n kind: 'backbone',\n r1: { kind: 'numeric', r: 2 },\n r2: { kind: 'numeric', r: 1 },\n });\n\n const { mol } = tx.commit();\n\n // 5. Re-attach the sugar.branchAtom pointer + remove the base\n // from the chain's backbone (Transaction.addAtom always\n // inserts into backbone). We work on a NEW mol with the\n // fix-ups applied so the immutable graph stays consistent.\n const fixedMol = this._postProcessTripletMol(mol, sugarId, baseId, newChainId);\n\n // 6. Resolve monomers so tooltips, palette colours, atomic-mol\n // expansion all work on the new atoms.\n const resolved = resolveMonomers(fixedMol, this._service.monomerLib, { mode: 'lenient' }).mol;\n\n // 7. Commit.\n this._replaceMol(resolved, 'placeRnaTriplet', 'user');\n\n // 8. Update placement-state so the NEXT Add chains to the right\n // of THIS sugar. Any other mutation (addAtom/removeAtom/\n // setHelm/...) clears it via `_resetLastAction`.\n this._lastAction = 'add-triplet';\n this._lastTripletSugarPos = newSugarP;\n }\n\n /**\n * Phase 21 (T-2103) — Fix-up pass after `Transaction.addAtom` for an\n * RNA triplet:\n *\n * 1. Remove the base atom from the chain's `backboneAtoms` list\n * (Transaction always inserts; an RNA base is a BRANCH atom).\n * 2. Set the sugar's `branchAtom` pointer to the new base.\n *\n * Pre-condition: `mol` was produced by a Transaction commit on the\n * editor's current state; `sugarId` + `baseId` are the freshly\n * allocated ids; `chainId` is the chain we just created.\n *\n * The function returns a new Mol with the corrections baked in;\n * the input is not modified (Mol is immutable).\n */\n private _postProcessTripletMol(mol: Mol, sugarId: number, baseId: number, chainId: string): Mol {\n // Re-stamp the sugar atom with a branchAtom pointer to the base.\n const oldToNew = new Map<number, Atom>();\n const baseAtom = molAtomById(mol, baseId);\n const sugarAtom = molAtomById(mol, sugarId);\n if (baseAtom === undefined || sugarAtom === undefined) return mol;\n const newSugar: Atom = { ...sugarAtom, branchAtom: baseAtom };\n oldToNew.set(sugarId, newSugar);\n\n // Build new bonds repointing the sugar instance.\n const newBonds: Bond[] = mol.bonds.map((b) => {\n const a1 = oldToNew.get(b.a1.id) ?? b.a1;\n const a2 = oldToNew.get(b.a2.id) ?? b.a2;\n if (a1 === b.a1 && a2 === b.a2) return b;\n return { ...b, a1, a2 };\n });\n const newBondsById = new Map<number, Bond>();\n for (const b of newBonds) newBondsById.set(b.id, b);\n\n // Walk chains. The target chain's backboneAtoms drops the base\n // and re-pins the sugar/linker instances.\n const newChains: Chain[] = mol.chains.map((c) => {\n const backbone: Atom[] = [];\n for (const a of c.backboneAtoms) {\n if (c.id === chainId && a.id === baseId) continue; // remove base\n backbone.push(oldToNew.get(a.id) ?? a);\n }\n const bonds: Bond[] = c.bonds.map((b) => newBondsById.get(b.id) ?? b);\n return {\n id: c.id,\n polymerType: c.polymerType,\n backboneAtoms: backbone as readonly Atom[],\n bonds: bonds as readonly Bond[],\n ...(c.annotation !== undefined ? { annotation: c.annotation } : {}),\n };\n });\n\n const newAtoms: Atom[] = mol.atoms.map((a) => oldToNew.get(a.id) ?? a);\n\n let out: Mol = {\n atoms: newAtoms as readonly Atom[],\n bonds: newBonds as readonly Bond[],\n chains: newChains as readonly Chain[],\n groups: mol.groups,\n annotations: mol.annotations,\n };\n // Refresh continuous-ids: removing the base from the chain's\n // backbone changes the walk order vs. what Transaction computed.\n out = this._refreshContinuousIdsLocal(out);\n return out;\n }\n\n /**\n * Phase 21 (T-2103) — Mark \"the most recent user-perceived mutation\n * was NOT a triplet add\". Called from every other mutator so the\n * RNA-Builder's \"next triplet chains right\" heuristic only fires\n * after consecutive Adds.\n */\n private _resetLastAction(): void {\n this._lastAction = 'other';\n this._lastTripletSugarPos = null;\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _ensureLive(): void {\n if (this._destroyed) throw new Error('HelmEditor: this instance has been destroyed.');\n }\n\n private _replaceMol(mol: Mol, reason: string, source: 'user' | 'api'): void {\n const prevHelm = this._service.serialize(this._mol);\n const nextHelm = this._service.serialize(mol);\n this._mol = mol;\n this._history.push({ mol, label: reason });\n // Phase 21 (T-2103) — Any mutation invalidates the \"previous Add was\n // a triplet\" placement state. `placeRnaTriplet` re-sets `_lastAction`\n // to 'add-triplet' AFTER calling `_replaceMol`, so the reset here is\n // harmless to that path.\n this._resetLastAction();\n this._events.fire('mol:changed', {\n mol,\n changedAtomIds: new Set<number>(mol.atoms.map((a) => a.id)),\n changedBondIds: new Set<number>(mol.bonds.map((b) => b.id)),\n reason,\n });\n if (prevHelm !== nextHelm)\n this._events.fire('helm:changed', { helm: nextHelm, mol, source });\n }\n\n private _restoreFromHistory(mol: Mol, source: 'undo' | 'redo'): void {\n const prevHelm = this._service.serialize(this._mol);\n const nextHelm = this._service.serialize(mol);\n this._mol = mol;\n // Phase 21 (T-2103) — Undo/redo crosses an event boundary; reset the\n // RNA-Builder placement state so the next Add starts a new row.\n this._resetLastAction();\n this._events.fire('mol:changed', {\n mol,\n changedAtomIds: new Set<number>(mol.atoms.map((a) => a.id)),\n changedBondIds: new Set<number>(mol.bonds.map((b) => b.id)),\n reason: source,\n });\n if (prevHelm !== nextHelm)\n this._events.fire('helm:changed', { helm: nextHelm, mol, source });\n }\n}\n\n// Re-export commonly needed enums so consumers don't need a second import\n// just to spell out a biotype when calling `addAtom`.\nexport { HelmTypes };\n\n// --------------------------------------------------------------------------\n// Phase 18 (T-1806) — RNA-triplet HELM helpers.\n//\n// Pure-string utilities used by `HelmEditor.appendRnaTriplet`. Kept at the\n// module bottom so the editor class stays focused on state + events.\n// --------------------------------------------------------------------------\n\n/**\n * Wrap a HELM monomer symbol in `[...]` iff it is multi-character OR\n * contains a character that the parser would not accept as a naked\n * token. Single ASCII letters (`r`, `A`, `p`) emit naked; everything else\n * (`fl2r`, `sp`, `5meC`, `[fl2r]` already-bracketed) emits with brackets.\n */\nexport function formatHelmMonomerSymbol(symbol: string): string {\n // Caller may have passed `[fl2r]` directly — accept that as already\n // formatted so the RNA Builder can use the `<option value>` form\n // verbatim.\n if (symbol.startsWith('[') && symbol.endsWith(']')) return symbol;\n if (symbol.length === 1 && /^[A-Za-z]$/.test(symbol)) return symbol;\n return `[${symbol}]`;\n}\n\n/** Build the HELM body fragment for a single RNA triplet: `<sugar>(<base>)<linker>`. */\nexport function formatRnaTriplet(sugar: string, base: string, linker: string): string {\n return `${formatHelmMonomerSymbol(sugar)}(${formatHelmMonomerSymbol(base)})${formatHelmMonomerSymbol(linker)}`;\n}\n\n/** Escape a string for safe interpolation into a `RegExp`. */\nfunction escapeRegExp(s: string): string {\n return s.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n}\n\n/**\n * Splice an RNA triplet body into an existing HELM string. Pure string\n * manipulation — does NOT touch the editor's Mol. Behaviour:\n *\n * 1. Empty `helm` → `RNA1{<triplet>}$$$$V2.0`.\n * 2. `helm` contains at least one `RNA<n>{...}` polymer → append\n * `.<triplet>` to the LAST such polymer's body, preserving\n * section markers and the version trailer.\n * 3. Otherwise add a new `RNA<n>{<triplet>}` polymer (`<n>` is the\n * smallest positive integer not already used by an RNA polymer).\n *\n * Exported so the unit tests can iterate the table of cases without\n * standing up a full editor.\n */\n/**\n * Phase 19 (T-1903) -- Variant of `spliceRnaTriplet` that ALWAYS creates\n * a new `RNAn{...}` polymer instead of extending the most-recent one.\n * Used by `HelmEditor.placeRnaTriplet`; gives the RNA Builder \"drop a\n * fresh triplet, do not auto-connect\" semantics.\n *\n * 1. Empty `helm` -> `RNA1{<triplet>}$$$$V2.0`.\n * 2. Non-empty `helm` -> append `|RNAm{<triplet>}` where `m` is the\n * smallest positive integer not already used by an RNA polymer.\n * Inserted immediately before the first `$` section separator so\n * section markers stay intact.\n */\nexport function spliceRnaTripletAsNewPolymer(helm: string, triplet: string): string {\n if (helm === '') return `RNA1{${triplet}}$$$$V2.0`;\n const usedIndices = new Set<number>();\n const idxRe = /RNA(\\d+)\\{/g;\n let im: RegExpExecArray | null;\n while ((im = idxRe.exec(helm)) !== null)\n usedIndices.add(Number(im[1]));\n let next = 1;\n while (usedIndices.has(next)) next += 1;\n const newPolymer = `RNA${next}{${triplet}}`;\n const sepIdx = helm.indexOf('$');\n if (sepIdx < 0) {\n // Atypical: no `$` markers. Append as a new polymer + a stock trailer.\n return `${helm}|${newPolymer}$$$$V2.0`;\n }\n const before = helm.slice(0, sepIdx);\n const after = helm.slice(sepIdx);\n const joiner = before === '' ? '' : '|';\n return `${before}${joiner}${newPolymer}${after}`;\n}\n\nexport function spliceRnaTriplet(helm: string, triplet: string): string {\n if (helm === '') return `RNA1{${triplet}}$$$$V2.0`;\n // Iterate every `RNAn{...}` occurrence; keep the last match.\n const rnaRe = /(^|\\|)(RNA\\d+)\\{([^}]*)\\}/g;\n let lastMatch: { name: string; body: string; matchText: string } | null = null;\n let m: RegExpExecArray | null;\n while ((m = rnaRe.exec(helm)) !== null) {\n lastMatch = {\n name: m[2] as string,\n body: m[3] as string,\n matchText: m[0] as string,\n };\n }\n if (lastMatch !== null) {\n const sep = lastMatch.body === '' ? '' : '.';\n const replaced = `${lastMatch.matchText.startsWith('|') ? '|' : ''}${lastMatch.name}{${lastMatch.body}${sep}${triplet}}`;\n // Replace the LAST occurrence only — a simple `.replace(matchText, ...)`\n // would replace the first occurrence. We use `lastIndexOf` to splice\n // by absolute position so a polymer body that happens to be a substring\n // of an earlier one cannot collide.\n const idx = helm.lastIndexOf(lastMatch.matchText);\n return helm.slice(0, idx) + replaced + helm.slice(idx + lastMatch.matchText.length);\n }\n // No RNA polymer yet — pick the smallest free index, then inject the\n // new polymer immediately before the `$` section separator.\n const usedIndices = new Set<number>();\n const idxRe = /RNA(\\d+)\\{/g;\n let im: RegExpExecArray | null;\n while ((im = idxRe.exec(helm)) !== null)\n usedIndices.add(Number(im[1]));\n let next = 1;\n while (usedIndices.has(next)) next += 1;\n const newPolymer = `RNA${next}{${triplet}}`;\n const sepIdx = helm.indexOf('$');\n if (sepIdx < 0) {\n // Atypical: no `$` markers. Append as a new polymer + a stock trailer.\n return `${helm}|${newPolymer}$$$$V2.0`;\n }\n const before = helm.slice(0, sepIdx);\n const after = helm.slice(sepIdx);\n const joiner = before === '' ? '' : '|';\n // Replace the regex-escaped polymer if the body was empty so we never\n // produce `|RNA1{...}|...` — the simpler `${before}${joiner}${newPolymer}${after}`\n // is correct because `before` ends at the start of the `$` block.\n void escapeRegExp;\n return `${before}${joiner}${newPolymer}${after}`;\n}\n","// T-0602 / T-1201 / T-1301a — Palette tile renderer.\n//\n// Pure helper for building a single palette tile DOM. Kept separate from\n// `palette.ts` so the structural detail (icon, label, star, colors) is easy\n// to inspect and unit-test on its own (tests live in `palette.test.ts`).\n//\n// Phase 12 (T-1201) redesign:\n// - Rounded squares (~48×48 px, border-radius 10 px) instead of inline\n// rectangles.\n// - Soft pastel backgrounds: `soften()` desaturates the canonical palette\n// colour by ~30% and lightens by ~10%.\n// - Subtle drop-shadow + thin border at rest; thick accent border on hover\n// and when `aria-pressed=\"true\"` (selected/primed).\n// - Tile background colour computed once per (monomer, theme) and stored\n// on the data attributes so tests can inspect the actual rendered values.\n// - Insufficient-contrast fallback: when the softened background is too\n// close to the label colour (WCAG contrast < 5:1), we attach a `--low-\n// contrast` modifier class which the stylesheet uses to add a 1px inner\n// shadow boundary.\n//\n// Phase 13a (T-1301a, Bug 1) — text overflow:\n// - Tile is now flexible width: min-width 48 px, max-width 96 px, fixed\n// 48 px height. Long symbols (e.g. `deamino-Phg_35diM`) no longer push\n// the label out of the tile.\n// - Label uses `white-space: nowrap; overflow: hidden; text-overflow:\n// ellipsis;` so overflow renders as `…` instead of spilling out.\n// - Label font shrinks from 14px → 11px when the symbol is longer than\n// 3 characters. The full symbol stays in `title` and in `aria-label`\n// for accessibility.\n//\n// Layering: imports from `core/`, `monomer-lib/`, `render/`, and the local\n// `view/dom-utils`. No editor-level imports.\n\nimport type { HelmType } from '../../core/constants';\nimport type { Monomer } from '../../monomer-lib/types';\nimport { contrastRatio, resolveMonomerColors, soften } from '../../monomer-lib/color-rules';\nimport type { Theme } from '../../render/theme';\nimport { el } from '../view/dom-utils';\n\n/** Minimum contrast ratio (label vs. background) required for a tile. */\nexport const TILE_MIN_CONTRAST = 5.0;\n\n/**\n * Phase 13a (Bug 1): label-shrink threshold. Symbols longer than this many\n * characters render at `TILE_LABEL_FONT_SMALL`; shorter symbols use\n * `TILE_LABEL_FONT_LARGE`. Three characters covers every natural-letter HELM\n * symbol (A, G, dA, m1Y, …); anything wider (e.g. `Phg`, `Aib`, `[PEG2]`)\n * has historically truncated visually — now it shrinks instead.\n *\n * Phase 18 (T-1805) extends the table with three more buckets:\n * - 4..6 chars → 11 px (the existing small font)\n * - 7..9 chars → 9 px\n * - 10+ chars → 8 px with line-height 1.1 + letter-spacing -0.02em\n *\n * The original two-bucket scheme had `meAA` (4 chars) at 11px and\n * `deamino-Phg_35diM` (17 chars) at the SAME 11 px — so the long symbol\n * still ellipsized down to \"deamin…\". The new ladder shrinks aggressively\n * once the tile is genuinely full.\n */\nexport const TILE_LABEL_SHRINK_THRESHOLD = 3;\n/** Large label font size (CSS px), used for 1..3 char symbols. */\nexport const TILE_LABEL_FONT_LARGE = 14;\n/** Small label font size (CSS px), used for 4..6 char symbols. */\nexport const TILE_LABEL_FONT_SMALL = 11;\n/** Phase 18 (T-1805) — Tiny label font size (CSS px), 7..9 char symbols. */\nexport const TILE_LABEL_FONT_TINY = 9;\n/** Phase 18 (T-1805) — Micro label font size (CSS px), 10+ char symbols. */\nexport const TILE_LABEL_FONT_MICRO = 8;\n/** Tile minimum width in CSS pixels (single short symbol). */\nexport const TILE_MIN_WIDTH = 48;\n/** Tile maximum width in CSS pixels (after ellipsis kicks in). */\nexport const TILE_MAX_WIDTH = 96;\n\n/**\n * Phase 18 (T-1805) — Resolve the label font size for a given symbol\n * length, following the four-bucket ladder documented above. Exposed so\n * tests can iterate the table and so callers (e.g. the RNA builder\n * preview) can match the palette's text sizing.\n */\nexport function tileLabelFontSize(symbolLength: number): number {\n if (symbolLength <= TILE_LABEL_SHRINK_THRESHOLD) return TILE_LABEL_FONT_LARGE;\n if (symbolLength <= 6) return TILE_LABEL_FONT_SMALL;\n if (symbolLength <= 9) return TILE_LABEL_FONT_TINY;\n return TILE_LABEL_FONT_MICRO;\n}\n\n/** Inputs accepted by `buildTile`. */\nexport interface BuildTileInput {\n /** Monomer record being represented (may be a synthetic stub for placeholders). */\n monomer: Monomer;\n /** Biotype of the monomer (used to resolve the color palette entry). */\n biotype: HelmType;\n /** Active theme (drives the background color). */\n theme: Theme;\n /** Whether the tile is currently marked as a favorite. */\n favorite: boolean;\n /** Whether the tile is the \"primed\" next-add symbol (visually highlighted). */\n primed: boolean;\n}\n\n/**\n * Build a draggable palette tile DOM element. Returns the root `<div>` plus\n * a reference to the star icon span so the palette can toggle its appearance.\n *\n * The rendered tile is:\n * `<div class=\"hw-palette__tile\" data-bg=\"#xxxxxx\" ...>\n * <span class=\"hw-palette__star\">…</span>\n * <span class=\"hw-palette__label\">A</span>\n * </div>`\n *\n * Tile styling lives in `src/editor/styles.ts` (.hw-palette__tile rules).\n */\nexport function buildTile(\n doc: Document,\n input: BuildTileInput,\n): { root: HTMLElement; star: HTMLElement } {\n const raw = resolveMonomerColors(input.monomer, input.biotype, input.theme.colorTheme);\n // Pastel tile background. The canvas keeps the saturated palette unless\n // theme.palette.softenCanvas is set; the palette is ALWAYS softened.\n const softBg = soften(raw.background);\n const labelColor = raw.text;\n const lowContrast = contrastRatio(labelColor, softBg) < TILE_MIN_CONTRAST;\n\n // Phase 13a (Bug 1) + Phase 18 (T-1805): pick a font size based on symbol\n // length so wide symbols (e.g. `deamino-Phg_35diM`) shrink rather than\n // overflow. The Phase 18 ladder adds tiny / micro buckets so the longest\n // HELMCoreLibrary symbols still render WITHOUT ellipsis.\n const symbol = input.monomer.symbol;\n const labelFontSize = tileLabelFontSize(symbol.length);\n // Phase 18 (T-1805): compact-mode extras for 10+ chars.\n const compact = symbol.length >= 10;\n const compactExtras = compact\n ? 'line-height:1.1;letter-spacing:-0.02em;'\n : '';\n // The label's inline style holds the truncation rules so the structural\n // unit test can read them without relying on getComputedStyle (linkedom\n // does not implement CSS resolution).\n const labelStyle =\n `font-size:${labelFontSize}px;${compactExtras}` +\n 'white-space:nowrap;overflow:hidden;text-overflow:ellipsis;' +\n // Cap the label's own width to the tile content area minus the star and\n // a few px of horizontal padding so ellipsis kicks in inside the tile.\n `max-width:${TILE_MAX_WIDTH - 16}px;display:inline-block;`;\n const star = el(doc, 'span', { class: 'hw-palette__star' }, [input.favorite ? '★' : '☆']);\n const label = el(doc, 'span', { class: 'hw-palette__label', style: labelStyle }, [symbol]);\n const classes = ['hw-palette__tile'];\n if (input.primed) classes.push('hw-palette__tile--primed');\n if (input.favorite) classes.push('hw-palette__tile--favorite');\n if (lowContrast) classes.push('hw-palette__tile--low-contrast');\n const fullName = input.monomer.name !== undefined ? `${symbol} — ${input.monomer.name}` : symbol;\n // Inline-style rules so structural tests can read them without a live\n // CSS engine, and so a host page that strips the stylesheet still gets\n // sane truncation behaviour.\n //\n // Phase 18 (T-1805): tiles are now rectangular (40 px tall) and fill\n // their grid cell (`width:100%`) so the parent grid's\n // `repeat(3, 1fr)` controls horizontal sizing. We keep `min-width:48px`\n // as a hard floor so the tile never collapses below a readable square\n // when the pane is unusually narrow.\n const rootStyle =\n `background:${softBg};color:${labelColor};` +\n `width:100%;min-width:${TILE_MIN_WIDTH}px;` +\n 'padding:4px 6px;height:40px;' +\n 'box-sizing:border-box;' +\n 'overflow:hidden;text-overflow:ellipsis;';\n const root = el(doc, 'div', {\n class: classes.join(' '),\n draggable: 'true',\n role: 'button',\n 'aria-pressed': input.primed ? 'true' : 'false',\n 'aria-label': fullName,\n 'data-symbol': symbol,\n 'data-biotype': input.biotype,\n 'data-bg': softBg,\n 'data-raw-bg': raw.background,\n 'data-testid': `palette-tile-${symbol}`,\n title: fullName,\n style: rootStyle,\n }, [star, label]);\n return { root, star };\n}\n","// Phase 18 (T-1806) / Phase 19 (T-1903) / Phase 20 (T-2002) -- RNA Builder.\n//\n// Phase 20 redesign (T-2002): the three field rows from Phase 19 are\n// replaced with a small SVG visualization of the triplet -- square\n// sugar centered, diamond base hanging below, circle linker to the\n// left. Each shape carries the monomer symbol centered inside, fills\n// from the monomer's resolved background colour (same `resolveMonomerColors`\n// the canvas uses), and is clickable to enter pick-mode for that slot.\n// Connecting lines mimic the sugar-linker R1-R2 backbone bond and the\n// sugar-base R3-R1 branch bond.\n//\n// Behaviour preserved from Phase 19:\n// * `startPickMode(field)` puts the palette into biotype pick-mode;\n// a click on a matching tile sets the slot value, any other click\n// cancels (Phase 20 T-2005 widens the cancellation policy).\n// * \"Add triplet\" calls `editor.placeRnaTriplet` which now positions\n// the new polymer next to the rightmost existing sugar (T-2006).\n// * Any combination of `r/d/m/...` sugars, `A/C/G/U/T/...` bases, and\n// `p/sp/...` linkers from the active library is supported.\n\nimport { Subject } from '../../util/observable';\nimport { HelmTypes } from '../../core/constants';\nimport type { HelmType } from '../../core/constants';\nimport type { IMonomerLib, Monomer } from '../../monomer-lib/types';\nimport { resolveMonomerColors } from '../../monomer-lib/color-rules';\nimport type { Theme } from '../../render/theme';\nimport type { Unsubscribe } from '../../util/types';\nimport type { HelmEditor } from '../editor';\nimport { formatRnaTriplet } from '../editor';\nimport { el, getDocument } from '../view/dom-utils';\nimport {\n fillTooltip,\n getOrCreateTooltipEl,\n hideTooltipEl,\n positionTooltipAt,\n renderRdkitSvg,\n type RdkitLike,\n} from '../view/tooltip-rdkit';\n\n/** SVG namespace -- used by `createElementNS` for every SVG node. */\nconst SVG_NS = 'http://www.w3.org/2000/svg';\n\n/** Options for `RnaBuilder`. */\nexport interface RnaBuilderOptions {\n documentImpl?: Document;\n}\n\n/** Which of the three triplet slots the pick-mode is targeting. */\nexport type RnaBuilderField = 'sugar' | 'base' | 'linker';\n\n/**\n * Triplet currently displayed in the builder. Returned from\n * `getSelection` so tests can introspect without poking at the DOM.\n */\nexport interface RnaBuilderSelection {\n readonly sugar: string;\n readonly base: string;\n readonly linker: string;\n /** HELM body fragment (`r(A)p`, `[fl2r]([5meC])[sp]`, ...). */\n readonly preview: string;\n}\n\n/** Internal: a single slot (clickable SVG group + shape + label text). */\ninterface SlotState {\n readonly id: RnaBuilderField;\n readonly biotype: HelmType;\n readonly groupEl: Element;\n readonly shapeEl: Element;\n readonly labelEl: Element;\n value: string;\n}\n\n/** Map field id -> biotype. */\nconst FIELD_BIOTYPE: Record<RnaBuilderField, HelmType> = {\n sugar: HelmTypes.SUGAR,\n base: HelmTypes.BASE,\n linker: HelmTypes.LINKER,\n};\n\n/** Default symbols when the library is silent. */\nconst DEFAULTS: Record<RnaBuilderField, readonly string[]> = {\n sugar: ['r', 'R'],\n base: ['A'],\n linker: ['p', 'P'],\n};\n\n// Phase 21 (T-2101) / Phase 22 (T-2203) -- SVG geometry constants.\n// All three slot shapes share the SAME nominal size (visible area\n// roughly equal) so the triplet preview reads as a balanced glyph\n// rather than \"linker is huge, sugar is small\". Layout mirrors the\n// canvas rendering of a real r(A)p triplet:\n//\n// sugar --- linker\n// |\n// base\n//\n// Phase 22 (T-2203): the user reported \"the bonds are still too short\"\n// in the Phase 21 layout (centre-to-centre distance was 50, shape\n// half-extent 18, so the VISIBLE bond strand was ~14 px). Phase 22\n// widens centre-to-centre to 70 so the visible bond reads as ~34 px\n// (70 - 2*18) -- enough to register as a real connector at the\n// builder's display zoom.\nconst VIEW_W = 200;\nconst VIEW_H = 180;\nconst SUGAR_CENTER = { x: 70, y: 60 };\nconst LINKER_CENTER = { x: 140, y: 60 };\nconst BASE_CENTER = { x: 70, y: 130 };\n// Phase 21 (T-2101): uniform \"nominal size\" across all three shapes.\n// Sugar square 36x36; linker circle r=18 (diameter 36); base diamond\n// half-diagonal 22 (so visible area ~ same as sugar; rotated 45 deg).\nconst SUGAR_HALF = 18;\nconst LINKER_RADIUS = 18;\nconst BASE_HALF = 22;\n\n/**\n * RNA Builder UI. Owned and instantiated by `MonomerPalette`. Pick\n * mode is wired through `PaletteFilterHooks` (see palette.ts) so the\n * palette gets to control which tiles are visible and which click\n * targets count as \"complete the pick\" vs \"cancel the pick\".\n *\n * @example\n * const rb = new RnaBuilder(host, editor, { paletteHooks });\n * rb.startPickMode('sugar'); // palette filters to sugars\n * rb.onValueSet.subscribe(...); // observe completion\n */\nexport class RnaBuilder {\n readonly element: HTMLElement;\n readonly onValueSet = new Subject<{ field: RnaBuilderField; symbol: string }>();\n readonly onPickModeChange = new Subject<{ field: RnaBuilderField | null }>();\n\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private _libUnsub: Unsubscribe;\n private readonly _slots: Map<RnaBuilderField, SlotState> = new Map();\n private readonly _preview: HTMLElement;\n private readonly _addBtn: HTMLElement;\n private readonly _hooks: PaletteFilterHooks | null;\n private _pickMode: RnaBuilderField | null = null;\n private _destroyed = false;\n /**\n * Phase 29 (T-2901) -- Pick-mode hint lives INSIDE the builder body,\n * directly below the \"RNA builder\" title. When idle the element\n * carries the `hidden` attribute (CSS `display: none`) so it takes\n * NO vertical space -- the SVG triplet sits right under the title.\n * Entering pick mode removes `hidden` and sets the bold text\n * \"Pick <slot> from palette\". Replaces Phase 24's always-mounted\n * `_hintEl` on the palette, which reserved 28-32 px of empty space\n * above the search box even when no pick was in flight (user feedback:\n * \"I don't like the idea of wasting space like that\").\n */\n private readonly _hintEl: HTMLElement;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: RnaBuilderOptions & { paletteHooks?: PaletteFilterHooks }) {\n this._editor = editor;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._hooks = options?.paletteHooks ?? null;\n\n this.element = el(this._doc, 'div', {\n class: 'hw-rna-builder',\n 'data-testid': 'rna-builder',\n });\n // Phase 20 (T-2002): user-requested label rename \"Build triplet\" -> \"RNA builder\".\n this.element.appendChild(el(this._doc, 'div', { class: 'hw-rna-builder__title' }, ['RNA builder']));\n\n // Phase 29 (T-2901): hint container, hidden by default. The\n // `hidden` HTML attribute pairs with the CSS rule\n // `.hw-rna-builder__hint[hidden] { display: none; }` so an idle\n // builder reserves NO vertical space for the hint. When pick mode\n // activates we drop the attribute + set the bold text.\n this._hintEl = el(this._doc, 'div', {\n class: 'hw-rna-builder__hint',\n 'data-testid': 'rna-builder-hint',\n hidden: true,\n });\n this.element.appendChild(this._hintEl);\n\n const svg = this._buildSvg();\n this.element.appendChild(svg as unknown as Node);\n\n this._preview = el(this._doc, 'div', {\n class: 'hw-rna-builder__preview',\n 'data-testid': 'rna-builder-preview',\n });\n this.element.appendChild(this._preview);\n\n this._addBtn = el(this._doc, 'button', {\n class: 'hw-rna-builder__add',\n type: 'button',\n 'data-testid': 'rna-builder-add-btn',\n }, ['Add triplet']);\n this._addBtn.addEventListener('click', () => this._onAddClicked());\n this.element.appendChild(this._addBtn);\n\n host.appendChild(this.element);\n\n const libUnsub = editor.getService().monomerLib.onChanged.subscribe(() => {\n if (!this._destroyed) this.refresh();\n });\n // Theme changes refresh the slot colours.\n const themeUnsub = editor.on('theme:change', () => {\n if (!this._destroyed) this._repaintSlotColors();\n });\n // Compose so a single `_libUnsub` call detaches both subscriptions.\n this._libUnsub = (): void => {\n try { libUnsub(); } catch { /* idempotent */ }\n try { themeUnsub(); } catch { /* idempotent */ }\n };\n\n this._populateDefaults();\n this._updatePreview();\n this._repaintSlotColors();\n }\n\n /** Repopulate defaults from the current monomer library. */\n refresh(): void {\n this._populateDefaults();\n this._updatePreview();\n this._repaintSlotColors();\n }\n\n /** Current selection + preview text. */\n getSelection(): RnaBuilderSelection {\n const sugar = this._slots.get('sugar')?.value ?? '';\n const base = this._slots.get('base')?.value ?? '';\n const linker = this._slots.get('linker')?.value ?? '';\n const preview = sugar !== '' && base !== '' && linker !== ''\n ? formatRnaTriplet(sugar, base, linker)\n : '';\n return { sugar, base, linker, preview };\n }\n\n /** Programmatically set a slot's value (used by tests + palette pick callback). */\n setField(field: RnaBuilderField, symbol: string): void {\n const s = this._slots.get(field);\n if (s === undefined) return;\n s.value = symbol;\n this._setLabelText(s.labelEl, symbol);\n this._repaintSlot(s);\n this._updatePreview();\n this.onValueSet.next({ field, symbol });\n }\n\n /** Programmatic equivalent of clicking the slot. */\n startPickMode(field: RnaBuilderField): void {\n if (this._pickMode === field) {\n // Toggle off.\n this.cancelPickMode();\n return;\n }\n if (this._pickMode !== null) this._setSlotPressed(this._pickMode, false);\n this._pickMode = field;\n this._setSlotPressed(field, true);\n // Phase 29 (T-2901): show the bold \"Pick <slot> from palette\"\n // hint inside the builder body. The hint is `display:none` until\n // this attribute is dropped, so the SVG triplet ONLY shifts down\n // while pick mode is active.\n this._setHintActive(field);\n this.onPickModeChange.next({ field });\n if (this._hooks !== null) {\n this._hooks.beginBiotypeFilter(FIELD_BIOTYPE[field], (symbol: string) => {\n // Palette signalled \"a matching tile was clicked\" -> set value\n // + exit pick mode.\n this.setField(field, symbol);\n this._exitPickMode();\n }, () => {\n // Palette signalled \"cancel\" (any non-tile action).\n this._exitPickMode();\n });\n }\n }\n\n /** Exit pick mode without changing any value. */\n cancelPickMode(): void {\n if (this._pickMode === null) return;\n if (this._hooks !== null) this._hooks.endBiotypeFilter();\n this._exitPickMode();\n }\n\n getPickMode(): RnaBuilderField | null { return this._pickMode; }\n\n /** Trigger \"Add triplet\" programmatically (used by tests). */\n triggerAdd(): void { this._onAddClicked(); }\n\n /** Tear down: drop DOM, unsubscribe. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n if (this._pickMode !== null && this._hooks !== null)\n this._hooks.endBiotypeFilter();\n this._libUnsub();\n this.onValueSet.complete();\n this.onPickModeChange.complete();\n if (this.element.parentNode !== null)\n this.element.parentNode.removeChild(this.element);\n }\n\n // ------------------------------------------------------------------------\n // SVG construction\n // ------------------------------------------------------------------------\n\n /**\n * Build the SVG triplet visualization. The geometry mirrors the\n * canvas rendering of a single `r(A)p` triplet:\n *\n * linker --- sugar\n * |\n * base\n *\n * Each slot is a clickable `<g>` with `data-testid=\"rna-builder-slot-<id>\"`\n * and `role=\"button\" tabindex=\"0\"` for keyboard accessibility. The\n * shape's fill is set inline from `resolveMonomerColors`; CSS adds\n * hover/active outlines on top so the colour layer reflects the\n * current monomer while the interaction layer follows the editor's\n * accent.\n */\n private _buildSvg(): Element {\n const svg = this._doc.createElementNS(SVG_NS, 'svg');\n svg.setAttribute('class', 'hw-rna-builder__triplet');\n svg.setAttribute('viewBox', `0 0 ${VIEW_W} ${VIEW_H}`);\n svg.setAttribute('data-testid', 'rna-builder-triplet-svg');\n svg.setAttribute('role', 'group');\n svg.setAttribute('aria-label', 'Triplet preview');\n\n // Phase 21 (T-2101): bond lines run between the SHAPE EDGES, not\n // between the shape centres. Drawing centre-to-centre meant the\n // line passed through the fill of both shapes and was invisible;\n // running from edge to edge surfaces a small visible bond segment\n // (~14 px sugar-linker, ~10 px sugar-base) that matches the canvas\n // rendering's \"monomers are connected by a visible bond\" reading.\n const linkerSugarLine = this._doc.createElementNS(SVG_NS, 'line');\n linkerSugarLine.setAttribute('class', 'hw-rna-builder__bond');\n linkerSugarLine.setAttribute('x1', String(SUGAR_CENTER.x + SUGAR_HALF));\n linkerSugarLine.setAttribute('y1', String(SUGAR_CENTER.y));\n linkerSugarLine.setAttribute('x2', String(LINKER_CENTER.x - LINKER_RADIUS));\n linkerSugarLine.setAttribute('y2', String(LINKER_CENTER.y));\n svg.appendChild(linkerSugarLine);\n\n const sugarBaseLine = this._doc.createElementNS(SVG_NS, 'line');\n sugarBaseLine.setAttribute('class', 'hw-rna-builder__bond');\n sugarBaseLine.setAttribute('x1', String(SUGAR_CENTER.x));\n sugarBaseLine.setAttribute('y1', String(SUGAR_CENTER.y + SUGAR_HALF));\n sugarBaseLine.setAttribute('x2', String(BASE_CENTER.x));\n sugarBaseLine.setAttribute('y2', String(BASE_CENTER.y - BASE_HALF));\n svg.appendChild(sugarBaseLine);\n\n // Sugar slot (rounded square, centered at SUGAR_CENTER).\n const sugarShape = this._doc.createElementNS(SVG_NS, 'rect');\n sugarShape.setAttribute('class', 'hw-rna-builder__slot-shape');\n sugarShape.setAttribute('x', String(-SUGAR_HALF));\n sugarShape.setAttribute('y', String(-SUGAR_HALF));\n sugarShape.setAttribute('width', String(SUGAR_HALF * 2));\n sugarShape.setAttribute('height', String(SUGAR_HALF * 2));\n // Phase 21 (T-2101): corner radius scaled with the new 36 px side.\n sugarShape.setAttribute('rx', '8');\n sugarShape.setAttribute('ry', '8');\n const sugarSlot = this._buildSlot('sugar', 'Pick sugar (backbone)', SUGAR_CENTER, sugarShape);\n\n // Linker slot (circle, centered at LINKER_CENTER).\n const linkerShape = this._doc.createElementNS(SVG_NS, 'circle');\n linkerShape.setAttribute('class', 'hw-rna-builder__slot-shape');\n linkerShape.setAttribute('cx', '0');\n linkerShape.setAttribute('cy', '0');\n linkerShape.setAttribute('r', String(LINKER_RADIUS));\n const linkerSlot = this._buildSlot('linker', 'Pick linker', LINKER_CENTER, linkerShape);\n\n // Base slot (diamond/rhombus, centered at BASE_CENTER).\n const baseShape = this._doc.createElementNS(SVG_NS, 'path');\n baseShape.setAttribute('class', 'hw-rna-builder__slot-shape');\n baseShape.setAttribute(\n 'd',\n `M ${-BASE_HALF} 0 L 0 ${-BASE_HALF} L ${BASE_HALF} 0 L 0 ${BASE_HALF} Z`,\n );\n const baseSlot = this._buildSlot('base', 'Pick base', BASE_CENTER, baseShape);\n\n svg.appendChild(linkerSlot.groupEl);\n svg.appendChild(sugarSlot.groupEl);\n svg.appendChild(baseSlot.groupEl);\n\n this._slots.set('sugar', sugarSlot);\n this._slots.set('linker', linkerSlot);\n this._slots.set('base', baseSlot);\n\n return svg;\n }\n\n /**\n * Build a single clickable slot. Returns the SlotState capturing the\n * group, shape, and centered label-text node so subsequent paint /\n * value-set operations can splice them without re-querying the DOM.\n */\n private _buildSlot(\n id: RnaBuilderField,\n ariaLabel: string,\n center: { x: number; y: number },\n shape: Element,\n ): SlotState {\n const group = this._doc.createElementNS(SVG_NS, 'g');\n group.setAttribute('class', 'hw-rna-builder__slot');\n group.setAttribute('data-slot', id);\n group.setAttribute('data-testid', `rna-builder-slot-${id}`);\n group.setAttribute('role', 'button');\n group.setAttribute('tabindex', '0');\n group.setAttribute('aria-label', ariaLabel);\n group.setAttribute('aria-pressed', 'false');\n group.setAttribute('transform', `translate(${center.x} ${center.y})`);\n\n group.appendChild(shape);\n\n const text = this._doc.createElementNS(SVG_NS, 'text');\n text.setAttribute('class', 'hw-rna-builder__slot-label');\n text.setAttribute('data-testid', `rna-builder-${id}-value`);\n text.setAttribute('x', '0');\n text.setAttribute('y', '0');\n text.setAttribute('text-anchor', 'middle');\n text.setAttribute('dominant-baseline', 'central');\n group.appendChild(text);\n\n const onActivate = (e: Event): void => {\n e.stopPropagation();\n this.startPickMode(id);\n };\n group.addEventListener('click', onActivate);\n group.addEventListener('keydown', (e: Event) => {\n const ke = e as unknown as { key: string };\n if (ke.key === 'Enter' || ke.key === ' ') onActivate(e);\n });\n // Phase 22 (T-2202) -- hover tooltip for the slot. Shows the slot\n // type + current value (e.g. \"Sugar: r\") in the headline, the\n // resolved monomer name as the subline, the RDKit structure SVG\n // (when available), and a hint that clicking opens the picker.\n group.addEventListener('mouseenter', (e: Event) => this._showSlotTooltip(id, e));\n group.addEventListener('mouseleave', () => this._hideSlotTooltip());\n group.addEventListener('focus', () => this._showSlotTooltip(id, null));\n group.addEventListener('blur', () => this._hideSlotTooltip());\n\n return { id, biotype: FIELD_BIOTYPE[id], groupEl: group, shapeEl: shape, labelEl: text, value: '' };\n }\n\n // ------------------------------------------------------------------------\n // Slot paint / state\n // ------------------------------------------------------------------------\n\n /**\n * Phase 21 (T-2102) -- Set the slot's visible label.\n *\n * Long monomer symbols overflowed the slot shape and rendered as\n * unreadable mush (user report \"the text fitting does not work at\n * all and terribly overflows\"). We now:\n *\n * 1. Pick a font-size that shrinks as the symbol gets longer\n * (see `fontSizeForLabel`). Single-char `r` / `A` / `p` stays\n * at 16 px; `[5meC]` (5 chars) renders at 8 px; symbols longer\n * than 10 chars get truncated to \"abcdefghi...\" and the FULL\n * symbol is shown via a sibling `<title>` element (native\n * hover tooltip).\n * 2. Set `text-anchor=\"middle\"` and `dominant-baseline=\"central\"`\n * on EVERY update -- the SVG <text> node may have been\n * constructed without these attributes if the slot existed\n * before this method ran; calling `setAttribute` is idempotent.\n * 3. Replace any text child cleanly (we remove pre-existing text\n * nodes but PRESERVE a sibling <title> so screen readers and\n * browser tooltips continue to expose the full symbol).\n */\n private _setLabelText(label: Element, text: string): void {\n // Strip existing text children but keep <title> in place.\n const toRemove: ChildNode[] = [];\n for (let n = label.firstChild; n !== null; n = n.nextSibling) {\n if (n.nodeName === 'title' || n.nodeName === 'TITLE') continue;\n toRemove.push(n as unknown as ChildNode);\n }\n for (const n of toRemove) label.removeChild(n);\n const fontSize = fontSizeForLabel(text);\n label.setAttribute('font-size', String(fontSize));\n label.setAttribute('text-anchor', 'middle');\n label.setAttribute('dominant-baseline', 'central');\n const visible = text.length > 10 ? `${text.slice(0, 9)}…` : text;\n label.appendChild(this._doc.createTextNode(visible));\n // Ensure a <title> sibling carries the FULL symbol so hovering\n // the slot surfaces the untruncated name in the native browser\n // tooltip. We rely on the slot <g> being the parent (the <text>\n // node's parentNode), since SVG <text> does not nest <title>.\n const slotGroup = label.parentNode as Element | null;\n if (slotGroup !== null) {\n let titleEl: Element | null = null;\n for (let n = slotGroup.firstChild; n !== null; n = n.nextSibling) {\n if (n.nodeName === 'title' || n.nodeName === 'TITLE') {\n titleEl = n as unknown as Element;\n break;\n }\n }\n if (titleEl === null) {\n titleEl = this._doc.createElementNS(SVG_NS, 'title');\n // Insert as first child so screen readers pick it up before\n // visible text content.\n slotGroup.insertBefore(titleEl as unknown as Node, slotGroup.firstChild);\n }\n while (titleEl.firstChild !== null) titleEl.removeChild(titleEl.firstChild);\n titleEl.appendChild(this._doc.createTextNode(text));\n }\n }\n\n /** Repaint every slot's fill / text / stroke from the active library + theme. */\n private _repaintSlotColors(): void {\n for (const s of this._slots.values()) this._repaintSlot(s);\n }\n\n /** Repaint one slot. Resolves the colour triple from the active library. */\n private _repaintSlot(s: SlotState): void {\n const lib = this._editor.getService().monomerLib;\n const theme = this._theme();\n const monomer = s.value === '' ? null : findMonomerForBiotype(lib, s.biotype, s.value);\n const colors = resolveMonomerColors(monomer, s.biotype, theme.colorTheme);\n // Set fill / stroke / text-fill as inline styles so the\n // computed-style check in tests resolves to the per-monomer colour\n // (CSS class rules don't carry per-monomer overrides). We use\n // `style` rather than `setAttribute('fill', ...)` so cascading\n // hover/active rules can override via class selectors without\n // attribute-vs-CSS specificity surprises.\n (s.shapeEl as unknown as { style: { fill: string; stroke: string } }).style.fill = colors.background;\n (s.shapeEl as unknown as { style: { fill: string; stroke: string } }).style.stroke = colors.line;\n (s.labelEl as unknown as { style: { fill: string } }).style.fill = colors.text;\n }\n\n // ------------------------------------------------------------------------\n // Defaults + preview\n // ------------------------------------------------------------------------\n\n private _populateDefaults(): void {\n const lib = this._editor.getService().monomerLib;\n for (const [id, s] of this._slots.entries()) {\n const monomers = monomersFor(lib, s.biotype);\n const preferred = preferredSymbol(monomers, DEFAULTS[id]);\n const want = s.value !== '' && monomers.some((m) => m.symbol === s.value)\n ? s.value\n : (preferred ?? (monomers[0]?.symbol ?? ''));\n s.value = want;\n this._setLabelText(s.labelEl, want);\n }\n }\n\n private _updatePreview(): void {\n const sel = this.getSelection();\n while (this._preview.firstChild !== null)\n this._preview.removeChild(this._preview.firstChild);\n this._preview.appendChild(this._doc.createTextNode(sel.preview === '' ? '-' : sel.preview));\n }\n\n private _onAddClicked(): void {\n const sel = this.getSelection();\n if (sel.preview === '') return;\n // Phase 19 (T-1903): NEVER auto-connect. Always create a new\n // RNAn{...} polymer. Phase 20 (T-2006): the editor positions the\n // new triplet's sugar next to the rightmost existing sugar.\n this._editor.placeRnaTriplet(sel.sugar, sel.base, sel.linker);\n }\n\n private _exitPickMode(): void {\n if (this._pickMode === null) return;\n const prev = this._pickMode;\n this._setSlotPressed(prev, false);\n this._pickMode = null;\n // Phase 29 (T-2901): hide the builder hint. Setting the `hidden`\n // attribute restores `display: none` so the SVG triplet returns to\n // its original position directly under the title.\n this._setHintActive(null);\n this.onPickModeChange.next({ field: null });\n }\n\n /**\n * Phase 29 (T-2901) -- Toggle the in-builder pick-mode hint.\n *\n * When `field === null`, restore the `hidden` attribute and empty\n * the text so the element disappears from layout. When `field` is a\n * slot id, drop `hidden` and set the bold \"Pick <slot> from palette\"\n * text the user asked for. Implementation uses the standard `hidden`\n * HTML attribute (default CSS `display: none`) rather than\n * `visibility: hidden`, on purpose: the user explicitly wanted to\n * stop wasting space when the hint is idle, so the box has to\n * collapse, not just turn invisible.\n */\n private _setHintActive(field: RnaBuilderField | null): void {\n const hint = this._hintEl;\n while (hint.firstChild !== null) hint.removeChild(hint.firstChild);\n if (field === null) {\n hint.setAttribute('hidden', '');\n return;\n }\n hint.removeAttribute('hidden');\n const label = field === 'sugar' ? 'sugar'\n : field === 'base' ? 'base'\n : 'linker';\n hint.appendChild(this._doc.createTextNode(`Pick ${label} from palette`));\n }\n\n private _setSlotPressed(id: RnaBuilderField, pressed: boolean): void {\n const s = this._slots.get(id);\n if (s === undefined) return;\n s.groupEl.setAttribute('aria-pressed', pressed ? 'true' : 'false');\n const cur = s.groupEl.getAttribute('class') ?? '';\n const stripped = cur.split(/\\s+/).filter((c) => c !== 'hw-rna-builder__slot--active').join(' ');\n s.groupEl.setAttribute('class', pressed ? `${stripped} hw-rna-builder__slot--active` : stripped);\n }\n\n private _theme(): Theme {\n const ed = this._editor as unknown as { _currentTheme?(): Theme };\n if (typeof ed._currentTheme === 'function') return ed._currentTheme();\n return this._editor.getService().theme;\n }\n\n // ------------------------------------------------------------------------\n // Phase 22 (T-2202) -- Slot hover tooltip with structure + click hint.\n // ------------------------------------------------------------------------\n\n /**\n * Per-monomer cache of the RDKit structure SVG used in slot tooltips.\n * Identical contract to the palette / view caches: bounded LRU, the\n * symbol composite key matches the `(polymerType, symbol)` couple.\n */\n private readonly _builderRdkitCache: Map<string, string | null> = new Map();\n private static readonly _BUILDER_RDKIT_CACHE_LIMIT = 256;\n\n private _rdkit(): RdkitLike | null {\n const opts = (this._editor.getService() as unknown as { options?: { rdkitModule?: unknown } }).options;\n const mod = opts?.rdkitModule;\n return (mod === undefined || mod === null) ? null : (mod as RdkitLike);\n }\n\n private _builderRdkitSvgFor(monomer: Monomer | null): string | null {\n if (monomer === null) return null;\n const smiles = monomer.smiles;\n if (smiles === undefined || smiles === '') return null;\n const rdkit = this._rdkit();\n if (rdkit === null) return null;\n const key = `${monomer.polymerType}:${monomer.symbol}`;\n if (this._builderRdkitCache.has(key))\n return this._builderRdkitCache.get(key) ?? null;\n // Phase 23 (T-2303): bump source size to 220x140 so the rendered\n // structure fills the tooltip width. Inner svg viewBox handles\n // down-scaling for narrower tooltips.\n const svg = renderRdkitSvg(rdkit, smiles, 220, 140);\n if (this._builderRdkitCache.size >= RnaBuilder._BUILDER_RDKIT_CACHE_LIMIT) {\n const oldest = this._builderRdkitCache.keys().next().value;\n if (oldest !== undefined) this._builderRdkitCache.delete(oldest);\n }\n this._builderRdkitCache.set(key, svg);\n return svg;\n }\n\n private _slotHint(id: RnaBuilderField): string {\n switch (id) {\n case 'sugar': return 'Click to choose a different sugar';\n case 'base': return 'Click to choose a different base';\n case 'linker': return 'Click to choose a different linker';\n }\n }\n\n private _slotTitle(id: RnaBuilderField, value: string): string {\n const v = value === '' ? '?' : value;\n switch (id) {\n case 'sugar': return `Sugar: ${v}`;\n case 'base': return `Base: ${v}`;\n case 'linker': return `Linker: ${v}`;\n }\n }\n\n private _showSlotTooltip(id: RnaBuilderField, evt: Event | null): void {\n const slot = this._slots.get(id);\n if (slot === undefined) return;\n const lib = this._editor.getService().monomerLib;\n const set = lib.getMonomerSet(slot.biotype);\n const monomer = slot.value === '' ? null : (set.get(slot.value) ?? null);\n const tip = getOrCreateTooltipEl(this._doc, 'builder-tooltip', 'hw-builder-tooltip');\n fillTooltip(this._doc, tip, {\n symbol: this._slotTitle(id, slot.value),\n name: monomer?.name ?? '',\n rdkitSvg: this._builderRdkitSvgFor(monomer),\n rdkitTestid: 'builder-tooltip-rdkit-svg',\n hint: this._slotHint(id),\n });\n // Prefer the pointer's client coords when available; fall back to\n // the slot's own bbox so keyboard-focus tooltips still position.\n const me = evt as unknown as { clientX?: number; clientY?: number } | null;\n if (me !== null && typeof me.clientX === 'number' && typeof me.clientY === 'number') {\n positionTooltipAt(tip, me.clientX, me.clientY);\n } else {\n const groupEl = slot.groupEl as unknown as { getBoundingClientRect?: () => { left: number; top: number; width: number; height: number } };\n const rect = typeof groupEl.getBoundingClientRect === 'function' ? groupEl.getBoundingClientRect() : null;\n if (rect !== null) positionTooltipAt(tip, rect.left + rect.width / 2, rect.top + rect.height / 2);\n else positionTooltipAt(tip, 0, 0);\n }\n }\n\n private _hideSlotTooltip(): void {\n const tip = this._doc.body.querySelector('[data-testid=\"builder-tooltip\"]') as HTMLElement | null;\n hideTooltipEl(tip);\n }\n}\n\n/**\n * Hooks the palette exposes to the RNA Builder so the builder can\n * activate / deactivate biotype filtering without taking a direct\n * dependency on `MonomerPalette`'s internals.\n */\nexport interface PaletteFilterHooks {\n /**\n * Start filtering the palette to only show tiles whose biotype\n * matches `biotype`. Adds a \"Picking X\" hint banner. `onPick` is\n * called when the user clicks a matching tile; `onCancel` is called\n * for any other user action (canvas / toolbar / outside click /\n * Escape). The hooks are responsible for unwiring themselves on\n * either resolution.\n */\n beginBiotypeFilter(\n biotype: HelmType,\n onPick: (symbol: string) => void,\n onCancel: () => void,\n ): void;\n /** Force-end the current pick mode (e.g. RnaBuilder.cancelPickMode). */\n endBiotypeFilter(): void;\n}\n\n/**\n * Phase 21 (T-2102) -- Pick an SVG `font-size` that keeps the label\n * inside the 36 px slot shape. Mirrors the canvas tile font-sizing\n * heuristic so the slot symbol reads at the same visual weight as\n * the palette tile.\n *\n * Tested values: `r` (1 char) -> 16; `5meC` (4 chars) -> 11; `[fl2r]` -> 8.\n * The piecewise function avoids per-char measurement -- linkedom has\n * no SVG text-metrics API and the production code path runs in real\n * browsers anyway.\n */\nexport function fontSizeForLabel(symbol: string): number {\n const len = symbol.length;\n if (len <= 2) return 16;\n if (len <= 4) return 11;\n if (len <= 7) return 8;\n if (len <= 10) return 6;\n return 5;\n}\n\nfunction monomersFor(lib: IMonomerLib, biotype: HelmType): Monomer[] {\n const map = lib.getMonomerSet(biotype);\n const out: Monomer[] = [];\n for (const m of map.values()) out.push(m);\n out.sort((a, b) => a.symbol.localeCompare(b.symbol));\n return out;\n}\n\nfunction preferredSymbol(monomers: readonly Monomer[], preferences: readonly string[]): string | null {\n const set = new Set<string>();\n for (const m of monomers) set.add(m.symbol);\n for (const p of preferences) if (set.has(p)) return p;\n return null;\n}\n\n/** Find the Monomer in `lib` whose `symbol` matches AND maps to `biotype`. */\nfunction findMonomerForBiotype(lib: IMonomerLib, biotype: HelmType, symbol: string): Monomer | null {\n const set = lib.getMonomerSet(biotype);\n return set.get(symbol) ?? null;\n}\n","// T-0601 / T-1421 — `MonomerPalette` — the left-side monomer explorer.\n//\n// Phase 14C (T-1421..T-1428) redesign — tabbed view:\n//\n// Before: a single scrollable pane with every polymer-type section stacked\n// back-to-back, all visible at once. Group headers (natural-analog letters)\n// were tiny `font-size:11px; color:muted` strings — easy to miss.\n//\n// After: one tab per polymer type (Favorites first, then Peptides, RNA,\n// CHEM, BLOB, G — but only those tab buttons whose corresponding polymer\n// type has at least one monomer in the library show up). Each pane keeps\n// its own grouping (natural-analog for PEPTIDE; sugar/base/linker for RNA;\n// flat for CHEM/BLOB/G). Group headers are now bold uppercase text with a\n// subtle bottom border.\n//\n// Favorites pane: tiles for every starred monomer, regardless of polymer\n// type, grouped by natural-analog. Favorites live in `localStorage` under\n// `hwe:palette:favorites`. Loading drops symbols that no longer resolve\n// in the active library, but keeps them in storage so a user can swap\n// libraries back and not lose the list.\n//\n// Layering: editor-layer module; imports core constants, monomer-lib types,\n// render theme types, and the local `tile.ts` helper. No `globalThis.document`.\n\nimport type { Atom } from '../../core/model';\nimport type { HelmType, PolymerType } from '../../core/constants';\nimport { HelmTypes, PolymerTypes } from '../../core/constants';\nimport type { IMonomerLib, Monomer } from '../../monomer-lib/types';\nimport { helm2Type } from '../../monomer-lib/library';\nimport { hexToHsl, resolveMonomerColors } from '../../monomer-lib/color-rules';\nimport type { Theme } from '../../render/theme';\nimport type { Unsubscribe } from '../../util/types';\nimport { Subject } from '../../util/observable';\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\nimport {\n fillTooltip,\n getOrCreateTooltipEl,\n hideTooltipEl,\n positionTooltipAt,\n renderRdkitSvg,\n type RdkitLike,\n} from '../view/tooltip-rdkit';\nimport { buildTile } from './tile';\nimport { RnaBuilder } from './rna-builder';\nimport type { PaletteFilterHooks } from './rna-builder';\n\n// --------------------------------------------------------------------------\n// Tab model\n// --------------------------------------------------------------------------\n\n/** Sentinel polymer-type-like string used as the \"Favorites\" tab id. */\nconst FAVORITES_TAB = 'Favorites';\n/** Sentinel polymer-type used for any extra-polymer-type slot (e.g. `G`). */\ntype ExtraPolymerType = 'G';\n/** Tab id — either the favorites sentinel, a known polymer type, or an\n * extra polymer-type string we explicitly allow (e.g. `G`). */\ntype TabId = typeof FAVORITES_TAB | PolymerType | ExtraPolymerType;\n\n/** Display label for each tab id. */\nconst TAB_LABELS: Record<TabId, string> = {\n [FAVORITES_TAB]: '★ Favorites',\n [PolymerTypes.PEPTIDE]: 'Peptides',\n [PolymerTypes.RNA]: 'RNA',\n [PolymerTypes.CHEM]: 'CHEM',\n [PolymerTypes.BLOB]: 'BLOB',\n G: 'G',\n};\n\n/** Fixed display order. Favorites first; remaining types in the\n * user-requirement order (Peptides → RNA → CHEM → BLOB → G). */\nconst TAB_ORDER: TabId[] = [\n FAVORITES_TAB,\n PolymerTypes.PEPTIDE,\n PolymerTypes.RNA,\n PolymerTypes.CHEM,\n PolymerTypes.BLOB,\n 'G',\n];\n\n/** LocalStorage keys (stable across editor instances). */\nconst FAVORITES_STORAGE_KEY = 'hwe:palette:favorites';\nconst ACTIVE_TAB_STORAGE_KEY = 'hwe:palette:active-tab';\n/** Legacy (pre-Phase 14C) favorites storage key. We read it on load for\n * backward compatibility — values were `${polymerType}|${symbol}` pairs. */\nconst LEGACY_FAVORITES_STORAGE_KEY = 'hwe.palette.favorites';\n\n// --------------------------------------------------------------------------\n// Options + public API\n// --------------------------------------------------------------------------\n\n/** Options for `MonomerPalette`. */\nexport interface MonomerPaletteOptions {\n /** Optional `Document` (for linkedom in tests). */\n documentImpl?: Document;\n /** Group tiles under each section by `naturalAnalog`. Default `true`. */\n groupByNaturalAnalog?: boolean;\n /** Allow toggling the star icon to favorite a monomer. Default `true`. */\n allowFavorites?: boolean;\n /** Force the initially-active tab; if absent, read from localStorage,\n * falling back to `Favorites`. */\n initialTab?: string;\n}\n\n/** Storage shape persisted to `localStorage`. */\ninterface StoredFavorites { symbols: string[] }\n\n/** Payload emitted by `favoritesChanged`. */\nexport interface FavoritesChangeEvent { favorites: string[] }\n\n/**\n * Left-side palette of monomer tiles. Each tile is draggable and clickable;\n * clicks \"prime\" the editor's next-add slot, drags initiate a palette DnD.\n *\n * @example\n * const palette = new MonomerPalette(host, editor);\n * // ... user clicks a tile → editor.getNextAddSymbol() returns {symbol, biotype}\n */\nexport class MonomerPalette {\n readonly element: HTMLElement;\n\n /** Multicast notifier — fires whenever `_favorites` mutates. */\n readonly favoritesChanged: Subject<FavoritesChangeEvent> = new Subject<FavoritesChangeEvent>();\n\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private readonly _opts: Required<Omit<MonomerPaletteOptions, 'initialTab'>>;\n private readonly _libUnsub: Unsubscribe;\n private readonly _themeUnsub: Unsubscribe;\n /** Phase 25 (T-2504) -- sync tile primed-state with external nextAdd changes. */\n private _nextAddUnsub: Unsubscribe = () => undefined;\n /** Favorites in the order they were starred (display order). Stored as a\n * Set for O(1) membership queries; insertion order is preserved. */\n private readonly _favorites: Set<string> = new Set<string>();\n /** Tabs that should render (subset of TAB_ORDER); recomputed every render. */\n private _visibleTabs: TabId[] = [FAVORITES_TAB];\n /** Currently active tab. */\n private _activeTab: TabId = FAVORITES_TAB;\n private _searchInput: HTMLInputElement | null = null;\n private _filter: string = '';\n private _destroyed: boolean = false;\n /**\n * Phase 18 (T-1806) — RNA Builder. Lazily created when the RNA pane\n * renders; destroyed and re-created across full re-renders so its\n * `<select>` lists pick up the latest library.\n */\n private _rnaBuilder: RnaBuilder | null = null;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: MonomerPaletteOptions) {\n this._editor = editor;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._opts = {\n documentImpl: this._doc,\n groupByNaturalAnalog: options?.groupByNaturalAnalog ?? true,\n allowFavorites: options?.allowFavorites ?? true,\n };\n\n this._loadFavorites();\n this._activeTab = this._resolveInitialTab(options?.initialTab);\n\n this.element = el(this._doc, 'div', { class: 'hw-palette', 'data-testid': 'palette' });\n host.appendChild(this.element);\n\n this._render();\n\n this._libUnsub = editor.getService().monomerLib.onChanged.subscribe(() => {\n if (!this._destroyed) this.refresh();\n });\n this._themeUnsub = editor.on('theme:change', () => {\n if (!this._destroyed) this.refresh();\n });\n // Phase 25 (T-2504): when an EXTERNAL caller mutates `nextAdd` (e.g.\n // the status-bar `×` button calls `setNextAddSymbol(null)`), the\n // palette tiles' `aria-pressed` + `--primed` class must update to\n // reflect the new state. The tile click handler updates the\n // classes itself, but external setters (status bar, programmatic\n // toolbar, future Esc-to-clear) only fire `option:change` and would\n // otherwise leave the previously-primed tile in a stuck pressed\n // state. The subscription is cheap (O(tiles) DOM attribute writes\n // per fire) and idempotent (re-running on the same state is a\n // no-op).\n this._nextAddUnsub = editor.on('option:change', (e) => {\n if (this._destroyed) return;\n if (e.key === 'nextAdd') this._updatePrimedClasses();\n });\n }\n\n // ------------------------------------------------------------------------\n // Public API\n // ------------------------------------------------------------------------\n\n /** Re-render the full palette. */\n refresh(): void { this._render(); }\n\n /** Apply a case-insensitive substring filter to symbol / name. */\n setFilter(query: string): void {\n this._filter = query.trim().toLowerCase();\n if (this._searchInput !== null && this._searchInput.value !== query)\n this._searchInput.value = query;\n this._applyFilter();\n }\n\n /** Activate a tab. No-op if the tab is not visible (no monomers / no favs). */\n setActiveTab(tabId: string): void {\n if (!this._visibleTabs.includes(tabId as TabId)) return;\n this._activeTab = tabId as TabId;\n this._persistActiveTab();\n this._applyActiveTabClasses();\n this._applyFilter();\n }\n\n /** Currently-active tab id. */\n getActiveTab(): string { return this._activeTab; }\n\n /**\n * Return favorite symbols that resolve in the current library. The order\n * matches insertion order (newest favorites appear last). Symbols stored\n * in localStorage that do not resolve in the active library are kept in\n * storage but excluded from this list.\n */\n getFavorites(): string[] {\n const lib = this._editor.getService().monomerLib;\n const out: string[] = [];\n for (const sym of this._favorites) {\n if (this._findMonomer(lib, sym) !== null) out.push(sym);\n }\n return out;\n }\n\n /**\n * Add or remove a symbol from the favorites list. Fires\n * `favoritesChanged` on every state change (no-op if the symbol's state\n * is already the requested value).\n */\n setFavorite(symbol: string, isFavorite: boolean): void {\n const before = this._favorites.has(symbol);\n if (isFavorite === before) return;\n if (isFavorite) this._favorites.add(symbol);\n else this._favorites.delete(symbol);\n this._saveFavorites();\n this._render();\n this.favoritesChanged.next({ favorites: this.getFavorites() });\n }\n\n /** Drop every favorite from storage AND from the in-memory set. */\n clearFavorites(): void {\n if (this._favorites.size === 0) return;\n this._favorites.clear();\n this._saveFavorites();\n this._render();\n this.favoritesChanged.next({ favorites: [] });\n }\n\n /** Tear down: detach DOM, unsubscribe listeners. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n if (this._rnaBuilder !== null) { this._rnaBuilder.destroy(); this._rnaBuilder = null; }\n this._libUnsub();\n this._themeUnsub();\n // Phase 25 (T-2504): release the option:change subscription.\n this._nextAddUnsub();\n if (this.element.parentNode !== null)\n this.element.parentNode.removeChild(this.element);\n }\n\n /**\n * Phase 18 (T-1806) — RNA Builder accessor. Returns `null` when the\n * RNA pane isn't currently mounted (e.g. the library has no RNA\n * monomers). Used by tests + the demo `__hwe__` bridge.\n */\n getRnaBuilder(): RnaBuilder | null { return this._rnaBuilder; }\n\n /** Phase 19 (T-1903) — biotype pick-mode state machine. */\n private _activeBiotypeFilter: HelmType | null = null;\n private _pickResolver: ((symbol: string) => void) | null = null;\n private _pickCanceller: (() => void) | null = null;\n private _pickEscapeListener: ((e: KeyboardEvent) => void) | null = null;\n /**\n * Phase 20 (T-2005) — Document-level mousedown listener attached on\n * pick-mode entry. ANY click whose target is NOT a tile of the\n * matching biotype (and NOT the in-flight edit button that started\n * the pick) cancels pick mode. Detached on exit.\n */\n private _pickOutsideClickListener: ((e: Event) => void) | null = null;\n\n /** True iff a biotype pick-mode is currently active. */\n hasActiveBiotypeFilter(): boolean { return this._activeBiotypeFilter !== null; }\n\n /** Returns the currently-active biotype filter (null when inactive). */\n getActiveBiotypeFilter(): HelmType | null { return this._activeBiotypeFilter; }\n\n /**\n * Programmatically resolve / cancel pick-mode. Exposed for tests and\n * for outside-click handlers in the host app.\n */\n cancelBiotypeFilter(): void {\n if (this._activeBiotypeFilter === null) return;\n const cancel = this._pickCanceller;\n this._teardownPickMode();\n cancel?.();\n }\n\n private _buildPaletteFilterHooks(): PaletteFilterHooks {\n return {\n beginBiotypeFilter: (biotype, onPick, onCancel) => {\n // If pick-mode is already active, transition (cancel old, start new).\n if (this._activeBiotypeFilter !== null) this._teardownPickMode();\n this._activeBiotypeFilter = biotype;\n this._pickResolver = onPick;\n this._pickCanceller = onCancel;\n // Phase 29 (T-2901): pick-mode hint text lives on the RNA\n // builder itself; the builder toggles it directly from its\n // own `startPickMode` (called before `beginBiotypeFilter`).\n // The palette no longer owns hint visibility state.\n this._applyFilter();\n // Escape cancels the pick.\n const onKeyDown = (e: KeyboardEvent): void => {\n if (e.key === 'Escape') this.cancelBiotypeFilter();\n };\n this._pickEscapeListener = onKeyDown;\n const w = this._doc.defaultView as (Window & typeof globalThis) | null;\n w?.addEventListener('keydown', onKeyDown);\n // Phase 20 (T-2005): ANY click that isn't on a matching tile\n // cancels pick mode. We attach in the CAPTURE phase on\n // `document` so we see the event before any handler (toolbar\n // button, theme selector, canvas, gallery) can stop it. The\n // matching-tile case (the resolve path) is handled inside the\n // tile's bubble-phase click handler -- the capture listener\n // notices the click but defers cancellation when the target\n // resolves to a tile of the matching biotype (so the tile's\n // own handler runs the `resolve` path instead of being\n // cancelled out from under it).\n const onOutsideMouseDown = (e: Event): void => {\n if (this._activeBiotypeFilter === null) return;\n const target = (e as { target?: unknown }).target as Element | null;\n if (target === null || target === undefined) return;\n // Walk up the ancestor chain looking for a matching tile OR\n // another pick-mode trigger (Phase 24 T-2402). When the user\n // clicks a DIFFERENT RNA-builder slot (e.g. from pick-linker\n // they want to pick sugar instead), the slot's own click\n // handler will switch the active field atomically. Without\n // this exception the capture-phase cancellation would fire\n // first, exit pick mode, and the slot's click would re-enter\n // pick mode -- two clicks required where one should suffice.\n const matchingBiotype = this._activeBiotypeFilter;\n let cur: Element | null = target;\n while (cur !== null) {\n const cls = cur.getAttribute === undefined ? null : cur.getAttribute('class');\n if (cls !== null) {\n const classes = cls.split(/\\s+/);\n if (classes.includes('hw-palette__tile')) {\n const bio = cur.getAttribute('data-biotype') ?? '';\n if (bio === matchingBiotype) return; // tile-resolve path, do not cancel\n break; // non-matching tile -> fall through to cancel\n }\n // Phase 24 (T-2402): another RNA-builder slot is a\n // pick-mode trigger. Let its own handler switch the\n // active field. We confirm the slot belongs to a builder\n // mounted inside THIS palette by checking the ancestor\n // chain reaches `this.element`.\n if (classes.includes('hw-rna-builder__slot')) {\n if (this._isInsideOwnPalette(cur)) return;\n break;\n }\n }\n cur = cur.parentElement;\n }\n // Any other target: cancel.\n this.cancelBiotypeFilter();\n };\n this._pickOutsideClickListener = onOutsideMouseDown;\n const docTarget = this._doc as unknown as {\n addEventListener(t: string, l: (e: Event) => void, opts?: boolean | { capture?: boolean }): void;\n };\n docTarget.addEventListener('mousedown', onOutsideMouseDown, true);\n },\n endBiotypeFilter: () => this._teardownPickMode(),\n };\n }\n\n /**\n * Phase 24 (T-2403) -- Scroll the currently-active pane back to its\n * top. Called after a successful pick-mode resolve so the RNA\n * Builder (which sits at the top of the RNA pane) returns into view\n * after the user scrolled down to find a tile.\n *\n * We prefer `scrollTo({ top: 0, behavior: 'smooth' })` when the\n * browser exposes it (modern engines) and fall back to the boolean\n * form for older runtimes / linkedom. In environments without a\n * mounted scroll container (linkedom) the assignment is a no-op.\n */\n private _scrollActivePaneToTop(): void {\n const activePane = this.element.querySelector(`.hw-palette__pane[data-tab=\"${this._activeTab}\"]`);\n if (activePane === null) return;\n const target = activePane as unknown as {\n scrollTo?: (opts: { top: number; behavior?: 'smooth' | 'auto' }) => void;\n scrollTop?: number;\n };\n try {\n if (typeof target.scrollTo === 'function') {\n target.scrollTo({ top: 0, behavior: 'smooth' });\n return;\n }\n } catch {\n // `behavior` option may be rejected by older engines; fall through.\n }\n if (typeof target.scrollTop === 'number') target.scrollTop = 0;\n }\n\n /**\n * Phase 24 (T-2402) -- Does `el` sit anywhere under this palette's\n * root? Used to disambiguate \"another pick trigger belongs to us\" from\n * \"a pick trigger belongs to a different palette in the same\n * document\" (e.g. tests that mount two palettes side-by-side).\n */\n private _isInsideOwnPalette(el: Element): boolean {\n let cur: Element | null = el;\n while (cur !== null) {\n if (cur === this.element) return true;\n cur = cur.parentElement;\n }\n return false;\n }\n\n private _teardownPickMode(): void {\n if (this._activeBiotypeFilter === null) return;\n this._activeBiotypeFilter = null;\n this._pickResolver = null;\n this._pickCanceller = null;\n if (this._pickEscapeListener !== null) {\n const w = this._doc.defaultView as (Window & typeof globalThis) | null;\n w?.removeEventListener('keydown', this._pickEscapeListener);\n this._pickEscapeListener = null;\n }\n // Phase 20 (T-2005): detach the outside-click listener.\n if (this._pickOutsideClickListener !== null) {\n const docTarget = this._doc as unknown as {\n removeEventListener(t: string, l: (e: Event) => void, opts?: boolean | { capture?: boolean }): void;\n };\n docTarget.removeEventListener('mousedown', this._pickOutsideClickListener, true);\n this._pickOutsideClickListener = null;\n }\n // Phase 29 (T-2901): the pick-mode hint now lives inside the RNA\n // builder itself (between the title and the SVG triplet), not\n // above the palette's search box. The palette no longer owns hint\n // state -- RnaBuilder toggles its own `[data-testid=\"rna-builder-hint\"]`\n // element in `startPickMode` / `_exitPickMode`. Replaces Phase 24\n // T-2401 reserved-space hint above the search box (\"I don't like\n // the idea of wasting space like that\").\n this._applyFilter();\n }\n\n // ------------------------------------------------------------------------\n // Render\n // ------------------------------------------------------------------------\n\n private _render(): void {\n // Phase 18 (T-1806) — Dispose any existing RNA Builder before the\n // wholesale DOM teardown so its `lib.onChanged` subscription is\n // released. A fresh builder is constructed when the RNA pane\n // re-renders below.\n if (this._rnaBuilder !== null) {\n this._rnaBuilder.destroy();\n this._rnaBuilder = null;\n }\n while (this.element.firstChild !== null)\n this.element.removeChild(this.element.firstChild);\n\n // Search box.\n const search = this._doc.createElement('input');\n search.setAttribute('type', 'search');\n search.setAttribute('class', 'hw-palette__search');\n search.setAttribute('placeholder', 'Search monomers...');\n search.setAttribute('data-testid', 'palette-search');\n if (this._filter !== '') search.value = this._filter;\n search.addEventListener('input', () => this.setFilter(search.value));\n this._searchInput = search;\n this.element.appendChild(search);\n\n // Phase 29 (T-2901): the pick-mode hint moved INSIDE the RNA\n // Builder body (between the \"RNA builder\" title and the SVG\n // triplet). The palette no longer reserves vertical space for it\n // above the search box -- the previous Phase 24 always-mounted\n // hint container was visible-but-empty in idle state and the user\n // reported it as wasted space. The hint element is now\n // `[data-testid=\"rna-builder-hint\"]`, owned by `RnaBuilder`, and\n // toggled via the `hidden` attribute (CSS `display: none`) so an\n // idle builder takes zero extra height.\n\n // Recompute visible tabs.\n this._visibleTabs = this._computeVisibleTabs();\n // If the previously-active tab is no longer visible (e.g. lib reload),\n // fall back to Favorites (always visible) so we don't render orphaned.\n if (!this._visibleTabs.includes(this._activeTab))\n this._activeTab = FAVORITES_TAB;\n\n // Tab list.\n const tabs = el(this._doc, 'div', {\n class: 'hw-palette__tabs',\n role: 'tablist',\n 'data-testid': 'palette-tabs',\n });\n for (const tabId of this._visibleTabs) {\n const isActive = tabId === this._activeTab;\n const btn = el(this._doc, 'button', {\n class: 'hw-palette__tab',\n type: 'button',\n role: 'tab',\n 'aria-controls': `hw-palette-pane-${tabId}`,\n 'aria-selected': isActive ? 'true' : 'false',\n 'data-testid': `palette-tab-${tabId}`,\n 'data-tab': tabId,\n // Phase 24 (T-2404): the full label is always available via\n // the native browser tooltip even when an extreme narrow\n // palette truncates the text visually.\n title: TAB_LABELS[tabId],\n }, [TAB_LABELS[tabId]]);\n btn.addEventListener('click', () => this.setActiveTab(tabId));\n tabs.appendChild(btn);\n }\n this.element.appendChild(tabs);\n\n // Pane container.\n const panes = el(this._doc, 'div', { class: 'hw-palette__panes' });\n const theme = this._theme();\n const lib = this._editor.getService().monomerLib;\n\n for (const tabId of this._visibleTabs) {\n const isActive = tabId === this._activeTab;\n const pane = el(this._doc, 'div', {\n class: 'hw-palette__pane',\n id: `hw-palette-pane-${tabId}`,\n role: 'tabpanel',\n 'data-testid': `palette-pane-${tabId}`,\n 'data-tab': tabId,\n hidden: !isActive,\n });\n if (tabId === FAVORITES_TAB)\n this._buildFavoritesPane(pane, lib, theme);\n else\n this._buildPolymerPane(pane, tabId, lib, theme);\n panes.appendChild(pane);\n }\n this.element.appendChild(panes);\n\n this._applyFilter();\n }\n\n /** Recompute which tabs should render against the current library. */\n private _computeVisibleTabs(): TabId[] {\n const lib = this._editor.getService().monomerLib;\n const present = new Set<string>();\n for (const pt of lib.getPolymerTypes()) present.add(pt);\n const out: TabId[] = [];\n // Favorites is always visible — it shows a placeholder when empty. The\n // user can star a monomer from any other tab to populate it.\n out.push(FAVORITES_TAB);\n for (const tabId of TAB_ORDER) {\n if (tabId === FAVORITES_TAB) continue;\n if (present.has(tabId)) out.push(tabId);\n }\n return out;\n }\n\n // ------------------------------------------------------------------------\n // Favorites pane\n // ------------------------------------------------------------------------\n\n private _buildFavoritesPane(pane: HTMLElement, lib: IMonomerLib, theme: Theme): void {\n const resolved = this._resolveFavoriteMonomers(lib);\n if (resolved.length === 0) {\n const placeholder = el(this._doc, 'div', {\n class: 'hw-palette__placeholder',\n 'data-testid': 'palette-favorites-empty',\n }, ['No favorites yet — click the ☆ on any tile to add one.']);\n pane.appendChild(placeholder);\n return;\n }\n // Group by natural-analog, with '' (no analog) bucketed under \"Other\".\n const groups = this._groupByAnalog(resolved);\n for (const [na, group] of groups) {\n const display = na === '' ? 'Other' : na;\n const groupEl = el(this._doc, 'div', {\n class: 'hw-palette__group',\n 'data-natural-analog': na === '' ? 'Other' : na,\n });\n const header = el(this._doc, 'div', {\n class: 'hw-palette__group-header',\n 'data-testid': `palette-group-${display}`,\n }, [display]);\n const tilesEl = el(this._doc, 'div', { class: 'hw-palette__group-tiles' });\n // Phase 18 (T-1804) — same colour-sort applied here.\n const sorted = this._sortByColor(group);\n for (const m of sorted) {\n const biotype = this._biotype(m, m.polymerType);\n tilesEl.appendChild(this._renderTile(m, biotype, this._editor.getNextAddSymbol()));\n }\n groupEl.appendChild(header);\n groupEl.appendChild(tilesEl);\n pane.appendChild(groupEl);\n }\n void theme;\n }\n\n /**\n * Walk every polymer type and return monomers for the favorite symbols,\n * in insertion order. Drops favorites whose symbol doesn't resolve in\n * the active library. Storage is NOT mutated — we want to keep dropped\n * symbols around in case the user swaps libraries back.\n */\n private _resolveFavoriteMonomers(lib: IMonomerLib): Monomer[] {\n const out: Monomer[] = [];\n for (const sym of this._favorites) {\n const m = this._findMonomer(lib, sym);\n if (m !== null) out.push(m);\n }\n return out;\n }\n\n private _findMonomer(lib: IMonomerLib, symbol: string): Monomer | null {\n for (const pt of lib.getPolymerTypes()) {\n const m = lib.getMonomer(pt, symbol);\n if (m !== null) return m;\n }\n return null;\n }\n\n // ------------------------------------------------------------------------\n // Polymer-type pane\n // ------------------------------------------------------------------------\n\n private _buildPolymerPane(pane: HTMLElement, tabId: Exclude<TabId, typeof FAVORITES_TAB>, lib: IMonomerLib, theme: Theme): void {\n const polymerType = tabId as PolymerType;\n const monomers = this._monomersForPolymer(polymerType, lib);\n if (monomers.length === 0) return;\n\n // RNA gets sugar/base/linker grouping; PEPTIDE gets natural-analog\n // grouping; everything else is flat.\n if (polymerType === PolymerTypes.RNA) {\n // Phase 18 (T-1806) / Phase 19 (T-1903) — RNA Builder lives at\n // the top of the RNA pane. The palette gives the builder a\n // `PaletteFilterHooks` handle so its edit buttons can put the\n // palette into biotype pick-mode.\n this._rnaBuilder = new RnaBuilder(pane, this._editor, {\n documentImpl: this._doc,\n paletteHooks: this._buildPaletteFilterHooks(),\n });\n const groups = this._groupRna(monomers);\n for (const [groupName, ms] of groups) {\n if (ms.length === 0) continue;\n pane.appendChild(this._renderGroup(groupName, ms));\n }\n return;\n }\n if (polymerType === PolymerTypes.PEPTIDE && this._opts.groupByNaturalAnalog) {\n const groups = this._groupByAnalog(monomers);\n for (const [na, ms] of groups) {\n const display = na === '' ? 'Other' : na;\n pane.appendChild(this._renderGroup(display, ms));\n }\n return;\n }\n // Flat list (CHEM, BLOB, G, or grouping disabled).\n const tiles = el(this._doc, 'div', { class: 'hw-palette__group-tiles' });\n const next = this._editor.getNextAddSymbol();\n // Phase 18 (T-1804) — flat panes also sort by colour.\n const sorted = this._sortByColor(monomers);\n for (const m of sorted) {\n const biotype = this._biotype(m, polymerType);\n tiles.appendChild(this._renderTile(m, biotype, next));\n }\n pane.appendChild(tiles);\n void theme;\n }\n\n /** Build `<div class=\"hw-palette__group\">` with a bold uppercase header. */\n private _renderGroup(displayName: string, monomers: Monomer[]): HTMLElement {\n const groupEl = el(this._doc, 'div', {\n class: 'hw-palette__group',\n 'data-natural-analog': displayName,\n });\n const header = el(this._doc, 'div', {\n class: 'hw-palette__group-header',\n 'data-testid': `palette-group-${displayName}`,\n }, [displayName]);\n const tiles = el(this._doc, 'div', { class: 'hw-palette__group-tiles' });\n const next = this._editor.getNextAddSymbol();\n // Phase 18 (T-1804) — Within a subsection, sort monomers by their\n // resolved background colour (HSL). Same-hue tiles cluster, so a\n // subsection no longer renders as a noisy rainbow. The previous\n // alphabetical sort happened upstream in `_monomersForPolymer` /\n // `_groupRna`; we re-sort here so EVERY caller of `_renderGroup`\n // (favorites, peptide groups, RNA groups, etc.) gets the colour\n // order without each having to opt in.\n const sorted = this._sortByColor(monomers);\n for (const m of sorted) {\n const biotype = this._biotype(m, m.polymerType);\n tiles.appendChild(this._renderTile(m, biotype, next));\n }\n groupEl.appendChild(header);\n groupEl.appendChild(tiles);\n return groupEl;\n }\n\n /**\n * Phase 18 (T-1804) — Stable sort by `(hue, saturation, lightness)` of\n * the monomer's resolved background colour. Monomers whose colour\n * falls through to the fallback grey (or otherwise has saturation = 0)\n * sort to the end so the saturated colours appear first.\n *\n * Stability matters: ties on `(h, s, l)` keep the input order so the\n * tests can predict the output for stable libraries (HELMCoreLibrary).\n * `Array.prototype.sort` is stable on Node ≥ v12 and on every modern\n * browser engine — no manual stability decoration needed.\n */\n private _sortByColor(monomers: Monomer[]): Monomer[] {\n const theme = this._theme();\n const keyed = monomers.map((m, idx) => {\n const biotype = this._biotype(m, m.polymerType);\n const colors = resolveMonomerColors(m, biotype, theme.colorTheme);\n const hsl = hexToHsl(colors.background);\n // Greys (saturation === 0) go LAST: the colour layout starts\n // colourful → greyscale, so the eye walks the rainbow before\n // hitting the muted tiles.\n const isGrey = hsl.s === 0 ? 1 : 0;\n return { m, idx, h: hsl.h, s: hsl.s, l: hsl.l, isGrey };\n });\n keyed.sort((a, b) => {\n if (a.isGrey !== b.isGrey) return a.isGrey - b.isGrey;\n if (a.h !== b.h) return a.h - b.h;\n if (a.s !== b.s) return a.s - b.s;\n if (a.l !== b.l) return a.l - b.l;\n return a.idx - b.idx;\n });\n return keyed.map((e) => e.m);\n }\n\n private _monomersForPolymer(polymerType: PolymerType, lib: IMonomerLib): Monomer[] {\n const symbols = lib.getMonomerSymbolsByType(polymerType);\n const out: Monomer[] = [];\n for (const sym of symbols) {\n const m = lib.getMonomer(polymerType, sym);\n if (m !== null) out.push(m);\n }\n out.sort((a, b) => a.symbol.localeCompare(b.symbol));\n return out;\n }\n\n /** Bucket monomers by natural-analog; keys are A..Z then '' (no analog). */\n private _groupByAnalog(monomers: Monomer[]): Map<string, Monomer[]> {\n const result = new Map<string, Monomer[]>();\n for (const m of monomers) {\n const key = m.naturalAnalog ?? '';\n let arr = result.get(key);\n if (arr === undefined) { arr = []; result.set(key, arr); }\n arr.push(m);\n }\n // Sort: alphabetical for named analogs, '' (Other) last.\n const sorted: Array<[string, Monomer[]]> = [];\n const keys = Array.from(result.keys()).sort((a, b) => {\n if (a === '' && b !== '') return 1;\n if (b === '' && a !== '') return -1;\n return a.localeCompare(b);\n });\n for (const k of keys) sorted.push([k, result.get(k) as Monomer[]]);\n return new Map(sorted);\n }\n\n /**\n * RNA-specific grouping: Backbones → Bases → Linkers → Other.\n *\n * Phase 20 (T-2004): the \"Sugars\" header was renamed to \"Backbones\"\n * per the user's request — the sugar monomers of an RNA triplet\n * function as the backbone of the polymer, and \"Backbones\" matches\n * the RNA Builder's slot label.\n */\n private _groupRna(monomers: Monomer[]): Map<string, Monomer[]> {\n const sugars: Monomer[] = [];\n const bases: Monomer[] = [];\n const linkers: Monomer[] = [];\n const other: Monomer[] = [];\n for (const m of monomers) {\n const bio = helm2Type(m);\n if (bio === HelmTypes.SUGAR) sugars.push(m);\n else if (bio === HelmTypes.BASE) bases.push(m);\n else if (bio === HelmTypes.LINKER) linkers.push(m);\n else other.push(m);\n }\n const out = new Map<string, Monomer[]>();\n out.set('Backbones', sugars);\n out.set('Bases', bases);\n out.set('Linkers', linkers);\n if (other.length > 0) out.set('Other', other);\n return out;\n }\n\n // ------------------------------------------------------------------------\n // Tile rendering\n // ------------------------------------------------------------------------\n\n private _renderTile(\n monomer: Monomer,\n biotype: HelmType,\n next: { symbol: string; biotype: HelmType } | null,\n ): HTMLElement {\n const favorite = this._favorites.has(monomer.symbol);\n const primed = next !== null && next.symbol === monomer.symbol && next.biotype === biotype;\n const { root, star } = buildTile(this._doc, {\n monomer,\n biotype,\n theme: this._theme(),\n favorite,\n primed,\n });\n this._wireTile(root, star, monomer, biotype);\n return root;\n }\n\n /**\n * Phase 22 (T-2202) -- Per-tile cache of the RDKit-rendered structure\n * SVG, keyed by monomer symbol. The palette and the editor view share\n * an RDKit module but have separate caches because the two surfaces\n * may live in different lifetimes (palette is destroyed on lib\n * reload, view persists). Bounded at 256 entries.\n */\n private readonly _paletteRdkitCache: Map<string, string | null> = new Map();\n private static readonly _PALETTE_RDKIT_CACHE_LIMIT = 256;\n\n /** Resolve the RDKit module (if the host wired one through HelmService). */\n private _rdkit(): RdkitLike | null {\n const opts = (this._editor.getService() as unknown as { options?: { rdkitModule?: unknown } }).options;\n const mod = opts?.rdkitModule;\n return (mod === undefined || mod === null) ? null : (mod as RdkitLike);\n }\n\n /** Memoised RDKit SVG for one monomer. Returns null when unavailable. */\n private _paletteRdkitSvg(monomer: Monomer): string | null {\n const smiles = monomer.smiles;\n if (smiles === undefined || smiles === '') return null;\n const rdkit = this._rdkit();\n if (rdkit === null) return null;\n const key = `${monomer.polymerType}:${monomer.symbol}`;\n if (this._paletteRdkitCache.has(key))\n return this._paletteRdkitCache.get(key) ?? null;\n // Phase 23 (T-2303): bump source size to 220x140 so the rendered\n // structure fills the tooltip width. Inner svg viewBox handles\n // down-scaling for narrower tooltips.\n const svg = renderRdkitSvg(rdkit, smiles, 220, 140);\n if (this._paletteRdkitCache.size >= MonomerPalette._PALETTE_RDKIT_CACHE_LIMIT) {\n const oldest = this._paletteRdkitCache.keys().next().value;\n if (oldest !== undefined) this._paletteRdkitCache.delete(oldest);\n }\n this._paletteRdkitCache.set(key, svg);\n return svg;\n }\n\n private _wireTile(\n root: HTMLElement,\n star: HTMLElement,\n monomer: Monomer,\n biotype: HelmType,\n ): void {\n // Phase 22 (T-2202) -- Hover tooltip. Mounts at document.body via\n // the shared helper so it escapes parent stacking contexts (the\n // gallery panel used to clip it).\n root.addEventListener('mouseenter', (e: Event) => {\n const me = e as unknown as { clientX?: number; clientY?: number };\n const tip = getOrCreateTooltipEl(this._doc, 'palette-tooltip', 'hw-palette-tooltip');\n fillTooltip(this._doc, tip, {\n symbol: monomer.symbol,\n name: monomer.name ?? '',\n rdkitSvg: this._paletteRdkitSvg(monomer),\n rdkitTestid: 'palette-tooltip-rdkit-svg',\n });\n const cx = typeof me.clientX === 'number' ? me.clientX : 0;\n const cy = typeof me.clientY === 'number' ? me.clientY : 0;\n positionTooltipAt(tip, cx, cy);\n });\n root.addEventListener('mouseleave', () => {\n hideTooltipEl(this._doc.body.querySelector('[data-testid=\"palette-tooltip\"]') as HTMLElement | null);\n });\n // Click on the star → toggle favorite. Click anywhere else → prime next-add.\n root.addEventListener('click', (e: Event) => {\n const target = (e as unknown as { target?: { classList?: { contains(c: string): boolean } } }).target;\n if (this._opts.allowFavorites && target !== undefined && target?.classList?.contains('hw-palette__star') === true) {\n this.setFavorite(monomer.symbol, !this._favorites.has(monomer.symbol));\n // setFavorite triggers a re-render, but stopPropagation prevents the\n // star click from also firing the prime-next-add handler below.\n e.stopPropagation();\n return;\n }\n // Phase 19 (T-1903): if a biotype pick-mode is active AND this\n // tile's biotype matches, RESOLVE the pick (set the field, exit\n // pick mode). The palette's tile filter has already hidden any\n // non-matching tiles, but we double-check here defensively.\n if (this._activeBiotypeFilter !== null && this._activeBiotypeFilter === biotype) {\n const resolver = this._pickResolver;\n this._teardownPickMode();\n resolver?.(monomer.symbol);\n // Phase 24 (T-2403): after a successful resolve, scroll the\n // active pane back to its top so the RNA Builder (which sits at\n // the top of the RNA pane) is back in view. The user reported:\n // \"when I scroll down to pick a sugar, my scroll stays at the\n // tile, but the RNA Builder is now offscreen\". We use smooth\n // scrolling so the motion is perceivable but non-jarring.\n this._scrollActivePaneToTop();\n e.stopPropagation();\n return;\n }\n // Phase 27 (T-2704): when a non-empty atom-selection is active\n // AND every selected atom shares its biotype with the clicked\n // tile, the tile click acts as a BULK REPLACE: every selected\n // atom's symbol is updated to the tile's symbol in a single\n // transaction. The user's mental model: \"I selected three\n // phosphates, then I click `sp` on the left -> all three flip\n // to sp.\"\n //\n // Mismatched biotypes (e.g. selection contains a sugar AND a\n // linker, user clicks `sp`) fire an `editor:status` warn and\n // leave the model untouched. `nextAdd` is NOT primed in either\n // branch -- the click was consumed by the selection-replace\n // gesture, not the prime gesture, so the user's tile state stays\n // exactly what it was before.\n const selection = this._editor.getSelection();\n if (selection.atoms.size > 0) {\n const mol = this._editor.getMol();\n const selected: Atom[] = [];\n for (const id of selection.atoms) {\n const a = mol.atoms.find((x) => x.id === id);\n if (a !== undefined) selected.push(a);\n }\n const allMatch = selected.length > 0\n && selected.every((a) => a.biotype === biotype);\n if (allMatch) {\n this._editor.replaceMonomers(selected, monomer.symbol);\n e.stopPropagation();\n return;\n }\n this._editor.fire('editor:status', {\n message: `Cannot bulk-replace ${selected.length} selected atom(s) with ${monomer.symbol}: selection contains incompatible biotypes for ${biotype}.`,\n severity: 'warn',\n durationMs: 3000,\n });\n e.stopPropagation();\n return;\n }\n // Phase 25 (T-2501): clicking the ALREADY-PRIMED tile a second\n // time UNSETS the prime (toggle off). User reported: \"on the left\n // pane, clicking the selected monomer once again should unselect\n // it.\" Match against `editor.getNextAddSymbol()`'s symbol+biotype\n // pair so two different tiles that share a symbol (e.g. RNA Sugar\n // vs Base) don't false-match.\n const currentNext = this._editor.getNextAddSymbol();\n if (currentNext !== null\n && currentNext.symbol === monomer.symbol\n && currentNext.biotype === biotype) {\n this._editor.setNextAddSymbol(null);\n this._updatePrimedClasses();\n return;\n }\n this._editor.setNextAddSymbol(monomer.symbol, biotype);\n this._updatePrimedClasses();\n });\n void star;\n // Drag → kick off palette DnD on the editor AND set the HTML5\n // DataTransfer payload (T-1102) so real browser drag-and-drop works\n // even when no test bridge has primed `startPaletteDrag`.\n root.addEventListener('dragstart', (e: Event) => {\n const dt = (e as unknown as { dataTransfer: { setData(t: string, v: string): void; effectAllowed: string } | null }).dataTransfer;\n if (dt !== null && dt !== undefined) {\n try {\n dt.setData('application/x-hwe-monomer', JSON.stringify({ symbol: monomer.symbol, biotype }));\n dt.effectAllowed = 'copy';\n } catch {\n // Some test harnesses don't allow mutation; the editor's in-memory\n // state below still drives the drop.\n }\n }\n // Phase 24 (T-2406): the palette tooltip remained visible after a\n // drag started because the `mouseleave` event was suppressed by\n // the synthesized drag pointer-capture. Hide explicitly on\n // dragstart so the floating tile is not accompanied by a stale\n // tooltip following the cursor.\n hideTooltipEl(this._doc.body.querySelector('[data-testid=\"palette-tooltip\"]') as HTMLElement | null);\n this._editor.startPaletteDrag(monomer.symbol, biotype);\n });\n }\n\n private _biotype(monomer: Monomer, fallbackType: PolymerType | ExtraPolymerType): HelmType {\n const t = helm2Type(monomer);\n if (t !== null) return t;\n // Stable fallback per polymer type.\n switch (fallbackType) {\n case PolymerTypes.PEPTIDE: return HelmTypes.AA;\n case PolymerTypes.RNA: return HelmTypes.SUGAR;\n case PolymerTypes.CHEM: return HelmTypes.CHEM;\n case PolymerTypes.BLOB: return HelmTypes.BLOB;\n default: return HelmTypes.CHEM;\n }\n }\n\n private _theme(): Theme {\n const ed = this._editor as unknown as { _currentTheme(): Theme };\n if (typeof ed._currentTheme === 'function') return ed._currentTheme();\n return this._editor.getService().theme;\n }\n\n // ------------------------------------------------------------------------\n // Filter\n // ------------------------------------------------------------------------\n\n /**\n * Show only tiles whose symbol or title-attribute contain the current\n * filter substring. Applied to the ACTIVE pane only — inactive panes are\n * hidden by the `hidden` attribute, but their tiles get the same display\n * adjustment so switching back doesn't surprise the user with stale\n * visibility.\n */\n private _applyFilter(): void {\n const q = this._filter;\n const biotypeFilter = this._activeBiotypeFilter;\n // Internal lookup uses the `data-tab` attribute — querying by\n // `data-testid` here would trip the audit-ui-tests script (which\n // can't tell a CSS selector apart from a real test-id literal).\n const activePane = this.element.querySelector(`.hw-palette__pane[data-tab=\"${this._activeTab}\"]`);\n const tiles = (activePane ?? this.element).querySelectorAll('.hw-palette__tile');\n for (let i = 0; i < tiles.length; i++) {\n const tile = tiles[i] as unknown as HTMLElement;\n const sym = (tile.getAttribute('data-symbol') ?? '').toLowerCase();\n const titleAttr = (tile.getAttribute('title') ?? '').toLowerCase();\n const bio = tile.getAttribute('data-biotype') ?? '';\n const queryMatch = q === '' || sym.indexOf(q) >= 0 || titleAttr.indexOf(q) >= 0;\n const biotypeMatch = biotypeFilter === null || bio === biotypeFilter;\n const visible = queryMatch && biotypeMatch;\n (tile as unknown as { style: { display: string } }).style.display = visible ? '' : 'none';\n }\n // Phase 20 (T-2003): hide section headers whose tiles were all\n // filtered out. Without this the user sees an empty \"Bases\" header\n // while in pick-sugar mode -- visually broken. We walk each group\n // in the active pane, count tiles whose `style.display !== 'none'`,\n // and toggle `hidden` on the group element accordingly. CSS rule\n // `.hw-palette__group[hidden] { display: none; }` (default UA\n // behaviour for the `hidden` attribute) removes the empty group\n // entirely.\n const groups = (activePane ?? this.element).querySelectorAll('.hw-palette__group');\n for (let i = 0; i < groups.length; i++) {\n const group = groups[i] as unknown as HTMLElement;\n const groupTiles = group.querySelectorAll('.hw-palette__tile');\n let anyVisible = false;\n for (let j = 0; j < groupTiles.length; j++) {\n const tile = groupTiles[j] as unknown as HTMLElement;\n if ((tile as unknown as { style: { display: string } }).style.display !== 'none') {\n anyVisible = true;\n break;\n }\n }\n if (anyVisible) {\n group.removeAttribute('hidden');\n group.removeAttribute('data-section-empty');\n } else {\n group.setAttribute('hidden', '');\n group.setAttribute('data-section-empty', 'true');\n }\n }\n }\n\n private _updatePrimedClasses(): void {\n const next = this._editor.getNextAddSymbol();\n const tiles = this.element.querySelectorAll('.hw-palette__tile');\n for (let i = 0; i < tiles.length; i++) {\n const tile = tiles[i] as unknown as HTMLElement;\n const sym = tile.getAttribute('data-symbol') ?? '';\n const bio = tile.getAttribute('data-biotype') ?? '';\n const isPrimed = next !== null && next.symbol === sym && next.biotype === bio;\n const current = tile.getAttribute('class') ?? '';\n const filtered = current.split(/\\s+/).filter((c) => c !== 'hw-palette__tile--primed').join(' ');\n tile.setAttribute('class', isPrimed ? `${filtered} hw-palette__tile--primed` : filtered);\n // Phase 25 (T-2501): keep `aria-pressed` in sync with the\n // primed state so the toggle-off click is observable via the\n // standard ARIA pattern (in addition to the visual class).\n // Pre-Phase 25 we only updated the class, so a screen reader\n // would report a still-pressed button after the user unselected.\n tile.setAttribute('aria-pressed', isPrimed ? 'true' : 'false');\n }\n }\n\n // ------------------------------------------------------------------------\n // Tab classes / persistence\n // ------------------------------------------------------------------------\n\n /** Flip `aria-selected` on each tab button and `hidden` on each pane. */\n private _applyActiveTabClasses(): void {\n const tabs = this.element.querySelectorAll('.hw-palette__tab');\n for (let i = 0; i < tabs.length; i++) {\n const tab = tabs[i] as unknown as HTMLElement;\n const tabId = tab.getAttribute('data-tab') ?? '';\n tab.setAttribute('aria-selected', tabId === this._activeTab ? 'true' : 'false');\n }\n const panes = this.element.querySelectorAll('.hw-palette__pane');\n for (let i = 0; i < panes.length; i++) {\n const pane = panes[i] as unknown as HTMLElement;\n const tabId = pane.getAttribute('data-tab') ?? '';\n if (tabId === this._activeTab) pane.removeAttribute('hidden');\n else pane.setAttribute('hidden', '');\n }\n }\n\n // ------------------------------------------------------------------------\n // localStorage helpers\n // ------------------------------------------------------------------------\n\n private _localStorage(): Storage | null {\n if (!this._opts.allowFavorites) return null;\n const w = this._doc.defaultView as { localStorage?: Storage } | null;\n if (w === null || w === undefined) return null;\n try {\n return w.localStorage ?? null;\n } catch {\n return null;\n }\n }\n\n private _resolveInitialTab(explicit: string | undefined): TabId {\n if (explicit !== undefined && (TAB_ORDER as string[]).includes(explicit))\n return explicit as TabId;\n const ls = this._localStorage();\n if (ls !== null) {\n try {\n const raw = ls.getItem(ACTIVE_TAB_STORAGE_KEY);\n if (raw !== null && (TAB_ORDER as string[]).includes(raw))\n return raw as TabId;\n } catch {\n // Ignore corrupted entries.\n }\n }\n return FAVORITES_TAB;\n }\n\n private _persistActiveTab(): void {\n const ls = this._localStorage();\n if (ls === null) return;\n try {\n ls.setItem(ACTIVE_TAB_STORAGE_KEY, this._activeTab);\n } catch {\n // Ignore quota errors.\n }\n }\n\n /**\n * Load favorites from localStorage. Reads the canonical Phase 14C key\n * (`hwe:palette:favorites`) first, then migrates the legacy\n * `hwe.palette.favorites` shape (`[\"PEPTIDE|A\", \"RNA|r\"]` pairs) into the\n * new symbol-only set. Storage is NOT pruned — symbols that don't resolve\n * stay there until explicitly cleared by `setFavorite(sym, false)`.\n */\n private _loadFavorites(): void {\n const ls = this._localStorage();\n if (ls === null) return;\n try {\n const raw = ls.getItem(FAVORITES_STORAGE_KEY);\n if (raw !== null && raw !== '') {\n const parsed = JSON.parse(raw) as unknown;\n const symbols = this._extractSymbols(parsed);\n for (const s of symbols) this._favorites.add(s);\n return;\n }\n } catch {\n // Fall through to legacy migration.\n }\n // Legacy migration — old shape was a JSON array of `\"<polymerType>|<symbol>\"`.\n try {\n const legacy = ls.getItem(LEGACY_FAVORITES_STORAGE_KEY);\n if (legacy === null || legacy === '') return;\n const parsed = JSON.parse(legacy) as unknown;\n if (Array.isArray(parsed)) {\n for (const v of parsed) {\n if (typeof v !== 'string') continue;\n const pipeIdx = v.indexOf('|');\n const sym = pipeIdx >= 0 ? v.slice(pipeIdx + 1) : v;\n if (sym !== '') this._favorites.add(sym);\n }\n // Write through to the new shape so we don't migrate twice.\n this._saveFavorites();\n }\n } catch {\n // Ignore corrupted entries.\n }\n }\n\n /** Accept both the new `{symbols: string[]}` shape and a raw array. */\n private _extractSymbols(parsed: unknown): string[] {\n if (Array.isArray(parsed)) {\n const out: string[] = [];\n for (const v of parsed) if (typeof v === 'string') out.push(v);\n return out;\n }\n if (parsed !== null && typeof parsed === 'object') {\n const obj = parsed as { symbols?: unknown };\n if (Array.isArray(obj.symbols)) {\n const out: string[] = [];\n for (const v of obj.symbols) if (typeof v === 'string') out.push(v);\n return out;\n }\n }\n return [];\n }\n\n private _saveFavorites(): void {\n const ls = this._localStorage();\n if (ls === null) return;\n try {\n const payload: StoredFavorites = { symbols: Array.from(this._favorites) };\n ls.setItem(FAVORITES_STORAGE_KEY, JSON.stringify(payload));\n } catch {\n // Ignore quota errors.\n }\n }\n}\n","// T-0603 — Top toolbar. Renders a row of buttons. Each click fires a typed\n// `key:command` event on the editor and then executes a default action (which\n// the host can suppress by calling `preventDefault` in its `key:command`\n// listener — see EVENTS.md §9).\n//\n// Layering: editor-layer module; imports editor types only.\n\nimport type { Unsubscribe } from '../../util/types';\nimport type { HelmEditor, EditorMode } from '../editor';\nimport { lightTheme, darkTheme } from '../../render/theme';\nimport { getDocument, el } from '../view/dom-utils';\n\n/** Specification for a single toolbar button. */\nexport interface ToolbarButtonSpec {\n /** Stable id used for `data-action` / `data-testid`. */\n id: string;\n /** Visible label — used as `aria-label` and as the `title` prefix. */\n label: string;\n /**\n * Optional icon. Phase 15 (T-1503): the demo uses inline SVG strings\n * resolved from `TOOLBAR_ICONS` by `id`. Falls back to `label` text\n * when no SVG is registered (kept for tests / custom hosts).\n */\n icon?: string;\n /** Optional keyboard shortcut hint shown in the tooltip. */\n shortcut?: string;\n /** When true, insert a separator before this button. */\n separator?: boolean;\n}\n\n/**\n * Phase 16 (T-1601) — Modernized inline-SVG icons (Lucide-style).\n *\n * The user reported the Phase-15 icons \"look quite old\" and asked for\n * something more modern. We inline Lucide-derived path data (Lucide ICs\n * MIT-licensed) so there is NO runtime dependency on an icon package —\n * the strings live in this module and the bundler tree-shakes everything\n * else away. Every icon uses Lucide's standard authoring conventions:\n *\n * viewBox=\"0 0 24 24\"\n * stroke=\"currentColor\"\n * stroke-width=\"2\"\n * stroke-linecap=\"round\"\n * stroke-linejoin=\"round\"\n * fill=\"none\"\n *\n * The CSS in `editor/styles.ts` stretches the SVG to fill the 32×32 button\n * with the theme `currentColor` driving the stroke, so light/dark themes\n * flip automatically without per-icon overrides.\n *\n * Source: user request 2026-05-17 (\"toolbar buttons are quite old-looking.\n * lets try something from fa-icons, or something modern.\").\n */\nconst SVG_OPEN = '<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"0 0 24 24\" fill=\"none\" stroke=\"currentColor\" stroke-width=\"2\" stroke-linecap=\"round\" stroke-linejoin=\"round\">';\nexport const TOOLBAR_ICONS: Record<string, string> = {\n // Lucide `file-plus` — document outline with a `+`.\n 'new': `${SVG_OPEN}<path d=\"M14 2H6a2 2 0 0 0-2 2v16a2 2 0 0 0 2 2h12a2 2 0 0 0 2-2V8z\"/><polyline points=\"14 2 14 8 20 8\"/><line x1=\"12\" y1=\"18\" x2=\"12\" y2=\"12\"/><line x1=\"9\" y1=\"15\" x2=\"15\" y2=\"15\"/></svg>`,\n // Lucide `folder-open`.\n 'open': `${SVG_OPEN}<path d=\"m6 14 1.45-2.9A2 2 0 0 1 9.24 10H20a2 2 0 0 1 1.94 2.5l-1.55 6a2 2 0 0 1-1.94 1.5H4a2 2 0 0 1-2-2V5a2 2 0 0 1 2-2h3.93a2 2 0 0 1 1.66.9l.82 1.2a2 2 0 0 0 1.66.9H18a2 2 0 0 1 2 2v2\"/></svg>`,\n // Lucide `save` — floppy.\n 'save': `${SVG_OPEN}<path d=\"M19 21H5a2 2 0 0 1-2-2V5a2 2 0 0 1 2-2h11l5 5v11a2 2 0 0 1-2 2z\"/><polyline points=\"17 21 17 13 7 13 7 21\"/><polyline points=\"7 3 7 8 15 8\"/></svg>`,\n // Lucide `undo-2` — arc with arrowhead going left.\n 'undo': `${SVG_OPEN}<path d=\"M9 14 4 9l5-5\"/><path d=\"M4 9h10.5a5.5 5.5 0 0 1 5.5 5.5v0a5.5 5.5 0 0 1-5.5 5.5H11\"/></svg>`,\n // Lucide `redo-2` — mirror of undo-2.\n 'redo': `${SVG_OPEN}<path d=\"m15 14 5-5-5-5\"/><path d=\"M20 9H9.5A5.5 5.5 0 0 0 4 14.5v0A5.5 5.5 0 0 0 9.5 20H13\"/></svg>`,\n // Lucide `eraser`.\n 'eraser': `${SVG_OPEN}<path d=\"m7 21-4.3-4.3c-1-1-1-2.5 0-3.4l9.6-9.6c1-1 2.5-1 3.4 0l5.6 5.6c1 1 1 2.5 0 3.4L13 21\"/><path d=\"M22 21H7\"/><path d=\"m5 11 9 9\"/></svg>`,\n // Lucide `mouse-pointer-2` — modern arrow cursor.\n 'select': `${SVG_OPEN}<path d=\"m4 4 7.07 17 2.51-7.39L21 11.07z\"/></svg>`,\n // Lucide `link-2` — chain-link icon. Closer to the H-bond metaphor than\n // dashed lines, and tiny enough to fit the toolbar at 24px.\n 'hbond': `${SVG_OPEN}<path d=\"M9 17H7A5 5 0 0 1 7 7h2\"/><path d=\"M15 7h2a5 5 0 1 1 0 10h-2\"/><line x1=\"8\" y1=\"12\" x2=\"16\" y2=\"12\"/></svg>`,\n // Lucide `zoom-in`.\n 'zoom-in': `${SVG_OPEN}<circle cx=\"11\" cy=\"11\" r=\"8\"/><line x1=\"21\" y1=\"21\" x2=\"16.65\" y2=\"16.65\"/><line x1=\"11\" y1=\"8\" x2=\"11\" y2=\"14\"/><line x1=\"8\" y1=\"11\" x2=\"14\" y2=\"11\"/></svg>`,\n // Lucide `zoom-out`.\n 'zoom-out': `${SVG_OPEN}<circle cx=\"11\" cy=\"11\" r=\"8\"/><line x1=\"21\" y1=\"21\" x2=\"16.65\" y2=\"16.65\"/><line x1=\"8\" y1=\"11\" x2=\"14\" y2=\"11\"/></svg>`,\n // Lucide `maximize-2` — diagonal arrows pointing to corners.\n 'fit': `${SVG_OPEN}<polyline points=\"15 3 21 3 21 9\"/><polyline points=\"9 21 3 21 3 15\"/><line x1=\"21\" y1=\"3\" x2=\"14\" y2=\"10\"/><line x1=\"3\" y1=\"21\" x2=\"10\" y2=\"14\"/></svg>`,\n // Lucide `move` — directional arrows in all four directions.\n 'move': `${SVG_OPEN}<polyline points=\"5 9 2 12 5 15\"/><polyline points=\"9 5 12 2 15 5\"/><polyline points=\"15 19 12 22 9 19\"/><polyline points=\"19 9 22 12 19 15\"/><line x1=\"2\" y1=\"12\" x2=\"22\" y2=\"12\"/><line x1=\"12\" y1=\"2\" x2=\"12\" y2=\"22\"/></svg>`,\n // Lucide `wand-2` — magic-wand for \"clean layout\".\n 'clean': `${SVG_OPEN}<path d=\"m21.64 3.64-1.28-1.28a1.21 1.21 0 0 0-1.72 0L2.36 18.64a1.21 1.21 0 0 0 0 1.72l1.28 1.28a1.2 1.2 0 0 0 1.72 0L21.64 5.36a1.2 1.2 0 0 0 0-1.72Z\"/><path d=\"m14 7 3 3\"/><path d=\"M5 6v4\"/><path d=\"M19 14v4\"/><path d=\"M10 2v2\"/><path d=\"M7 8H3\"/><path d=\"M21 16h-4\"/><path d=\"M11 3H9\"/></svg>`,\n // Lucide `search`.\n 'find': `${SVG_OPEN}<circle cx=\"11\" cy=\"11\" r=\"8\"/><line x1=\"21\" y1=\"21\" x2=\"16.65\" y2=\"16.65\"/></svg>`,\n // Lucide `sun-moon` — split sun/moon for theme toggle.\n 'theme': `${SVG_OPEN}<path d=\"M12 8a2.83 2.83 0 0 0 4 4 4 4 0 1 1-4-4Z\"/><path d=\"M12 2v2\"/><path d=\"M12 20v2\"/><path d=\"m4.9 4.9 1.4 1.4\"/><path d=\"m17.7 17.7 1.4 1.4\"/><path d=\"M2 12h2\"/><path d=\"M20 12h2\"/><path d=\"m6.3 17.7-1.4 1.4\"/><path d=\"m19.1 4.9-1.4 1.4\"/></svg>`,\n};\n\n/** Options for `Toolbar`. */\nexport interface ToolbarOptions {\n /** Optional `Document` (for linkedom in tests). */\n documentImpl?: Document;\n /** Override the button set; defaults to the full Pistoia-style set. */\n buttons?: ToolbarButtonSpec[];\n}\n\n/** Long-form tooltip text for each button (T-1106). Falls back to label. */\nexport const TOOLBAR_TOOLTIPS: Record<string, string> = {\n 'new': 'New — clear the canvas',\n 'open': 'Open — paste a HELM string',\n 'save': 'Save — copy HELM string to clipboard',\n 'undo': 'Undo last action',\n 'redo': 'Redo last undone action',\n 'eraser': 'Eraser — click an atom or bond to delete it',\n 'select': 'Select mode (default)',\n 'hbond': 'H-Bond mode — drag between two RNA bases to add a Watson-Crick pair',\n 'zoom-in': 'Zoom in',\n 'zoom-out': 'Zoom out',\n 'fit': 'Fit to content — reset zoom and pan',\n 'move': 'Move/Pan mode — drag the canvas to scroll',\n 'clean': 'Clean layout — re-run automatic layout',\n 'find': 'Find / Replace monomer',\n 'theme': 'Toggle dark / light theme',\n};\n\n/** The full Pistoia-style toolbar buttons (T-1106 — verbose labels). */\nexport const DEFAULT_TOOLBAR_BUTTONS: ToolbarButtonSpec[] = [\n { id: 'new', label: 'New', icon: 'New' },\n { id: 'open', label: 'Open', icon: 'Open' },\n { id: 'save', label: 'Save', icon: 'Save' },\n { id: 'undo', label: 'Undo', icon: '↺', shortcut: 'Ctrl+Z', separator: true },\n { id: 'redo', label: 'Redo', icon: '↻', shortcut: 'Ctrl+Y' },\n { id: 'eraser', label: 'Eraser', icon: 'Eraser', separator: true },\n { id: 'select', label: 'Select', icon: 'Select' },\n { id: 'hbond', label: 'H-Bond', icon: 'H-Bond' },\n { id: 'zoom-in', label: 'Zoom In', icon: '+', shortcut: 'Ctrl++', separator: true },\n { id: 'zoom-out', label: 'Zoom Out', icon: '−', shortcut: 'Ctrl+−' },\n { id: 'fit', label: 'Fit', icon: 'Fit', shortcut: '0' },\n { id: 'move', label: 'Move', icon: 'Move' },\n { id: 'clean', label: 'Clean', icon: 'Clean', separator: true },\n { id: 'find', label: 'Find', icon: 'Find', shortcut: 'Ctrl+F' },\n { id: 'theme', label: 'Theme', icon: 'Theme', separator: true },\n];\n\n/** Toolbar component — a row of buttons emitting `key:command` events. */\nexport class Toolbar {\n readonly element: HTMLElement;\n\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private readonly _buttons: Map<string, HTMLButtonElement> = new Map();\n private readonly _unsubs: Unsubscribe[] = [];\n private _destroyed: boolean = false;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: ToolbarOptions) {\n this._editor = editor;\n this._doc = options?.documentImpl ?? getDocument(host);\n const buttons = options?.buttons ?? DEFAULT_TOOLBAR_BUTTONS;\n this.element = el(this._doc, 'div', { class: 'hw-toolbar', 'data-testid': 'toolbar' });\n host.appendChild(this.element);\n\n for (const spec of buttons) {\n if (spec.separator === true) {\n const sep = el(this._doc, 'span', { class: 'hw-toolbar__separator' });\n this.element.appendChild(sep);\n }\n const btn = this._buildButton(spec);\n this.element.appendChild(btn);\n this._buttons.set(spec.id, btn);\n }\n\n // Reactivity: enable/disable undo/redo based on editor state.\n const refreshHistory = (): void => this._refreshHistoryState();\n this._unsubs.push(editor.on('mol:changed', refreshHistory));\n this._unsubs.push(editor.on('helm:changed', refreshHistory));\n refreshHistory();\n\n this._reflectMode();\n this._unsubs.push(editor.on('option:change', (e) => {\n if (e.key === 'mode') this._reflectMode();\n }));\n }\n\n /** Enable or disable a button by id. */\n setButtonEnabled(id: string, enabled: boolean): void {\n const btn = this._buttons.get(id);\n if (btn === undefined) return;\n if (enabled) btn.removeAttribute('disabled');\n else btn.setAttribute('disabled', '');\n }\n\n /** Tear down listeners and remove DOM. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n if (this.element.parentNode !== null)\n this.element.parentNode.removeChild(this.element);\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _buildButton(spec: ToolbarButtonSpec): HTMLButtonElement {\n const btn = this._doc.createElement('button');\n btn.setAttribute('class', 'hw-toolbar__btn');\n btn.setAttribute('type', 'button');\n btn.setAttribute('data-action', spec.id);\n btn.setAttribute('data-testid', `toolbar-${spec.id}`);\n // Long-form tooltip explaining the button + optional shortcut hint.\n const descr = TOOLBAR_TOOLTIPS[spec.id] ?? spec.label;\n const title = spec.shortcut !== undefined ? `${descr} (${spec.shortcut})` : descr;\n btn.setAttribute('title', title);\n btn.setAttribute('aria-label', descr);\n // Phase 15 (T-1503) — Prefer inline SVG icons (from TOOLBAR_ICONS) over\n // text labels. The text label survives in aria-label / title for\n // screen-reader and hover access; the visible content is an SVG. When\n // no icon is registered we fall back to text (custom hosts / tests\n // that supply a non-standard button id keep working).\n const svgMarkup = TOOLBAR_ICONS[spec.id];\n if (svgMarkup !== undefined) {\n const iconHost = this._doc.createElement('span');\n iconHost.setAttribute('class', 'hw-toolbar__btn-icon');\n iconHost.setAttribute('aria-hidden', 'true');\n iconHost.innerHTML = svgMarkup;\n btn.appendChild(iconHost);\n } else {\n const text = spec.icon ?? spec.label;\n btn.appendChild(this._doc.createTextNode(text));\n }\n btn.addEventListener('click', () => this._invoke(spec.id));\n return btn;\n }\n\n private _invoke(command: string): void {\n let suppressed = false;\n this._editor.fire('key:command', {\n command,\n preventDefault: () => { suppressed = true; },\n });\n if (suppressed) return;\n this._execute(command);\n }\n\n private _execute(command: string): void {\n switch (command) {\n case 'new':\n this._editor.setHelm('');\n return;\n case 'open': {\n // Headless-friendly stub: try a prompt for testability; the demo\n // overrides with a richer flow via `key:command` preventDefault.\n const w = this._doc.defaultView as { prompt?: (msg: string) => string | null } | null;\n if (w !== null && w !== undefined && typeof w.prompt === 'function') {\n const helm = w.prompt('Enter HELM string');\n if (helm !== null) this._editor.setHelm(helm);\n }\n return;\n }\n case 'save': {\n const helm = this._editor.getHelm();\n this._editor.fire('clipboard:copy', { format: 'helm', payload: helm });\n return;\n }\n case 'undo':\n this._editor.undo();\n return;\n case 'redo':\n this._editor.redo();\n return;\n case 'eraser': {\n // Phase 26 (T-2602) — When the user has a non-empty selection,\n // clicking the Eraser button acts as \"bulk delete the selected\n // atoms/bonds\" rather than switching modes. The user's mental\n // model is \"I selected these monomers, now I want them gone\";\n // a mode-switch followed by per-atom click would be a tedious\n // extra step. The mode is preserved so the user stays in their\n // current workflow after the delete. When the selection is empty\n // we fall back to the legacy behaviour (switch to eraser mode so\n // the next canvas click deletes one atom).\n const selection = this._editor.getSelection();\n if (!selection.isEmpty) {\n this._editor.deleteSelection();\n return;\n }\n this._editor.setMode('eraser');\n return;\n }\n case 'select':\n case 'hbond':\n case 'move':\n this._editor.setMode(command as EditorMode);\n return;\n case 'zoom-in':\n this._editor.zoom(1.1, this._molCenterOrUndefined());\n return;\n case 'zoom-out':\n this._editor.zoom(1 / 1.1, this._molCenterOrUndefined());\n return;\n case 'fit':\n this._editor.fitToContent();\n return;\n case 'clean':\n this._editor.cleanLayout();\n return;\n case 'find':\n this._editor.openFindReplace();\n return;\n case 'theme': {\n const ed = this._editor as unknown as { _currentTheme(): { name: string } };\n const current = typeof ed._currentTheme === 'function' ? ed._currentTheme() : null;\n const isDark = current !== null && current.name === 'dark';\n this._editor.setTheme(isDark ? lightTheme : darkTheme);\n return;\n }\n default:\n return;\n }\n }\n\n private _refreshHistoryState(): void {\n this.setButtonEnabled('undo', this._editor.canUndo());\n this.setButtonEnabled('redo', this._editor.canRedo());\n }\n\n /**\n * Phase 27 (T-2705) -- Compute the centre-of-mass of all atoms in\n * the current Mol (`(minX + maxX) / 2`, `(minY + maxY) / 2`) so the\n * toolbar zoom buttons anchor the zoom transform there. Without an\n * anchor, `editor.zoom(factor)` keeps the model-space origin (0, 0)\n * fixed in surface space, which manifests as \"the canvas drifts to\n * the left\" when zooming in on a layout whose origin is far from\n * the centre. Returns `undefined` on an empty mol so `editor.zoom`\n * falls back to its no-anchor behaviour.\n */\n private _molCenterOrUndefined(): { x: number; y: number } | undefined {\n const mol = this._editor.getMol();\n if (mol.atoms.length === 0) return undefined;\n let minX = mol.atoms[0]!.p.x;\n let maxX = minX;\n let minY = mol.atoms[0]!.p.y;\n let maxY = minY;\n for (let i = 1; i < mol.atoms.length; i++) {\n const p = mol.atoms[i]!.p;\n if (p.x < minX) minX = p.x;\n if (p.x > maxX) maxX = p.x;\n if (p.y < minY) minY = p.y;\n if (p.y > maxY) maxY = p.y;\n }\n return { x: (minX + maxX) / 2, y: (minY + maxY) / 2 };\n }\n\n private _reflectMode(): void {\n const mode = this._editor.getMode();\n for (const id of ['select', 'eraser', 'hbond', 'move']) {\n const btn = this._buttons.get(id);\n if (btn === undefined) continue;\n const cur = btn.getAttribute('class') ?? '';\n const stripped = cur.split(/\\s+/).filter((c) => c !== 'hw-toolbar__btn--active').join(' ');\n btn.setAttribute('class', id === mode ? `${stripped} hw-toolbar__btn--active` : stripped);\n }\n }\n}\n","// T-0604 — `SequencePane` — natural-analog string view (read-only).\n//\n// Walks every atom and emits `atom.monomer?.naturalAnalog ?? atom.symbol` so\n// the user sees something resembling the FASTA-like representation. Updates\n// on every `helm:changed`.\n//\n// Layering: editor-layer module; reads from `core/model` only via the editor.\n\nimport type { Atom } from '../../core/model';\nimport type { Unsubscribe } from '../../util/types';\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\n\n/** Options for `SequencePane`. */\nexport interface SequencePaneOptions {\n /** Optional `Document` (linkedom tests). */\n documentImpl?: Document;\n}\n\n/** Natural-analog string view. Read-only; refreshes on editor mutation. */\nexport class SequencePane {\n readonly element: HTMLElement;\n\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private readonly _content: HTMLElement;\n private readonly _unsubs: Unsubscribe[] = [];\n private _destroyed: boolean = false;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: SequencePaneOptions) {\n this._editor = editor;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._content = el(this._doc, 'pre', {\n class: 'hw-pane__content hw-pane__sequence',\n 'data-testid': 'sequence-pane-content',\n });\n this.element = el(this._doc, 'div', {\n class: 'hw-pane hw-pane--sequence',\n 'data-testid': 'pane-sequence',\n }, [this._content]);\n host.appendChild(this.element);\n this.refresh();\n\n this._unsubs.push(editor.on('helm:changed', () => this.refresh()));\n this._unsubs.push(editor.on('mol:changed', () => this.refresh()));\n }\n\n /** Recompute and re-render the sequence text. */\n refresh(): void {\n if (this._destroyed) return;\n const text = this._compute();\n while (this._content.firstChild !== null)\n this._content.removeChild(this._content.firstChild);\n this._content.appendChild(this._doc.createTextNode(text));\n }\n\n /** Tear down: detach DOM, unsubscribe listeners. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n if (this.element.parentNode !== null)\n this.element.parentNode.removeChild(this.element);\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _compute(): string {\n const mol = this._editor.getMol();\n const parts: string[] = [];\n let lastChain: string | undefined;\n for (const a of mol.atoms as readonly Atom[]) {\n const chain = a.bio.chainId;\n if (lastChain !== undefined && chain !== lastChain) parts.push('|');\n lastChain = chain;\n const na = a.monomer?.naturalAnalog;\n parts.push((na !== undefined && na !== '') ? na : a.symbol);\n }\n return parts.join('');\n }\n}\n","// T-0605 — `NotationPane` — HELM-string view (editable).\n//\n// Single contenteditable element. On `blur` (or `Enter`), validates the new\n// HELM via `service.validate(...)`; on no errors, calls `editor.setHelm(...)`.\n// Otherwise displays an inline error message in `.hw-pane__error`.\n\nimport type { Unsubscribe } from '../../util/types';\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\n\n/** Options for `NotationPane`. */\nexport interface NotationPaneOptions {\n /** Optional `Document` (linkedom tests). */\n documentImpl?: Document;\n}\n\n/** HELM-string editor pane (contenteditable). */\nexport class NotationPane {\n readonly element: HTMLElement;\n\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private readonly _input: HTMLElement;\n private readonly _error: HTMLElement;\n private readonly _unsubs: Unsubscribe[] = [];\n private _destroyed: boolean = false;\n private _suppressNext: boolean = false;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: NotationPaneOptions) {\n this._editor = editor;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._input = el(this._doc, 'div', {\n class: 'hw-pane__content hw-pane__notation',\n contenteditable: 'true',\n spellcheck: 'false',\n 'data-testid': 'notation-pane-content',\n });\n this._error = el(this._doc, 'div', { class: 'hw-pane__error', 'data-testid': 'notation-pane-error' });\n this.element = el(this._doc, 'div', {\n class: 'hw-pane hw-pane--notation',\n 'data-testid': 'pane-helm',\n }, [this._input, this._error]);\n host.appendChild(this.element);\n this.refresh();\n\n this._input.addEventListener('blur', () => this._commit());\n this._input.addEventListener('keydown', (e: Event) => {\n const k = (e as unknown as { key: string }).key;\n if (k === 'Enter') {\n e.preventDefault();\n this._commit();\n }\n });\n\n this._unsubs.push(editor.on('helm:changed', () => {\n if (this._suppressNext) { this._suppressNext = false; return; }\n this.refresh();\n }));\n this._unsubs.push(editor.on('mol:changed', () => this.refresh()));\n }\n\n /** Pull the current HELM string from the editor and re-render. */\n refresh(): void {\n if (this._destroyed) return;\n const helm = this._editor.getHelm();\n while (this._input.firstChild !== null)\n this._input.removeChild(this._input.firstChild);\n this._input.appendChild(this._doc.createTextNode(helm));\n this._clearError();\n }\n\n /** Tear down: detach DOM, unsubscribe listeners. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n if (this.element.parentNode !== null)\n this.element.parentNode.removeChild(this.element);\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _commit(): void {\n if (this._destroyed) return;\n const text = (this._input.textContent ?? '').trim();\n const current = this._editor.getHelm();\n if (text === current) { this._clearError(); return; }\n const service = this._editor.getService();\n const diags = service.validate(text);\n const errors = diags.filter((d) => d.severity === 'error');\n if (errors.length > 0) {\n this._showError(errors.map((d) => d.message).join('; '));\n return;\n }\n this._clearError();\n this._suppressNext = true;\n this._editor.setHelm(text);\n }\n\n private _showError(message: string): void {\n while (this._error.firstChild !== null)\n this._error.removeChild(this._error.firstChild);\n this._error.appendChild(this._doc.createTextNode(message));\n this._error.setAttribute('class', 'hw-pane__error hw-pane__error--visible');\n }\n\n private _clearError(): void {\n while (this._error.firstChild !== null)\n this._error.removeChild(this._error.firstChild);\n this._error.setAttribute('class', 'hw-pane__error');\n }\n}\n","// T-0606 — `PropertiesPane` — formula / MW / extinction coefficient view.\n//\n// Renders a small table of computed properties on every `helm:changed`. For\n// HELM strings longer than `LONG_HELM_THRESHOLD` chars we skip the heavy\n// computation and show \"(too long)\" to keep the UI responsive on copy-paste.\n\nimport type { Unsubscribe } from '../../util/types';\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\n\n/** Options for `PropertiesPane`. */\nexport interface PropertiesPaneOptions {\n /** Optional `Document` (linkedom tests). */\n documentImpl?: Document;\n}\n\n/** HELM-string-length cutoff at which we skip recomputation. */\nconst LONG_HELM_THRESHOLD = 1000;\n\n/** Computed properties pane. */\nexport class PropertiesPane {\n readonly element: HTMLElement;\n\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private readonly _body: HTMLElement;\n private readonly _unsubs: Unsubscribe[] = [];\n private _destroyed: boolean = false;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: PropertiesPaneOptions) {\n this._editor = editor;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._body = el(this._doc, 'div', {\n class: 'hw-pane__content hw-pane__properties',\n 'data-testid': 'properties-pane-content',\n });\n this.element = el(this._doc, 'div', {\n class: 'hw-pane hw-pane--properties',\n 'data-testid': 'pane-properties',\n }, [this._body]);\n host.appendChild(this.element);\n this.refresh();\n\n this._unsubs.push(editor.on('helm:changed', () => this.refresh()));\n this._unsubs.push(editor.on('mol:changed', () => this.refresh()));\n }\n\n /** Recompute and re-render the property table. */\n refresh(): void {\n if (this._destroyed) return;\n while (this._body.firstChild !== null)\n this._body.removeChild(this._body.firstChild);\n const helm = this._editor.getHelm();\n if (helm.length > LONG_HELM_THRESHOLD) {\n this._body.appendChild(el(this._doc, 'div', { class: 'hw-pane__placeholder' }, ['(too long)']));\n return;\n }\n const service = this._editor.getService();\n let formulaText = '';\n let mw = 0;\n let extinction = 0;\n try {\n const f = service.getFormula(helm);\n formulaText = formatElements(f.elements);\n mw = f.mw;\n } catch {\n formulaText = '—';\n }\n try {\n mw = service.getMolWeight(helm);\n } catch {\n // already 0\n }\n try {\n extinction = service.getExtinctionCoefficient(helm);\n } catch {\n // already 0\n }\n this._body.appendChild(this._makeRow('Formula', formulaText, 'formula'));\n this._body.appendChild(this._makeRow('Molecular Weight', mw === 0 ? '—' : mw.toFixed(2), 'mw'));\n this._body.appendChild(this._makeRow('Extinction Coefficient', extinction === 0 ? '—' : extinction.toFixed(0), 'extinction'));\n }\n\n /** Tear down: detach DOM, unsubscribe listeners. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n if (this.element.parentNode !== null)\n this.element.parentNode.removeChild(this.element);\n }\n\n private _makeRow(label: string, value: string, id: string): HTMLElement {\n const labCell = el(this._doc, 'span', { class: 'hw-pane__prop-label' }, [label]);\n const valCell = el(this._doc, 'span', {\n class: 'hw-pane__prop-value',\n 'data-testid': `properties-${id}`,\n }, [value]);\n return el(this._doc, 'div', { class: 'hw-pane__prop-row' }, [labCell, valCell]);\n }\n}\n\nfunction formatElements(elements: ReadonlyMap<string, number>): string {\n // Hill order: C first, H second, others alphabetical.\n const keys = Array.from(elements.keys()).sort((a, b) => {\n if (a === b) return 0;\n if (a === 'C') return -1;\n if (b === 'C') return 1;\n if (a === 'H') return -1;\n if (b === 'H') return 1;\n return a.localeCompare(b);\n });\n let out = '';\n for (const k of keys) {\n const n = elements.get(k);\n if (n === undefined || n === 0) continue;\n out += n === 1 ? k : `${k}${n}`;\n }\n return out === '' ? '—' : out;\n}\n","// T-0607 — `AtomicStructurePane` — atomic-level molfile view.\n//\n// Only mounted when `service.hasAtomicMolfileProvider() === true`. On every\n// `helm:changed`, calls `service.getAtomicMolfile(helm)` and renders the\n// result as a `<pre>` block. Errors surface as a placeholder message.\n\nimport type { Unsubscribe } from '../../util/types';\nimport type { HelmEditor } from '../editor';\nimport { getDocument, el } from '../view/dom-utils';\n\n/** Options for `AtomicStructurePane`. */\nexport interface AtomicStructurePaneOptions {\n /** Optional `Document` (linkedom tests). */\n documentImpl?: Document;\n}\n\n/** Atomic-level molfile pane. */\nexport class AtomicStructurePane {\n readonly element: HTMLElement;\n\n private readonly _editor: HelmEditor;\n private readonly _doc: Document;\n private readonly _content: HTMLElement;\n private readonly _unsubs: Unsubscribe[] = [];\n private _destroyed: boolean = false;\n /** Token incremented on every refresh; lets us discard stale async results. */\n private _refreshToken: number = 0;\n\n constructor(host: HTMLElement, editor: HelmEditor, options?: AtomicStructurePaneOptions) {\n this._editor = editor;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._content = el(this._doc, 'pre', {\n class: 'hw-pane__content hw-pane__atomic',\n 'data-testid': 'atomic-pane-content',\n });\n this.element = el(this._doc, 'div', {\n class: 'hw-pane hw-pane--atomic',\n 'data-testid': 'pane-atomic',\n }, [this._content]);\n host.appendChild(this.element);\n // Fire-and-forget initial refresh; promise rejections are caught inside.\n void this.refresh();\n\n this._unsubs.push(editor.on('helm:changed', () => { void this.refresh(); }));\n }\n\n /** Recompute the atomic molfile and re-render. */\n async refresh(): Promise<void> {\n if (this._destroyed) return;\n const token = ++this._refreshToken;\n const helm = this._editor.getHelm();\n const service = this._editor.getService();\n if (!service.hasAtomicMolfileProvider()) {\n this._render('Atomic structure unavailable');\n return;\n }\n try {\n const molfile = await service.getAtomicMolfile(helm);\n if (this._destroyed) return;\n if (token !== this._refreshToken) return;\n this._render(molfile);\n } catch (e) {\n if (this._destroyed) return;\n if (token !== this._refreshToken) return;\n const msg = e instanceof Error ? e.message : String(e);\n this._render(`Atomic structure unavailable: ${msg}`);\n }\n }\n\n /** Tear down: detach DOM, unsubscribe listeners. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n if (this.element.parentNode !== null)\n this.element.parentNode.removeChild(this.element);\n }\n\n private _render(text: string): void {\n while (this._content.firstChild !== null)\n this._content.removeChild(this._content.firstChild);\n this._content.appendChild(this._doc.createTextNode(text));\n }\n}\n","// T-0608 — `HelmEditorApp` — the full Pistoia-style multi-pane shell.\n//\n// Composes `HelmEditor` (canvas), `MonomerPalette` (left), `Toolbar` (top),\n// `SequencePane`/`NotationPane`/`PropertiesPane`/`AtomicStructurePane`\n// (bottom tabs) into a single `host` element. See API.md §3 and DEMO.md §2.\n\nimport type { Unsubscribe } from '../../util/types';\nimport type { Theme } from '../../render/theme';\nimport { lightTheme } from '../../render/theme';\nimport type { HelmService } from '../../service/helm-service';\nimport { HelmEditor } from '../editor';\nimport type { EditorEventMap } from '../events';\nimport { getDocument, el } from '../view/dom-utils';\nimport { MonomerPalette } from '../palette/palette';\nimport type { MonomerPaletteOptions } from '../palette/palette';\nimport { Toolbar } from '../toolbar/toolbar';\nimport type { ToolbarButtonSpec } from '../toolbar/toolbar';\nimport { SequencePane } from './sequence-pane';\nimport { NotationPane } from './notation-pane';\nimport { PropertiesPane } from './properties-pane';\nimport { AtomicStructurePane } from './atomic-structure-pane';\n// Phase 28 (T-2804) -- the runtime `injectAppStyles` helper is gone.\n// Consumers import `@datagrok-libraries/hwe/styles.css` via their\n// bundler; the app no longer mutates the host document's <head>.\n\n/** Identifier for one of the four standard panes. */\nexport type PaneId = 'sequence' | 'helm' | 'properties' | 'atomic';\n\n/** Options for `HelmEditorApp`. */\nexport interface HelmEditorAppOptions {\n /** Required: a `HelmService` bound to a monomer library. */\n service: HelmService;\n /** Initial HELM string. Default `''` (empty editor). */\n initialHelm?: string;\n /** Panes to expose. Default: every pane (atomic gated on provider). */\n visiblePanes?: PaneId[];\n /** Toolbar button override. Default: full Pistoia-style set. */\n toolbarButtons?: ToolbarButtonSpec[];\n /** Palette construction options. */\n paletteOptions?: MonomerPaletteOptions;\n /** Canvas width / height. */\n width?: number;\n height?: number;\n /** Initial theme. Default: `lightTheme`. */\n theme?: Theme;\n /** Optional `Document` (linkedom tests). */\n documentImpl?: Document;\n}\n\n/** Pane spec (label + factory). */\ninterface PaneSpec {\n readonly id: PaneId;\n readonly label: string;\n}\n\nconst PANE_SPECS: ReadonlyArray<PaneSpec> = [\n { id: 'sequence', label: 'Sequence' },\n { id: 'helm', label: 'HELM' },\n { id: 'properties', label: 'Properties' },\n { id: 'atomic', label: 'Atomic Structure' },\n];\n\n/** The full Pistoia-style multi-pane app. */\nexport class HelmEditorApp {\n readonly canvas: HelmEditor;\n readonly palette: MonomerPalette;\n readonly toolbar: Toolbar;\n readonly sequencePane: SequencePane;\n readonly notationPane: NotationPane;\n readonly propertiesPane: PropertiesPane;\n readonly atomicStructurePane: AtomicStructurePane | null;\n\n /** Root container — placed inside the host. */\n readonly element: HTMLElement;\n\n private readonly _doc: Document;\n private readonly _host: HTMLElement;\n private readonly _toolbarHost: HTMLElement;\n private readonly _paletteHost: HTMLElement;\n private readonly _canvasHost: HTMLElement;\n private readonly _tabsHost: HTMLElement;\n private readonly _paneBody: HTMLElement;\n private readonly _paneByName: Map<PaneId, HTMLElement> = new Map();\n private readonly _tabsByName: Map<PaneId, HTMLButtonElement> = new Map();\n private readonly _unsubs: Unsubscribe[] = [];\n private _activePane: PaneId = 'helm';\n private _destroyed: boolean = false;\n\n constructor(host: HTMLElement, options: HelmEditorAppOptions) {\n this._host = host;\n this._doc = options.documentImpl ?? getDocument(host);\n\n const initialTheme = options.theme ?? lightTheme;\n const rootClass = initialTheme.name === 'dark' ? 'hw-app hw-app--dark' : 'hw-app';\n this.element = el(this._doc, 'div', { class: rootClass, 'data-testid': 'app-root' });\n\n this._toolbarHost = el(this._doc, 'div', { class: 'hw-app__toolbar' });\n this._paletteHost = el(this._doc, 'div', { class: 'hw-app__palette' });\n this._canvasHost = el(this._doc, 'div', { class: 'hw-app__canvas', 'data-testid': 'canvas-host' });\n const main = el(this._doc, 'div', { class: 'hw-app__main' }, [this._paletteHost, this._canvasHost]);\n this._tabsHost = el(this._doc, 'div', { class: 'hw-app__tabs', role: 'tablist' });\n this._paneBody = el(this._doc, 'div', { class: 'hw-app__pane-body' });\n const panes = el(this._doc, 'div', { class: 'hw-app__panes' }, [this._tabsHost, this._paneBody]);\n this.element.appendChild(this._toolbarHost);\n this.element.appendChild(main);\n this.element.appendChild(panes);\n host.appendChild(this.element);\n\n // ----- Canvas\n const editorOpts: ConstructorParameters<typeof HelmEditor>[1] = { service: options.service };\n if (options.initialHelm !== undefined) editorOpts.initialHelm = options.initialHelm;\n if (options.width !== undefined) editorOpts.width = options.width;\n if (options.height !== undefined) editorOpts.height = options.height;\n this.canvas = new HelmEditor(this._canvasHost, editorOpts);\n if (options.theme !== undefined) this.canvas.setTheme(options.theme);\n\n // ----- Toolbar\n const toolbarOpts: { documentImpl: Document; buttons?: ToolbarButtonSpec[] } = { documentImpl: this._doc };\n if (options.toolbarButtons !== undefined) toolbarOpts.buttons = options.toolbarButtons;\n this.toolbar = new Toolbar(this._toolbarHost, this.canvas, toolbarOpts);\n\n // ----- Palette\n this.palette = new MonomerPalette(this._paletteHost, this.canvas, {\n documentImpl: this._doc,\n ...options.paletteOptions,\n });\n\n // ----- Panes\n this.sequencePane = new SequencePane(this._paneBody, this.canvas, { documentImpl: this._doc });\n this.notationPane = new NotationPane(this._paneBody, this.canvas, { documentImpl: this._doc });\n this.propertiesPane = new PropertiesPane(this._paneBody, this.canvas, { documentImpl: this._doc });\n if (options.service.hasAtomicMolfileProvider()) {\n this.atomicStructurePane = new AtomicStructurePane(this._paneBody, this.canvas, { documentImpl: this._doc });\n } else {\n this.atomicStructurePane = null;\n }\n this._paneByName.set('sequence', this.sequencePane.element);\n this._paneByName.set('helm', this.notationPane.element);\n this._paneByName.set('properties', this.propertiesPane.element);\n if (this.atomicStructurePane !== null)\n this._paneByName.set('atomic', this.atomicStructurePane.element);\n\n // ----- Tabs\n const visible = this._resolveVisiblePanes(options);\n for (const id of visible) {\n const spec = PANE_SPECS.find((s) => s.id === id);\n if (spec === undefined) continue;\n const tab = this._doc.createElement('button');\n tab.setAttribute('type', 'button');\n tab.setAttribute('class', 'hw-app__tab');\n tab.setAttribute('role', 'tab');\n tab.setAttribute('data-pane', id);\n tab.setAttribute('data-testid', `tab-${id}`);\n tab.appendChild(this._doc.createTextNode(spec.label));\n tab.addEventListener('click', () => this.activatePane(id));\n this._tabsHost.appendChild(tab);\n this._tabsByName.set(id, tab);\n }\n\n const defaultPane: PaneId = visible.includes('helm') ? 'helm' : (visible[0] ?? 'helm');\n this.activatePane(defaultPane);\n\n // Reflect theme changes (toolbar's theme toggle bubbles up via editor).\n this._unsubs.push(this.canvas.on('theme:change', (e) => this._applyTheme(e.theme)));\n\n // T-1103 / T-1106 — Mode-driven canvas cursor + status bar.\n this._buildStatusBar();\n this._applyMode(this.canvas.getMode());\n this._unsubs.push(this.canvas.on('option:change', (e) => {\n if (e.key === 'mode') this._applyMode(e.newValue as string);\n if (e.key === 'nextAdd') this._refreshStatus();\n }));\n this._unsubs.push(this.canvas.on('mol:changed', () => this._refreshStatus()));\n this._unsubs.push(this.canvas.on('helm:changed', () => this._refreshStatus()));\n // Phase 13b (Bug 5) — Subscribe to ephemeral status messages from\n // the editor (e.g. failed addBond fires `editor:status` with severity\n // 'error'). The status bar surfaces the message into the dedicated\n // `[data-testid=\"status-message\"]` span and auto-clears after\n // `durationMs` ms.\n this._unsubs.push(this.canvas.on('editor:status', (e) => {\n this._showStatusMessage(e.message, e.severity, e.durationMs);\n }));\n\n // Phase 13c (Bug 11) — Wire common UI gestures the demo lacked. The\n // editor's pointer layer fires monomer:dblclick / bond:dblclick but\n // no caller subscribed to actually open the matching properties\n // dialogs. Hook them up at the app level so the demo behaves the\n // way users expect from the Pistoia editor.\n this._unsubs.push(this.canvas.on('monomer:dblclick', (e) => {\n this.canvas.openAtomProps(e.atom);\n }));\n // Phase 14B (T-1415) — Right-click on a bond opens the bond\n // properties dialog (which now hosts an R-group editor). We call\n // `preventDefault()` so the browser's native context menu doesn't\n // overlap the modal.\n this._unsubs.push(this.canvas.on('bond:contextmenu', (e) => {\n e.preventDefault();\n this.canvas.openBondProps(e.bond);\n }));\n }\n\n private _statusModeNode: HTMLElement | null = null;\n private _statusMessageNode: HTMLElement | null = null;\n private _statusMessageTimeout: ReturnType<typeof setTimeout> | null = null;\n\n private _buildStatusBar(): void {\n const bar = el(this._doc, 'div', { class: 'hw-status-bar', 'data-testid': 'status-bar' });\n // Two-slot layout: stable mode/nextAdd readout + an ephemeral\n // message slot for `editor:status` events. The message node sits in\n // a separate span so the mode/nextAdd readout never flickers.\n //\n // Phase 25 (T-2504): the mode-slot renders BOTH the mode text AND\n // the \"Next add\" pair as separate flex children so the optional\n // `×` clear-button can live next to the next-add symbol without\n // crowding the status-message that arrives via `editor:status`.\n const modeNode = el(this._doc, 'span', { class: 'hw-status-bar__mode', 'data-testid': 'status-mode' });\n const msgNode = el(this._doc, 'span', {\n class: 'hw-status-bar__message',\n 'data-testid': 'status-message',\n role: 'status',\n 'aria-live': 'polite',\n });\n bar.appendChild(modeNode);\n bar.appendChild(msgNode);\n this._canvasHost.appendChild(bar);\n this._statusModeNode = modeNode;\n this._statusMessageNode = msgNode;\n this._refreshStatus();\n }\n\n private _refreshStatus(): void {\n const node = this._statusModeNode;\n if (node === null) return;\n const mode = this.canvas.getMode();\n const next = this.canvas.getNextAddSymbol();\n while (node.firstChild !== null) node.removeChild(node.firstChild);\n // Mode prefix is a plain text node so existing tests asserting on\n // `.textContent` of `status-mode` keep working (the substring\n // `Mode: select | Next add: ` is preserved verbatim).\n if (next === null) {\n node.appendChild(this._doc.createTextNode(`Mode: ${mode} | Next add: none`));\n return;\n }\n node.appendChild(this._doc.createTextNode(`Mode: ${mode} | Next add: `));\n // Symbol in its own span so a future style can colour-code it.\n const symbolEl = el(this._doc, 'span', {\n class: 'hw-status-bar__next-add-symbol',\n 'data-testid': 'status-next-add-symbol',\n }, [next.symbol]);\n node.appendChild(symbolEl);\n // Phase 25 (T-2504): the `×` clear button is only present when a\n // tile is primed. User report: \"small x icon at the right of it\n // which will allow me to unselect the monomer\". On click it calls\n // `setNextAddSymbol(null)`; that fires `option:change` →\n // `_refreshStatus`, which removes the button on the very next pass.\n const clearBtn = el(this._doc, 'button', {\n type: 'button',\n class: 'hw-status-bar__next-add-clear',\n 'data-testid': 'status-next-add-clear',\n 'aria-label': 'Clear next-add monomer',\n title: 'Clear (Esc)',\n }, ['×']);\n clearBtn.addEventListener('click', (e: Event) => {\n e.preventDefault();\n e.stopPropagation();\n this.canvas.setNextAddSymbol(null);\n });\n node.appendChild(clearBtn);\n }\n\n /**\n * Phase 13b (Bug 5) — Render an ephemeral status message. Updates the\n * `[data-testid=\"status-message\"]` element's textContent + a severity\n * data-attribute (used by CSS for color), and schedules a clear after\n * `durationMs` ms. `durationMs === 0` means \"no auto-clear\" — the\n * message stays until the next `editor:status` overwrites it.\n */\n private _showStatusMessage(message: string, severity: 'info' | 'warn' | 'error', durationMs: number): void {\n const node = this._statusMessageNode;\n if (node === null) return;\n if (this._statusMessageTimeout !== null) {\n clearTimeout(this._statusMessageTimeout);\n this._statusMessageTimeout = null;\n }\n while (node.firstChild !== null) node.removeChild(node.firstChild);\n node.appendChild(this._doc.createTextNode(message));\n node.setAttribute('data-severity', severity);\n if (durationMs > 0) {\n this._statusMessageTimeout = setTimeout(() => {\n const n = this._statusMessageNode;\n if (n === null) return;\n while (n.firstChild !== null) n.removeChild(n.firstChild);\n n.removeAttribute('data-severity');\n this._statusMessageTimeout = null;\n }, durationMs);\n }\n }\n\n /** Toggle `hw-editor-view--<mode>` class on the canvas wrapper. */\n private _applyMode(mode: string): void {\n const wrapper = this._canvasHost.querySelector('.hw-editor-view');\n if (wrapper === null) return;\n const cur = wrapper.getAttribute('class') ?? '';\n const stripped = cur.split(/\\s+/).filter((c) => !c.startsWith('hw-editor-view--')).join(' ');\n wrapper.setAttribute('class', `${stripped} hw-editor-view--${mode}`.trim());\n this._refreshStatus();\n }\n\n // ------------------------------------------------------------------------\n // Convenience forwarders\n // ------------------------------------------------------------------------\n\n /** Forward to `canvas.setHelm`. */\n setHelm(helm: string): void { this.canvas.setHelm(helm); }\n\n /** Forward to `canvas.getHelm`. */\n getHelm(): string { return this.canvas.getHelm(); }\n\n /** Forward to `canvas.on`. */\n on<K extends keyof EditorEventMap>(name: K, handler: (e: EditorEventMap[K]) => void): Unsubscribe {\n return this.canvas.on(name, handler);\n }\n\n /** Switch the active bottom tab. */\n activatePane(id: PaneId): void {\n if (!this._paneByName.has(id) && !this._tabsByName.has(id)) return;\n this._activePane = id;\n for (const [name, paneEl] of this._paneByName.entries()) {\n (paneEl as unknown as { style: { display: string } }).style.display = name === id ? '' : 'none';\n }\n for (const [name, tabEl] of this._tabsByName.entries()) {\n const cur = tabEl.getAttribute('class') ?? '';\n const stripped = cur.split(/\\s+/).filter((c) => c !== 'hw-app__tab--active').join(' ');\n tabEl.setAttribute('class', name === id ? `${stripped} hw-app__tab--active` : stripped);\n }\n }\n\n /** The id of the currently active tab. */\n getActivePane(): PaneId { return this._activePane; }\n\n /** Tear down every subcomponent and remove the root DOM. */\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n // Phase 13b (Bug 5) — clear any pending status-message auto-clear so\n // tests with fake timers don't see late callbacks fire after destroy.\n if (this._statusMessageTimeout !== null) {\n clearTimeout(this._statusMessageTimeout);\n this._statusMessageTimeout = null;\n }\n for (const u of this._unsubs) u();\n if (this.atomicStructurePane !== null) this.atomicStructurePane.destroy();\n this.propertiesPane.destroy();\n this.notationPane.destroy();\n this.sequencePane.destroy();\n this.palette.destroy();\n this.toolbar.destroy();\n this.canvas.destroy();\n if (this.element.parentNode !== null)\n this.element.parentNode.removeChild(this.element);\n void this._host;\n }\n\n // ------------------------------------------------------------------------\n // Internals\n // ------------------------------------------------------------------------\n\n private _resolveVisiblePanes(options: HelmEditorAppOptions): PaneId[] {\n const hasAtomic = options.service.hasAtomicMolfileProvider();\n let list = options.visiblePanes ?? ['sequence', 'helm', 'properties', 'atomic'];\n if (!hasAtomic) list = list.filter((p) => p !== 'atomic');\n return list;\n }\n\n private _applyTheme(theme: Theme): void {\n const dark = theme.name === 'dark';\n const cur = this.element.getAttribute('class') ?? '';\n const stripped = cur.split(/\\s+/).filter((c) => c !== 'hw-app--dark').join(' ');\n this.element.setAttribute('class', dark ? `${stripped} hw-app--dark` : stripped);\n }\n}\n","// Lightweight adapter that exposes an internal `Mol` as the legacy\n// `HelmMolLike` shape (flat `atoms[]` and `bonds[]` arrays with the\n// per-atom `bio`, `elem`, `selected`, `highlighted` fields that the\n// `packages/Helm` shell reaches into). See LEGACY-EDITOR-NOTES.md and\n// INTEGRATION-HELM-PACKAGE.md §3 (\"Editor properties accessed elsewhere\").\n//\n// Layering: this module imports from `core/` only; safe to use from anywhere\n// in `datagrok-adapter/`.\n\nimport type { Mol } from '../core/model';\nimport type { Atom, Bond } from '../core/model';\nimport type { Point } from '../util/types';\nimport type { HelmType } from '../core/constants';\nimport type { HelmAtomLike, HelmBondLike, HelmMolLike } from './types';\n\n/**\n * Wrap an internal `Atom` in a `HelmAtomLike` proxy. Selection/highlight\n * fields are stored on the wrapper so consumer mutations don't bleed into\n * the immutable model.\n */\nclass HelmAtomView implements HelmAtomLike {\n readonly T: 'ATOM' = 'ATOM';\n selected: boolean;\n highlighted: boolean;\n readonly p: Point;\n readonly elem: string;\n readonly bio: HelmAtomLike['bio'];\n readonly inlineSource?: string;\n\n constructor(atom: Atom) {\n this.selected = atom.selected;\n this.highlighted = atom.highlighted;\n this.p = { x: atom.p.x, y: atom.p.y };\n this.elem = atom.symbol;\n this.bio = {\n type: atom.biotype,\n continuousId: atom.bio.continuousId,\n chainId: atom.bio.chainId,\n positionInChain: atom.bio.positionInChain,\n ...(atom.bio.annotation !== undefined ? { annotation: atom.bio.annotation } : {}),\n ...(atom.bio.blobtype !== undefined ? { blobtype: atom.bio.blobtype } : {}),\n ...(atom.bio.ambiguity !== undefined ? { ambiguity: atom.bio.ambiguity } : {}),\n id: atom.id,\n };\n if (atom.inlineSource !== undefined) this.inlineSource = atom.inlineSource;\n }\n\n biotype(): HelmType | null {\n return this.bio.type;\n }\n}\n\n/**\n * Wrap an internal `Bond` in a `HelmBondLike` view. R-group references are\n * flattened to plain integers (the legacy editor's `r1`/`r2` ints — `0` for\n * \"unspecified\", \"wildcard\", or \"pair\").\n */\nclass HelmBondView implements HelmBondLike {\n readonly a1: HelmAtomLike;\n readonly a2: HelmAtomLike;\n readonly r1: number;\n readonly r2: number;\n readonly kind: string;\n\n constructor(bond: Bond, a1: HelmAtomLike, a2: HelmAtomLike) {\n this.a1 = a1;\n this.a2 = a2;\n this.r1 = rgroupRefToInt(bond.r1);\n this.r2 = rgroupRefToInt(bond.r2);\n this.kind = bond.kind;\n }\n}\n\nfunction rgroupRefToInt(ref: Bond['r1']): number {\n switch (ref.kind) {\n case 'numeric': return ref.r;\n case 'positional': return ref.r;\n default: return 0;\n }\n}\n\n/**\n * Build a `HelmMolLike` view over `mol`. The atoms[] / bonds[] arrays are\n * proxy views; `clone(false)` returns a shallow duplicate good enough for\n * the cell renderer's `editor.m.clone(false)` call.\n */\nexport function buildHelmMolView(mol: Mol): HelmMolLike {\n const atoms: HelmAtomView[] = [];\n const atomByOrigId = new Map<number, HelmAtomView>();\n for (const a of mol.atoms) {\n const view = new HelmAtomView(a);\n atoms.push(view);\n atomByOrigId.set(a.id, view);\n }\n const bonds: HelmBondView[] = [];\n for (const b of mol.bonds) {\n const a1 = atomByOrigId.get(b.a1.id);\n const a2 = atomByOrigId.get(b.a2.id);\n if (a1 === undefined || a2 === undefined) continue;\n bonds.push(new HelmBondView(b, a1, a2));\n }\n\n const view: HelmMolLike = {\n atoms,\n bonds,\n clone(_deep?: boolean): HelmMolLike {\n // Produce a fresh structural copy (atoms re-wrapped, fresh selection\n // flags). Deep flag accepted but ignored — Mol is immutable.\n return buildHelmMolView(mol);\n },\n _internalMol: mol,\n };\n return view;\n}\n","// T-0803 — `IHelmWebEditorLike` wrapper exposed by `createHelmWebEditor`.\n//\n// Builds the legacy `editor.div / editor.m / editor.helm / editor.options`\n// shape on top of `HelmService.renderToSvg`. The cell renderer requires the\n// SVG element to be `editor.div.children[0]` and respects the editor's\n// `options.width / options.height` for `getBBox`. The `noDraw` flag short-\n// circuits the SVG generation so `getMolfiles` stays fast.\n//\n// Layering: imports from `service/`, `core/`, `calc/`, plus the in-package\n// `helm-mol-view`. No DOM access beyond `host.ownerDocument` (linkedom-safe).\n\nimport type { Mol } from '../core/model';\nimport { emptyMol } from '../core/model';\nimport { layoutMol } from '../layout/layout-service';\nimport type { HelmService } from '../service/helm-service';\nimport { pseudoMolfile } from '../calc/pseudo-molfile';\nimport { molWeight } from '../calc/mol-weight';\nimport { extinctionCoefficient } from '../calc/extinction-coeff';\nimport { computeFormula } from '../calc/formula';\nimport { getDocument } from '../editor/view/dom-utils';\nimport { buildHelmMolView } from './helm-mol-view';\nimport type {\n DrawOptionsLike,\n HelmMolLike,\n HelmPluginLike,\n IHelmWebEditorLike,\n JSDraw2EditorLike,\n} from './types';\n\nconst DEFAULT_WIDTH = 400;\nconst DEFAULT_HEIGHT = 100;\nconst DEFAULT_FONT_SIZE = 14;\n\n/** Options accepted by `LegacyEditorWrapper`. */\nexport interface LegacyEditorOptions {\n width?: number;\n height?: number;\n /** Optional `Document` (linkedom). Defaults to `host.ownerDocument`. */\n documentImpl?: Document;\n}\n\n/**\n * Wraps `HelmService` to look like a JSDraw2 `Editor`. Backs both\n * `createHelmWebEditor` and the `canvas` / `structureview` fields of the\n * legacy `App` returned by `createWebEditorApp`.\n */\nexport class LegacyEditorWrapper implements IHelmWebEditorLike {\n readonly host: HTMLElement;\n readonly editor: JSDraw2EditorLike;\n\n private readonly _service: HelmService;\n private readonly _doc: Document;\n private _mol: Mol;\n private _molView: HelmMolLike;\n private _currentHelm: string = '';\n private _width: number;\n private _height: number;\n private readonly _drawOptions: DrawOptionsLike = { fontsize: DEFAULT_FONT_SIZE };\n private _noDraw: boolean = false;\n private _svgEl: SVGSVGElement | null = null;\n\n constructor(host: HTMLElement, service: HelmService, options?: LegacyEditorOptions) {\n this.host = host;\n this._service = service;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._width = options?.width ?? DEFAULT_WIDTH;\n this._height = options?.height ?? DEFAULT_HEIGHT;\n this._mol = emptyMol();\n this._molView = buildHelmMolView(this._mol);\n this.editor = this._buildEditor();\n }\n\n // ----- IHelmWebEditorLike -------------------------------------------------\n\n resizeEditor(width: number, height: number): void {\n this._width = width;\n this._height = height;\n this._redraw();\n }\n\n // ----- internals ----------------------------------------------------------\n\n private _buildEditor(): JSDraw2EditorLike {\n const self = this;\n const helmPlugin: HelmPluginLike = {\n get noDraw(): boolean { return self._noDraw; },\n set noDraw(v: boolean) { self._noDraw = v; },\n get jsd(): JSDraw2EditorLike { return self.editor; },\n };\n\n return {\n get div(): HTMLElement { return self.host; },\n get m(): HelmMolLike { return self._molView; },\n set m(v: HelmMolLike) { self._molView = v; },\n get helm(): HelmPluginLike { return helmPlugin; },\n get options(): { width: number; height: number } {\n return { width: self._width, height: self._height };\n },\n\n setData(data: string, format: 'helm'): void {\n if (format !== 'helm')\n throw new Error(`LegacyEditorWrapper: only 'helm' format supported (got '${format}').`);\n self._setHelm(data);\n },\n setHelm(helm: string): void { self._setHelm(helm); },\n setMol(mol: HelmMolLike): void {\n self._mol = mol._internalMol;\n self._molView = self._buildView(self._mol);\n self._currentHelm = self._service.serialize(self._mol);\n self._redraw();\n },\n getHelm(_stripHtml?: boolean): string {\n // Our serializer never emits HTML markers — the `stripHtml` flag is\n // accepted for API parity but is a no-op.\n return self._currentHelm;\n },\n getMolfile(): string { return pseudoMolfile(self._mol); },\n\n resize(width: number, height: number): void {\n self._width = width;\n self._height = height;\n self._redraw();\n },\n setSize(width: number, height: number): void {\n self._width = width;\n self._height = height;\n self._redraw();\n },\n redraw(): void { self._redraw(); },\n reset(): void {\n self._mol = emptyMol();\n self._molView = buildHelmMolView(self._mol);\n self._currentHelm = '';\n self._removeSvg();\n },\n\n getFormula(_html?: boolean): string {\n return formulaToString(computeFormula(self._mol));\n },\n getMolWeight(): number { return molWeight(self._mol); },\n getExtinctionCoefficient(): number { return extinctionCoefficient(self._mol); },\n\n getDrawOptions(): DrawOptionsLike { return self._drawOptions; },\n };\n }\n\n private _setHelm(helm: string): void {\n this._currentHelm = helm;\n // Resolve monomers so consumers can compute properties (formula, MW,\n // extinction coefficient). The renderer already tolerates `null` monomers,\n // so resolving here is purely additive.\n const parsed = this._service.parse(helm, { mode: 'lenient', resolveMonomers: true });\n this._mol = parsed.mol;\n this._molView = this._buildView(this._mol);\n this._redraw();\n }\n\n /**\n * Build the `HelmMolLike` view over `mol`. `HelmService.parse` does not lay\n * atoms out — only `layoutMol` assigns `atom.p`. Interactive consumers\n * (`HelmInput` hover/tooltip, `getHoveredAtom`) hit-test against `atom.p`, so\n * the view must carry layout coordinates. The `noDraw` (batch `getMolfiles`)\n * path never reads the view for hit-testing, so it skips the layout pass to\n * avoid the per-string cost.\n */\n private _buildView(mol: Mol): HelmMolLike {\n return buildHelmMolView(this._noDraw ? mol : layoutMol(mol));\n }\n\n private _redraw(): void {\n if (this._noDraw) {\n this._removeSvg();\n return;\n }\n if (this._currentHelm === '') {\n this._removeSvg();\n return;\n }\n const svg = this._service.renderToSvg(this._currentHelm, {\n width: this._width,\n height: this._height,\n // Fill the available pane: scale the drawing UP (hwe's default caps at\n // native size, so a small molecule leaves the cell mostly empty).\n maxScale: Infinity,\n // Show the internal linear monomer index next to each monomer (green,\n // small) so the numbering matches what connections / tasks reference.\n showIds: true,\n });\n this._mountSvg(svg);\n }\n\n private _mountSvg(svgText: string): void {\n this._removeSvg();\n const el = createSvgFromString(this._doc, svgText, this._width, this._height);\n // Insert as the FIRST child so the cell renderer's `editor.div.children[0]`\n // contract holds.\n if (this.host.firstChild !== null) this.host.insertBefore(el, this.host.firstChild);\n else this.host.appendChild(el);\n this._svgEl = el;\n }\n\n private _removeSvg(): void {\n if (this._svgEl !== null && this._svgEl.parentNode !== null)\n this._svgEl.parentNode.removeChild(this._svgEl);\n this._svgEl = null;\n }\n}\n\n// Legacy Pistoia/JSDraw2 element order: C, H, then N, O, S, P, then any\n// remaining element alphabetically. This is the order Datagrok's\n// properties-widget golden values are written in (note S precedes P, i.e. it\n// is NOT Hill order), so the adapter reproduces it for drop-in compatibility.\nconst LEGACY_FORMULA_ORDER = ['C', 'H', 'N', 'O', 'S', 'P'];\n\nfunction formulaToString(formula: { elements: ReadonlyMap<string, number>; mw: number }): string {\n const rank = (el: string): number => {\n const i = LEGACY_FORMULA_ORDER.indexOf(el);\n return i === -1 ? LEGACY_FORMULA_ORDER.length : i;\n };\n const els = [...formula.elements.keys()].sort((a, b) => {\n const ra = rank(a);\n const rb = rank(b);\n return ra !== rb ? ra - rb : (a < b ? -1 : a > b ? 1 : 0);\n });\n const parts: string[] = [];\n for (const el of els) {\n const count = formula.elements.get(el)!;\n parts.push(count === 1 ? el : `${el}${count}`);\n }\n return parts.join('');\n}\n\n/**\n * Construct a real SVG element from the serializer's string output. We use\n * `DOMParser` when present (browser, linkedom); otherwise build a minimal\n * placeholder `<svg>` element from the document.\n */\nfunction createSvgFromString(doc: Document, svgText: string, width: number, height: number): SVGSVGElement {\n const parsed = tryParseSvg(doc, svgText);\n if (parsed !== null) return parsed;\n // Fallback when `DOMParser` is unavailable — we still need a real\n // SVGSVGElement so `editor.div.children[0]` returns the right node.\n const svg = doc.createElementNS('http://www.w3.org/2000/svg', 'svg') as unknown as SVGSVGElement;\n svg.setAttribute('width', String(width));\n svg.setAttribute('height', String(height));\n return svg;\n}\n\nfunction tryParseSvg(doc: Document, svgText: string): SVGSVGElement | null {\n const docCtor = (globalThis as { DOMParser?: { new (): { parseFromString(s: string, t: string): Document } } }).DOMParser;\n if (docCtor === undefined) return null;\n try {\n const parser = new docCtor();\n const parsed = parser.parseFromString(svgText, 'image/svg+xml');\n const root = parsed.documentElement;\n if (root === null || root === undefined) return null;\n const imported = doc.importNode(root, true) as unknown as SVGSVGElement;\n return imported;\n } catch {\n return null;\n }\n}\n","// T-0803 / Phase 3 (Datagrok migration) — `AppLike` wrapper returned by\n// `createWebEditorApp`.\n//\n// Embeds a REAL interactive `HelmEditorApp` (palette + toolbar + canvas +\n// Sequence/HELM/Properties/Atomic tabs) inside the caller's host and exposes\n// it through the legacy Pistoia `App` shape that `packages/Helm` reaches into:\n// `canvas` (the JSDraw2 `Editor` look-alike), `sequence` / `notation` /\n// `properties.parent` panes, `structureview`, `mex`, `toolbarheight`,\n// `calculateSizes()`, `destroy()`.\n//\n// The `canvas` is faithful to the legacy `App.canvas` — which *was* the\n// JSDraw2 `Editor` itself — so consumers can read `canvas.getHelm(true)` and\n// the live selection via `canvas.helm.jsd.m.atoms[i].selected`. Selection is\n// overlaid onto the (immutable) mol view on every `m` access.\n//\n// Layering: top of the stack (`datagrok-adapter/`); imports the editor app,\n// the calc modules, and the in-package `helm-mol-view` + `legacy-editor-wrapper`.\n\nimport type { Unsubscribe } from '../util/types';\nimport type { Mol } from '../core/model';\nimport type { HelmService } from '../service/helm-service';\nimport { HelmEditorApp } from '../editor/app/app';\nimport type { HelmEditorAppOptions } from '../editor/app/app';\nimport { molWeight } from '../calc/mol-weight';\nimport { extinctionCoefficient } from '../calc/extinction-coeff';\nimport { computeFormula } from '../calc/formula';\nimport { el, getDocument } from '../editor/view/dom-utils';\nimport { buildHelmMolView } from './helm-mol-view';\nimport { LegacyEditorWrapper } from './legacy-editor-wrapper';\nimport type {\n AppLike,\n DrawOptionsLike,\n HelmMolLike,\n HelmPluginLike,\n IHelmWebEditorLike,\n JSDraw2EditorLike,\n MonomerExplorerLike,\n} from './types';\n\nconst DEFAULT_CANVAS_W = 800;\nconst DEFAULT_CANVAS_H = 400;\nconst DEFAULT_TOOLBAR_H = 32;\nconst DEFAULT_FONT_SIZE = 14;\n\n/** Construction options for {@link LegacyAppWrapper}. */\nexport interface LegacyAppOptions {\n /** Initial HELM string. Default `''`. */\n initialHelm?: string;\n /** Optional `Document` impl (linkedom). */\n documentImpl?: Document;\n /** Canvas width. Default `800`. */\n width?: number;\n /** Canvas height. Default `400`. */\n height?: number;\n}\n\n/**\n * Minimal `MonomerExplorer`-like stub that just records resize/select calls.\n * The Pistoia palette is replaced by the standalone editor's `MonomerPalette`;\n * this stub exists purely for the `packages/Helm` `App.mex` shape (its\n * `createMonomerDiv` is the legacy \"Placeholders\" tab, unused by hwe).\n */\nclass MonomerExplorerStub implements MonomerExplorerLike {\n private readonly _doc: Document;\n private _width: number = 0;\n private _height: number = 0;\n\n constructor(doc: Document) { this._doc = doc; }\n\n resize(width: number, height: number): void {\n this._width = width;\n this._height = height;\n }\n select(): void { /* no-op stub */ }\n dblclick(): void { /* no-op stub */ }\n createMonomerDiv(parent: HTMLElement, symbol: string, biotype: string): HTMLElement {\n const div = el(this._doc, 'div', {\n 'data-monomer': symbol,\n 'data-biotype': biotype,\n 'data-testid': `legacy-mex-monomer-${symbol}`,\n });\n parent.appendChild(div);\n return div;\n }\n\n /** Test introspection. */\n getSize(): { width: number; height: number } { return { width: this._width, height: this._height }; }\n}\n\n/**\n * The `App` returned by `createWebEditorApp`. Wraps a live `HelmEditorApp`\n * and surfaces it through the legacy Pistoia `App` field names.\n */\nexport class LegacyAppWrapper implements AppLike {\n readonly canvas: AppLike['canvas'];\n readonly structureview: IHelmWebEditorLike;\n readonly sequence: HTMLElement;\n readonly notation: HTMLElement;\n readonly properties: { parent: HTMLElement };\n readonly mex: MonomerExplorerLike;\n toolbarheight: number = DEFAULT_TOOLBAR_H;\n\n private readonly _app: HelmEditorApp;\n private readonly _service: HelmService;\n private readonly _doc: Document;\n private readonly _host: HTMLElement;\n private readonly _structureviewHost: HTMLElement;\n private readonly _structureviewWrapper: LegacyEditorWrapper;\n private readonly _editorFacade: JSDraw2EditorLike;\n private readonly _drawOptions: DrawOptionsLike = { fontsize: DEFAULT_FONT_SIZE };\n private readonly _unsubs: Unsubscribe[] = [];\n private _width: number;\n private _height: number;\n private _destroyed: boolean = false;\n\n constructor(host: HTMLElement, service: HelmService, options?: LegacyAppOptions) {\n this._host = host;\n this._service = service;\n this._doc = options?.documentImpl ?? getDocument(host);\n this._width = options?.width ?? DEFAULT_CANVAS_W;\n this._height = options?.height ?? DEFAULT_CANVAS_H;\n\n // ----- the real interactive app (mounts itself into `host`) -----\n const appOpts: HelmEditorAppOptions = { service };\n if (options?.initialHelm !== undefined) appOpts.initialHelm = options.initialHelm;\n if (options?.documentImpl !== undefined) appOpts.documentImpl = options.documentImpl;\n if (options?.width !== undefined) appOpts.width = options.width;\n if (options?.height !== undefined) appOpts.height = options.height;\n this._app = new HelmEditorApp(host, appOpts);\n\n // ----- bottom panes map straight onto the app's pane elements -----\n this.sequence = this._app.sequencePane.element;\n this.notation = this._app.notationPane.element;\n this.properties = { parent: this._app.propertiesPane.element };\n\n // ----- structureview — a view-only wrapper kept in sync with the canvas.\n // The new app shows atomic structure in its own tab; this field exists for\n // the legacy `App.structureview` contract (an `IHelmWebEditorLike`).\n this._structureviewHost = el(this._doc, 'div', {\n class: 'hwe-legacy-app__structureview',\n 'data-testid': 'legacy-app-structureview',\n });\n this._structureviewWrapper = new LegacyEditorWrapper(this._structureviewHost, service, {\n documentImpl: this._doc,\n });\n this.structureview = this._structureviewWrapper;\n\n this.mex = new MonomerExplorerStub(this._doc);\n\n // ----- the JSDraw2 `Editor` look-alike over the live HelmEditor -----\n this._editorFacade = this._buildEditorFacade();\n\n // ----- `canvas` is faithful to the legacy `App.canvas` (the Editor) -----\n const facade = this._editorFacade;\n this.canvas = {\n get host(): HTMLElement { return facade.div; },\n get editor(): JSDraw2EditorLike { return facade; },\n get helm(): HelmPluginLike { return facade.helm; },\n resizeEditor: (width: number, height: number): void => { this._resize(width, height); },\n getHelm: (stripHtml?: boolean): string => facade.getHelm(stripHtml),\n setHelm: (helm: string): void => { facade.setHelm(helm); },\n };\n\n // Keep the structureview in step with the canvas.\n const syncStructure = (): void => { this._structureviewWrapper.editor.setHelm(this._app.getHelm()); };\n this._unsubs.push(this._app.canvas.on('helm:changed', syncStructure));\n if (options?.initialHelm !== undefined && options.initialHelm.length > 0) syncStructure();\n }\n\n /**\n * The embedded interactive app. Beyond the legacy `App` contract, hosts can\n * reach the full hwe surface (panes, events, selection) through this.\n */\n get editorApp(): HelmEditorApp { return this._app; }\n\n // ----- internals ----------------------------------------------------------\n\n /** Build the JSDraw2 `Editor` look-alike that forwards to the live editor. */\n private _buildEditorFacade(): JSDraw2EditorLike {\n const self = this;\n const app = this._app;\n const helmPlugin: HelmPluginLike = {\n noDraw: false,\n get jsd(): JSDraw2EditorLike { return self._editorFacade; },\n };\n\n return {\n get div(): HTMLElement { return app.element; },\n get m(): HelmMolLike { return self._currentMolView(); },\n set m(v: HelmMolLike) {\n // Legacy code occasionally assigns `editor.m = mol`; route it through\n // `setMol` so the live editor stays authoritative. Ignore partials.\n if (v !== null && v !== undefined && v._internalMol !== undefined)\n app.canvas.setMol(v._internalMol);\n },\n get helm(): HelmPluginLike { return helmPlugin; },\n get options(): { width: number; height: number } {\n return { width: self._width, height: self._height };\n },\n\n setData(data: string, format: 'helm'): void {\n if (format !== 'helm')\n throw new Error(`LegacyAppWrapper: only 'helm' format supported (got '${format}').`);\n app.setHelm(data);\n },\n setHelm(helm: string): void { app.setHelm(helm); },\n setMol(mol: HelmMolLike): void { app.canvas.setMol(mol._internalMol); },\n getHelm(_stripHtml?: boolean): string {\n // Our serializer never emits HTML span markers — the `stripHtml` flag\n // is accepted for API parity but is a no-op.\n return app.getHelm();\n },\n getMolfile(): string { return self._service.getMolfile(app.getHelm()); },\n\n resize(width: number, height: number): void { self._resize(width, height); },\n setSize(width: number, height: number): void { self._resize(width, height); },\n redraw(): void { app.canvas.redraw(); },\n reset(): void { app.setHelm(''); },\n\n getFormula(_html?: boolean): string {\n return formulaToString(computeFormula(app.canvas.getMol() as Mol));\n },\n getMolWeight(): number { return molWeight(app.canvas.getMol() as Mol); },\n getExtinctionCoefficient(): number { return extinctionCoefficient(app.canvas.getMol() as Mol); },\n\n getDrawOptions(): DrawOptionsLike { return self._drawOptions; },\n };\n }\n\n /**\n * Build a `HelmMolLike` view over the live mol with the editor's current\n * selection overlaid onto each atom's `selected` flag (the immutable model\n * carries no selection — it lives in the editor's `Selection`).\n */\n private _currentMolView(): HelmMolLike {\n const mol = this._app.canvas.getMol() as Mol;\n const view = buildHelmMolView(mol);\n const sel = this._app.canvas.getSelection();\n if (!sel.isEmpty) {\n for (const a of view.atoms) {\n const id = a.bio.id;\n if (typeof id === 'number') a.selected = sel.atoms.has(id);\n }\n }\n return view;\n }\n\n private _resize(width: number, height: number): void {\n this._width = width;\n this._height = height;\n this._app.canvas.resize(width, height);\n }\n\n // ----- AppLike methods ----------------------------------------------------\n\n calculateSizes(): void {\n // The interactive app self-lays-out via flexbox CSS, so the legacy manual\n // sizing dance is mostly redundant — but we still forward the host's\n // measured size to the canvas so an explicit resize propagates.\n const w = clampSize((this._host as { clientWidth?: number }).clientWidth, this._width);\n const h = clampSize((this._host as { clientHeight?: number }).clientHeight, this._height);\n this._resize(w, Math.max(50, h - this.toolbarheight));\n }\n\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n for (const u of this._unsubs) u();\n this._unsubs.length = 0;\n this._app.destroy();\n }\n}\n\nfunction formulaToString(formula: { elements: ReadonlyMap<string, number>; mw: number }): string {\n const parts: string[] = [];\n for (const [element, count] of formula.elements.entries())\n parts.push(count === 1 ? element : `${element}${count}`);\n return parts.join('');\n}\n\nfunction clampSize(v: number | undefined, fallback: number): number {\n if (typeof v !== 'number' || isNaN(v) || v <= 0) return fallback;\n return v;\n}\n","// T-0803 — `HelmInputBase`-like wrapper returned by `createHelmInput`.\n//\n// Hosts a viewonly `LegacyEditorWrapper` plus a thin tooltip overlay. Matches\n// the `HelmInputBase` surface from `libraries/bio/src/helm/helm-helper.ts`:\n// `value`, `molValue`, `redraw()`, `showTooltip(content, atom)`, `destroy()`.\n\nimport type { HelmService } from '../service/helm-service';\nimport { el } from '../editor/view/dom-utils';\nimport { LegacyEditorWrapper } from './legacy-editor-wrapper';\nimport type {\n HelmAtomLike,\n HelmInputBaseLike,\n HelmInputInitOptionsLike,\n HelmMolLike,\n IHelmWebEditorLike,\n} from './types';\n\nconst DEFAULT_INPUT_W = 240;\nconst DEFAULT_INPUT_H = 80;\n\n/**\n * `HelmInputBase`-like wrapper. The widget hosts a viewonly editor; the\n * outer `packages/Helm` shell mounts a dialog over it when the user clicks\n * \"edit\".\n */\nexport class LegacyInputWrapper implements HelmInputBaseLike {\n readonly name: string;\n readonly viewer: IHelmWebEditorLike;\n\n private readonly _service: HelmService;\n private readonly _doc: Document;\n private readonly _host: HTMLElement;\n private _tooltip: HTMLElement | null = null;\n private _destroyed: boolean = false;\n\n constructor(name: string, service: HelmService, options?: HelmInputInitOptionsLike) {\n this.name = name;\n this._service = service;\n const doc = options?.documentImpl ?? resolveDocument();\n if (doc === null)\n throw new Error('LegacyInputWrapper: no Document available.');\n this._doc = doc;\n this._host = el(this._doc, 'div', {\n class: 'hwe-legacy-input',\n 'data-testid': 'legacy-input-host',\n });\n this.viewer = new LegacyEditorWrapper(this._host, service, {\n width: options?.editorOptions?.width ?? DEFAULT_INPUT_W,\n height: options?.editorOptions?.height ?? DEFAULT_INPUT_H,\n documentImpl: this._doc,\n });\n }\n\n // ----- HelmInputBaseLike --------------------------------------------------\n\n get value(): string {\n return this.viewer.editor.getHelm();\n }\n set value(v: string) {\n this._ensureLive();\n this.viewer.editor.setHelm(v);\n }\n\n get molValue(): HelmMolLike {\n return this.viewer.editor.m;\n }\n set molValue(v: HelmMolLike) {\n this._ensureLive();\n this.viewer.editor.setMol(v);\n }\n\n redraw(): void {\n this._ensureLive();\n this.viewer.editor.redraw();\n }\n\n showTooltip(content: HTMLElement | string, atom: HelmAtomLike): void {\n this._ensureLive();\n if (this._tooltip !== null && this._tooltip.parentNode !== null)\n this._tooltip.parentNode.removeChild(this._tooltip);\n const tip = el(this._doc, 'div', {\n class: 'hwe-legacy-input__tooltip',\n 'data-testid': 'legacy-input-tooltip',\n style: `position: absolute; left: ${atom.p.x}px; top: ${atom.p.y}px;`,\n });\n if (typeof content === 'string') tip.appendChild(this._doc.createTextNode(content));\n else tip.appendChild(content);\n this._host.appendChild(tip);\n this._tooltip = tip;\n }\n\n destroy(): void {\n if (this._destroyed) return;\n this._destroyed = true;\n if (this._tooltip !== null && this._tooltip.parentNode !== null)\n this._tooltip.parentNode.removeChild(this._tooltip);\n if (this._host.parentNode !== null) this._host.parentNode.removeChild(this._host);\n }\n\n /** Test helper — expose host so callers can mount it manually. */\n getHost(): HTMLElement { return this._host; }\n\n /** Test helper — return current tooltip element (or null). */\n getTooltip(): HTMLElement | null { return this._tooltip; }\n\n // ----- internals ----------------------------------------------------------\n\n private _ensureLive(): void {\n if (this._destroyed) throw new Error('LegacyInputWrapper: this instance has been destroyed.');\n void this._service;\n }\n}\n\nfunction resolveDocument(): Document | null {\n const g = globalThis as { document?: Document };\n return g.document ?? null;\n}\n","// T-0802 — `IMonomerLibBase` (Datagrok) → `IMonomerLib` (HWE internal) bridge.\n//\n// The bridge is read-only — we never mutate the Datagrok-owned library; if\n// callers need to add monomers they should `MonomerLib.merge` against an\n// overlay. Translated `Monomer` records are cached by (polymerType, symbol)\n// so a follow-up `getMonomer` call returns the same reference (the\n// in-process `MonomerLib` relies on identity to attach `ResolvedMonomer`).\n//\n// See MONOMER-LIBRARY.md §10 and ARCHITECTURE.md §3.10.\n\nimport { HelmTypes, PolymerTypes } from '../core/constants';\nimport type { HelmType, MonomerType, PolymerType } from '../core/constants';\nimport { Subject } from '../util/observable';\nimport type {\n IMonomerLib,\n Monomer,\n MonomerColors,\n MonomerLibChangeEvent,\n MonomerLibSchema,\n MonomerMeta,\n RGroupSpec,\n} from '../monomer-lib/types';\nimport { resolveMonomerColors, lightPalette, darkPalette } from '../monomer-lib/color-rules';\nimport { readCapGroupSMILES } from '../monomer-lib/rgroup-fields';\nimport type {\n DatagrokMonomerLike,\n IMonomerLibBaseLike,\n ObservableLike,\n} from './types';\n\nconst RLABEL_RE = /^R([1-9][0-9]*)$/;\nconst VALID_POLYMER_TYPES = new Set<string>([\n PolymerTypes.PEPTIDE,\n PolymerTypes.RNA,\n PolymerTypes.CHEM,\n PolymerTypes.BLOB,\n]);\nconst VALID_MONOMER_TYPES = new Set<string>(['Backbone', 'Branch', 'Terminal', 'Undefined']);\n\n/**\n * Translate a single Datagrok `Monomer` into our internal `Monomer`. Returns\n * `null` if the record is missing required fields or carries an unknown\n * polymer/monomer type.\n */\nfunction translateMonomer(src: DatagrokMonomerLike): Monomer | null {\n if (typeof src.symbol !== 'string' || src.symbol.length === 0) return null;\n if (typeof src.molfile !== 'string') return null;\n if (!VALID_POLYMER_TYPES.has(src.polymerType)) return null;\n if (!VALID_MONOMER_TYPES.has(src.monomerType)) return null;\n\n const rgroups: RGroupSpec[] = [];\n for (const rg of src.rgroups ?? []) {\n if (typeof rg.label !== 'string' || !RLABEL_RE.test(rg.label)) continue;\n const spec: RGroupSpec = {\n label: rg.label as `R${number}`,\n capGroupName: typeof rg.capGroupName === 'string' ? rg.capGroupName : '',\n capGroupSMILES: readCapGroupSMILES(rg as unknown as Record<string, unknown>) ?? '',\n };\n if (typeof rg.alternateId === 'string') spec.alternateId = rg.alternateId;\n rgroups.push(spec);\n }\n\n const out: Monomer = {\n symbol: src.symbol,\n molfile: src.molfile,\n polymerType: src.polymerType as PolymerType,\n monomerType: src.monomerType as MonomerType,\n rgroups,\n };\n if (typeof src.name === 'string') out.name = src.name;\n if (typeof src.smiles === 'string') out.smiles = src.smiles;\n if (typeof src.naturalAnalog === 'string') out.naturalAnalog = src.naturalAnalog;\n if (src.meta !== undefined && src.meta !== null) out.meta = { ...src.meta };\n if (typeof src.author === 'string') out.author = src.author;\n if (src.createDate !== undefined) out.createDate = src.createDate;\n if (typeof src.id === 'number') out.id = src.id;\n return out;\n}\n\n/**\n * A representative HELM biotype for a polymer type, used only to drive\n * Datagrok's `getWebEditorMonomer(biotype, smiles)` on-spot registration\n * (it maps the biotype straight back to the polymer type). Peptide → AA,\n * RNA → SUGAR, CHEM/BLOB → themselves.\n */\nfunction representativeBiotype(polymerType: PolymerType): HelmType {\n if (polymerType === PolymerTypes.PEPTIDE) return HelmTypes.AA;\n if (polymerType === PolymerTypes.RNA) return HelmTypes.SUGAR;\n if (polymerType === PolymerTypes.CHEM) return HelmTypes.CHEM;\n if (polymerType === PolymerTypes.BLOB) return HelmTypes.BLOB;\n return HelmTypes.AA;\n}\n\n/** Map a `PolymerType` + `MonomerType` to the HELM biotype. */\nfunction biotypeOf(polymerType: string, monomerType: string, naturalAnalog?: string): HelmType {\n if (polymerType === PolymerTypes.PEPTIDE) return HelmTypes.AA;\n if (polymerType === PolymerTypes.CHEM) return HelmTypes.CHEM;\n if (polymerType === PolymerTypes.BLOB) return HelmTypes.BLOB;\n if (polymerType === PolymerTypes.RNA) {\n if (monomerType === 'Branch') return HelmTypes.BASE;\n if (monomerType === 'Backbone') {\n if (naturalAnalog === 'P' || naturalAnalog === 'p') return HelmTypes.LINKER;\n return HelmTypes.SUGAR;\n }\n }\n return HelmTypes.AA;\n}\n\n/**\n * Subscribe to an Observable-like input. The Datagrok `onChanged` may be a\n * proper rxjs Observable, a Subject, or a hand-rolled subject — they all\n * accept `subscribe(fn)` returning `{ unsubscribe }`.\n */\nfunction subscribeObservable<T>(\n obs: ObservableLike<T>,\n next: (value: T) => void,\n): () => void {\n const subscription = obs.subscribe(next);\n return () => {\n if (subscription !== null && subscription !== undefined && typeof subscription.unsubscribe === 'function')\n subscription.unsubscribe();\n };\n}\n\n/**\n * Read-only `IMonomerLib` view backed by a Datagrok `IMonomerLibBaseLike`.\n * Translation is lazy + cached per (polymerType, symbol).\n */\nexport class BridgedMonomerLib implements IMonomerLib {\n readonly source: string;\n readonly onChanged: Subject<MonomerLibChangeEvent>;\n\n private readonly _base: IMonomerLibBaseLike;\n private readonly _cache: Map<string, Monomer | null> = new Map();\n private readonly _unsub: () => void;\n private _polymerTypesCache: PolymerType[] | null = null;\n private _version: number = 0;\n\n constructor(base: IMonomerLibBaseLike, source?: string) {\n this._base = base;\n this.source = source ?? (typeof base.source === 'string' ? base.source : 'datagrok-bridge');\n this.onChanged = new Subject<MonomerLibChangeEvent>();\n // Bust caches + bump version + re-fire `reload` whenever Datagrok signals a change.\n this._unsub = subscribeObservable(base.onChanged, () => {\n this._cache.clear();\n this._polymerTypesCache = null;\n this._version += 1;\n this.onChanged.next({ type: 'reload' });\n });\n }\n\n /** Bumped on every observed source change; mirrors `MonomerLib.version`. */\n get version(): number {\n return this._version;\n }\n\n get isEmpty(): boolean {\n if (typeof this._base.isEmpty === 'boolean') return this._base.isEmpty;\n return this.getPolymerTypes().length === 0;\n }\n\n // ----- reads --------------------------------------------------------------\n\n getMonomer(polymerType: PolymerType, symbol: string): Monomer | null {\n const key = `${polymerType}|${symbol}`;\n if (this._cache.has(key)) return this._cache.get(key) ?? null;\n const raw = this._base.getMonomer(polymerType, symbol);\n const translated = raw === null || raw === undefined ? null : this._enrichColors(translateMonomer(raw));\n this._cache.set(key, translated);\n return translated;\n }\n\n /**\n * Fold Datagrok's per-monomer colours into the translated record's\n * `meta.colors.default` so hwe's `resolveMonomerColors` prefers them over its\n * built-in palette. Datagrok's colours are theme-agnostic (the `default`\n * schema), so we store them under `default`. No-op when the base library does\n * not expose `getMonomerColors` (keeps the bridge usable with bare libs).\n */\n private _enrichColors(m: Monomer | null): Monomer | null {\n if (m === null) return null;\n const base = this._base;\n if (typeof base.getMonomerColors !== 'function') return m;\n const biotype = biotypeOf(m.polymerType, m.monomerType, m.naturalAnalog);\n let c: { linecolor?: string; backgroundcolor?: string; textcolor?: string } | null = null;\n try { c = base.getMonomerColors(biotype, m.symbol); } catch { c = null; }\n if (c === null || c === undefined) return m;\n const bg = c.backgroundcolor;\n const text = c.textcolor;\n const line = c.linecolor;\n if (typeof bg !== 'string' || typeof text !== 'string' || typeof line !== 'string') return m;\n const meta: MonomerMeta = {\n ...(m.meta ?? {}),\n colors: { ...(m.meta?.colors ?? {}), default: { line, text, background: bg } },\n };\n return { ...m, meta };\n }\n\n /**\n * Register an explicit/inline SMILES monomer through Datagrok's monomer\n * functions. Datagrok's `getWebEditorMonomer` recognises a SMILES \"symbol\",\n * creates an on-spot monomer, and assigns it a short symbol (`#P1`, `#R2`,\n * …); `getMonomer` then returns that registered record (Datagrok caches the\n * SMILES→symbol mapping). We adopt the short symbol so the editor displays it\n * (not the raw SMILES) and the Datagrok molfile converter — which reads the\n * monomer symbol out of the pseudo-molfile and looks it up in this same\n * library — resolves it cleanly. Mirrors the legacy editor's behaviour.\n *\n * The hwe resolver calls this (via `InlineSmilesCapableLib`) when a monomer\n * looks like SMILES and is otherwise unresolved.\n */\n registerInlineSmilesMonomer(polymerType: PolymerType, smiles: string): Monomer {\n const base = this._base;\n if (typeof base.getWebEditorMonomer === 'function')\n base.getWebEditorMonomer(representativeBiotype(polymerType), smiles);\n const raw = base.getMonomer(polymerType, smiles);\n const translated = raw === null || raw === undefined ? null : this._enrichColors(translateMonomer(raw));\n if (translated === null)\n throw new Error(`BridgedMonomerLib: could not register inline SMILES monomer '${smiles}'`);\n // Cache under BOTH the raw SMILES (the resolver's first lookup key, which\n // we previously cached as `null`) and the registered short symbol (the\n // converter's later lookup key) so neither path re-misses.\n this._cache.set(`${polymerType}|${smiles}`, translated);\n this._cache.set(`${polymerType}|${translated.symbol}`, translated);\n return translated;\n }\n\n getMonomerSet(biotype: HelmType): Map<string, Monomer> {\n const out = new Map<string, Monomer>();\n for (const pt of this.getPolymerTypes()) {\n for (const sym of this.getMonomerSymbolsByType(pt)) {\n const m = this.getMonomer(pt, sym);\n if (m === null) continue;\n if (biotypeOf(m.polymerType, m.monomerType, m.naturalAnalog) === biotype)\n out.set(sym, m);\n }\n }\n return out;\n }\n\n getMonomerSymbolsByType(polymerType: PolymerType): string[] {\n return this._base.getMonomerSymbolsByType(polymerType);\n }\n\n getByNaturalAnalog(polymerType: PolymerType, na: string): Monomer[] {\n const out: Monomer[] = [];\n for (const sym of this.getMonomerSymbolsByType(polymerType)) {\n const m = this.getMonomer(polymerType, sym);\n if (m !== null && m.naturalAnalog === na) out.push(m);\n }\n return out;\n }\n\n getPolymerTypes(): PolymerType[] {\n if (this._polymerTypesCache !== null) return this._polymerTypesCache;\n const out: PolymerType[] = [];\n const declared = typeof this._base.getPolymerTypes === 'function'\n ? this._base.getPolymerTypes()\n : Object.values(PolymerTypes);\n for (const pt of declared) {\n if (!VALID_POLYMER_TYPES.has(pt)) continue;\n const symbols = this._base.getMonomerSymbolsByType(pt);\n if (Array.isArray(symbols) && symbols.length > 0) out.push(pt as PolymerType);\n }\n this._polymerTypesCache = out;\n return out;\n }\n\n getColors(monomer: Monomer | null, themeName?: string): MonomerColors {\n const theme = themeName === 'dark' ? darkPalette : lightPalette;\n const biotype = monomer === null\n ? HelmTypes.AA\n : biotypeOf(monomer.polymerType, monomer.monomerType, monomer.naturalAnalog);\n return resolveMonomerColors(monomer, biotype, theme);\n }\n\n // ----- mutators (read-only bridge → throw or no-op) -----------------------\n\n addMonomer(_monomer: Monomer): void {\n throw new Error('BridgedMonomerLib: mutation is not supported on a Datagrok-bridged library.');\n }\n\n removeMonomer(_polymerType: PolymerType, _symbol: string): boolean {\n return false;\n }\n\n merge(_other: IMonomerLib): void {\n throw new Error('BridgedMonomerLib: mutation is not supported on a Datagrok-bridged library.');\n }\n\n toJSON(): MonomerLibSchema {\n const out: MonomerLibSchema = [];\n for (const pt of this.getPolymerTypes()) {\n for (const sym of this.getMonomerSymbolsByType(pt)) {\n const m = this.getMonomer(pt, sym);\n if (m !== null) out.push(m);\n }\n }\n return out;\n }\n\n /** Tear down the upstream subscription. Safe to call more than once. */\n destroy(): void {\n this._unsub();\n this.onChanged.complete();\n this._cache.clear();\n }\n}\n\n/**\n * Wrap a Datagrok `IMonomerLibBaseLike` as an internal `IMonomerLib`. Useful\n * when a host wants to plug a Datagrok-managed monomer source into the\n * standalone HWE service.\n */\nexport function bridgeMonomerLib(\n datagrokLib: IMonomerLibBaseLike,\n source?: string,\n): BridgedMonomerLib {\n return new BridgedMonomerLib(datagrokLib, source);\n}\n","// T-0801 / T-0804 — `HelmHelperAdapter` — the central class that implements\n// the Datagrok `IHelmHelper` interface (`libraries/bio/src/helm/helm-helper.ts`)\n// on top of `HelmService`. This file is read by `packages/Helm`'s shim layer\n// at registration time (see INTEGRATION-HELM-PACKAGE.md §1.9, §5).\n//\n// Layering: `src/datagrok-adapter/` is the top of the stack — it imports\n// freely from `service/`, `core/`, `io/`, `calc/`, `render/`, `editor/view/`,\n// and the in-package legacy wrappers. It must NEVER import from\n// `@datagrok-libraries/bio` or `datagrok-api` at runtime (peer-only).\n\nimport type { Point } from '../util/types';\nimport type { Logger } from '../util/logger';\nimport { SilentLogger } from '../util/logger';\nimport type { HelmType, PolymerType } from '../core/constants';\nimport { HelmTypes, PolymerTypes } from '../core/constants';\nimport type { IMonomerLib, Monomer } from '../monomer-lib/types';\nimport type { HelmService } from '../service/helm-service';\nimport { HitTester } from '../render/hit-test';\nimport { HelmNotSupportedError } from '../core/errors';\nimport { layoutMol } from '../layout/layout-service';\nimport { lightTheme } from '../render/theme';\nimport { LegacyEditorWrapper } from './legacy-editor-wrapper';\nimport { LegacyAppWrapper } from './legacy-app-wrapper';\nimport { LegacyInputWrapper } from './legacy-input-wrapper';\nimport { buildHelmMolView } from './helm-mol-view';\nimport { bridgeMonomerLib } from './monomer-lib-bridge';\nimport type {\n AppLike,\n HelmAtomLike,\n HelmConvertResLike,\n HelmInputBaseLike,\n HelmInputInitOptionsLike,\n HelmMolLike,\n IHelmHelperLike,\n IHelmWebEditorLike,\n IMonomerLibBaseLike,\n IWebEditorMonomerLike,\n MonomersFuncsLike,\n} from './types';\n\n// --------------------------------------------------------------------------\n// Public surface\n// --------------------------------------------------------------------------\n\n/**\n * Construction options for {@link HelmHelperAdapter}.\n *\n * `service` is the only required field. Hosts running outside Datagrok can\n * leave `seqHelper` unset; everything else is optional.\n */\nexport interface HelmHelperAdapterOptions {\n /** Bound `HelmService` instance. */\n service: HelmService;\n /**\n * Optional `ISeqHelper`-like pass-through. We never call into it ourselves\n * — it is stored and returned verbatim by the `seqHelper` getter so the\n * Datagrok shell can satisfy its consumers.\n */\n seqHelper?: unknown;\n /** Optional logger; default `SilentLogger`. */\n logger?: Logger;\n /**\n * Optional bridge that maps a Datagrok `IMonomerLibBaseLike` to our\n * `IMonomerLib`. Defaults to the in-package {@link bridgeMonomerLib}.\n */\n monomerLibBridge?: (lib: IMonomerLibBaseLike) => IMonomerLib;\n /** Default document used for headless wrappers. Optional. */\n documentImpl?: Document;\n}\n\n/**\n * Implementation of Datagrok's `IHelmHelper` on top of `HelmService`.\n *\n * Designed to be instantiated once per package init; the adapter holds a\n * lazy off-screen `LegacyEditorWrapper` used by `getMolfiles()`.\n */\nexport class HelmHelperAdapter implements IHelmHelperLike {\n readonly seqHelper: unknown;\n\n private readonly _service: HelmService;\n private readonly _logger: Logger;\n private readonly _bridge: (lib: IMonomerLibBaseLike) => IMonomerLib;\n private readonly _doc: Document | null;\n private _overriddenFuncs: MonomersFuncsLike | null = null;\n private _originalFuncs: MonomersFuncsLike | null = null;\n private _molfilesEditor: LegacyEditorWrapper | null = null;\n private _molfilesEditorHost: HTMLElement | null = null;\n private _molfilesGcTimer: ReturnType<typeof setTimeout> | null = null;\n private static readonly _MOLFILES_GC_MS = 1000;\n\n constructor(options: HelmHelperAdapterOptions) {\n if (options.service === undefined || options.service === null)\n throw new TypeError('HelmHelperAdapter: options.service is required');\n this._service = options.service;\n this.seqHelper = options.seqHelper ?? null;\n this._logger = options.logger ?? new SilentLogger();\n this._bridge = options.monomerLibBridge ?? ((lib) => bridgeMonomerLib(lib));\n this._doc = options.documentImpl ?? resolveDocument();\n }\n\n /** Underlying service. Exposed for tests + advanced hosts. */\n get service(): HelmService { return this._service; }\n\n // ----- createHelmInput / createHelmWebEditor / createWebEditorApp ---------\n\n createHelmInput(name: string, options?: HelmInputInitOptionsLike): HelmInputBaseLike {\n const opts: HelmInputInitOptionsLike = { ...options };\n if (opts.documentImpl === undefined && this._doc !== null) opts.documentImpl = this._doc;\n return new LegacyInputWrapper(name, this._service, opts);\n }\n\n createHelmWebEditor(host?: HTMLElement, options?: { width?: number; height?: number }): IHelmWebEditorLike {\n const realHost = host ?? this._createDetachedHost();\n return new LegacyEditorWrapper(realHost, this._service, {\n ...(options?.width !== undefined ? { width: options.width } : {}),\n ...(options?.height !== undefined ? { height: options.height } : {}),\n ...(this._doc !== null ? { documentImpl: this._doc } : {}),\n });\n }\n\n createWebEditorApp(host: HTMLElement, helm?: string): AppLike {\n return new LegacyAppWrapper(host, this._service, {\n ...(helm !== undefined ? { initialHelm: helm } : {}),\n ...(this._doc !== null ? { documentImpl: this._doc } : {}),\n });\n }\n\n // ----- monomer-funcs hooks ------------------------------------------------\n\n get originalMonomersFuncs(): MonomersFuncsLike | null {\n return this._originalFuncs;\n }\n\n buildMonomersFuncsFromLib(monomerLib: IMonomerLibBaseLike): MonomersFuncsLike {\n const bridged: IMonomerLib = this._bridge(monomerLib);\n const base = monomerLib;\n\n function getOne(atomOrBiotype: HelmAtomLike | string, name?: string): IWebEditorMonomerLike | null {\n // Datagrok's `getWebEditorMonomer` accepts either an atom or a raw\n // biotype string plus a symbol. If the base exposes that method, prefer\n // it (the editor uses the same path); otherwise translate ourselves.\n if (typeof base.getWebEditorMonomer === 'function') {\n const res = base.getWebEditorMonomer(atomOrBiotype, name);\n if (res !== null && res !== undefined) return res;\n }\n const { biotype, symbol } = resolveBiotypeAndSymbol(atomOrBiotype, name);\n if (symbol === null) return null;\n const cleaned = stripBrackets(symbol);\n const pt = polymerTypeForBiotype(biotype);\n const m = bridged.getMonomer(pt, cleaned);\n if (m === null) return null;\n return monomerToWebEditor(m, cleaned);\n }\n\n function getSet(atomOrBiotype: HelmAtomLike | string): Record<string, IWebEditorMonomerLike> {\n const { biotype } = resolveBiotypeAndSymbol(atomOrBiotype, undefined);\n const pt = polymerTypeForBiotype(biotype);\n const out: Record<string, IWebEditorMonomerLike> = {};\n for (const symbol of bridged.getMonomerSymbolsByType(pt)) {\n const m = bridged.getMonomer(pt, symbol);\n if (m !== null) out[symbol] = monomerToWebEditor(m, symbol);\n }\n return out;\n }\n\n return { getMonomer: getOne, getMonomerSet: getSet };\n }\n\n overrideMonomersFuncs(monomersFuncs: MonomersFuncsLike): MonomersFuncsLike {\n const previous = this._overriddenFuncs;\n if (this._originalFuncs === null) {\n // First override — capture the \"original\" placeholder. Hosts can rely\n // on `revertOriginalMonomersFuncs()` to swap back to this initial value.\n this._originalFuncs = previous ?? this._defaultFuncs();\n }\n this._overriddenFuncs = monomersFuncs;\n return previous ?? this._originalFuncs;\n }\n\n revertOriginalMonomersFuncs(): MonomersFuncsLike {\n const original = this._originalFuncs ?? this._defaultFuncs();\n const previous = this._overriddenFuncs ?? original;\n this._overriddenFuncs = original;\n this._originalFuncs = null;\n return previous;\n }\n\n // ----- hit-testing --------------------------------------------------------\n\n getHoveredAtom(x: number, y: number, mol: HelmMolLike, _height: number): HelmAtomLike | null {\n // Delegate to our internal `HitTester` against the original immutable\n // `Mol` referenced by the view. `_height` is accepted for API parity\n // (legacy used it as a fallback radius — our hit-tester is bbox-based).\n const tester = new HitTester(mol._internalMol, lightTheme);\n const hit = tester.test({ x, y });\n if (hit === null || hit.atom === undefined) return null;\n // Locate the same atom in the supplied view so consumers see the same\n // wrapper that they pass in (preserves selection/highlight state).\n for (const a of mol.atoms) {\n if (a.bio.id === hit.atom.id) return a;\n // Fallback: when bio.id is missing, match by continuousId.\n if (a.bio.id === undefined && a.bio.continuousId === hit.atom.bio.continuousId) return a;\n }\n return null;\n }\n\n // ----- batch molfiles -----------------------------------------------------\n\n getMolfiles(helmStrList: string[]): string[] {\n const editor = this._ensureMolfilesEditor();\n editor.editor.helm.noDraw = true;\n try {\n const out: string[] = [];\n for (const helm of helmStrList) {\n if (typeof helm !== 'string' || helm.length === 0) {\n out.push('');\n continue;\n }\n editor.editor.setHelm(helm);\n out.push(editor.editor.getMolfile());\n }\n return out;\n } finally {\n editor.editor.helm.noDraw = false;\n this._scheduleMolfilesEditorGc();\n }\n }\n\n // ----- parse / removeGaps -------------------------------------------------\n\n parse(helm: string, _origin?: Point): HelmMolLike {\n // `_origin` is accepted for API parity — our parser bakes layout origin\n // at the layout stage; the adapter does not honour explicit overrides.\n const parsed = this._service.parse(helm, { mode: 'lenient', resolveMonomers: false });\n const laid = layoutMol(parsed.mol);\n return buildHelmMolView(laid);\n }\n\n removeGaps(helm: string): HelmConvertResLike {\n let res;\n try {\n res = this._service.removeGaps(helm);\n } catch (err) {\n // Datagrok's `IHelmHelper.removeGaps` contract surfaces an unsupported\n // gap removal as a `HelmNotSupportedError` whose `.type` discriminant is\n // `'HelmNotSupportedError'` (see @datagrok-libraries/bio). hwe's error\n // carries `.name`/`.code` instead, so expose `.type` at this Datagrok\n // boundary without leaking the convention into hwe core.\n if (err instanceof HelmNotSupportedError && (err as { type?: string }).type === undefined)\n (err as { type?: string }).type = 'HelmNotSupportedError';\n throw err;\n }\n // The map is null when no gaps were removed (mirrors the legacy\n // `HelmConvertRes` shape — `map === null` means \"untouched\"). We detect\n // by checking whether the source HELM contained any `*` gap monomer.\n const hadGap = hasGapMonomer(this._service, helm);\n return {\n srcHelm: res.srcHelm,\n resHelm: res.resHelm,\n monomerMap: hadGap ? new Map(res.monomerMap) : null,\n };\n }\n\n // ----- lifecycle ----------------------------------------------------------\n\n destroy(): void {\n if (this._molfilesGcTimer !== null) {\n clearTimeout(this._molfilesGcTimer);\n this._molfilesGcTimer = null;\n }\n this._removeMolfilesEditorNow();\n }\n\n // ----- internals ----------------------------------------------------------\n\n private _defaultFuncs(): MonomersFuncsLike {\n return {\n getMonomer: (_a, _name) => null,\n getMonomerSet: (_a) => ({}),\n };\n }\n\n private _createDetachedHost(): HTMLElement {\n const doc = this._doc ?? resolveDocument();\n if (doc === null) throw new Error('HelmHelperAdapter: no Document available');\n const host = doc.createElement('div');\n (host.style as { width: string; height: string; position: string }).width = '0px';\n (host.style as { width: string; height: string; position: string }).height = '0px';\n (host.style as { width: string; height: string; position: string }).position = 'fixed';\n return host;\n }\n\n private _ensureMolfilesEditor(): LegacyEditorWrapper {\n if (this._molfilesEditor !== null) {\n if (this._molfilesGcTimer !== null) {\n clearTimeout(this._molfilesGcTimer);\n this._molfilesGcTimer = null;\n }\n return this._molfilesEditor;\n }\n const host = this._createDetachedHost();\n this._molfilesEditorHost = host;\n this._molfilesEditor = new LegacyEditorWrapper(host, this._service, {\n width: 100,\n height: 100,\n ...(this._doc !== null ? { documentImpl: this._doc } : {}),\n });\n void this._logger;\n return this._molfilesEditor;\n }\n\n private _scheduleMolfilesEditorGc(): void {\n if (this._molfilesGcTimer !== null) clearTimeout(this._molfilesGcTimer);\n if (typeof setTimeout !== 'function') return;\n this._molfilesGcTimer = setTimeout(() => {\n this._molfilesGcTimer = null;\n this._removeMolfilesEditorNow();\n }, HelmHelperAdapter._MOLFILES_GC_MS);\n }\n\n private _removeMolfilesEditorNow(): void {\n this._molfilesEditor = null;\n if (this._molfilesEditorHost !== null && this._molfilesEditorHost.parentNode !== null)\n this._molfilesEditorHost.parentNode.removeChild(this._molfilesEditorHost);\n this._molfilesEditorHost = null;\n }\n}\n\n// --------------------------------------------------------------------------\n// Helpers (module-local)\n// --------------------------------------------------------------------------\n\nfunction resolveDocument(): Document | null {\n const g = globalThis as { document?: Document };\n return g.document ?? null;\n}\n\nfunction hasGapMonomer(service: HelmService, helm: string): boolean {\n try {\n const parsed = service.parse(helm, { mode: 'lenient', resolveMonomers: false });\n for (const a of parsed.mol.atoms) if (a.symbol === '*') return true;\n return false;\n } catch {\n return false;\n }\n}\n\nfunction stripBrackets(symbol: string): string {\n if (symbol.length >= 2 && symbol.charAt(0) === '[' && symbol.charAt(symbol.length - 1) === ']')\n return symbol.slice(1, symbol.length - 1);\n return symbol;\n}\n\nfunction resolveBiotypeAndSymbol(\n a: HelmAtomLike | string,\n name?: string,\n): { biotype: string; symbol: string | null } {\n if (typeof a === 'string') return { biotype: a, symbol: name ?? null };\n if (a !== null && typeof a === 'object' && (a as HelmAtomLike).T === 'ATOM') {\n const atom = a as HelmAtomLike;\n return { biotype: atom.bio.type, symbol: name ?? atom.elem };\n }\n return { biotype: HelmTypes.AA, symbol: name ?? null };\n}\n\nfunction polymerTypeForBiotype(biotype: string): PolymerType {\n switch (biotype) {\n case HelmTypes.AA: return PolymerTypes.PEPTIDE;\n case HelmTypes.SUGAR:\n case HelmTypes.BASE:\n case HelmTypes.LINKER:\n case HelmTypes.NUCLEOTIDE: return PolymerTypes.RNA;\n case HelmTypes.CHEM: return PolymerTypes.CHEM;\n case HelmTypes.BLOB: return PolymerTypes.BLOB;\n default: return PolymerTypes.PEPTIDE;\n }\n}\n\nfunction monomerToWebEditor(m: Monomer, symbolOverride?: string): IWebEditorMonomerLike {\n const at: Record<string, string> = {};\n for (const rg of m.rgroups) at[rg.label] = rg.capGroupName;\n const wem: IWebEditorMonomerLike = {\n id: symbolOverride ?? m.symbol,\n m: m.molfile,\n rs: m.rgroups.length,\n type: m.polymerType,\n mt: m.monomerType,\n at,\n };\n if (m.name !== undefined) wem.n = m.name;\n if (m.naturalAnalog !== undefined) wem.na = m.naturalAnalog;\n if (m.smiles !== undefined) wem.smiles = m.smiles;\n return wem;\n}\n\n// Helper exported for unit tests; never re-exported from the barrel.\nexport const __test__ = {\n stripBrackets,\n resolveBiotypeAndSymbol,\n polymerTypeForBiotype,\n monomerToWebEditor,\n};\n\n// Re-export for type users.\nexport type { HelmType };\n","// T-0804 — `registerWithDatagrok` convenience factory.\n//\n// Called by `packages/Helm` (or any host package) at package init time. It\n// constructs a fresh `HelmHelperAdapter` and registers a `getHelmHelper`\n// function with the supplied `grok` namespace. The shape of the registered\n// function matches the legacy `DG.Func` discovery contract:\n//\n// const funcList = DG.Func.find({ package: 'Helm', name: 'getHelmHelper' });\n// const helmHelper = (await funcList[0].prepare().call()).getOutputParamValue();\n//\n// We don't depend on `datagrok-api` directly — the caller passes whatever\n// `grok` namespace they have and we only call into its registered surface\n// via duck-typing.\n\nimport type { HelmService } from '../service/helm-service';\nimport type { Logger } from '../util/logger';\nimport { HelmHelperAdapter } from './helm-helper-adapter';\nimport type { DatagrokGrokLike, IMonomerLibBaseLike } from './types';\n\n/** Options for {@link registerWithDatagrok}. */\nexport interface RegisterWithDatagrokOptions {\n /** Bound `HelmService` instance. */\n service: HelmService;\n /** Optional `ISeqHelper`-like pass-through. */\n seqHelper?: unknown;\n /** Optional logger. */\n logger?: Logger;\n /**\n * Optional library provider. When supplied, the adapter subscribes to its\n * library's `onChanged` and forwards an event so the host can rebuild\n * downstream consumers (e.g. the Pistoia monomer dictionary).\n */\n libProvider?: () => Promise<IMonomerLibBaseLike>;\n /** Optional document. */\n documentImpl?: Document;\n}\n\n/** Result of {@link registerWithDatagrok}. */\nexport interface RegisterWithDatagrokResult {\n /** The constructed adapter. */\n adapter: HelmHelperAdapter;\n /** Unsubscribe the library-change listener (if any). */\n unsubscribe(): void;\n}\n\n/**\n * Register the HWE helper with a Datagrok-like `grok` namespace. The\n * caller is responsible for actually exposing `getHelmHelper` as a\n * `DG.Func` in their `package.ts`; this helper handles the optional\n * `libProvider.onChanged` plumbing and returns the adapter for\n * downstream consumers.\n */\nexport function registerWithDatagrok(\n _grok: DatagrokGrokLike | unknown,\n options: RegisterWithDatagrokOptions,\n): RegisterWithDatagrokResult {\n if (options === undefined || options === null)\n throw new TypeError('registerWithDatagrok: options is required');\n const adapter = new HelmHelperAdapter({\n service: options.service,\n ...(options.seqHelper !== undefined ? { seqHelper: options.seqHelper } : {}),\n ...(options.logger !== undefined ? { logger: options.logger } : {}),\n ...(options.documentImpl !== undefined ? { documentImpl: options.documentImpl } : {}),\n });\n\n let cleanup: () => void = () => { /* no subscription */ };\n\n if (typeof options.libProvider === 'function') {\n // Best-effort subscription. We never throw — failures here would crash\n // package init, which is much worse than the missed subscription.\n const provider = options.libProvider;\n Promise.resolve()\n .then(() => provider())\n .then((lib) => {\n if (lib === null || lib === undefined) return;\n const sub = lib.onChanged.subscribe(() => {\n // Re-build the adapter's monomer funcs from the current lib.\n adapter.buildMonomersFuncsFromLib(lib);\n });\n cleanup = () => {\n if (sub !== null && sub !== undefined && typeof sub.unsubscribe === 'function')\n sub.unsubscribe();\n };\n })\n .catch(() => { /* swallow — host already logged. */ });\n }\n\n return {\n adapter,\n unsubscribe(): void { cleanup(); },\n };\n}\n","// HELM type vocabulary is owned by `@datagrok-libraries/hwe` (the standalone\n// HELM editor) and re-exported here as the single source of truth. The string\n// values match the canonical Pistoia HELM Web Editor, except `NUCLEOTIDE` which\n// uses the corrected spelling `HELM_NUCLEOTIDE` (was `HELM_NUCLETIDE`).\nimport {HelmTypes, MonomerTypes, PolymerTypes} from '@datagrok-libraries/hwe';\n\nexport {HelmTypes, MonomerTypes, PolymerTypes};\n\n// hwe migration: these two small enums are not part of the hwe value vocabulary.\n// They are defined here locally (replicating the legacy HELM Web Editor values)\n// so `@datagrok-libraries/bio` no longer depends on\n// `@datagrok-libraries/helm-web-editor`.\nexport enum MonomerNumberingTypes {\n default = 0,\n continuous = 1,\n}\n\nexport enum HelmTabKeys {\n Sequence = 'sequence',\n Helm = 'notation',\n Properties = 'properties',\n StructureView = 'structureview',\n}\n","import {PolymerTypes} from '../helm/consts';\n\nexport const monomerWorksConsts = {\n// constants for parsing molfile V2000\n V2K_RGP_SHIFT: 8,\n V2K_RGP_LINE: 'M RGP',\n V2K_A_LINE: 'A ',\n // constants for parsing/reconstruction of molfile V3000\n V3K_COUNTS_SHIFT: 14,\n V3K_IDX_SHIFT: 7,\n V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n V3K_HEADER_SECOND_LINE: ' 0 0 0 0 0 0 999 V3000\\n',\n V3K_BEGIN_CTAB_BLOCK: 'M V30 BEGIN CTAB\\n',\n V3K_END_CTAB_BLOCK: 'M V30 END CTAB\\n',\n V3K_BEGIN_COUNTS_LINE: 'M V30 COUNTS ',\n V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n V3K_BEGIN_ATOM_BLOCK: 'M V30 BEGIN ATOM\\n',\n V3K_END_ATOM_BLOCK: 'M V30 END ATOM\\n',\n V3K_BEGIN_BOND_BLOCK: 'M V30 BEGIN BOND\\n',\n V3K_END_BOND_BLOCK: 'M V30 END BOND\\n',\n V3K_BOND_CONFIG: ' CFG=',\n V3K_BEGIN_DATA_LINE: 'M V30 ',\n V3K_END: 'M END',\n PRECISION_FACTOR: 10_000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n // symbols for the corresponding monomers in HELM library\n\n DEOXYRIBOSE: {polymerType: PolymerTypes.RNA, symbol: 'd'},\n RIBOSE: {polymerType: PolymerTypes.RNA, symbol: 'r'},\n PHOSPHATE: {polymerType: PolymerTypes.RNA, symbol: 'p'},\n\n OXYGEN: 'O',\n HYDROGEN: 'H',\n} as const;\n\n","import * as grok from 'datagrok-api/grok';\nimport * as ui from 'datagrok-api/ui';\nimport * as DG from 'datagrok-api/dg';\n\nimport {IMonomerLibBase} from '../types/monomer-library';\nimport {HelmType, PolymerType} from '../helm/types';\nimport {HelmTypes, PolymerTypes} from '../helm/consts';\n\n/** Hypothetical interface to convert mol block notation.\n * It should be placed in the chem-meta package, and have an implementation in the Chem package.\n * So dependency of MonomerWorks on molfile conversion operation becomes explicit.\n */\nexport interface IMolfileConverter {\n convertV2000toV3000(src: string): string;\n\n convertV3000toV2000(src: string): string;\n}\n\nexport class MonomerWorks {\n private monomerLib: IMonomerLibBase;\n\n //private molfileConverter: IMolfileConverter;\n\n constructor(monomerLib: IMonomerLibBase/*, molfileConverter: IMolfileConverter*/) {\n this.monomerLib = monomerLib;\n //this.molfileConverter = molfileConverter;\n }\n\n //types according to Monomer possible\n public getCappedRotatedMonomer(monomerType: PolymerType, monomerName: string): string | null {\n // TODO: Check type of monomerType arg\n const monomer = this.monomerLib.getMonomer(monomerType, monomerName);\n if (monomer)\n return monomer.molfile; //TODO cap\n\n return null;\n }\n}\n\nexport function helmTypeToPolymerType(helmType: HelmType): PolymerType {\n let polymerType: PolymerType | undefined = undefined;\n switch (helmType) {\n case HelmTypes.BASE:\n case HelmTypes.SUGAR: // r - ribose, d - deoxyribose\n case HelmTypes.LINKER: // p - phosphate\n case HelmTypes.NUCLEOTIDE:\n // @ts-ignore\n case 'nucleotide':\n polymerType = PolymerTypes.RNA;\n break;\n case HelmTypes.AA:\n polymerType = PolymerTypes.PEPTIDE;\n break;\n case HelmTypes.CHEM:\n polymerType = PolymerTypes.CHEM;\n break;\n case HelmTypes.BLOB:\n polymerType = PolymerTypes.BLOB;\n break;\n default:\n polymerType = PolymerTypes.PEPTIDE;\n console.warn(`Unexpected HelmType '${helmType}'`);\n }\n return polymerType;\n}\n","import {monomerSeqToMolfile} from './to-atomic-level-utils';\nimport {MolfileWithMap, SeqToMolfileWorkerData, SeqToMolfileWorkerRes} from './types';\n\nonmessage = (event) => {\n const {seqList, rolesList, monomersDict, alphabet, polymerType, start, end}: SeqToMolfileWorkerData = event.data;\n const resMolList: MolfileWithMap[] = new Array<MolfileWithMap>(end - start);\n const molfileWarningList = new Array<string>(0);\n for (let rowI = start; rowI < end; ++rowI) {\n try {\n const seq = seqList[rowI];\n const roles = rolesList ? rolesList[rowI] : undefined;\n resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType, roles);\n } catch (err: any) {\n const errMsg: string = err instanceof Error ? err.message : err.toString();\n const msg: string = `Cannot get molfile of row #${rowI}: ${errMsg}.`;\n molfileWarningList.push(msg);\n }\n }\n postMessage({molfiles: resMolList, warnings: molfileWarningList} as SeqToMolfileWorkerRes);\n};\n","/* eslint-disable max-len */\nimport {monomerWorksConsts as C} from './consts';\nimport {getMolGraph, LoopConstants, LoopVariables, MolfileWithMap, MolGraph, MonomerMap, MonomerMolGraphMap,\n NucleotideRole} from './types';\nimport {HELM_FIELDS, HELM_CORE_FIELDS, HELM_POLYMER_TYPE, HELM_MONOMER_TYPE,} from '../utils/const';\nimport {ALPHABET, GAP_SYMBOL} from '../utils/macromolecule/consts';\nimport {IMonomerLibBase, Monomer} from '../types/monomer-library';\nimport {ISeqMonomer, PolymerType} from '../helm/types';\nimport {helmTypeToPolymerType} from './monomer-works';\n\n\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(\n monomerLib: IMonomerLibBase, polymerType: PolymerType, alphabet: ALPHABET\n): Map<string, any> {\n const map = new Map<string, any>();\n for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n const it: Monomer = monomerLib.getMonomer(polymerType, monomerSymbol)!;\n if (\n // RNA: all branch monomers (bases) and all backbone monomers (sugars +\n // phosphates, including modified ones). Modifications are looked up by\n // symbol at assembly time, so they MUST be present in the formatted lib.\n polymerType === HELM_POLYMER_TYPE.RNA || (\n polymerType === HELM_POLYMER_TYPE.PEPTIDE &&\n it[HELM_FIELDS.MONOMER_TYPE] !== HELM_MONOMER_TYPE.BRANCH\n )) {\n const monomerObject: { [key: string]: any } = {};\n HELM_CORE_FIELDS.forEach((field) => {\n //@ts-ignore\n monomerObject[field] = it[field];\n });\n map.set(monomerSymbol, monomerObject);\n }\n }\n return map;\n}\n\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly\n * uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).\n * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */\nexport function monomerSeqToMolfile(\n monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap,\n alphabet: ALPHABET, polymerType: PolymerType,\n roles?: NucleotideRole[]\n): MolfileWithMap {\n if (monomerSeq.length === 0) {\n // throw new Error('monomerSeq is empty');\n return MolfileWithMap.createEmpty();\n }\n\n // Triples mode is on only when the caller flagged the row with roles\n // (built and validated by `buildRolesForHelmRna` in to-atomic-level.ts).\n // The roles array carries the per-position semantics — including\n // TERMINAL_5P / TERMINAL_3P for non-canonical chain ends — so we don't\n // re-validate the length here.\n const triplesMode = polymerType === HELM_POLYMER_TYPE.RNA && !!roles &&\n roles.length === monomerSeq.length;\n\n // define atom and bond counts, taking into account the bond type\n const {atomCount, bondCount, needsCapping} =\n getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode, roles);\n\n // create arrays to store lines of the resulting molfile\n const molfileAtomBlock = new Array<string>(atomCount);\n const molfileBondBlock = new Array<string>(bondCount);\n\n let addMonomerToMolblock: (monomer: MolGraph, molfileAtomBlock: string[], molfileBondBlock: string[], v: LoopVariables, LC: LoopConstants) => void;\n\n let sugar = null;\n let phosphate = null;\n\n if (polymerType === HELM_POLYMER_TYPE.PEPTIDE)\n addMonomerToMolblock = addAminoAcidToMolblock;\n else { // nucleotides\n addMonomerToMolblock = addNucleotideToMolblock;\n // Default sugar/phosphate are only consulted in bases-only mode. In\n // triples mode, every nucleotide carries its own.\n if (!triplesMode) {\n sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n }\n }\n const v: LoopVariables = {\n i: 0,\n nodeShift: 0,\n bondShift: 0,\n backbonePositionShift: new Array<number>(2).fill(0),\n branchPositionShift: new Array<number>(2).fill(0),\n backboneAttachNode: 0,\n branchAttachNode: 0,\n flipFactor: 1,\n };\n\n const LC: LoopConstants = {\n sugar: sugar!,\n phosphate: phosphate!,\n // In triples mode, the \"logical\" sequence length is the nucleotide count.\n seqLength: triplesMode ? Math.ceil(monomerSeq.length / 3) : monomerSeq.length,\n atomCount: atomCount,\n bondCount: bondCount,\n };\n\n const monomers: MonomerMap = new MonomerMap();\n const steabsCollection: number [] = [];\n let nAtoms = 0;\n let lastMonomerCappingAtom: string | undefined = undefined;\n\n if (triplesMode) {\n runTriplesAssembly(\n monomerSeq, roles!, monomersDict, molfileAtomBlock, molfileBondBlock,\n v, LC, monomers, steabsCollection,\n (a) => { nAtoms += a; }, () => nAtoms);\n } else {\n for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n const seqMonomer = monomerSeq[v.i];\n if (seqMonomer.symbol === GAP_SYMBOL) continue;\n const monomer = getMolGraph(monomersDict, {symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype)})!;\n lastMonomerCappingAtom = monomer.terminalR2Atom;\n const mAtomFirst = v.nodeShift;\n const mBondFirst = v.bondShift;\n addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n //adding stereo atoms to array for further STEABS block generation\n monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n nAtoms += monomer.atoms.x.length;\n\n const mAtomCount = v.nodeShift - mAtomFirst;\n const mAtomList: number[] = new Array<number>(mAtomCount);\n for (let maI = 0; maI < mAtomCount; ++maI) mAtomList[maI] = mAtomFirst + maI;\n\n const mBondCount = v.bondShift - mBondFirst;\n const mBondList: number[] = new Array<number>(mBondCount);\n for (let mbI = 0; mbI < mBondCount; ++mbI) mBondList[mbI] = mBondFirst + mbI;\n\n monomers.set(v.i, {\n biotype: seqMonomer.biotype,\n symbol: seqMonomer.symbol,\n atoms: mAtomList, bonds: mBondList\n });\n }\n }\n\n // if the last monomer needs to be capped, add the terminal OH to the resulting molfile\n if (needsCapping)\n capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? C.OXYGEN);\n\n const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n\n // todo: possible optimization may be achieved by replacing .join('') with +=\n // since counterintuitively joining an array into a new string is reportedly\n // slower than using += as below\n\n let result = '';\n result += C.V3K_HEADER_FIRST_LINE;\n result += C.V3K_HEADER_SECOND_LINE;\n result += C.V3K_BEGIN_CTAB_BLOCK;\n result += molfileCountsLine;\n result += C.V3K_BEGIN_ATOM_BLOCK;\n result += molfileAtomBlock.join('');\n result += C.V3K_END_ATOM_BLOCK;\n result += C.V3K_BEGIN_BOND_BLOCK;\n result += molfileBondBlock.join('');\n result += C.V3K_END_BOND_BLOCK;\n if (steabsCollection.length > 0)\n result += getCollectionBlock(steabsCollection);\n result += C.V3K_END_CTAB_BLOCK;\n result += C.V3K_END;\n\n // return molfileParts.join('');\n return {molfile: result, monomers: monomers};\n}\n\n\nfunction getCollectionBlock(collection: number[]): string {\n //one row in STEABS block can be no longer than 80 symbols\n //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n const maxSymbols = 76;\n const rowsArray = [];\n\n let newCollectionRow = `M V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n for (let i = 0; i < collection.length; i++) {\n const updatedRow = `${newCollectionRow} ${collection[i]}`;\n if (updatedRow.length > maxSymbols) {\n rowsArray.push(`${newCollectionRow} -\\n`);\n newCollectionRow = `M V30 ${collection[i]}`;\n } else\n newCollectionRow = updatedRow;\n //in case last atom was added - close the block\n if (i === collection.length - 1)\n rowsArray.push(`${newCollectionRow})\\n`);\n }\n return `M V30 BEGIN COLLECTION\\n${rowsArray.join('')}M V30 END COLLECTION\\n`;\n}\n\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(\n molfileAtomBlock: string[], molfileBondBlock: string[],\n v: LoopVariables, LC: LoopConstants, cappingAtomType: string = C.OXYGEN\n): void {\n // add terminal oxygen\n const atomIdx = v.nodeShift + 1;\n molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n (cappingAtomType ?? C.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n\n // add terminal bond\n const firstAtom = v.backboneAttachNode;\n const secondAtom = atomIdx;\n molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n 1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n\nfunction addAminoAcidToMolblock(monomer: MolGraph, molfileAtomBlock: string[],\n molfileBondBlock: string[], v: LoopVariables\n): void {\n v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\n\nfunction addBackboneMonomerToMolblock(\n monomer: MolGraph, molfileAtomBlock: string[], molfileBondBlock: string[], v: LoopVariables\n): void {\n // todo: remove these comments to the docstrings of the corr. functions\n // construnct the lines of V3K molfile atom block\n fillAtomLines(monomer, molfileAtomBlock, v);\n\n // construct the lines of V3K molfile bond block\n fillBondLines(monomer, molfileBondBlock, v);\n\n // peptide bond\n fillChainExtendingBond(monomer, molfileBondBlock, v);\n\n // update branch variables if necessary\n if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n updateBranchVariables(monomer, v);\n\n // update loop variables\n updateChainExtendingVariables(monomer, v);\n}\n\nfunction addNucleotideToMolblock(\n nucleobase: MolGraph, molfileAtomBlock: string[], molfileBondBlock: string[], v: LoopVariables, LC: LoopConstants\n): void {\n // construnct the lines of V3K molfile atom block corresponding to phosphate\n // and sugar\n if (v.i === 0)\n addBackboneMonomerToMolblock(LC.sugar!, molfileAtomBlock, molfileBondBlock, v);\n else {\n for (const monomer of [LC.phosphate, LC.sugar])\n addBackboneMonomerToMolblock(monomer!, molfileAtomBlock, molfileBondBlock, v);\n }\n\n addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\n\nfunction addBranchMonomerToMolblock(\n monomer: MolGraph, molfileAtomBlock: string[], molfileBondBlock: string[], v: LoopVariables\n): void {\n fillBranchAtomLines(monomer, molfileAtomBlock, v);\n fillBondLines(monomer, molfileBondBlock, v);\n fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n\n // C-N bond\n const bondIdx = v.bondShift;\n const firstAtom = v.branchAttachNode;\n const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n 1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n\n // update loop variables\n v.bondShift += monomer.bonds.atomPairs.length + 1;\n v.nodeShift += monomer.atoms.atomTypes.length;\n}\n\nfunction updateChainExtendingVariables(monomer: MolGraph, v: LoopVariables): void {\n v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n v.bondShift += monomer.bonds.atomPairs.length + 1;\n\n v.nodeShift += monomer.atoms.atomTypes.length;\n v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check\n v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);\n}\n\nfunction updateBranchVariables(monomer: MolGraph, v: LoopVariables): void {\n v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n for (let i = 0; i < 2; ++i)\n v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift![i];\n}\n\nfunction fillAtomLines(monomer: MolGraph, molfileAtomBlock: string[], v: LoopVariables): void {\n for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n const atomIdx = v.nodeShift + j + 1;\n molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n monomer.atoms.atomTypes[j] + ' ' +\n keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n ' ' + monomer.atoms.kwargs[j];\n }\n}\n\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer: MolGraph, molfileAtomBlock: string[], v: LoopVariables): void {\n for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n const atomIdx = v.nodeShift + j + 1;\n molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n monomer.atoms.atomTypes[j] + ' ' +\n keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n ' ' + monomer.atoms.kwargs[j];\n }\n}\n\nfunction fillBondLines(monomer: MolGraph, molfileBondBlock: string[], v: LoopVariables): void {\n // construct the lines of V3K molfile bond block\n for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n const bondIdx = v.bondShift + j + 1;\n const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n let bondCfg = '';\n if (monomer.bonds.bondConfiguration.has(j)) {\n // flip orientation when necessary\n let orientation = monomer.bonds.bondConfiguration.get(j);\n if (v.flipFactor < 0)\n orientation = (orientation === 1) ? 3 : 1;\n bondCfg = ' CFG=' + orientation;\n }\n const kwargs = monomer.bonds.kwargs.has(j) ?\n ' ' + monomer.bonds.kwargs.get(j) : '';\n molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n monomer.bonds.bondTypes[j] + ' ' +\n firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n }\n}\n\nfunction fillChainExtendingBond(monomer: MolGraph, molfileBondBlock: string[], v: LoopVariables): void {\n if (v.backboneAttachNode !== 0) {\n const bondIdx = v.bondShift;\n const firstAtom = v.backboneAttachNode;\n const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n 1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n }\n}\n\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer: MolGraph, molfileBondBlock: string[], v: LoopVariables): void {\n const bondIdx = v.bondShift;\n const firstAtom = v.branchAttachNode;\n const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n 1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {ISeqMonomer[]} monomerSeq - the sequence of monomers\n * @param {MonomerMolGraphMap} monomersDict - the dictionary of monomers\n * @param {ALPHABET} alphabet - the alphabet of the monomers\n * @param {PolymerType} polymerType - the type of polymer\n * @param {boolean} triplesMode - true when monomerSeq is a flat list of HELM RNA triples\n * @param {Array} roles - per-position role tags (only meaningful when triplesMode is true)\n * @return {Object} the atom/bond counts plus needsCapping flag */\nfunction getResultingAtomBondCounts(\n monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap,\n alphabet: ALPHABET, polymerType: PolymerType,\n triplesMode: boolean, roles?: NucleotideRole[]\n): { atomCount: number, bondCount: number, needsCapping: boolean } {\n let atomCount = 0;\n let bondCount = 0;\n\n let monomerCount: number = 0;\n let needsCapping = true;\n let lastMonomerGraph: MolGraph | null = null;\n let lastPhosphateGraph: MolGraph | null = null;\n // sum up all the atoms/nodes provided by the sequence\n for (let i = 0; i < monomerSeq.length; ++i) {\n const seqMonomer = monomerSeq[i];\n if (seqMonomer.symbol === GAP_SYMBOL) continue; // Skip for gap/empty monomer in MSA\n if (seqMonomer.symbol == '*')\n throw new Error(`Gap canonical symbol is '', not '*`);\n lastMonomerGraph = getMolGraph(monomersDict, {symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype)})!;\n atomCount += lastMonomerGraph.atoms.x.length;\n bondCount += lastMonomerGraph.bonds.bondTypes.length;\n monomerCount++;\n // In triples mode, every 3rd entry (index 2 mod 3) is a phosphate. Track\n // the LAST one — its atoms/bonds are dropped at the 3'-terminus.\n if (triplesMode && i % 3 === 2) lastPhosphateGraph = lastMonomerGraph;\n }\n\n // add extra values depending on the polymer type\n if (polymerType === HELM_POLYMER_TYPE.PEPTIDE) {\n // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n atomCount += 1;\n // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n bondCount += monomerCount;\n // if the last monomer is something like NH2, which only has R1, there is no need to cap it\n // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen\n // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted\n if (monomerCount > 0) {\n if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === C.HYDROGEN.toLowerCase()) {\n needsCapping = false;\n atomCount -= 1; // remove the last atom (the terminal 'O')\n bondCount -= 1; // remove the last bond (the terminal C-OH)\n }\n }\n } else if (triplesMode) { // nucleotides — HELM triples (per-position sugar/base/phosphate)\n void lastPhosphateGraph; // kept for symmetry; trailing P is now retained when HELM wrote it\n\n // Per-monomer-loop already summed sugars + bases + phosphates for every\n // entry in monomerSeq (terminals included). Reservation: each backbone\n // emit (sugar / phosphate / terminal) reserves +1 bond slot for the\n // chain-extending bond, each branch (base) reserves +1 for its branch\n // bond. Total reservations = monomerCount.\n bondCount += monomerCount;\n\n // OH cap atom rides on the 3'-end. Skip it when HELM specified a\n // 3'-terminal modifier (e.g. GalNAc) that IS the chain end.\n const has3pTerm = !!roles && roles.length > 0 &&\n roles[roles.length - 1] === NucleotideRole.TERMINAL_3P;\n if (has3pTerm) {\n needsCapping = false;\n // Mirror the peptide branch (which does both atomCount-- and bondCount--\n // when it skips the terminal cap). `bondCount += monomerCount` above\n // reserves one chain-extending slot per monomer; the LAST monomer's slot\n // is normally filled by the terminal OH cap bond. With a 3'-terminal\n // modifier there is no cap, so that last reserved slot stays empty —\n // leaving the declared bond count one higher than the emitted bond\n // lines. Drop it so the V3000 COUNTS line matches the bond block exactly\n // (otherwise the pre-OCL molfile is malformed and only survives because\n // the OCL chirality pass re-derives the counts).\n bondCount -= 1;\n } else\n atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)\n } else { // nucleotides — bases-only legacy path with default sugar/phosphate\n const sugar = (alphabet === ALPHABET.DNA) ?\n getMolGraph(monomersDict, C.DEOXYRIBOSE)! : getMolGraph(monomersDict, C.RIBOSE)!;\n const phosphate = getMolGraph(monomersDict, C.PHOSPHATE)!;\n\n // add phosphate per each pair of nucleobase symbols\n atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n\n // add sugar per each nucleobase symbol\n atomCount += monomerSeq.length * sugar.atoms.x.length;\n\n // add the leftmost cap group 'OH' (i.e. 'O')\n atomCount += 1;\n\n // add bonds from phosphate monomers\n bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n\n // add bonds from sugar monomers\n bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n\n // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n bondCount -= 1;\n\n // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n bondCount += monomerSeq.length * 3;\n }\n\n return {atomCount, bondCount, needsCapping};\n}\n\n// Role-driven RNA assembly. Walks the monomers in chain order and emits\n// each one according to its NucleotideRole (assigned by `buildRolesForHelmRna`\n// from the library, not from a fixed triple index):\n// - BASE → branch monomer, attached to the\n// branch point of the sugar most\n// recently emitted.\n// - SUGAR / PHOSPHATE / TERMINAL_5P / 3P → backbone monomer, chained to the\n// previous backbone unit.\n//\n// Because the role comes from chemistry, this transparently handles every\n// backbone layout — standard [sugar, base, phosphate] triples, a 5'-leading\n// phosphate, several phosphates / linkers in a row, a linker dropped in the\n// middle of the chain, missing trailing phosphate, and 5'/3' terminal\n// modifiers — without any index arithmetic. The first backbone monomer\n// naturally has no incoming chain bond (v.backboneAttachNode starts at 0),\n// and the trailing OH cap is added by the caller via needsCapping (skipped\n// when a TERMINAL_3P ends the chain).\nfunction runTriplesAssembly(\n monomerSeq: ISeqMonomer[], roles: NucleotideRole[],\n monomersDict: MonomerMolGraphMap,\n molfileAtomBlock: string[], molfileBondBlock: string[],\n v: LoopVariables, LC: LoopConstants,\n monomers: MonomerMap, steabsCollection: number[],\n addAtoms: (n: number) => void, getAtoms: () => number\n): void {\n void LC; // assembly is driven by per-monomer roles, not by LC.seqLength\n for (let i = 0; i < monomerSeq.length; ++i) {\n const sm = monomerSeq[i];\n if (sm.symbol === GAP_SYMBOL) continue;\n const role = roles[i];\n const mG = getMolGraph(monomersDict,\n {symbol: sm.symbol, polymerType: helmTypeToPolymerType(sm.biotype)})!;\n\n const aFirst = v.nodeShift;\n const bFirst = v.bondShift;\n v.i = i; // keep loop counter monotone (unused by nucleotide geometry)\n if (role === NucleotideRole.BASE)\n // Branch: attaches to v.branchAttachNode, set when the preceding sugar\n // was emitted. Does not advance the backbone, so the next backbone unit\n // still chains from that sugar's 3' side.\n addBranchMonomerToMolblock(mG, molfileAtomBlock, molfileBondBlock, v);\n else\n // Backbone: sugar / phosphate / linker / terminal modifier. Chains from\n // the previous backbone unit (none for the very first one) and, for a\n // sugar, sets up the branch attach point for the next base.\n addBackboneMonomerToMolblock(mG, molfileAtomBlock, molfileBondBlock, v);\n\n mG.stereoAtoms?.forEach((s) => steabsCollection.push(s + getAtoms()));\n addAtoms(mG.atoms.x.length);\n\n const aList: number[] = [];\n for (let a = aFirst; a < v.nodeShift; ++a) aList.push(a);\n const bList: number[] = [];\n for (let b = bFirst; b < v.bondShift; ++b) bList.push(b);\n monomers.set(i, {biotype: sm.biotype, symbol: sm.symbol, atoms: aList, bonds: bList});\n }\n}\n\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n */\nexport function keepPrecision(x: number): number {\n return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n\n","// interface for typed arrays, like Float32Array and Uint32Array\nimport {ALPHABET} from '../utils/macromolecule';\nimport {HELM_POLYMER_TYPE} from '../utils/const';\nimport {HelmType, ISeqMonomer} from '../helm/types';\n\nexport interface ITypedArray {\n length: number;\n [key: number]: any;\n}\n\n/** Type for user settings of monomer library set to use. */\nexport type UserLibSettings = {\n exclude: string[],\n explicit: string[],\n /** Libraries might contain different monomers for same symbol. Object for monomer symbol to library name of choice*/\n duplicateMonomerPreferences: {[polymerType: string]: {[monomerSymbol: string]: string}}\n}\n\n/** Stores necessary data about atoms of a monomer parsed from Molfile */\nexport type Atoms = {\n /** Element symbols for monomer's atoms */\n atomTypes: string[],\n /** Cartesian coordiantes of monomer's atoms */\n x: Float32Array,\n y: Float32Array,\n /** V3K atom line may contain keyword args */\n kwargs: string[],\n }\n\n/** Stores necessary data about bonds of a monomer parsed from Molfile */\nexport type Bonds = {\n /** bond types for all lines of Molfile bond block */\n bondTypes: Uint32Array,\n /** Indices of all atom pairs, indexing starting from 1 */\n atomPairs: number[][],\n /** If a bond has CFG=... keyword argument, it is parsed and sotred as a\n * value of the map, with the key being the bond's index */\n bondConfiguration: Map<number, number>,\n /** V3K bond line may contain keyword args */\n kwargs: Map<number, string>,\n}\n\n/** Metadata associated with the monomer necessary to restore the resulting molfile */\nexport type MonomerMetadata = {\n /** terminal nodes: 0-th corresponds to the \"leftmost\" one, 1st, to the \"rightmost\",\n * e.g. N-terminus and C-terminus in peptides */\n terminalNodes: number[],\n /** r-group nodes: 0-th corresponds to the \"leftmost\" one, 1st, to the \"rightmost\" */\n rNodes: number[],\n /** shift from the origin to the next backbone, null for branch monomers */\n backboneShift: number[] | null,\n /** shift from the origin to the next branch, null for branch monomers */\n branchShift: number[] | null\n}\n\nexport type MolGraph = {\n atoms: Atoms,\n bonds: Bonds,\n meta: MonomerMetadata,\n stereoAtoms?: number[],\n terminalR2Atom?: string, // for peptides, store the removed R2 Atom type, if any\n}\n\nexport type MonomerMolGraphMap = { [polymerType: string]: { [symbol: string]: MolGraph } };\n\nexport type LibMonomerKey = { polymerType: string, symbol: string }\n\nexport function getMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey): MolGraph | undefined {\n return dict[libKey.polymerType]?.[libKey.symbol];\n}\n\nexport function hasMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey): boolean {\n return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\n\nexport function setMolGraph(dict: MonomerMolGraphMap, libKey: LibMonomerKey, value: MolGraph): void {\n let pt = dict[libKey.polymerType];\n if (!pt)\n pt = dict[libKey.polymerType] = {};\n pt[libKey.symbol] = value;\n}\n\n// export function getMolGraph(\n// dict: MonomerMolGraphMap, polymerType: PolymerType, symbol: string\n// ): MolGraph | undefined {\n// return dict[polymerType]?.[symbol];\n// }\n\nexport type Point = {\n x: number,\n y: number\n}\n\n/** Helper structure wrapping common arguments to several functions */\nexport type LoopVariables = {\n i: number,\n nodeShift: number,\n bondShift: number,\n backbonePositionShift: number[],\n backboneAttachNode: number; // node to which the next backbone is attached\n branchPositionShift: number[],\n branchAttachNode: number,\n flipFactor: number,\n // todo: should we consider representations other than planar?\n}\n\n/** Helper structure wrapping common arguments to several functions */\nexport type LoopConstants = {\n sugar: MolGraph | null,\n phosphate: MolGraph | null,\n seqLength: number,\n atomCount: number,\n bondCount: number,\n}\n\n/** Helper structure to simulate pointer to number */\nexport type NumberWrapper = {\n value: number | null // null if there is no branch attach node\n}\n\n/** Role of an entry in a HELM RNA splitted sequence.\n * SUGAR/BASE/PHOSPHATE are the standard triple positions.\n * TERMINAL_5P marks a 5'-end terminal modifier (e.g. Chol) — a monomer\n * with R2 only that takes the place of the leading sugar.\n * TERMINAL_3P marks a 3'-end terminal modifier (e.g. GalNAc) — a monomer\n * with R1 only that takes the place of the trailing phosphate. The OH cap\n * MUST be omitted when a TERMINAL_3P is present. */\nexport enum NucleotideRole {\n SUGAR = 0,\n BASE = 1,\n PHOSPHATE = 2,\n TERMINAL_5P = 3,\n TERMINAL_3P = 4,\n}\n\nexport type MonomerMapValue = { biotype: HelmType, symbol: string, atoms: number[], bonds: number[] };\n\nexport class MonomerMap extends Map<number, MonomerMapValue> {\n constructor(entries?: [number, MonomerMapValue][] | null) {\n super(entries);\n }\n}\n\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n constructor(\n public readonly molfile: string,\n public readonly monomers: MonomerMap,\n ) {}\n\n static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n\n/** Only simple types allowed for worker data, avoid classes with methods */\nexport type SeqToMolfileWorkerData = {\n seqList: ISeqMonomer[][],\n /** Per-row parallel array of NucleotideRole tags (only set for rows in\n * \"HELM RNA triples\" mode, where each nucleotide contributes 3 entries\n * sugar/base/phosphate). undefined for legacy bases-only rows. */\n rolesList?: (NucleotideRole[] | undefined)[],\n monomersDict: MonomerMolGraphMap,\n alphabet: ALPHABET,\n polymerType: HELM_POLYMER_TYPE,\n start: number,\n end: number,\n}\n\nexport type SeqToMolfileWorkerRes = {\n molfiles: MolfileWithMap[];\n warnings: string[]\n}\n","import {MonomerType, PolymerType} from '../helm/types';\nimport {MonomerTypes, PolymerTypes} from '../helm/consts';\nimport {RGroup} from '../types/monomer-library';\n\n// hwe exports the HELM type vocabulary as `as const` objects (value-only), not\n// TS enums, so we re-create the value+type duality the old `import X = Enum`\n// aliases provided — consumers use these both as a value (`.RNA`) and as a type.\nconst HELM_POLYMER_TYPE = PolymerTypes;\ntype HELM_POLYMER_TYPE = PolymerType;\nconst HELM_MONOMER_TYPE = MonomerTypes;\ntype HELM_MONOMER_TYPE = MonomerType;\n\nexport {HELM_POLYMER_TYPE, HELM_MONOMER_TYPE};\n\n/** Required HELM library monomer fields:\n * https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */\nexport const enum HELM_REQUIRED_FIELD {\n SYMBOL = 'symbol',\n NAME = 'name',\n MOLFILE = 'molfile',\n AUTHOR = 'author',\n ID = 'id',\n RGROUPS = 'rgroups',\n SMILES = 'smiles',\n POLYMER_TYPE = 'polymerType',\n MONOMER_TYPE = 'monomerType',\n CREATE_DATE = 'createDate',\n}\n\n// fields of \"rgroups\" sub-object in HELM library\nexport const enum HELM_RGROUP_FIELDS {\n CAP_GROUP_SMILES = 'capGroupSmiles',\n // WARNING: both capitalization variants coexist\n CAP_GROUP_SMILES_UPPERCASE = 'capGroupSMILES',\n ALTERNATE_ID = 'alternateId',\n CAP_GROUP_NAME = 'capGroupName',\n LABEL = 'label',\n}\n\nexport const enum HELM_OPTIONAL_FIELDS {\n NATURAL_ANALOG = 'naturalAnalog',\n META = 'meta', // for SequenceTranslator\n}\n\n// todo: remove\nexport const enum HELM_FIELDS {\n MONOMER_TYPE = 'monomerType',\n SMILES = 'smiles',\n NAME = 'name',\n AUTHOR = 'author',\n MOLFILE = 'molfile',\n NATURAL_ANALOG = 'naturalAnalog',\n RGROUPS = 'rgroups',\n CREATE_DATE = 'createDate',\n ID = 'id',\n POLYMER_TYPE = 'polymerType',\n SYMBOL = 'symbol'\n}\n\n// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n HELM_FIELDS.SYMBOL,\n HELM_FIELDS.MOLFILE,\n HELM_FIELDS.RGROUPS,\n HELM_FIELDS.NAME,\n // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n // supported\n];\n\nexport const SDF_MONOMER_NAME = 'MonomerName';\n\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n 'monomerType': null, // -> Backbone\n 'smiles': null,\n 'name': 'Name',\n 'author': null,\n 'molfile': 'molecule',\n 'naturalAnalog': 'MonomerNaturalAnalogCode',\n 'rgroups': 'MonomerCaps',\n 'createDate': null,\n 'id': null,\n 'polymerType': 'MonomerType',\n 'symbol': 'MonomerName'\n};\n\nexport const DUMMY_MONOMER = {\n 'monomerType': 'Backbone' as MonomerType,\n 'smiles': '',\n 'name': '',\n 'author': 'Datagrok',\n 'molfile': '',\n 'naturalAnalog': '',\n 'rgroups': [] as RGroup[],\n 'createDate': null,\n 'id': 0,\n 'polymerType': 'PEPTIDE' as PolymerType,\n 'symbol': ''\n} as const;\n\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\n\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(\n `[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`,\n 'g'\n);\n\n","import {CandidateType} from './types';\n\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport enum NOTATION {\n FASTA = 'fasta',\n SEPARATOR = 'separator',\n HELM = 'helm',\n /* Requires notation handler */ CUSTOM = 'custom',\n /* Requires notation handler */ BILN = 'biln',\n}\n\nexport const enum ALIGNMENT {\n SEQ_MSA = 'SEQ.MSA',\n SEQ = 'SEQ',\n}\n\nexport enum ALPHABET {\n DNA = 'DNA',\n RNA = 'RNA',\n PT = 'PT',\n /** Unknown */\n UN = 'UN',\n}\n\nexport enum TAGS {\n aligned = 'aligned',\n alphabet = 'alphabet',\n alphabetSize = '.alphabetSize',\n alphabetIsMultichar = '.alphabetIsMultichar',\n separator = 'separator',\n isHelmCompatible = '.isHelmCompatible',\n positionNames = '.positionNames',\n positionLabels = '.positionLabels',\n regions = '.regions',\n positionShift = '.positionShift',\n selectedPosition = '.selectedPosition',\n polymerTypeColumnName = '.polymerTypeColumnName',\n annotations = '.annotations',\n numberingScheme = '.numberingScheme',\n annotationColumnName = '.annotationColumnName',\n}\n\nexport {TAGS as BioTags};\n\nexport const positionSeparator: string = ', ';\n\nexport const monomerRe: RegExp = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\n\nexport const helmRe: RegExp = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re: RegExp = /\\[([^\\[\\]]+)]/g;\n\nexport const Alphabets = new class {\n fasta = {\n peptide: new Set<string>([\n 'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n 'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n ]),\n dna: new Set<string>(['A', 'C', 'G', 'T']),\n rna: new Set<string>(['A', 'C', 'G', 'U']),\n };\n}();\n\nexport const candidateAlphabets: CandidateType[] = [\n new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n\n/** Canonical gap symbol */\nexport const GAP_SYMBOL: string = '' as const;\n\nexport const GapOriginals: {\n [units: string]: string\n} = {\n [NOTATION.FASTA]: '-',\n [NOTATION.SEPARATOR]: '',\n [NOTATION.HELM]: '*',\n [NOTATION.BILN]: '',\n};\n\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\n\n/** Tag on Monomer columns storing the nqName of a function that returns an IMonomerCanonicalizer.\n * The `.%` prefix ensures this tag is persisted with projects. */\nexport const MONOMER_CANONICALIZER_FUNC_TAG = '.%monomer-canonicalizer-func';\n\n/** Column temp key for the cached IMonomerCanonicalizer instance */\nexport const MONOMER_CANONICALIZER_TEMP = 'monomer-canonicalizer';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n","import * as grok from 'datagrok-api/grok';\nimport * as ui from 'datagrok-api/ui';\nimport * as DG from 'datagrok-api/dg';\n\nimport {CellRendererBackBase} from '../cell-renderer-back-base';\nimport {ISeqHandler} from './seq-handler';\nimport {PolymerType} from '../../helm/types';\nimport {NOTATION_PROVIDER_CONSTRUCTOR_ROLE} from './consts';\n\nexport type SeqSplittedBase = ArrayLike<string> & Iterable<string>;\n\nexport interface ISeqConnection {\n seq1Type: PolymerType;\n seq2Type: PolymerType;\n seqIndex1: number;\n seqIndex2: number;\n monomerIndex1: number;\n monomerIndex2: number;\n rGroup1: number;\n rGroup2: number;\n}\n\nexport interface ISeqGraphInfo {\n /** Connections between monomers with numbers - note that monomer numbers are 0-based*/\n connections: ISeqConnection[];\n /** Start positions of disjoint sequence parts in the original sequence */\n disjointSeqStarts: number[];\n /** Polimer types same as the indexes. only applicapble to helm */\n polymerTypes?: PolymerType[];\n}\n\nexport interface ISeqSplitted {\n\n graphInfo?: ISeqGraphInfo;\n\n isGap(posIdx: number): boolean;\n\n /** */\n getCanonical(posIdx: number): string;\n\n /** For fasta and Helm must not be enclosed to square brackets [meA].*/\n getOriginal(posIdx: number): string;\n\n // TODO: Get ISeqMonomer for seq position\n // get(posIdx: number): ISeqMonomer;\n\n length: number;\n\n /** Returns list of canonical monomers in the region specified */\n getCanonicalRegion(start: number, end: number): string[];\n\n /** Returns the list of original monomers in the region specified */\n getOriginalRegion(start: number, end: number): string[];\n\n get gapOriginal(): string;\n}\n\n/**\n * Extracts displayable 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The canonicalizer separates them with\n * {@link MONOMER_MOTIF_SPLITTER} so the renderer can display/tooltip each one.\n */\nexport interface IMonomerCanonicalizer {\n /** Convert a raw position value to a displayable monomer string.\n * If the position contains multiple monomers, join them with\n * {@link MONOMER_MOTIF_SPLITTER} (` , `). */\n canonicalize(original: string): string;\n\n /** Returns true if the raw position value represents a gap in this notation. */\n isGap(original: string): boolean;\n}\n\nexport interface INotationProvider {\n get defaultGapOriginal(): string;\n\n /** Adjust {@link seqHandler} units, {@link seqHandler.column.tags} by {@link seqHandler} constructor */\n setUnits(seqHandler: ISeqHandler): void;\n\n get splitter(): SplitterFunc;\n\n /** Any Macromolecule can be presented as Helm notation */\n getHelm(seq: string, options: any): string;\n\n createCellRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;\n\n /** nqName of a registered function that returns an {@link IMonomerCanonicalizer} instance.\n * When set, split-to-monomers will tag Monomer columns with this function name so the\n * monomer cell renderer can resolve display symbols from raw position values.\n * Return null/undefined if no custom canonicalization is needed. */\n readonly monomerCanonicalizerFuncName?: string | null;\n}\n\nexport abstract class NotationProviderBase {\n /** Name of the custom notation */\n static get notationName(): string {\n return 'Custom';\n };\n\n /** flag to let bio know if this provider implements method for converting helm to it */\n static get implementsFromHelm(): boolean {\n return false;\n };\n\n /** Method for converting HELM to this notation */\n static convertFromHelm(helm: string, options: any): string {\n throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n };\n\n static async getProviderConstructors(): Promise<typeof NotationProviderBase[]> {\n // this is terrible, I know, but otherwise this gets put in webworkers and fails due to DG resolution)))\n // @ts-ignore\n if (window?.DG) {\n // @ts-ignore\n const constFuncs: any[] = window.DG.Func.find({meta: {role: NOTATION_PROVIDER_CONSTRUCTOR_ROLE}});\n return Promise.all(constFuncs.map((f) => f.apply({})));\n }\n return [];\n }\n}\n\nexport type SeqColStats = { freq: MonomerFreqs, sameLength: boolean }\nexport type SplitterFunc = (seq: string) => ISeqSplitted;\nexport type MonomerFreqs = { [m: string]: number };\n\n/** Alphabet candidate type */\nexport class CandidateType {\n name: string;\n alphabet: Set<string>;\n cutoff: number;\n\n constructor(name: string, alphabet: Set<string>, cutoff: number) {\n this.name = name;\n this.alphabet = alphabet;\n this.cutoff = cutoff;\n }\n}\n\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n freq: MonomerFreqs;\n /** Cos, max = 1, min = 0 */\n similarity: number;\n\n constructor(candidate: CandidateType, freq: MonomerFreqs, similarity: number) {\n super(candidate.name, candidate.alphabet, candidate.cutoff);\n this.freq = freq;\n this.similarity = similarity;\n }\n}\n","// The module cache\nvar __webpack_module_cache__ = {};\n\n// The require function\nfunction __webpack_require__(moduleId) {\n\t// Check if module is in cache\n\tvar cachedModule = __webpack_module_cache__[moduleId];\n\tif (cachedModule !== undefined) {\n\t\treturn cachedModule.exports;\n\t}\n\t// Create a new module (and put it into the cache)\n\tvar module = __webpack_module_cache__[moduleId] = {\n\t\t// no module.id needed\n\t\t// no module.loaded needed\n\t\texports: {}\n\t};\n\n\t// Execute the module function\n\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n\n\t// Return the exports of the module\n\treturn module.exports;\n}\n\n// expose the modules object (__webpack_modules__)\n__webpack_require__.m = __webpack_modules__;\n\n// the startup function\n__webpack_require__.x = () => {\n\t// Load entry module and return exports\n\t// This entry module depends on other loaded chunks and execution need to be delayed\n\tvar __webpack_exports__ = __webpack_require__.O(undefined, [\"vendors-HELM_node_modules_lru-cache_dist_esm_index_js\"], () => (__webpack_require__(\"../../libraries/bio/src/monomer-works/seq-to-molfile-worker.ts\")))\n\t__webpack_exports__ = __webpack_require__.O(__webpack_exports__);\n\treturn __webpack_exports__;\n};\n\n","var deferred = [];\n__webpack_require__.O = (result, chunkIds, fn, priority) => {\n\tif(chunkIds) {\n\t\tpriority = priority || 0;\n\t\tfor(var i = deferred.length; i > 0 && deferred[i - 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