@datagrok/bio 2.27.2 → 2.27.4

package/CLAUDE.md

@@ -15,6 +15,7 @@ Category: **Bioinformatics**. Top menu: `Bio | ...`.
 - `@datagrok-libraries/chem-meta` — RDKit API types (`RDModule`)
 - `@datagrok-libraries/tutorials` — tutorial framework
 - `@biowasm/aioli` — WebAssembly runtime for kalign (MSA)
+- `immunum` — WebAssembly antibody/TCR numbering (IMGT/Kabat) — run in a worker via `src/utils/antibody-numbering/`
 - `ajv` / `ajv-errors` — JSON schema validation for monomer libraries
 - `openchemlib` — molfile conversion, chirality engine
 
@@ -59,6 +60,9 @@ Other packages depend on these implementations: **Helm**, **Peptides**, **Biostr
 | `Bio \| Manage \| Monomer Libraries` | `manageLibrariesView` | Full monomer library management UI |
 | `Bio \| Manage \| Monomers` | `manageMonomersView` | Individual monomer CRUD editor |
 | `Bio \| Manage \| Match with Monomer Library...` | `matchWithMonomerLibrary` | Matches molecules to library monomers |
+| `Bio \| Annotate \| Apply Numbering Scheme...` | `applyNumberingScheme` | Assigns antibody numbering (IMGT/Kabat/Chothia/AHo) via any registered engine |
+| `Bio \| Annotate \| Scan Liabilities...` | `scanLiabilities` | Scans macromolecule sequences for deamidation / oxidation / other liabilities |
+| `Bio \| Annotate \| Manage Annotations...` | `manageAnnotations` | View and manage sequence annotations on macromolecule columns |
 
 **Registered Viewers:**
 - `WebLogo` → `WebLogoViewer` — sequence logo with entropy/full-height modes
@@ -210,6 +214,48 @@ static async myAligner(
 
 See `pepseaMsa()` in `package.ts` and `alignWithPepsea()` in `pepsea.ts` for a complete reference implementation.
 
+#### Antibody Numbering
+
+| File | Purpose |
+|---|---|
+| `utils/annotations/numbering-ui.ts` | `showNumberingSchemeDialog()` — generic dialog for applying antibody numbering. Discovers registered engines via `DG.Func.find({meta: {role: 'antibodyNumbering'}})`, reads the selected engine's `scheme` parameter `choices` to populate the scheme dropdown (updates when the engine changes), runs the chosen engine, and applies the result (regions/annotations + aligned column). |
+| `utils/antibody-numbering/number-antibody.ts` | `numberAntibodyColumn()` — built-in Bio engine. Runs immunum in a worker, builds the result DataFrame in the shape the dialog expects (`position_names`, `chain_type`, `annotations_json`, `numbering_detail`, `numbering_map`). |
+| `utils/antibody-numbering/immunum-client.ts` | Worker client: spawns a **fresh worker per call** and terminates it before returning so the WASM instance is freed. Request/response is one `MessageChannel` round-trip. |
+| `utils/antibody-numbering/immunum.worker.ts` | Worker entry — fetches `immunum_bg.wasm` from the dist/ directory (resolved via `self.location`), initializes the module, caches an `Annotator` per (scheme, chains) tuple for the lifetime of the worker, converts immunum's `Map<posCode, residue>` + `query_start` into the per-row result shape. |
+| `utils/antibody-numbering/immunum-glue.js` | Browser/worker-safe port of `node_modules/immunum/immunum.js`. Byte-identical wasm-bindgen glue — only the Node-only `require('fs').readFileSync` top-level loader is replaced with an explicit `initImmunum(bytes)` entry point. |
+| `utils/antibody-numbering/types.ts` | `ImmunumNumberingRow`, `ImmunumWorkerRequest`/`ImmunumWorkerResponse`, `IMMUNUM_SCHEMES`. |
+
+**Expected output shape (matches antpack reference script `scripts/number_antibody.py`):**
+
+A `DG.DataFrame` with 5 string columns, one row per input sequence:
+
+| Column | Example | Purpose |
+|---|---|---|
+| `position_names` | `"1, 2, 3, ..., 27A, ..."` | Comma-separated scheme position codes, in order |
+| `chain_type` | `"Heavy"` / `"Light"` / `""` | UI-facing chain group (immunum `H` → Heavy; `K`/`L` → Light) |
+| `annotations_json` | JSON array of FR/CDR region defs | Scheme-specific FR1-4 / CDR1-3 with `start`/`end` as *position codes* (not char indices); resolved via `numbering_map` |
+| `numbering_detail` | JSON `[{position, aa}, ...]` | Per-residue position → amino acid |
+| `numbering_map` | JSON `{posCode: charIdx}` | Char index into the **extracted** (gap-free, uppercased) input sequence |
+
+The numbering-ui dialog remaps `numbering_map` indices from ungapped to gapped via `buildUngappedToGappedMap()` so aligned MSA source columns still line up.
+
+##### Adding a New Antibody Numbering Engine
+
+Antibody numbering engines are discovered dynamically via `DG.Func.find({meta: {role: 'antibodyNumbering'}})`.
+To add a new engine (in this package or any other):
+
+1. Register a function with `meta.role: 'antibodyNumbering'` that takes `(df: DG.DataFrame, seqCol: DG.Column<string>, scheme: string)` and returns a `DG.DataFrame`.
+2. Declare the **supported schemes** on the `scheme` parameter via the `choices` option (e.g. `{choices: ['imgt', 'kabat'], initialValue: 'imgt'}`). The dialog reads these at open time and when the user switches engines, so only schemes your engine actually supports show up in the dropdown.
+3. The returned DataFrame **must** have the 5 string columns listed above with exactly those names — the numbering-ui dialog reads them by name.
+4. `position_names` / `numbering_detail` / `numbering_map` must agree: every code in `position_names` must key `numbering_map` and have a matching entry in `numbering_detail`.
+5. `annotations_json` is a JSON-serialized array of region definitions with `start` / `end` as scheme position codes (strings like `"1"`, `"105"`), **not** char indices. Use `SCHEME_REGIONS` from `@datagrok-libraries/bio/src/utils/macromolecule/numbering-schemes` for the canonical boundaries.
+
+Reference implementation: `immunumAntibodyNumbering()` in `package.ts` and `numberAntibodyColumn()` in `utils/antibody-numbering/number-antibody.ts`.
+
+Existing engines:
+- **Bio** — `immunumAntibodyNumbering` (WASM, in-worker, IMGT/Kabat only — advertised via the `scheme` param's `choices`)
+- **scripts/number_antibody.py** — Python/AntPack reference (non-commercial license, not shipped in production; kept for correctness cross-checks only)
+
 #### Seq Helper — `src/utils/seq-helper/`
 
 | File | Purpose |
@@ -308,6 +354,7 @@ Test entry point: `src/package-test.ts` — imports all test files, exports `tes
 | `helm-tests.ts` | HELM-specific operations |
 | `msa-tests.ts` | Multiple sequence alignment |
 | `pepsea-tests.ts` | PepSeA Docker MSA |
+| `antibody-numbering-tests.ts` | Immunum antibody numbering worker + DataFrame shape (IMGT/Kabat, heavy/light, empty-input handling) |
 | `to-atomic-level-tests.ts` | Sequence → molfile conversion |
 | `to-atomic-level-ui-tests.ts` | Atomic level UI widgets |
 | `activity-cliffs-tests.ts` | Activity cliff detection |
@@ -382,6 +429,9 @@ Test entry point: `src/package-test.ts` — imports all test files, exports `tes
 | MSA (kalign) | `src/utils/multiple-sequence-alignment.ts` |
 | MSA (PepSeA Docker) | `src/utils/pepsea.ts` + `pepseaMsa()` in `src/package.ts` |
 | Adding MSA engines | See "Adding a New MSA Engine" in Multiple Sequence Alignment section |
+| Antibody numbering dialog | `src/utils/annotations/numbering-ui.ts` (`showNumberingSchemeDialog`) |
+| Antibody numbering (immunum WASM in worker) | `src/utils/antibody-numbering/` (`immunum.worker.ts`, `immunum-client.ts`, `number-antibody.ts`, `immunum-glue.js`) |
+| Adding antibody numbering engines | See "Adding a New Antibody Numbering Engine" in Antibody Numbering section |
 | Notation conversion | `src/utils/convert.ts` |
 | Seq → molfile conversion | `src/utils/sequence-to-mol.ts` |
 | HELM → molfile pipeline | `src/utils/helm-to-molfile/converter/` |

package/agents/package-knowledge.yaml

@@ -0,0 +1,53 @@
+packageName: Bio
+description: Bioinformatics for macromolecules — sequence similarity/diversity/subsequence/substructure search, notation conversion (FASTA, HELM, BILN, separator), MSA (kalign, MAFFT/PepSeA), WebLogo, composition analysis, sequence space, activity cliffs, antibody numbering (IMGT/Kabat/Chothia/AHo), liability scanning, HELM↔atomic-level conversion, and monomer library management
+keywords:
+  - bioinformatics
+  - macromolecule
+  - sequence
+  - peptide
+  - protein
+  - dna
+  - rna
+  - sar
+  - fasta
+  - helm
+  - biln
+  - separator notation
+  - notation conversion
+  - bam import
+  - sequence similarity search
+  - sequence diversity search
+  - subsequence search
+  - substructure search
+  - identity
+  - msa
+  - multiple sequence alignment
+  - kalign
+  - pepsea
+  - mafft
+  - weblogo
+  - composition analysis
+  - sequence space
+  - activity cliffs
+  - region extraction
+  - vd regions
+  - compare sequences
+  - antibody numbering
+  - IMGT
+  - Kabat
+  - Chothia
+  - AHo
+  - liability scanning
+  - deamidation
+  - oxidation
+  - annotations
+  - immunum
+  - atomic level
+  - molecules to helm
+  - sequence to molecule
+  - monomer library
+  - monomer collection
+  - monomer rendering
+  - sequence cell renderer
+apiRef: src/package-api.ts
+docsRef: ../../help/datagrok/solutions/domains/bio/bio.md

package/dist/455.js

@@ -1,2 +1,2 @@
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utils/macromolecule/consts.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/utils/const.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/types.js","webpack://bio/./node_modules/@datagrok-libraries/js-draw-lite/src/types/org.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/monomer-works.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/seq-to-molfile-worker.js"],"sourcesContent":["export 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: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'd' },\n    RIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'r' },\n    PHOSPHATE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n    TAGS[\"annotations\"] = \".annotations\";\n    TAGS[\"numberingScheme\"] = \".numberingScheme\";\n    TAGS[\"annotationColumnName\"] = \".annotationColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\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(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\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/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\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/** Column temp key for the cached IMonomerCanonicalizer instance */\nexport const MONOMER_CANONICALIZER_TEMP = 'monomer-canonicalizer';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n//# sourceMappingURL=consts.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\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};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\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;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { NOTATION_PROVIDER_CONSTRUCTOR_ROLE } from './consts';\nexport class NotationProviderBase {\n    /** Name of the custom notation */\n    static get notationName() {\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() {\n        return false;\n    }\n    ;\n    /** Method for converting HELM to this notation */\n    static convertFromHelm(helm, options) {\n        throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n    }\n    ;\n    static async getProviderConstructors() {\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 = 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/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","export var HelmTypes;\n(function (HelmTypes) {\n    HelmTypes[\"BASE\"] = \"HELM_BASE\";\n    HelmTypes[\"SUGAR\"] = \"HELM_SUGAR\";\n    HelmTypes[\"LINKER\"] = \"HELM_LINKER\";\n    HelmTypes[\"AA\"] = \"HELM_AA\";\n    HelmTypes[\"CHEM\"] = \"HELM_CHEM\";\n    HelmTypes[\"BLOB\"] = \"HELM_BLOB\";\n    HelmTypes[\"NUCLEOTIDE\"] = \"HELM_NUCLETIDE\";\n})(HelmTypes || (HelmTypes = {}));\n//# sourceMappingURL=org.js.map","import { HelmTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\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        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = 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 = \"RNA\" /* PolymerTypes.RNA */;\n            break;\n        case HelmTypes.AA:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = \"CHEM\" /* PolymerTypes.CHEM */;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = \"BLOB\" /* PolymerTypes.BLOB */;\n            break;\n        default:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap } from './types';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\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(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                alphabet === ALPHABET.DNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE.symbol ||\n                alphabet === ALPHABET.RNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE.symbol ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE.symbol) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\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/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @return {string} - Molfile V3000*/\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount, needsCapping } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */)\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        seqLength: monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const seqMonomer = monomerSeq[v.i];\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            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        const mAtomCount = v.nodeShift - mAtomFirst;\n        const mAtomList = new Array(mAtomCount);\n        for (let maI = 0; maI < mAtomCount; ++maI)\n            mAtomList[maI] = mAtomFirst + maI;\n        const mBondCount = v.bondShift - mBondFirst;\n        const mBondList = new Array(mBondCount);\n        for (let mbI = 0; mbI < mBondCount; ++mbI)\n            mBondList[mbI] = mBondFirst + mbI;\n        monomers.set(v.i, {\n            biotype: seqMonomer.biotype,\n            symbol: seqMonomer.symbol,\n            atoms: mAtomList, bonds: mBondList\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    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\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    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    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\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    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 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** 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(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\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    // 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}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\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    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\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    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\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    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\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}\nfunction updateBranchVariables(monomer, v) {\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}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\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// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\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}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\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}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\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// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\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/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {string[]}monomerSeq - the sequence of monomers\n * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers\n * @param {ALPHABET}alphabet - the alphabet of the monomers\n * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer\n * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (const seqMonomer of monomerSeq) {\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            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    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* 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    }\n    else { // nucleotides\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\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) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const seq = seqList[rowI];\n            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? 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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: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'd' },\n    RIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'r' },\n    PHOSPHATE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\n/** Role of an entry in a HELM RNA splitted sequence (sugar, base, phosphate). */\nexport var NucleotideRole;\n(function (NucleotideRole) {\n    NucleotideRole[NucleotideRole[\"SUGAR\"] = 0] = \"SUGAR\";\n    NucleotideRole[NucleotideRole[\"BASE\"] = 1] = \"BASE\";\n    NucleotideRole[NucleotideRole[\"PHOSPHATE\"] = 2] = \"PHOSPHATE\";\n})(NucleotideRole || (NucleotideRole = {}));\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n    TAGS[\"annotations\"] = \".annotations\";\n    TAGS[\"numberingScheme\"] = \".numberingScheme\";\n    TAGS[\"annotationColumnName\"] = \".annotationColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\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(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\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/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\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/** Column temp key for the cached IMonomerCanonicalizer instance */\nexport const MONOMER_CANONICALIZER_TEMP = 'monomer-canonicalizer';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n//# sourceMappingURL=consts.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\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};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\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;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { NOTATION_PROVIDER_CONSTRUCTOR_ROLE } from './consts';\nexport class NotationProviderBase {\n    /** Name of the custom notation */\n    static get notationName() {\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() {\n        return false;\n    }\n    ;\n    /** Method for converting HELM to this notation */\n    static convertFromHelm(helm, options) {\n        throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n    }\n    ;\n    static async getProviderConstructors() {\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 = 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/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","export var HelmTypes;\n(function (HelmTypes) {\n    HelmTypes[\"BASE\"] = \"HELM_BASE\";\n    HelmTypes[\"SUGAR\"] = \"HELM_SUGAR\";\n    HelmTypes[\"LINKER\"] = \"HELM_LINKER\";\n    HelmTypes[\"AA\"] = \"HELM_AA\";\n    HelmTypes[\"CHEM\"] = \"HELM_CHEM\";\n    HelmTypes[\"BLOB\"] = \"HELM_BLOB\";\n    HelmTypes[\"NUCLEOTIDE\"] = \"HELM_NUCLETIDE\";\n})(HelmTypes || (HelmTypes = {}));\n//# sourceMappingURL=org.js.map","import { HelmTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\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        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = 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 = \"RNA\" /* PolymerTypes.RNA */;\n            break;\n        case HelmTypes.AA:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = \"CHEM\" /* PolymerTypes.CHEM */;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = \"BLOB\" /* PolymerTypes.BLOB */;\n            break;\n        default:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap } from './types';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\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(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = 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 === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Backbone\" /* HELM_MONOMER_TYPE.BACKBONE */) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\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/** 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(monomerSeq, monomersDict, alphabet, polymerType, roles) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // Triples mode is on only when (a) caller flagged the row with roles, and\n    // (b) the row's length is a positive multiple of 3 (sugar/base/phosphate triples).\n    // in edge cases, terminal phosphate may be missing, so we also allow length % 3 === 2, but only if roles are present to disambiguate the monomers.\n    const triplesMode = polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ && !!roles &&\n        roles.length === monomerSeq.length && (monomerSeq.length % 3 === 0 || monomerSeq.length % 3 === 2);\n    // define atom and bond counts, taking into account the bond type\n    const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* 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 = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\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    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    if (triplesMode) {\n        runTriplesAssembly(monomerSeq, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, (a) => { nAtoms += a; }, () => nAtoms);\n    }\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)\n                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            const mAtomCount = v.nodeShift - mAtomFirst;\n            const mAtomList = new Array(mAtomCount);\n            for (let maI = 0; maI < mAtomCount; ++maI)\n                mAtomList[maI] = mAtomFirst + maI;\n            const mBondCount = v.bondShift - mBondFirst;\n            const mBondList = new Array(mBondCount);\n            for (let mbI = 0; mbI < mBondCount; ++mbI)\n                mBondList[mbI] = mBondFirst + mbI;\n            monomers.set(v.i, {\n                biotype: seqMonomer.biotype,\n                symbol: seqMonomer.symbol,\n                atoms: mAtomList, bonds: mBondList\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    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\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    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    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\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    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 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** 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(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\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    // 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}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\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    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\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    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\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    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\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}\nfunction updateBranchVariables(monomer, v) {\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}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\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// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\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}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\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}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\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// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\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/** 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 * @return {Object} the atom/bond counts plus needsCapping flag */\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    let lastPhosphateGraph = 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)\n            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)\n            lastPhosphateGraph = lastMonomerGraph;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* 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    }\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        // Per-monomer-loop already summed sugars + bases + phosphates for every\n        // entry in monomerSeq. Reservation: each backbone (sugar/phosphate)\n        // reserves +1 bond slot for the chain-extending bond, each branch (base)\n        // reserves +1 for its branch bond. Total reservations = monomerCount.\n        //   length === 3N      → trailing P emitted, monomerCount = 3N.\n        //   length === 3N - 1  → trailing P absent, monomerCount = 3N - 1.\n        // Either way, bondCount = sum_bonds + monomerCount.\n        atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)\n        bondCount += monomerCount;\n    }\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        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\n}\n/** Triples-mode RNA assembly. Iterate by NUCLEOTIDE; each nucleotide normally\n * contributes 3 entries from monomerSeq in order [sugar, base, phosphate].\n * The LAST nucleotide may omit its trailing phosphate (length === 3N - 1) —\n * in that case HELM specified an unphosphorylated 3'-end and we cap on the\n * last sugar's R2 instead of on a final phosphate.\n *\n * @param {ISeqMonomer[]} monomerSeq - flat sugar/base/[phosphate] entries\n * @param {MonomerMolGraphMap} monomersDict - monomer dictionary\n * @param {string[]} molfileAtomBlock - output atom block buffer\n * @param {string[]} molfileBondBlock - output bond block buffer\n * @param {LoopVariables} v - mutable loop variables\n * @param {LoopConstants} LC - loop constants (seqLength = nucleotide count)\n * @param {MonomerMap} monomers - per-position monomer index map (filled in)\n * @param {number[]} steabsCollection - stereo atoms collected for STEABS block\n * @param {Function} addAtoms - callback to bump per-row atom counter for stereo offsets\n * @param {Function} getAtoms - callback to read current atom counter */\nfunction runTriplesAssembly(monomerSeq, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, addAtoms, getAtoms) {\n    const N = LC.seqLength;\n    // length === 3N → trailing P present. length === 3N-1 → trailing P absent.\n    const hasTrailingP = monomerSeq.length === 3 * N;\n    for (let n = 0; n < N; ++n) {\n        v.i = n;\n        const sugarSm = monomerSeq[3 * n];\n        const baseSm = monomerSeq[3 * n + 1];\n        const sugarG = getMolGraph(monomersDict, { symbol: sugarSm.symbol, polymerType: helmTypeToPolymerType(sugarSm.biotype) });\n        const baseG = getMolGraph(monomersDict, { symbol: baseSm.symbol, polymerType: helmTypeToPolymerType(baseSm.biotype) });\n        // The previous nucleotide's trailing phosphate is the linker into THIS\n        // nucleotide's sugar. It always exists for n >= 1 because only the\n        // very LAST nucleotide is permitted to omit its phosphate.\n        const prevPhosG = (n === 0) ? null :\n            getMolGraph(monomersDict, { symbol: monomerSeq[3 * (n - 1) + 2].symbol,\n                polymerType: helmTypeToPolymerType(monomerSeq[3 * (n - 1) + 2].biotype) });\n        // emit prevPhosphate (chain linker), then sugar, then base\n        const seqStartIdx = 3 * n; // for keying the per-row monomer map by HELM splitter index\n        if (prevPhosG) {\n            const prevAtomFirst = v.nodeShift;\n            const prevBondFirst = v.bondShift;\n            addBackboneMonomerToMolblock(prevPhosG, molfileAtomBlock, molfileBondBlock, v);\n            prevPhosG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n            addAtoms(prevPhosG.atoms.x.length);\n            // The phosphate \"belongs to\" nucleotide n-1's HELM index (3*(n-1)+2).\n            const prevPhosKey = 3 * (n - 1) + 2;\n            const aList = [];\n            for (let a = prevAtomFirst; a < v.nodeShift; ++a)\n                aList.push(a);\n            const bList = [];\n            for (let b = prevBondFirst; b < v.bondShift; ++b)\n                bList.push(b);\n            monomers.set(prevPhosKey, {\n                biotype: monomerSeq[prevPhosKey].biotype,\n                symbol: monomerSeq[prevPhosKey].symbol,\n                atoms: aList, bonds: bList,\n            });\n        }\n        const sugarAtomFirst = v.nodeShift;\n        const sugarBondFirst = v.bondShift;\n        addBackboneMonomerToMolblock(sugarG, molfileAtomBlock, molfileBondBlock, v);\n        sugarG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(sugarG.atoms.x.length);\n        const sAList = [];\n        for (let a = sugarAtomFirst; a < v.nodeShift; ++a)\n            sAList.push(a);\n        const sBList = [];\n        for (let b = sugarBondFirst; b < v.bondShift; ++b)\n            sBList.push(b);\n        monomers.set(seqStartIdx, {\n            biotype: sugarSm.biotype, symbol: sugarSm.symbol,\n            atoms: sAList, bonds: sBList,\n        });\n        const baseAtomFirst = v.nodeShift;\n        const baseBondFirst = v.bondShift;\n        addBranchMonomerToMolblock(baseG, molfileAtomBlock, molfileBondBlock, v);\n        baseG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(baseG.atoms.x.length);\n        const bAList = [];\n        for (let a = baseAtomFirst; a < v.nodeShift; ++a)\n            bAList.push(a);\n        const bBList = [];\n        for (let b = baseBondFirst; b < v.bondShift; ++b)\n            bBList.push(b);\n        monomers.set(seqStartIdx + 1, {\n            biotype: baseSm.biotype, symbol: baseSm.symbol,\n            atoms: bAList, bonds: bBList,\n        });\n    }\n    // Emit the trailing phosphate (the LAST nucleotide's P) as the final\n    // backbone monomer ONLY if HELM explicitly wrote it. The OH cap then\n    // rides on its free oxygen (3'-phosphate-OH terminus). If HELM omitted\n    // the trailing phosphate, the cap rides on the last sugar's R2 — that\n    // requires no extra emission here, since v.backboneAttachNode already\n    // points at the last sugar's R2 attach.\n    if (hasTrailingP) {\n        const lastPhosKey = 3 * (N - 1) + 2;\n        const lastPhosSm = monomerSeq[lastPhosKey];\n        const lastPhosG = getMolGraph(monomersDict, { symbol: lastPhosSm.symbol, polymerType: helmTypeToPolymerType(lastPhosSm.biotype) });\n        const trailAtomFirst = v.nodeShift;\n        const trailBondFirst = v.bondShift;\n        addBackboneMonomerToMolblock(lastPhosG, molfileAtomBlock, molfileBondBlock, v);\n        lastPhosG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));\n        addAtoms(lastPhosG.atoms.x.length);\n        const tAList = [];\n        for (let a = trailAtomFirst; a < v.nodeShift; ++a)\n            tAList.push(a);\n        const tBList = [];\n        for (let b = trailBondFirst; b < v.bondShift; ++b)\n            tBList.push(b);\n        monomers.set(lastPhosKey, {\n            biotype: lastPhosSm.biotype, symbol: lastPhosSm.symbol,\n            atoms: tAList, bonds: tBList,\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) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, rolesList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(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        }\n        catch (err) {\n            const errMsg = err instanceof Error ? err.message : err.toString();\n            const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;\n            molfileWarningList.push(msg);\n        }\n    }\n    postMessage({ molfiles: resMolList, warnings: molfileWarningList });\n};\n//# sourceMappingURL=seq-to-molfile-worker.js.map"],"names":["monomerWorksConsts","V2K_RGP_SHIFT","V2K_RGP_LINE","V2K_A_LINE","V3K_COUNTS_SHIFT","V3K_IDX_SHIFT","V3K_HEADER_FIRST_LINE","V3K_HEADER_SECOND_LINE","V3K_BEGIN_CTAB_BLOCK","V3K_END_CTAB_BLOCK","V3K_BEGIN_COUNTS_LINE","V3K_COUNTS_LINE_ENDING","V3K_BEGIN_ATOM_BLOCK","V3K_END_ATOM_BLOCK","V3K_BEGIN_BOND_BLOCK","V3K_END_BOND_BLOCK","V3K_BOND_CONFIG","V3K_BEGIN_DATA_LINE","V3K_END","PRECISION_FACTOR","DEOXYRIBOSE","polymerType","symbol","RIBOSE","PHOSPHATE","OXYGEN","HYDROGEN","getMolGraph","dict","libKey","NucleotideRole","NOTATION","ALPHABET","TAGS","MonomerMap","Map","constructor","entries","super","MolfileWithMap","molfile","monomers","this","createEmpty","RegExp","CandidateType","name","alphabet","cutoff","Alphabets","fasta","peptide","Set","dna","rna","HelmTypes","helmTypeToPolymerType","helmType","BASE","SUGAR","LINKER","NUCLEOTIDE","AA","CHEM","BLOB","console","warn","monomerSeqToMolfile","monomerSeq","monomersDict","roles","length","triplesMode","atomCount","bondCount","needsCapping","monomerCount","lastMonomerGraph","lastPhosphateGraph","i","seqMonomer","Error","biotype","atoms","x","bonds","bondTypes","meta","rNodes","terminalR2Atom","toLowerCase","sugar","DNA","phosphate","getResultingAtomBondCounts","molfileAtomBlock","Array","molfileBondBlock","addMonomerToMolblock","addAminoAcidToMolblock","addNucleotideToMolblock","v","nodeShift","bondShift","backbonePositionShift","fill","branchPositionShift","backboneAttachNode","branchAttachNode","flipFactor","LC","seqLength","Math","ceil","steabsCollection","lastMonomerCappingAtom","nAtoms","addAtoms","getAtoms","N","hasTrailingP","n","sugarSm","baseSm","sugarG","baseG","prevPhosG","seqStartIdx","prevAtomFirst","prevBondFirst","addBackboneMonomerToMolblock","stereoAtoms","forEach","push","prevPhosKey","aList","a","bList","b","set","sugarAtomFirst","sugarBondFirst","sAList","sBList","baseAtomFirst","baseBondFirst","addBranchMonomerToMolblock","bAList","bBList","lastPhosKey","lastPhosSm","lastPhosG","trailAtomFirst","trailBondFirst","tAList","tBList","runTriplesAssembly","monomer","mAtomFirst","mBondFirst","mAtomCount","mAtomList","maI","mBondCount","mBondList","mbI","cappingAtomType","atomIdx","keepPrecision","firstAtom","secondAtom","capResultingMolblock","molfileCountsLine","result","join","collection","rowsArray","newCollectionRow","updatedRow","getCollectionBlock","j","atomTypes","y","kwargs","fillAtomLines","fillBondLines","bondIdx","terminalNodes","fillChainExtendingBond","branchShift","updateBranchVariables","atomPairs","backboneShift","updateChainExtendingVariables","nucleobase","fillBranchAtomLines","branchMonomer","fillBackboneToBranchBond","bondCfg","bondConfiguration","has","orientation","get","round","PT","RNA","FASTA","SEPARATOR","HELM","BILN","onmessage","event","seqList","rolesList","start","end","data","resMolList","molfileWarningList","rowI","seq","undefined","err","msg","message","toString","postMessage","molfiles","warnings"],"sourceRoot":""}

package/dist/682.js

@@ -1,2 +1,2 @@
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