@datagrok/helm 3.0.1 → 3.0.3

package/CHANGELOG.md

@@ -1,10 +1,23 @@
 # Helm changelog
 
+## 3.0.3
+
+* Moved the Helm Playwright E2E suite into the package (playwright/); helpers from @datagrok-libraries/test/src/playwright
+* Improved HELM layout engine for conjugate cases
+
 ## 3.0.1 (2026-06-20)
 
+### Features
+
 * Migration to Datagrok Helm Web Editor
 * Support for new Helm Service, editor, parsing and rendering
 * Helm editor panes including molecular structure, composition and conversion
+* Monomer highlighting in HELM grid cells: cells respond to macromolecule highlight events, drawing a translucent overlay around the highlighted monomers
+* Improved RNA splitting: support for complex RNA and complex triplets, and more inclusive matching
+
+### Bug Fixes
+
+* Fixed async renderer invalidation
 
 ## 2.13.4 (2026-03-31)
 

package/CLAUDE.md

@@ -2,111 +2,102 @@
 
 ## Overview
 
-**Helm** (`@datagrok/helm`) is a Datagrok plugin providing full support for **HELM notation** (Hierarchical Editing Language for Macromolecules) — importing, detecting, rendering, editing, and conversion. It wraps the Pistoia HELM Web Editor and Scilligence JSDraw2 libraries, integrating them into the Datagrok platform with custom cell renderers, input widgets, and monomer library management.
+**Helm** (`@datagrok/helm`) is a Datagrok plugin providing full support for **HELM notation** (Hierarchical Editing Language for Macromolecules) — importing, detecting, rendering, editing, and conversion. It is built on the **standalone Datagrok HELM Web Editor** (`@datagrok-libraries/hwe`), integrating it into the platform with a custom grid cell renderer, an input widget, a property panel, and HELM↔other-notation conversion.
+
+The legacy forked Pistoia HELM Web Editor + Scilligence JSDraw2 + Dojo toolkit stack has been **fully removed** (HWE migration, package v3.0). There are no more bundled `vendor/dojo-1.10.10/` or `helm/JSDraw/` sources and no `org.helm.webeditor` / `JSDraw2` / `scil` / `dojo` globals.
 
 Category: **Bioinformatics**.
 
+## The hwe library — `@datagrok-libraries/hwe`
+
+Every editor / parse / render / calculation path routes through the self-contained `@datagrok-libraries/hwe` package. It is an **external npm dependency** (not under this repo's `libraries/`) and injects no global scripts. The package consumes from it:
+
+| Export | Purpose |
+|---|---|
+| `HelmService` | Parses HELM, renders **synchronously** to a canvas (`renderToCanvas`), and computes molfiles / molecular properties. Reads monomers through `bridgeMonomerLib(...)` |
+| `HelmHelperAdapter` | Wraps a `HelmService` to expose Datagrok's `IHelmHelper` plus a legacy-compatible Pistoia `App` shape (`createWebEditorApp`), so existing dialog consumers swap in unchanged |
+| `bridgeMonomerLib(lib)` | Adapts Bio's `IMonomerLib` so the editor resolves exactly the same monomers as the rest of the platform |
+| `buildHelmMolView(mol)` | Builds a legacy-shaped (`atoms[].p` in model space) laid-out molecule used for hover hit-testing and the highlight overlay |
+| `PolymerTypes`; types `IMonomerLibBaseLike`, `MonomersFuncsLike`, `CanvasBounds` | Constants / type shims for the adapter and renderer |
+| `@datagrok-libraries/hwe/styles.css` | The editor's `.hw-*` stylesheet. **Must be imported** (hwe ships CSS as a bundler import only — no runtime injection) or the editor renders unstyled. Imported once in `src/package.ts` |
+
 ## Architecture
 
 ### Entry Point — `src/package.ts`
 
-`PackageFunctions` class registers all platform-visible functions via `@grok.decorators`:
-- `initHelm` — `@init`: loads RdKit, SeqHelper, MonomerLibHelper, initializes HELMWebEditor, creates `HelmHelper` singleton, patches Pistoia monomer system
-- `getHelmService` — `@func`: returns `HelmServiceBase` singleton for off-screen HELM rendering
+Imports `@datagrok-libraries/hwe/styles.css`. `PackageFunctions` class registers all platform-visible functions via `@grok.decorators`:
+- `initHelm` — `@init`: loads the RDKit module, `SeqHelper`, `MonomerLibHelper`; creates the `HelmHelper` singleton (passing `seqHelper`, logger, `rdKitModule`); then `_package.completeInit(helmHelper, libHelper)`. No Dojo/editor bootstrapping or Pistoia monomer patching.
 - `helmCellRenderer` — `@func` (role: `cellRenderer`): returns `HelmGridCellRenderer` for columns with `quality=Macromolecule, units=helm`
-- `editMoleculeCell` — `@func` (role: `cellEditor`): opens full-screen HELM Web Editor dialog for cell editing
-- `openEditor` (`Edit Helm...`) — `@func` (action): context-menu editor for Macromolecule columns, converts non-HELM notations to HELM before editing
-- `propertiesWidget` (`Properties`) — `@panel`: shows molecular formula, weight, extinction coefficient for Macromolecule values
-- `getMolfiles` — `@func`: converts a Macromolecule column to molfile strings
-- `helmInput` — `@func` (role: `valueEditor`): creates `HelmInput` widget for Macromolecule/HELM semtype
-- `getHelmHelper` — `@func`: returns `IHelmHelper` singleton
-- `measureCellRenderer` — `@func`: performance measurement utility for cell rendering
-- `highlightMonomers` — `@func`: test app that loads peptide data and calls `Bio:toAtomicLevel` with highlight
+- `editMoleculeCell` — `@func` (role: `cellEditor`): opens the full-screen HELM editor app dialog for cell editing (`openWebEditor`)
+- `openEditor` (`Edit Helm...`) — `@func` (action): context-menu editor for Macromolecule columns; converts non-HELM notations to HELM first, then writes the edited value back in the column's original notation
+- `propertiesWidget` (`Properties`) — `@panel`: molecular formula, weight, extinction coefficient for a Macromolecule value
+- `getMolfiles` — `@func`: converts a Macromolecule column to molfile strings via `helmHelper.getMolfiles()`
+- `helmInput` — `@func` (role: `valueEditor`): creates the `HelmInput` widget for Macromolecule/HELM semType
+- `getHelmHelper` — `@func`: returns the `IHelmHelper` singleton
+- `measureCellRenderer` — `@func`: cell-render performance benchmark
+- `highlightMonomers` (`Highlight Monomers`) — `@func`: test app that loads peptide data and calls `Bio:toAtomicLevel` with `highlight: true`
+
+> The legacy `getHelmService` function is **gone** — the off-screen render service now lives inside hwe and is owned by the helper's adapter.
 
 **Exports**: `_package` (instance of `HelmPackage`), auto-generated function wrappers from `package.g.ts`
 
 ### Detector — `detectors.js`
 
 `HelmPackageDetectors` class:
-- `autostart` — registers `ui.input.helmAsync` polyfill so other packages can create HELM inputs before this package fully loads
+- `autostart` (meta.role: autostart) — Helm bootstrap; registers the `ui.input.helmAsync` polyfill (delegates to `Helm:helmInput`) so other packages can create HELM inputs before this package fully loads. No semantic-type detector — HELM detection lives in Bio's `detectMacromolecule`.
 
-### Package Utilities — `src/package-utils.ts`
+### Package Singleton — `src/package-utils.ts`
 
 `HelmPackage` class (extends `DG.Package`) — the package singleton managing:
-- `helmHelper` / `seqHelper` — accessors for initialized helpers
-- `_libHelper` — monomer library helper
-- `monomerLib` — accessor for current `IMonomerLib`
-- `initHELMWebEditor()` — loads Dojo toolkit (bundled), JSDraw2 + HELM Web Editor, patches `dojox.gfx.svg.Text.getTextWidth` for hang prevention
-- `initHelmPatchScilAlert()` — suppresses Scilligence alert popups for missing monomers
-- `initHelmPatchPistoia()` — overrides `org.helm.webeditor.Monomers.getMonomer` to use Datagrok's monomer library instead of built-in dictionaries
-- `completeInit()` — ties helmHelper + libHelper together, rewrites Pistoia monomer dictionaries, subscribes to monomer lib changes
-- `monomerLibOnChangedHandler()` — resyncs Pistoia dictionaries when monomer library updates
-
-`initHelmLoadAndPatchDojo()` — complex initialization:
-1. Configures and loads bundled Dojo 1.10.10 with custom `loaderPatch.injectUrl`
-2. Requires Dojo modules (dojo/window, dojox/gfx, dijit/*, etc.)
-3. Waits for all modules to be ready
-4. Patches `dojox.gfx.svg.Text.prototype.getTextWidth` to prevent infinite loops
+- `helmHelper` / `seqHelper` — accessors for the initialized helpers
+- `_libHelper` — monomer library helper; `monomerLib` — accessor for the current `IMonomerLib`
+- `completeInit(helmHelper, libHelper)` — stores the helpers and subscribes to `monomerLib.onChanged`
+- `monomerLibOnChangedHandler()` — logs the new library summary and shows a "Monomer lib updated" info toast
 
-### HELM Helper — `src/helm-helper.ts`
+The legacy Dojo/JSDraw2 loader (`initHELMWebEditor`, `initHelmLoadAndPatchDojo`) and the `org.helm.webeditor.Monomers` patching (`initHelmPatchScilAlert`, `initHelmPatchPistoia`) are **gone** — hwe is self-contained and reads Bio's monomer library directly via `bridgeMonomerLib`.
 
-`HelmHelper` (implements `IHelmHelper`) — singleton providing:
-- `createHelmInput()` — creates `HelmInput` widget
-- `createHelmWebEditor()` — creates `HelmWebEditor` viewer instance
-- `createWebEditorApp()` — creates full HELM Web Editor app (with monomer explorer, tabs, sequence/notation views) for dialog-based editing. Includes custom "Placeholders" tab
-- `overrideMonomersFuncs()` / `revertOriginalMonomersFuncs()` — swap Pistoia's `getMonomer`/`getMonomerSet` with custom implementations
-- `buildMonomersFuncsFromLib()` — builds `getMonomer` function that reads from Datagrok's `IMonomerLib`
-- `getMolfiles()` — batch converts HELM strings to molfile format using a cached off-screen JSDraw2 editor
-- `parse()` — parses HELM string into `HelmMol` object model
-- `removeGaps()` — removes gap monomers from HELM, re-links bonds, returns mapping of old→new monomer positions
-- `getHoveredAtom()` — hit-tests a point against a `HelmMol` to find the nearest atom
+### HELM Helper — `src/helm-helper.ts`
 
-### HELM Web Editor Wrapper — `src/helm-web-editor.ts`
+`HelmHelper` (implements `IHelmHelper`) — singleton. Every editor / parse / calculation path runs through hwe via a lazily-built `HelmHelperAdapter` over a `HelmService` (the `editorAdapter` getter). The service is constructed with `bridgeMonomerLib(monomerLib)`, the RDKit module (for monomer-structure rendering), and an `extraPanes` map providing the editor's package-contributed tabs:
 
-`HelmWebEditor` (implements `IHelmWebEditor`) — lightweight wrapper around `JSDraw2.Editor`:
-- Creates a viewonly editor in a host div
-- Handles resize events to keep editor synced with container size
-- Exposes `editor` (the JSDraw2 `HelmEditor` instance) and `host` div
+| Pane | Source |
+|---|---|
+| **FASTA** / **BILN** | Read-only converted text via the seq handler's notation converters (BILN only for peptide chains; FASTA only for a single linear chain) |
+| **Molecular Structure** | `Bio:toAtomicLevelPanel` widget |
+| **Composition Analysis** | `Bio:compositionAnalysisWidget` widget |
+
+Methods:
+- `createHelmInput()` — creates the `HelmInput` widget
+- `createHelmWebEditor(host, options)` — view-only editor instance (`IHelmWebEditor`) from the adapter
+- `createWebEditorApp(host, helm)` — full editor app (palette + toolbar + canvas + built-in tabs + the extra panes above), wrapped in hwe's `LegacyAppWrapper` so it presents the legacy Pistoia `App` shape (`canvas.getHelm(true)`, `canvas.helm.jsd.m.atoms[i].selected`, …) — existing dialog consumers work unchanged
+- `getMolfiles()`, `parse(helm, origin)`, `removeGaps(srcHelm)` — delegate to the adapter
+- `getHoveredAtom(x, y, mol, height)` — delegates to `getHoveredMonomerFromEditorMol`
+- `originalMonomersFuncs` / `revertOriginalMonomersFuncs()` / `overrideMonomersFuncs()` / `buildMonomersFuncsFromLib()` — thin pass-throughs to the adapter, kept only for the `IHelmHelper` contract (hwe reads `bridgeMonomerLib(...)` directly, so there is no global monomer registry to patch)
+- private `_getSingleHelmDf()` / `_getSingleHelmDfSh()` — build a cached single-row HELM dataframe (tagged Macromolecule/helm; sets `.toAtomicWidgetWidth` to ~60% of window width) used by the Molecular-Structure / Composition / FASTA / BILN pane providers
 
 ## Utilities (`src/utils/`)
 
 | File | Purpose |
 |---|---|
-| `helm-grid-cell-renderer.ts` | `HelmGridCellRenderer` + `HelmGridCellRendererBack`: async cell renderer using SVG→image pipeline. Renders HELM structures in grid cells with LRU caching, handles mouse hover for monomer tooltips and hover links |
-| `helm-service.ts` | `HelmService` (extends `HelmServiceBase`): off-screen rendering service. Uses hidden JSDraw2 editors (LRU-cached per monomer lib) to render HELM→SVG→ImageData. Handles scaling/fitting within cell bounds |
-| `get-monomer.ts` | `rewriteLibraries()`: syncs Datagrok monomer library → Pistoia `org.helm.webeditor.Monomers` dictionary. `getMonomerOverrideAndLogAlert()`: temporary getMonomer override with alert suppression |
-| `get-hovered.ts` | `getHoveredMonomerFromEditorMol()`: nearest-atom hit testing in editor molecule coordinates. `getSeqMonomerFromHelmAtom()`: converts `HelmAtom` to `ISeqMonomer` with canonical symbol |
-| `index.ts` | HELM string parsing utilities: `parseHelm()` (extracts monomer symbols), `removeGapsFromHelm()` (regex gap removal), `findMonomers()` (finds missing monomers), `split()` / `detachAnnotation()` (HELM section tokenizer) |
-| `err-info.ts` | `defaultErrorHandler()`: logs errors via package logger + `grok.shell.error` |
+| `helm-grid-cell-renderer.ts` | `HelmGridCellRenderer` + `HelmGridCellRendererBack`: **synchronous** grid cell renderer painting straight into the grid canvas via hwe `HelmService.renderToCanvas` (no async SVG→image / ImageData round-trip). Keeps one hwe service per monomer-library source (`serviceByLib`) and per-cell-value layout bookkeeping (`auxList`) for hover + highlight. Subscribes to monomer-lib changes (invalidate all) and to `MACROMOLECULE_HIGHLIGHT_EVENT_ID`; `drawHighlightOverlay` paints translucent rings around highlighted monomers. `onMouseMove` hit-tests the laid-out mol and shows the monomer tooltip + hover links |
+| `get-hovered.ts` | `getHoveredMonomerFromEditorMol()`: nearest-atom hit testing (model coordinates) against a `HelmMol`. `getSeqMonomerFromHelmAtom()`: converts a `HelmAtom` to `ISeqMonomer` with canonical symbol (DNA/RNA sugar + phosphate aware) |
+| `index.ts` | HELM string utilities: `parseHelm()` (extracts monomer symbols, bracket/paren aware), `removeGapsFromHelm()` (regex gap removal), `findMonomers()` (resolves via `monomerLib.getMonomer`), `getParts()`, and the `split()` / `detachAnnotation()` HELM section tokenizer |
+| `err-info.ts` | `defaultErrorHandler()`: logs via the package logger + `grok.shell.error` |
 
 ## Widgets (`src/widgets/`)
 
 | File | Purpose |
 |---|---|
-| `helm-input.ts` | `HelmInput` (extends `HelmInputBase`): interactive HELM sequence input widget. Embeds a viewonly `HelmWebEditor`, shows monomer tooltips on hover, "Click to edit" hint opens full editor dialog. Supports `SeqValueBase` get/set, string get/set, `molValue` access. Handles mouse events for hover/click/tooltip |
-| `properties-widget.ts` | `getPropertiesWidget()`: property panel showing molecular formula, weight, and extinction coefficient. Uses off-screen JSDraw2 editor to compute properties. Limits to sequences <1000 chars |
+| `helm-input.ts` | `HelmInput` (extends `HelmInputBase`): interactive HELM input widget embedding a **view-only hwe editor** (`IHelmWebEditor`). Defaults to a compact 250×250 box; shows monomer tooltips on hover; "Click to edit" opens the full hwe editor app in a full-screen dialog and reads back the edited HELM + monomer selection (via the legacy `App` canvas shape). Re-fits the canvas on resize (`ui.onSizeChanged`). Supports `SeqValueBase`/string get/set and `molValue` |
+| `properties-widget.ts` | `getPropertiesWidget()` / `getPropertiesDict()`: **async** property panel — molecular formula, weight, extinction coefficient computed from an off-screen hwe editor (obtained via the async `getHelmHelper()` factory, replacing the old off-screen JSDraw2 editor). Limited to sequences <1000 chars |
 
 ## Constants — `src/constants.ts`
 
 - `jsonSdfMonomerLibDict` — mapping between SDF monomer fields and internal property names
-- `SMILES`, `RGROUPS`, `MONOMER_SYMBOL`, `RGROUP_*` — field name constants for monomer data
-- `SDF_MONOMER_NAME` — SDF field name
+- `SMILES`, `RGROUPS`, `MONOMER_SYMBOL`, `RGROUP_*`, `SDF_MONOMER_NAME` — field-name constants for monomer data
 - `TAGS.cellRendererRenderError` — tag for tracking render errors
 
-## Types — `src/types/index.ts`
-
-Re-exports from `@datagrok-libraries/bio/src/helm/types`:
-- `ScilModule` — Scilligence utility module (`scil.*`)
-- `JSDraw2Module` — JSDraw2 editor module (`JSDraw2.*`)
-- `OrgHelmModule` — Pistoia HELM module (`org.helm.*`)
-
-## Vendor Libraries
-
-### `vendor/dojo-1.10.10/`
-Bundled Dojo Toolkit (dijit, dojo, dojox) required by JSDraw2 and HELM Web Editor. Loaded via custom `dojoConfig.loaderPatch.injectUrl` to work within webpack bundle.
-
-### `helm/JSDraw/`
-Legacy uncompressed sources of Scilligence JSDraw2 Lite and Pistoia HELM Web Editor. Currently replaced by `@datagrok-libraries/helm-web-editor` npm package.
+> HELM types (`HelmType`, `HelmMol`, `HelmAtom`, `App`, `Point`, `MonomersFuncs`, `IHelmWebEditor`, …) are imported directly from `@datagrok-libraries/bio/src/helm/types`. The old `src/types/` re-export module (`ScilModule` / `JSDraw2Module` / `OrgHelmModule`) was removed in the migration.
 
 ## Tests (`src/tests/`)
 
@@ -115,38 +106,34 @@ Test entry point: `src/package-test.ts` — imports all test files, exports `tes
 | File | What it tests |
 |---|---|
 | `_first-tests.ts` | Package import sanity check |
-| `helm-tests.ts` | HELM parsing, parseHelm utility |
+| `helm-tests.ts` | HELM parsing, `parseHelm` utility |
 | `findMonomers-tests.ts` | Missing monomer detection |
-| `helm-service-tests.ts` | HelmService rendering |
 | `renderers-tests.ts` | Cell renderer behavior |
 | `get-molfiles-tests.ts` | HELM → molfile conversion |
 | `properties-widget-tests.ts` | Properties panel (formula, MW, ext. coeff.) |
-| `get-monomer-tests.ts` | Monomer lookup and library integration |
 | `parse-helm-tests.ts` | HELM string parsing edge cases |
-| `helm-web-editor-tests.ts` | Web editor widget creation |
-| `helm-input-tests.ts` | HelmInput widget behavior |
-| `helm-helper-tests.ts` | HelmHelper methods (parse, removeGaps, getMolfiles) |
+| `helm-web-editor-tests.ts` | hwe editor / web-editor widget creation |
+| `helm-input-tests.ts` | `HelmInput` widget behavior |
+| `helm-helper-tests.ts` | `HelmHelper` methods (parse, removeGaps, getMolfiles) |
 | `helm-substructure-filter.ts` | Substructure filtering for HELM |
 | `helm-activity-cliffs.ts` | Activity cliffs computation for HELM |
 | `to-atomic-level-ui-non-linear.ts` | Non-linear HELM → atomic level conversion |
+| `utils.ts` | Shared test helpers (not a `test()` suite) |
 
 ## Initialization Flow
 
-1. `detectors.js` `autostart` runs first — registers `ui.input.helmAsync` polyfill
-2. `initHelm()` called on package init → loads RdKit, SeqHelper, MonomerLibHelper
-3. `initHELMWebEditor()` → loads bundled Dojo, waits for all Dojo modules, patches SVG text width
-4. Loads `@datagrok-libraries/helm-web-editor` bundle, waits for `helmWebEditor$.initPromise`
-5. Creates `HelmHelper` singleton
-6. `completeInit()` → rewrites Pistoia monomer dictionaries from Datagrok lib, patches `getMonomer`, subscribes to lib changes
+1. `detectors.js` `autostart` runs first — registers the `ui.input.helmAsync` polyfill
+2. `initHelm()` on package init → loads the RDKit module, `SeqHelper`, `MonomerLibHelper`; creates `HelmHelper(seqHelper, logger, rdKitModule)`
+3. `completeInit(helmHelper, libHelper)` → wires the helpers and subscribes to monomer-library changes
+4. The hwe `HelmHelperAdapter` / `HelmService` is built **lazily** on first editor / parse / calculation use (after the library is available), reading Bio's monomer library via `bridgeMonomerLib`
 
 ## Key Dependencies
 
-- `@datagrok-libraries/bio` — macromolecule types, HELM types (`HelmType`, `HelmAtom`, `HelmMol`, `IHelmHelper`, `ISeqHelper`, `IMonomerLib`), cell renderer base classes, monomer hover links
-- `@datagrok-libraries/helm-web-editor` — bundled JSDraw2 + Pistoia HELM Web Editor
-- `@datagrok-libraries/chem-meta` — chemistry metadata
-- `@datagrok-libraries/utils` — SVG utilities (`svgToImage`), console helpers
+- `@datagrok-libraries/hwe` — the standalone Datagrok HELM Web Editor: HELM parsing, synchronous canvas rendering, molfile / property calculators, and the editor app (`HelmService`, `HelmHelperAdapter`, `bridgeMonomerLib`, `buildHelmMolView`, `PolymerTypes`, `styles.css`)
+- `@datagrok-libraries/bio` — macromolecule + HELM types (`HelmType`, `HelmAtom`, `HelmMol`, `IHelmHelper`, `ISeqHelper`, `IMonomerLib`), cell-renderer base classes, monomer hover links, macromolecule-highlight events/consts
+- `@datagrok-libraries/chem-meta` — RDKit API types (`RDModule`)
+- `@datagrok-libraries/utils` — error / console helpers
 - `cash-dom` — jQuery-like DOM manipulation
-- `lru-cache` — LRU caching for editors and rendered images
 - `wu` — lazy iteration
 - `rxjs` — reactive subscriptions
 
@@ -155,18 +142,17 @@ Test entry point: `src/package-test.ts` — imports all test files, exports `tes
 | Looking for... | Check first |
 |---|---|
 | Function/panel/renderer registration | `src/package.ts` |
-| Package singleton, Dojo/HWE loading | `src/package-utils.ts` (`HelmPackage`) |
-| HELM helper (parse, convert, getMolfiles) | `src/helm-helper.ts` |
-| Web editor wrapper | `src/helm-web-editor.ts` |
-| Grid cell renderer (async SVG→image) | `src/utils/helm-grid-cell-renderer.ts` |
-| Off-screen render service | `src/utils/helm-service.ts` |
-| Monomer library sync with Pistoia | `src/utils/get-monomer.ts` |
+| Package singleton, init wiring | `src/package-utils.ts` (`HelmPackage`) |
+| HELM helper + hwe adapter (parse, convert, getMolfiles, editor app, panes) | `src/helm-helper.ts` (`HelmHelper.editorAdapter`) |
+| The hwe editor / service / adapter | `@datagrok-libraries/hwe` (external) |
+| Grid cell renderer (synchronous canvas) | `src/utils/helm-grid-cell-renderer.ts` |
+| Monomer highlight overlay (event-driven) | `src/utils/helm-grid-cell-renderer.ts` (`handleHighlightEvent` / `drawHighlightOverlay`) |
 | Mouse hover / hit testing | `src/utils/get-hovered.ts` |
 | HELM string parsing | `src/utils/index.ts` |
 | HELM input widget | `src/widgets/helm-input.ts` |
 | Properties panel (MW, formula) | `src/widgets/properties-widget.ts` |
 | Constants (field names, tags) | `src/constants.ts` |
-| Type re-exports (Scil, JSDraw2, Org) | `src/types/index.ts` |
+| HELM types (`HelmMol`, `HelmAtom`, `App`, …) | `@datagrok-libraries/bio/src/helm/types` |
 | Auto-generated function wrappers | `src/package.g.ts` / `src/package-api.ts` |
 | Autostart / input polyfill | `detectors.js` |
 | Test entry point | `src/package-test.ts` |

package/dist/489.js

@@ -0,0 +1,2 @@
+var helm;(()=>{"use strict";"object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,new Set;const t="object"==typeof process&&process?process:{};let e=globalThis.AbortController,i=globalThis.AbortSignal;if(void 0===e){i=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(t,e){this._onabort.push(e)}},e=class{constructor(){s()}signal=new i;abort(t){if(!this.signal.aborted){this.signal.reason=t,this.signal.aborted=!0;for(const e of this.signal._onabort)e(t);this.signal.onabort?.(t)}}};let r="1"!==t.env?.LRU_CACHE_IGNORE_AC_WARNING;const s=()=>{r&&(r=!1,((e,i,r,s)=>{"function"==typeof t.emitWarning?t.emitWarning(e,i,r,s):console.error(`[${r}] ${i}: ${e}`)})("AbortController is not defined. If using lru-cache in node 14, load an AbortController polyfill from the `node-abort-controller` package. A minimal polyfill is provided for use by LRUCache.fetch(), but it should not be relied upon in other contexts (eg, passing it to other APIs that use AbortController/AbortSignal might have undesirable effects). You may disable this with LRU_CACHE_IGNORE_AC_WARNING=1 in the env.","NO_ABORT_CONTROLLER","ENOTSUP",s))}}Symbol("type"),Symbol.iterator,Symbol.toStringTag;Error;new Map([[123,"lbrace"],[125,"rbrace"],[40,"lparen"],[41,"rparen"],[93,"rbracket"],[124,"pipe"],[46,"dot"],[44,"comma"],[43,"plus"],[58,"colon"],[45,"dash"],[36,"dollar"],[62,"gt"],[63,"question"],[42,"asterisk"],[95,"underscore"],[39,"apos"]]);new Map;var r="HELM_AA",s="HELM_SUGAR",l="HELM_BASE",o="HELM_LINKER",n="HELM_CHEM",a="HELM_BLOB",h="HELM_NUCLEOTIDE",d={PEPTIDE:"PEPTIDE",RNA:"RNA",CHEM:"CHEM",BLOB:"BLOB",G:"G"};var u=class{constructor(){this._listeners=new Set,this._completed=!1}subscribe(t){return this._completed?()=>{}:(this._listeners.add(t),()=>{this._listeners.delete(t)})}next(t){if(!this._completed)for(let e of[...this._listeners])e(t)}complete(){this._completed=!0,this._listeners.clear()}get observerCount(){return this._listeners.size}};function c(t){return{line:"#202020",text:"#000000",background:t}}function p(t){return{line:"#e0e0e0",text:"#ffffff",background:C(t,.25)}}function _(t){let e=/^#([0-9a-fA-F]{6})$/.exec(t),i=/^#([0-9a-fA-F]{3})$/.exec(t);if(null!==e){let t=e[1];return[parseInt(t.slice(0,2),16),parseInt(t.slice(2,4),16),parseInt(t.slice(4,6),16)]}if(null!==i){let t=i[1];return[parseInt(t[0]+t[0],16),parseInt(t[1]+t[1],16),parseInt(t[2]+t[2],16)]}return null}function b(t){return t.toString(16).padStart(2,"0")}function f(t,e,i){return`#${b(t)}${b(e)}${b(i)}`}function m(t,e,i){let r=t/255,s=e/255,l=i/255,o=Math.max(r,s,l),n=Math.min(r,s,l),a=(o+n)/2;if(o===n)return[0,0,a];let h,d=o-n;return h=o===r?60*((s-l)/d+(s<l?6:0)):o===s?60*((l-r)/d+2):60*((r-s)/d+4),[h,a>.5?d/(2-o-n):d/(o+n),a]}function g(t,e,i){let r=i;return r<0&&(r+=1),r>1&&(r-=1),r<1/6?t+6*(e-t)*r:r<.5?e:r<2/3?t+(e-t)*(2/3-r)*6:t}function y(t,e,i){if(0===e){let t=Math.round(255*i);return[t,t,t]}let r=i<.5?i*(1+e):i+e-i*e,s=2*i-r,l=t/360;return[Math.round(255*g(s,r,l+1/3)),Math.round(255*g(s,r,l)),Math.round(255*g(s,r,l-1/3))]}function v(t,e=.3,i=.1){let r=_(t);if(null===r)return t;let[s,l,o]=m(r[0],r[1],r[2]),n=Math.max(0,Math.min(1,l*(1-e))),a=Math.max(0,Math.min(.95,o+i*(1-o))),[h,d,u]=y(s,n,a);return f(h,d,u)}function w(t){let e=_(t);if(null===e)return 0;let i=t=>{let e=t/255;return e<=.03928?e/12.92:Math.pow((e+.055)/1.055,2.4)};return.2126*i(e[0])+.7152*i(e[1])+.0722*i(e[2])}function A(t){let e=_(t);if(null===e)return"#1f2937";let[i,r,s]=m(e[0],e[1],e[2]);if(s>.85||r<.15&&s>.7)return"#1f2937";let l=Math.max(.08,s-.3);return function(t){let e=(t.h%360+360)%360,i=Math.max(0,Math.min(1,t.s)),r=Math.max(0,Math.min(1,t.l)),[s,l,o]=y(e,i,r);return f(s,l,o)}({h:i,s:Math.min(1,r+.1),l})}function S(t){let e=function(t){let e=_(t);return null===e?null:{r:e[0]/255,g:e[1]/255,b:e[2]/255}}(t);if(null===e)return"#1f2937";let i=t=>t<=.03928?t/12.92:Math.pow((t+.055)/1.055,2.4),r=.2126*i(e.r)+.7152*i(e.g)+.0722*i(e.b);return 1.05/(r+.05)>(r+.05)/.05?"#ffffff":"#1f2937"}function C(t,e){let i=_(t);if(null===i)return t;let r=1-e;return f(Math.max(0,Math.min(255,Math.round(i[0]*r))),Math.max(0,Math.min(255,Math.round(i[1]*r))),Math.max(0,Math.min(255,Math.round(i[2]*r))))}var k={A:c("#A0A0FF"),G:c("#FF7070"),T:c("#A0FFA0"),C:c("#FF8C4B"),U:c("#FF8080")},T={R:c("#7a85c1"),r:c("#7a85c1")},E={P:c("#9aa5e1"),p:c("#9aa5e1")},N={A:c("#C8C8C8"),R:c("#145AFF"),N:c("#00DCDC"),D:c("#E60A0A"),C:c("#E6E600"),E:c("#00DCDC"),Q:c("#E60A0A"),G:c("#EBEBEB"),H:c("#8282D2"),I:c("#0F820F"),L:c("#0F820F"),K:c("#145AFF"),M:c("#E6E600"),F:c("#3232AA"),P:c("#DC9682"),S:c("#FA9600"),T:c("#FA9600"),W:c("#B45AB4"),Y:c("#3232AA"),V:c("#0F820F")},M={R:c("#eeeeee")},I={B:c("#999999"),G:c("#e2e2e2")},B={P:c("#9aa5e1")},x={name:"light",fallback:{line:"#202020",text:"#000000",background:"#eeeeee"},errorTriple:{line:"#cc0000",text:"#000000",background:"#FFFF00"},palette:{[l]:k,[s]:T,[o]:E,[r]:N,[n]:M,[a]:I,[h]:B}};function L(t){let e={};for(let[i,r]of Object.entries(t))e[i]=p(r.background);return e}var P={name:"dark",fallback:{line:"#e0e0e0",text:"#ffffff",background:C("#eeeeee",.5)},errorTriple:{line:"#ff5050",text:"#ffffff",background:C("#FFFF00",.4)},palette:{[l]:L(k),[s]:L(T),[o]:L(E),[r]:L(N),[n]:L(M),[a]:L(I),[h]:L(B)}};function F(t,e,i=x){if(null===t)return{...i.errorTriple};let r=t.meta?.colors;if(void 0!==r){let t="light"===i.name?r.light:"dark"===i.name?r.dark:void 0;if(void 0!==t)return{...t,line:A(t.background)};if(void 0!==r.default)return{...r.default,line:A(r.default.background)}}let s=t.naturalAnalog;if(void 0!==s&&""!==s){let t=i.palette[e];if(void 0!==t){let e=t[s];if(void 0!==e)return{...e,line:A(e.background),text:S(e.background)}}}return{...i.fallback,line:A(i.fallback.background),text:S(i.fallback.background)}}function $(t){switch(t.polymerType){case d.PEPTIDE:return r;case d.CHEM:return n;case d.BLOB:return a;case d.RNA:if("Branch"===t.monomerType)return l;if("Backbone"===t.monomerType){let e=t.naturalAnalog;return"P"===e||"p"===e?o:s}return null;default:return null}}new Set(["PEPTIDE","RNA","CHEM","BLOB"]),new Set(["Backbone","Branch","Terminal","Undefined"]);new Set(["?","*","_","X","N"]);Math.PI;function R(t,e){let i=Math.min(t.x,e.x),r=Math.min(t.y,e.y);return{x:i,y:r,width:Math.max(t.x+t.width,e.x+e.width)-i,height:Math.max(t.y+t.height,e.y+e.height)-r}}function O(t){if(Number.isInteger(t))return 0===t?"0":t.toString();if(!Number.isFinite(t)||Object.is(t,-0))return"0";let e=Math.round(1e3*t)/1e3;return 0===e?"0":e.toString()}function D(t){if(0===t.length)return"";let e=t[0],i=`M ${O(e.x)} ${O(e.y)}`;for(let e=1;e<t.length;e++){let r=t[e];i+=` L ${O(r.x)} ${O(r.y)}`}return i+=` L ${O(e.x)} ${O(e.y)} Z`,i}function V(t,e,i,r){let s=[],l=360/e;for(let o=0;o<e;o++){let e=(r+o*l)*Math.PI/180;s.push({x:t.x+i*Math.cos(e),y:t.y+i*Math.sin(e)})}return s}function K(t,e,i,r){let s=Math.abs(e)/2,l=Math.abs(i)/2,o=Math.max(0,Math.min(r,s,l)),n=t.x-s,a=t.y-l,h=n+2*s,d=a+2*l,u=`M ${O(n+o)} ${O(a)}`;return u+=` L ${O(h-o)} ${O(a)}`,u+=` A ${O(o)} ${O(o)} 0 0 1 ${O(h)} ${O(a+o)}`,u+=` L ${O(h)} ${O(d-o)}`,u+=` A ${O(o)} ${O(o)} 0 0 1 ${O(h-o)} ${O(d)}`,u+=` L ${O(n+o)} ${O(d)}`,u+=` A ${O(o)} ${O(o)} 0 0 1 ${O(n)} ${O(d-o)}`,u+=` L ${O(n)} ${O(a+o)}`,u+=` A ${O(o)} ${O(o)} 0 0 1 ${O(n+o)} ${O(a)}`,u+=" Z",u}function H(t,e,i){let r=Math.abs(e),s=Math.abs(i);return`M ${O(t.x-r)} ${O(t.y)} A ${O(r)} ${O(s)} 0 1 0 ${O(t.x+r)} ${O(t.y)} A ${O(r)} ${O(s)} 0 1 0 ${O(t.x-r)} ${O(t.y)} Z`}function G(t,e,i,r){switch(t){case"hexagon":{let t=i*Math.sqrt(3)/2,r=i;return{x:e.x-t,y:e.y-r,width:2*t,height:2*r}}case"diamond":return{x:e.x-i,y:e.y-i,width:2*i,height:2*i};case"pentagon":{let t=Math.cos(18*Math.PI/180)*i,r=-i,s=Math.sin(54*Math.PI/180)*i;return{x:e.x-t,y:e.y+r,width:2*t,height:s-r}}case"rounded-rect":case"blob":{let t=r??i,s=Math.abs(i)/2,l=Math.abs(t)/2;return{x:e.x-s,y:e.y-l,width:2*s,height:2*l}}case"ellipse":{let t=Math.abs(i),s=Math.abs(r??i);return{x:e.x-t,y:e.y-s,width:2*t,height:2*s}}case"circle":{let t=Math.abs(i);return{x:e.x-t,y:e.y-t,width:2*t,height:2*t}}}}var z='"Helvetica Neue", Helvetica, Arial, sans-serif';function U(t){return{aa:{size:.72*t,strokeWidth:5},sugar:{size:1.39*t,strokeWidth:5,cornerRadius:.3*t},base:{size:.88*t,strokeWidth:5},linker:{size:.63*t,strokeWidth:5},chem:{size:1.49*t,strokeWidth:5,cornerRadius:.5*t},blob:{size:1.64*t,strokeWidth:5,cornerRadius:.8*t},nucleotide:{size:.98*t,strokeWidth:5}}}var q={name:"light",background:"#ffffff",defaultStroke:"#202020",defaultFill:"#ffffff",selectionColor:"#FFC107",highlightColor:"#A4E2DC",errorColor:"#cc0000",fontSize:14,fontFamily:z,bondLength:28,textColor:"#000000",idColor:"#00aa00",annotationColor:"#FFA500",tagDotColor:"#dd2222",hbondColor:"#888888",nonCanonicalHbondColor:"#cc8800",crossPolymerBondColor:"#1f5fcd",colorTheme:x,palette:{softenCanvas:!1},shapes:U(14)};U(14);function j(t,e){switch(e){case r:return t.shapes.aa;case s:return t.shapes.sugar;case l:return t.shapes.base;case o:return t.shapes.linker;case n:return t.shapes.chem;case a:return t.shapes.blob;case h:return t.shapes.nucleotide}}function Y(t){switch(t){case r:return"hexagon";case s:return"rounded-rect";case l:return"diamond";case o:return"circle";case n:return"rounded-rect";case a:return"blob";case h:return"pentagon"}}function W(t,e,i=0){let r=j(e,t.biotype);if("*"===t.symbol)return function(t,e){return H(t,e,e)}(t.p,r.size+i);switch(Y(t.biotype)){case"hexagon":{let e=0===i?0:i/Math.cos(Math.PI/6);return function(t,e,i=-30){return D(V(t,6,e,i))}(t.p,r.size+e)}case"diamond":{let e=0===i?0:i/Math.cos(Math.PI/4);return function(t,e){return D([{x:t.x,y:t.y-e},{x:t.x+e,y:t.y},{x:t.x,y:t.y+e},{x:t.x-e,y:t.y}])}(t.p,r.size+e)}case"pentagon":{let e=0===i?0:i/Math.cos(Math.PI/5);return function(t,e,i=-90){return D(V(t,5,e,i))}(t.p,r.size+e)}case"rounded-rect":return K(t.p,r.size+2*i,r.size+2*i,(r.cornerRadius??0)+i);case"blob":return function(t,e,i,r){return K(t,e,i,r)}(t.p,r.size+2*i,r.size+2*i,(r.cornerRadius??0)+i);case"circle":return H(t.p,r.size+i,r.size+i)}}function X(t,e){let i,r=j(e,t.biotype),s="*"===t.symbol?"circle":Y(t.biotype);switch(s){case"hexagon":case"diamond":case"pentagon":case"circle":i=G(s,t.p,r.size);break;case"rounded-rect":case"blob":i=G(s,t.p,r.size,r.size)}let l=r.strokeWidth/2;return{x:i.x-l,y:i.y-l,width:i.width+2*l,height:i.height+2*l}}function Z(t,e){return j(e,t.biotype)}var J=/[&"'<>]/;function Q(t){return J.test(t)?t.replace(/&/g,"&amp;").replace(/"/g,"&quot;").replace(/'/g,"&apos;").replace(/</g,"&lt;").replace(/>/g,"&gt;"):t}function tt(t){if(Number.isInteger(t))return 0===t?"0":t.toString();if(!Number.isFinite(t)||Object.is(t,-0))return"0";let e=Math.round(1e3*t)/1e3;return 0===e?"0":e.toString()}function et(t,e,i){let r=`<${t}`;if(void 0!==e)for(let t in e){let i=e[t];if(void 0!==i&&!1!==i){if(!0===i){r+=` ${t}`;continue}r+="number"==typeof i?` ${t}="${tt(i)}"`:` ${t}="${Q(i)}"`}}return void 0===i?`${r}/>`:"string"==typeof i?`${r}>${i}</${t}>`:`${r}>${i.join("")}</${t}>`}function it(t,e,i){if(0===i.size)return et("g",{class:"hw-layer hw-highlights"},"");let r=[];for(let s of t.atoms){if(!i.has(s.id))continue;let t=W(s,e,(Z(s,e).strokeWidth+3)/2);r.push(et("path",{d:t,class:"hw-highlight",fill:"none",stroke:e.highlightColor,"stroke-width":3,"stroke-linejoin":"round","stroke-linecap":"round","data-symbol":s.symbol,"data-ring-atom-id":s.id,"data-testid":`highlight-ring-${s.id}`}))}return et("g",{class:"hw-layer hw-highlights"},r.join(""))}function rt(t,e,i){if(0===i.size)return et("g",{class:"hw-layer hw-selections"},"");let r=[];for(let s of t.atoms){if(!i.has(s.id))continue;let t=W(s,e,(Z(s,e).strokeWidth+3)/2);r.push(et("path",{d:t,class:"hw-selection",fill:"none",stroke:e.selectionColor,"stroke-width":3,"stroke-linejoin":"round","stroke-linecap":"round","data-symbol":s.symbol,"data-ring-atom-id":s.id,"data-testid":`selection-ring-${s.id}`}))}return et("g",{class:"hw-layer hw-selections"},r.join(""))}new WeakMap;new Map;var st=class{constructor(t,e){this.atoms=t,this.bonds=e,this.isEmpty=0===t.size&&0===e.size,Object.freeze(this)}};new st(new Set,new Set);function lt(t){let e=t.ownerDocument;if(null!=e)return e;let i=globalThis;if(void 0!==i.document)return i.document;throw new Error("EditorView: no Document available (host.ownerDocument is null).")}function ot(t,e,i,r){let s=t.createElement(e);if(void 0!==i)for(let t of Object.keys(i)){let e=i[t];!1===e||void 0===e||s.setAttribute(t,!0===e?"":String(e))}if(void 0!==r)for(let e of r)"string"==typeof e?s.appendChild(t.createTextNode(e)):s.appendChild(e);return s}function nt(t,e,i=220,r=140){if(null==t||""===e)return null;try{let s=t.get_mol(e);if(null===s)return null;let l=s.get_svg(i,r);return s.delete(),l}catch{return null}}function at(t,e,i){let r="data-testid";for(let i=0;i<t.body.children.length;i++){let s=t.body.children[i];if(void 0!==s&&s.getAttribute(r)===e)return s}let s=ot(t,"div",{class:i,[r]:e});return s.style.display="none",t.body.appendChild(s),s}function ht(t,e,i){for(;null!==e.firstChild;)e.removeChild(e.firstChild);if(e.appendChild(ot(t,"div",{class:"hw-tooltip__symbol"},[i.symbol])),void 0!==i.name&&""!==i.name&&i.name!==i.symbol&&e.appendChild(ot(t,"div",{class:"hw-tooltip__name"},[i.name])),void 0!==i.rdkitSvg&&null!==i.rdkitSvg&&""!==i.rdkitSvg){let r={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(r["data-testid"]=i.rdkitTestid);let s=ot(t,"div",r);s.innerHTML=i.rdkitSvg,e.appendChild(s)}void 0!==i.hint&&""!==i.hint&&e.appendChild(ot(t,"div",{class:"hw-tooltip__hint"},[i.hint]))}function dt(t,e,i){let r=t.style;r.display="block",r.left=`${e+12}px`,r.top=`${i+12}px`}function ut(t){null!==t&&(t.style.display="none")}function ct(t){let e=t.body;if(null!=e)for(let t=0;t<e.children.length;t++){let i=e.children[t];if(void 0===i)continue;let r=void 0===i.getAttribute?null:i.getAttribute("data-testid");null!=r&&r.endsWith("-tooltip")&&ut(i)}}var pt=class t{constructor(t,e,i){this._baseTransform="",this._viewport={scale:1,offset:{x:0,y:0}},this._pinnedBbox=null,this._tooltip=null,this._bondTooltip=null,this._rdkitSvgCache=new Map,this._unsubs=[],this._destroyed=!1,this.host=t,this._editor=e,this._doc=i?.documentImpl??lt(t),this._width=i?.width??400,this._height=i?.height??200,function(t){let e=lt(t);if(null!==e.querySelector("style[data-hw-editor-view-styles]"))return;let i=e.createElement("style");i.setAttribute("data-hw-editor-view-styles",""),i.textContent=".hw-editor-view{position:relative;display:block;overflow:hidden;outline:none;}.hw-editor-view svg{display:block;user-select:none;}.hw-editor-view.hw-view-only{cursor:default;}";let r=e.head??e.documentElement;null!==r&&r.appendChild(i)}(t);let r=this._doc.createElement("div");r.setAttribute("class","hw-editor-view"),t.appendChild(r),this._tooltip=at(this._doc,"atom-tooltip","hw-atom-tooltip"),this._bondTooltip=at(this._doc,"bond-tooltip","hw-bond-tooltip"),this._svgRoot=this._renderFresh(),this._unsubs.push(e.on("mol:changed",t=>{this._hideTooltip(),this._hideBondTooltip(),("setHelm"===t.reason||"cleanLayout"===t.reason||"initial"===t.reason)&&(this._pinnedBbox=null),this._renderFresh()})),this._unsubs.push(e.on("selection:change",t=>{this._refreshOverlays(t)})),this._unsubs.push(e.on("highlight:change",t=>{this._refreshOverlays(t)})),this._unsubs.push(e.on("theme:change",()=>{this._renderFresh()})),this._unsubs.push(e.on("view:resize",t=>{this._applyResize(t.width,t.height)})),this._unsubs.push(e.on("view:viewport-change",t=>{this._viewport=t.viewport,this._applyViewport(t.viewport)})),this._unsubs.push(e.on("view:fit-to-content",()=>{this._pinnedBbox=null,this._renderFresh()})),this._unsubs.push(e.on("monomer:hover",t=>{this._showTooltip(t.atom,t.clientX,t.clientY)})),this._unsubs.push(e.on("monomer:hover-end",()=>{this._hideTooltip()})),this._unsubs.push(e.on("bond:hover",t=>{this._showBondTooltip(t.bond,t.clientX,t.clientY)})),this._unsubs.push(e.on("bond:hover-end",()=>{this._hideBondTooltip()})),this._unsubs.push(e.on("bond:preview",t=>{this._paintBondPreview(t.start.p,t.cursor,null!==t.candidate)})),this._unsubs.push(e.on("bond:preview-end",()=>{this._clearBondPreview()})),this._unsubs.push(e.on("bond:cancel",()=>{this._clearBondPreview()})),this._unsubs.push(e.on("selection:rectangle-start",t=>{this._paintSelectionRect(t.origin,t.origin)})),this._unsubs.push(e.on("selection:rectangle-update",t=>{this._paintSelectionRectFromRect(t.rect)})),this._unsubs.push(e.on("selection:rectangle-end",()=>{this._clearSelectionRect()}))}get svgRoot(){return this._svgRoot}get width(){return this._width}get height(){return this._height}resize(t,e){this._destroyed||(this._width=t,this._height=e,this._renderFresh())}redraw(){this._destroyed||this._renderFresh()}destroy(){if(this._destroyed)return;this._destroyed=!0;for(let t of this._unsubs)t();this._unsubs.length=0;let t=this.host.querySelector(".hw-editor-view");null!==t&&null!==t.parentNode&&t.parentNode.removeChild(t),ut(this._tooltip),ut(this._bondTooltip),this._tooltip=null,this._bondTooltip=null}_renderFresh(){let t=this._editor.getService(),e=this._currentTheme(),i=this._editor.getMol();null===this._pinnedBbox&&(this._pinnedBbox=function(t,e=q){if(0===t.atoms.length)return{x:0,y:0,width:0,height:0};let i=X(t.atoms[0],e);for(let r=1;r<t.atoms.length;r++)i=R(i,X(t.atoms[r],e));return i}(i,e));let r=t.renderMol(i,{width:this._width,height:this._height,theme:e,fixedModelBbox:this._pinnedBbox});this._svgRoot=function(t,e){let i=lt(t),r=t.querySelector(".hw-editor-view");if(null===r)throw new Error("EditorView.replaceSvg: missing .hw-editor-view wrapper.");let s=i.createElement("div");s.innerHTML=e;let l=s.querySelector("svg");if(null===l)throw new Error("EditorView.replaceSvg: rendered output contained no <svg>.");for(;null!==r.firstChild;)r.removeChild(r.firstChild);return r.appendChild(l),l}(this.host,r);let s=this._svgRoot.querySelector(".hw-content");return this._baseTransform=null!==s?s.getAttribute("transform")??"":"",this._svgRoot.setAttribute("data-testid","editor-svg"),this._applyOverlaysToCurrent(),(1!==this._viewport.scale||0!==this._viewport.offset.x||0!==this._viewport.offset.y)&&this._applyViewport(this._viewport),this._svgRoot}_refreshOverlays(t){this._applyOverlaysToCurrent()}_applyOverlaysToCurrent(){let t=this._editor.getMol(),e=this._editor.getSelection(),i=function(t,e={}){let i=e.theme??q,r=e.selectedAtomIds??new Set;return{highlightLayer:it(t,i,e.highlightedAtomIds??new Set),selectionLayer:rt(t,i,r)}}(t,{theme:this._currentTheme(),selectedAtomIds:e.atoms,highlightedAtomIds:this._editorHighlights()});this._spliceLayer("hw-highlights",i.highlightLayer),this._spliceLayer("hw-selections",i.selectionLayer)}_spliceLayer(t,e){let i=this._svgRoot.querySelector(`.${t}`);if(null===i||null===i.parentNode)return;let r=this._doc.createElementNS("http://www.w3.org/2000/svg","svg");r.innerHTML=e;let s=r.querySelector(`.${t}`);null!==s&&i.parentNode.replaceChild(s,i)}_editorHighlights(){let t=this._editor;return"function"==typeof t._currentHighlights?t._currentHighlights():new Set}_currentTheme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_applyResize(t,e){this._width=t,this._height=e,this._pinnedBbox=null,this._renderFresh()}_applyViewport(t){let e=this._svgRoot.querySelector(".hw-content");if(null===e)return;let i=`translate(${t.offset.x} ${t.offset.y}) scale(${t.scale})`,r=""===this._baseTransform?i:`${i} ${this._baseTransform}`;e.setAttribute("transform",r)}_showTooltip(t,e,i){let r=this._tooltip;if(null===r)return;let s=""===t.symbol?"?":t.symbol,l=t.monomer?.name??"",o=t.bio.positionInChain,n=""===t.bio.chainId?"?":t.bio.chainId,a=""!==l&&l!==s?`${l} @ ${n}:${o}`:`${s} @ ${n}:${o}`,h=this._renderRdkitTooltipSvg(t);ht(this._doc,r,{symbol:s,name:a,rdkitSvg:h,rdkitTestid:"atom-tooltip-rdkit-svg"});let d=""!==l&&l!==s?`${s} — ${l}  @ ${n}:${o}`:`${s}  @ ${n}:${o}`,u=this._doc.createElement("div");u.setAttribute("class","hw-atom-tooltip__text"),u.style.display="none",u.appendChild(this._doc.createTextNode(d)),r.appendChild(u),dt(r,e,i)}_renderRdkitTooltipSvg(e){let i=this._editor.getService().options.rdkitModule;if(null==i)return null;let r=e.monomer;if(null===r)return null;let s=r.smiles;if(void 0===s||""===s)return null;let l=`${r.polymerType}:${r.symbol}`;if(this._rdkitSvgCache.has(l))return this._rdkitSvgCache.get(l)??null;let o=nt(i,s,220,140);if(this._rdkitSvgCache.size>=t._RDKIT_CACHE_LIMIT){let t=this._rdkitSvgCache.keys().next().value;void 0!==t&&this._rdkitSvgCache.delete(t)}return this._rdkitSvgCache.set(l,o),o}_hideTooltip(){ut(this._tooltip)}_showBondTooltip(t,e,i){let r=this._bondTooltip;if(null===r)return;let s=_t(t.r1),l=_t(t.r2),o=`${t.a1.symbol}@${t.a1.bio.chainId}:${t.a1.bio.positionInChain}`,n=`${t.a2.symbol}@${t.a2.bio.chainId}:${t.a2.bio.positionInChain}`;ht(this._doc,r,{symbol:`${s}-${l} (${t.kind})`,name:`${o} ↔ ${n}`}),dt(r,e,i)}_hideBondTooltip(){ut(this._bondTooltip)}_paintBondPreview(t,e,i){let r=this._svgRoot.querySelector(".hw-content");if(null===r)return;let s=r.querySelector(".hw-bond-preview");null===s&&(s=this._doc.createElementNS("http://www.w3.org/2000/svg","line"),s.setAttribute("class","hw-bond-preview"),s.setAttribute("data-testid","bond-preview"),s.setAttribute("stroke-dasharray","6 4"),s.setAttribute("stroke-width","2"),s.setAttribute("fill","none"),s.setAttribute("pointer-events","none"),r.appendChild(s)),s.setAttribute("x1",String(t.x)),s.setAttribute("y1",String(t.y)),s.setAttribute("x2",String(e.x)),s.setAttribute("y2",String(e.y)),s.setAttribute("stroke",i?"#1f5fcd":"#999999")}_clearBondPreview(){let t=this._svgRoot.querySelector(".hw-bond-preview");null!==t&&null!==t.parentNode&&t.parentNode.removeChild(t)}_paintSelectionRect(t,e){let i=Math.min(t.x,e.x),r=Math.min(t.y,e.y),s=Math.abs(t.x-e.x),l=Math.abs(t.y-e.y);this._paintSelectionRectAt(i,r,s,l)}_paintSelectionRectFromRect(t){this._paintSelectionRectAt(t.x,t.y,t.width,t.height)}_paintSelectionRectAt(t,e,i,r){let s=this._svgRoot.querySelector(".hw-content");if(null===s)return;let l=s.querySelector(".hw-selection-rect");null===l&&(l=this._doc.createElementNS("http://www.w3.org/2000/svg","rect"),l.setAttribute("class","hw-selection-rect"),l.setAttribute("data-testid","selection-rect"),l.setAttribute("fill","rgba(31, 95, 205, 0.08)"),l.setAttribute("stroke","#1f5fcd"),l.setAttribute("stroke-width","1"),l.setAttribute("stroke-dasharray","4 3"),l.setAttribute("pointer-events","none"),s.appendChild(l)),l.setAttribute("x",String(t)),l.setAttribute("y",String(e)),l.setAttribute("width",String(i)),l.setAttribute("height",String(r))}_clearSelectionRect(){let t=this._svgRoot.querySelector(".hw-selection-rect");null!==t&&null!==t.parentNode&&t.parentNode.removeChild(t)}};pt._RDKIT_CACHE_LIMIT=256;function _t(t){switch(t.kind){case"numeric":return`R${t.r}`;case"unspecified":return"?";case"wildcard":return"*";case"pair":return"pair";case"positional":return`${t.position}pos:R${t.r}`}}var bt=class t{constructor(t,e){this._onClose=null,this._primaryAction=null,this._host=t,this._doc=e.documentImpl??lt(t);let i=this._doc,r={class:"hw-modal-backdrop",role:"presentation"};void 0!==e.testId&&(r["data-testid"]=`dialog-${e.testId}`);let s=ot(i,"div",r),l={class:"hw-modal",role:"dialog","aria-modal":"true","aria-label":e.title};void 0!==e.testId&&(l["data-testid"]=`dialog-${e.testId}-frame`);let o=ot(i,"div",l),n=ot(i,"div",{class:"hw-modal__header"},[e.title]),a=ot(i,"div",{class:"hw-modal__body"});o.appendChild(n),o.appendChild(a),s.appendChild(o);let h=t=>{t.stopPropagation()};for(let t of["mousedown","mousemove","mouseup","mouseover","mouseenter","mouseleave","wheel","contextmenu","dblclick","keydown","keyup","keypress"])s.addEventListener(t,h);o.addEventListener("keydown",t=>{let e=t;if("Enter"!==e.key||"TEXTAREA"===e.target?.tagName)return;let i=this._primaryAction;null!==i&&(e.preventDefault?.(),e.stopImmediatePropagation?.(),i())}),s.addEventListener("click",t=>{t.target!==s?t.stopPropagation():this.close()}),this.root=s,this.body=a}static anyOpen(){return t._openStack.length>0}static closeTopmost(){let e=t._openStack[t._openStack.length-1];return void 0!==e&&(e.close(),!0)}open(e){this._onClose=e??null,null===this.root.parentNode&&this._host.appendChild(this.root),t._openStack.includes(this)||t._openStack.push(this),ct(this._doc)}close(){let e=t._openStack.indexOf(this);e>=0&&t._openStack.splice(e,1),null!==this.root.parentNode&&this.root.parentNode.removeChild(this.root);let i=this._onClose;this._onClose=null,null!==i&&i()}setPrimaryAction(t){this._primaryAction=t}get isOpen(){return null!==this.root.parentNode}};bt._openStack=[];Object.freeze(new Set);function ft(t){return t.startsWith("[")&&t.endsWith("]")||1===t.length&&/^[A-Za-z]$/.test(t)?t:`[${t}]`}function mt(t,e,i){return`${ft(t)}(${ft(e)})${ft(i)}`}var gt="http://www.w3.org/2000/svg",yt={sugar:s,base:l,linker:o},vt={sugar:["r","R"],base:["A"],linker:["p","P"]},wt={x:70,y:60},At={x:140,y:60},St={x:70,y:130},Ct=class t{constructor(t,e,i){this.onValueSet=new u,this.onPickModeChange=new u,this._slots=new Map,this._favStar=null,this._pickMode=null,this._destroyed=!1,this._builderRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??lt(t),this._hooks=i?.paletteHooks??null,this._favHooks=i?.favoriteHooks??null,this.element=ot(this._doc,"div",{class:"hw-rna-builder","data-testid":"rna-builder"});let r=ot(this._doc,"div",{class:"hw-rna-builder__header"});if(r.appendChild(ot(this._doc,"div",{class:"hw-rna-builder__title"},["RNA builder"])),null!==this._favHooks){let t=ot(this._doc,"span",{class:"hw-rna-builder__fav hw-rna-builder__fav--disabled",role:"button",tabindex:"0","data-testid":"rna-builder-fav-star",title:"Favorite this triplet","aria-pressed":"false","aria-disabled":"true"},["☆"]),e=t=>{t.stopPropagation();let e=this.getSelection();""===e.preview||null===this._favHooks||this._favHooks.toggleFavoriteTriplet(e.sugar,e.base,e.linker)};t.addEventListener("click",e),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&e(t)}),this._favStar=t,r.appendChild(t)}this.element.appendChild(r),this._hintEl=ot(this._doc,"div",{class:"hw-rna-builder__hint","data-testid":"rna-builder-hint",hidden:!0}),this.element.appendChild(this._hintEl);let s=this._buildSvg();this.element.appendChild(s),this._preview=ot(this._doc,"div",{class:"hw-rna-builder__preview","data-testid":"rna-builder-preview"}),this.element.appendChild(this._preview),this._addBtn=ot(this._doc,"button",{class:"hw-rna-builder__add",type:"button","data-testid":"rna-builder-add-btn"},["Add triplet"]),this._addBtn.addEventListener("click",()=>this._onAddClicked()),this.element.appendChild(this._addBtn),t.appendChild(this.element);let l=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),o=e.on("theme:change",()=>{this._destroyed||this._repaintSlotColors()});this._libUnsub=()=>{try{l()}catch{}try{o()}catch{}},this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}refresh(){this._populateDefaults(),this._updatePreview(),this._repaintSlotColors()}getSelection(){let t=this._slots.get("sugar")?.value??"",e=this._slots.get("base")?.value??"",i=this._slots.get("linker")?.value??"";return{sugar:t,base:e,linker:i,preview:""!==t&&""!==e&&""!==i?mt(t,e,i):""}}setField(t,e){let i=this._slots.get(t);void 0!==i&&(i.value=e,this._setLabelText(i.labelEl,e),this._repaintSlot(i),this._updatePreview(),this.onValueSet.next({field:t,symbol:e}))}startPickMode(t){this._pickMode!==t?(null!==this._pickMode&&this._setSlotPressed(this._pickMode,!1),this._pickMode=t,this._setSlotPressed(t,!0),this._setHintActive(t),this.onPickModeChange.next({field:t}),null!==this._hooks&&this._hooks.beginBiotypeFilter(yt[t],e=>{this.setField(t,e),this._exitPickMode()},()=>{this._exitPickMode()})):this.cancelPickMode()}cancelPickMode(){null!==this._pickMode&&(null!==this._hooks&&this._hooks.endBiotypeFilter(),this._exitPickMode())}getPickMode(){return this._pickMode}triggerAdd(){this._onAddClicked()}destroy(){this._destroyed||(this._destroyed=!0,null!==this._pickMode&&null!==this._hooks&&this._hooks.endBiotypeFilter(),this._libUnsub(),this.onValueSet.complete(),this.onPickModeChange.complete(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}_buildSvg(){let t=this._doc.createElementNS(gt,"svg");t.setAttribute("class","hw-rna-builder__triplet"),t.setAttribute("viewBox","0 0 200 180"),t.setAttribute("data-testid","rna-builder-triplet-svg"),t.setAttribute("role","group"),t.setAttribute("aria-label","Triplet preview");let e=this._doc.createElementNS(gt,"line");e.setAttribute("class","hw-rna-builder__bond"),e.setAttribute("x1",String(wt.x+18)),e.setAttribute("y1",String(wt.y)),e.setAttribute("x2",String(At.x-18)),e.setAttribute("y2",String(At.y)),t.appendChild(e);let i=this._doc.createElementNS(gt,"line");i.setAttribute("class","hw-rna-builder__bond"),i.setAttribute("x1",String(wt.x)),i.setAttribute("y1",String(wt.y+18)),i.setAttribute("x2",String(St.x)),i.setAttribute("y2",String(St.y-22)),t.appendChild(i);let r=this._doc.createElementNS(gt,"rect");r.setAttribute("class","hw-rna-builder__slot-shape"),r.setAttribute("x",String(-18)),r.setAttribute("y",String(-18)),r.setAttribute("width",String(36)),r.setAttribute("height",String(36)),r.setAttribute("rx","8"),r.setAttribute("ry","8");let s=this._buildSlot("sugar","Pick sugar (backbone)",wt,r),l=this._doc.createElementNS(gt,"circle");l.setAttribute("class","hw-rna-builder__slot-shape"),l.setAttribute("cx","0"),l.setAttribute("cy","0"),l.setAttribute("r",String(18));let o=this._buildSlot("linker","Pick linker",At,l),n=this._doc.createElementNS(gt,"path");n.setAttribute("class","hw-rna-builder__slot-shape"),n.setAttribute("d","M -22 0 L 0 -22 L 22 0 L 0 22 Z");let a=this._buildSlot("base","Pick base",St,n);return t.appendChild(o.groupEl),t.appendChild(s.groupEl),t.appendChild(a.groupEl),this._slots.set("sugar",s),this._slots.set("linker",o),this._slots.set("base",a),t}_buildSlot(t,e,i,r){let s=this._doc.createElementNS(gt,"g");s.setAttribute("class","hw-rna-builder__slot"),s.setAttribute("data-slot",t),s.setAttribute("data-testid",`rna-builder-slot-${t}`),s.setAttribute("role","button"),s.setAttribute("tabindex","0"),s.setAttribute("aria-label",e),s.setAttribute("aria-pressed","false"),s.setAttribute("transform",`translate(${i.x} ${i.y})`),s.appendChild(r);let l=this._doc.createElementNS(gt,"text");l.setAttribute("class","hw-rna-builder__slot-label"),l.setAttribute("data-testid",`rna-builder-${t}-value`),l.setAttribute("x","0"),l.setAttribute("y","0"),l.setAttribute("text-anchor","middle"),l.setAttribute("dominant-baseline","central"),s.appendChild(l);let o=e=>{e.stopPropagation(),this.startPickMode(t)};return s.addEventListener("click",o),s.addEventListener("keydown",t=>{let e=t;("Enter"===e.key||" "===e.key)&&o(t)}),s.addEventListener("mouseenter",e=>this._showSlotTooltip(t,e)),s.addEventListener("mouseleave",()=>this._hideSlotTooltip()),s.addEventListener("focus",()=>this._showSlotTooltip(t,null)),s.addEventListener("blur",()=>this._hideSlotTooltip()),{id:t,biotype:yt[t],groupEl:s,shapeEl:r,labelEl:l,value:""}}_setLabelText(t,e){let i=[];for(let e=t.firstChild;null!==e;e=e.nextSibling)"title"===e.nodeName||"TITLE"===e.nodeName||i.push(e);for(let e of i)t.removeChild(e);let r=function(t){let e=t.length;return e<=2?16:e<=4?11:e<=7?8:e<=10?6:5}(e);t.setAttribute("font-size",String(r)),t.setAttribute("text-anchor","middle"),t.setAttribute("dominant-baseline","central");let s=e.length>10?`${e.slice(0,9)}…`:e;t.appendChild(this._doc.createTextNode(s));let l=t.parentNode;if(null!==l){let t=null;for(let e=l.firstChild;null!==e;e=e.nextSibling)if("title"===e.nodeName||"TITLE"===e.nodeName){t=e;break}for(null===t&&(t=this._doc.createElementNS(gt,"title"),l.insertBefore(t,l.firstChild));null!==t.firstChild;)t.removeChild(t.firstChild);t.appendChild(this._doc.createTextNode(e))}}_repaintSlotColors(){for(let t of this._slots.values())this._repaintSlot(t)}_repaintSlot(t){let e=this._editor.getService().monomerLib,i=this._theme(),r=""===t.value?null:function(t,e,i){return t.getMonomerSet(e).get(i)??null}(e,t.biotype,t.value),s=F(r,t.biotype,i.colorTheme);t.shapeEl.style.fill=s.background,t.shapeEl.style.stroke=s.line,t.labelEl.style.fill=s.text}_populateDefaults(){let t=this._editor.getService().monomerLib;for(let[e,i]of this._slots.entries()){let r=Tt(t,i.biotype),s=Et(r,vt[e]),l=""!==i.value&&r.some(t=>t.symbol===i.value)?i.value:s??r[0]?.symbol??"";i.value=l,this._setLabelText(i.labelEl,l)}}_updatePreview(){let t=this.getSelection();for(;null!==this._preview.firstChild;)this._preview.removeChild(this._preview.firstChild);this._preview.appendChild(this._doc.createTextNode(""===t.preview?"-":t.preview)),this._updateFavStar(t)}_updateFavStar(t){if(null===this._favStar||null===this._favHooks)return;let e=""!==t.preview,i=e&&this._favHooks.isFavoriteTriplet(t.sugar,t.base,t.linker);for(;null!==this._favStar.firstChild;)this._favStar.removeChild(this._favStar.firstChild);this._favStar.appendChild(this._doc.createTextNode(i?"★":"☆")),this._favStar.setAttribute("aria-pressed",i?"true":"false"),e?this._favStar.removeAttribute("aria-disabled"):this._favStar.setAttribute("aria-disabled","true");let r="hw-rna-builder__fav"+(i?" hw-rna-builder__fav--active":"")+(e?"":" hw-rna-builder__fav--disabled");this._favStar.setAttribute("class",r)}_onAddClicked(){let t=this.getSelection();""!==t.preview&&this._editor.placeRnaTriplet(t.sugar,t.base,t.linker)}_exitPickMode(){if(null===this._pickMode)return;let t=this._pickMode;this._setSlotPressed(t,!1),this._pickMode=null,this._setHintActive(null),this.onPickModeChange.next({field:null})}_setHintActive(t){let e=this._hintEl;for(;null!==e.firstChild;)e.removeChild(e.firstChild);if(null===t)return void e.setAttribute("hidden","");e.removeAttribute("hidden");let i="sugar"===t?"sugar":"base"===t?"base":"linker";e.appendChild(this._doc.createTextNode(`Pick ${i} from palette`))}_setSlotPressed(t,e){let i=this._slots.get(t);if(void 0===i)return;i.groupEl.setAttribute("aria-pressed",e?"true":"false");let r=(i.groupEl.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-rna-builder__slot--active"!==t).join(" ");i.groupEl.setAttribute("class",e?`${r} hw-rna-builder__slot--active`:r)}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_builderRdkitSvgFor(e){if(null===e)return null;let i=e.smiles;if(void 0===i||""===i)return null;let r=this._rdkit();if(null===r)return null;let s=`${e.polymerType}:${e.symbol}`;if(this._builderRdkitCache.has(s))return this._builderRdkitCache.get(s)??null;let l=nt(r,i,220,140);if(this._builderRdkitCache.size>=t._BUILDER_RDKIT_CACHE_LIMIT){let t=this._builderRdkitCache.keys().next().value;void 0!==t&&this._builderRdkitCache.delete(t)}return this._builderRdkitCache.set(s,l),l}_slotHint(t){switch(t){case"sugar":return"Click to choose a different sugar";case"base":return"Click to choose a different base";case"linker":return"Click to choose a different linker"}}_slotTitle(t,e){let i=""===e?"?":e;switch(t){case"sugar":return`Sugar: ${i}`;case"base":return`Base: ${i}`;case"linker":return`Linker: ${i}`}}_showSlotTooltip(t,e){let i=this._slots.get(t);if(void 0===i)return;let r=this._editor.getService().monomerLib.getMonomerSet(i.biotype),s=""===i.value?null:r.get(i.value)??null,l=at(this._doc,"builder-tooltip","hw-builder-tooltip");ht(this._doc,l,{symbol:this._slotTitle(t,i.value),name:s?.name??"",rdkitSvg:this._builderRdkitSvgFor(s),rdkitTestid:"builder-tooltip-rdkit-svg",hint:this._slotHint(t)});let o=e;if(null!==o&&"number"==typeof o.clientX&&"number"==typeof o.clientY)dt(l,o.clientX,o.clientY);else{let t=i.groupEl,e="function"==typeof t.getBoundingClientRect?t.getBoundingClientRect():null;null!==e?dt(l,e.left+e.width/2,e.top+e.height/2):dt(l,0,0)}}_hideSlotTooltip(){ut(this._doc.body.querySelector('[data-testid="builder-tooltip"]'))}};Ct._BUILDER_RDKIT_CACHE_LIMIT=256;var kt=Ct;function Tt(t,e){let i=t.getMonomerSet(e),r=[];for(let t of i.values())r.push(t);return r.sort((t,e)=>t.symbol.localeCompare(e.symbol)),r}function Et(t,e){let i=new Set;for(let e of t)i.add(e.symbol);for(let t of e)if(i.has(t))return t;return null}var Nt="Favorites",Mt={[Nt]:"★ Favorites",[d.PEPTIDE]:"Peptides",[d.RNA]:"RNA",[d.CHEM]:"CHEM",[d.BLOB]:"BLOB",G:"G"},It=[Nt,d.PEPTIDE,d.RNA,d.CHEM,d.BLOB,"G"],Bt="hwe:palette:favorites",xt="hwe:palette:active-tab";function Lt(t){return`${t.sugar}|${t.base}|${t.linker}`}var Pt=class t{constructor(t,e,i){this.favoritesChanged=new u,this._nextAddUnsub=()=>{},this._favorites=new Set,this._favoriteTriplets=[],this._pendingRnaSelection=null,this._visibleTabs=[Nt],this._activeTab=Nt,this._searchInput=null,this._filter="",this._destroyed=!1,this._rnaBuilder=null,this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,this._pickEscapeListener=null,this._pickOutsideClickListener=null,this._paletteRdkitCache=new Map,this._editor=e,this._doc=i?.documentImpl??lt(t),this._opts={documentImpl:this._doc,groupByNaturalAnalog:i?.groupByNaturalAnalog??!0,allowFavorites:i?.allowFavorites??!0},this._loadFavorites(),this._activeTab=this._resolveInitialTab(i?.initialTab),this.element=ot(this._doc,"div",{class:"hw-palette","data-testid":"palette"}),t.appendChild(this.element),this._render(),this._libUnsub=e.getService().monomerLib.onChanged.subscribe(()=>{this._destroyed||this.refresh()}),this._themeUnsub=e.on("theme:change",()=>{this._destroyed||this.refresh()}),this._nextAddUnsub=e.on("option:change",t=>{this._destroyed||"nextAdd"===t.key&&this._updatePrimedClasses()})}refresh(){this._render()}setFilter(t){this._filter=t.trim().toLowerCase(),null!==this._searchInput&&this._searchInput.value!==t&&(this._searchInput.value=t),this._applyFilter()}setActiveTab(t){this._visibleTabs.includes(t)&&(this._activeTab=t,this._persistActiveTab(),this._applyActiveTabClasses(),this._applyFilter())}getActiveTab(){return this._activeTab}getFavorites(){let t=this._editor.getService().monomerLib,e=[];for(let i of this._favorites)null!==this._findMonomer(t,i)&&e.push(i);return e}setFavorite(t,e){e!==this._favorites.has(t)&&(e?this._favorites.add(t):this._favorites.delete(t),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}clearFavorites(){0===this._favorites.size&&0===this._favoriteTriplets.length||(this._favorites.clear(),this._favoriteTriplets.length=0,this._saveFavorites(),this._render(),this._emitFavoritesChanged())}getFavoriteTriplets(){return this._favoriteTriplets.map(t=>({...t}))}isFavoriteTriplet(t,e,i){let r=Lt({sugar:t,base:e,linker:i});return this._favoriteTriplets.some(t=>Lt(t)===r)}setFavoriteTriplet(t,e,i,r){let s=Lt({sugar:t,base:e,linker:i}),l=this._favoriteTriplets.findIndex(t=>Lt(t)===s);r!==l>=0&&(r?this._favoriteTriplets.push({sugar:t,base:e,linker:i}):this._favoriteTriplets.splice(l,1),this._saveFavorites(),this._hidePaletteTooltips(),this._render(),this._emitFavoritesChanged())}_hidePaletteTooltips(){let t=this._doc.body;ut(t.querySelector('[data-testid="palette-tooltip"]')),ut(t.querySelector('[data-testid="palette-triplet-tooltip"]'))}_emitFavoritesChanged(){this.favoritesChanged.next({favorites:this.getFavorites(),triplets:this.getFavoriteTriplets()})}destroy(){this._destroyed||(this._destroyed=!0,null!==this._rnaBuilder&&(this._rnaBuilder.destroy(),this._rnaBuilder=null),this._libUnsub(),this._themeUnsub(),this._nextAddUnsub(),null!==this.element.parentNode&&this.element.parentNode.removeChild(this.element))}getRnaBuilder(){return this._rnaBuilder}hasActiveBiotypeFilter(){return null!==this._activeBiotypeFilter}getActiveBiotypeFilter(){return this._activeBiotypeFilter}cancelBiotypeFilter(){if(null===this._activeBiotypeFilter)return;let t=this._pickCanceller;this._teardownPickMode(),t?.()}_buildPaletteFilterHooks(){return{beginBiotypeFilter:(t,e,i)=>{null!==this._activeBiotypeFilter&&this._teardownPickMode(),this._activeBiotypeFilter=t,this._pickResolver=e,this._pickCanceller=i,this._applyFilter();let r=t=>{"Escape"===t.key&&this.cancelBiotypeFilter()};this._pickEscapeListener=r,this._doc.defaultView?.addEventListener("keydown",r);let s=t=>{if(null===this._activeBiotypeFilter)return;let e=t.target;if(null==e)return;let i=this._activeBiotypeFilter,r=e;for(;null!==r;){let t=void 0===r.getAttribute?null:r.getAttribute("class");if(null!==t){let e=t.split(/\s+/);if(e.includes("hw-palette__tile")){if((r.getAttribute("data-biotype")??"")===i)return;break}if(e.includes("hw-rna-builder__slot")){if(this._isInsideOwnPalette(r))return;break}}r=r.parentElement}this.cancelBiotypeFilter()};this._pickOutsideClickListener=s,this._doc.addEventListener("mousedown",s,!0)},endBiotypeFilter:()=>this._teardownPickMode()}}_scrollActivePaneToTop(){let t=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`);if(null===t)return;let e=t;try{if("function"==typeof e.scrollTo)return void e.scrollTo({top:0,behavior:"smooth"})}catch{}"number"==typeof e.scrollTop&&(e.scrollTop=0)}_isInsideOwnPalette(t){let e=t;for(;null!==e;){if(e===this.element)return!0;e=e.parentElement}return!1}_teardownPickMode(){null!==this._activeBiotypeFilter&&(this._activeBiotypeFilter=null,this._pickResolver=null,this._pickCanceller=null,null!==this._pickEscapeListener&&(this._doc.defaultView?.removeEventListener("keydown",this._pickEscapeListener),this._pickEscapeListener=null),null!==this._pickOutsideClickListener&&(this._doc.removeEventListener("mousedown",this._pickOutsideClickListener,!0),this._pickOutsideClickListener=null),this._applyFilter())}_render(){for(null!==this._rnaBuilder&&(this._pendingRnaSelection=this._rnaBuilder.getSelection(),this._rnaBuilder.destroy(),this._rnaBuilder=null);null!==this.element.firstChild;)this.element.removeChild(this.element.firstChild);let t=this._doc.createElement("input");t.setAttribute("type","search"),t.setAttribute("class","hw-palette__search"),t.setAttribute("placeholder","Search monomers..."),t.setAttribute("data-testid","palette-search"),""!==this._filter&&(t.value=this._filter),t.addEventListener("input",()=>this.setFilter(t.value)),this._searchInput=t,this.element.appendChild(t),this._visibleTabs=this._computeVisibleTabs(),this._visibleTabs.includes(this._activeTab)||(this._activeTab=Nt);let e=ot(this._doc,"div",{class:"hw-palette__tabs",role:"tablist","data-testid":"palette-tabs"});for(let t of this._visibleTabs){let i=t===this._activeTab,r=ot(this._doc,"button",{class:"hw-palette__tab",type:"button",role:"tab","aria-controls":`hw-palette-pane-${t}`,"aria-selected":i?"true":"false","data-testid":`palette-tab-${t}`,"data-tab":t,title:Mt[t]},[Mt[t]]);r.addEventListener("click",()=>this.setActiveTab(t)),e.appendChild(r)}this.element.appendChild(e);let i=ot(this._doc,"div",{class:"hw-palette__panes"}),r=this._theme(),s=this._editor.getService().monomerLib;for(let t of this._visibleTabs){let e=t===this._activeTab,l=ot(this._doc,"div",{class:"hw-palette__pane",id:`hw-palette-pane-${t}`,role:"tabpanel","data-testid":`palette-pane-${t}`,"data-tab":t,hidden:!e});t===Nt?this._buildFavoritesPane(l,s,r):this._buildPolymerPane(l,t,s,r),i.appendChild(l)}this.element.appendChild(i),this._applyFilter()}_computeVisibleTabs(){let t=this._editor.getService().monomerLib,e=new Set;for(let i of t.getPolymerTypes())e.add(i);let i=[];i.push(Nt);for(let t of It)t!==Nt&&e.has(t)&&i.push(t);return i}_buildFavoritesPane(t,e,i){let r=this._resolveFavoriteMonomers(e),s=this._favoriteTriplets;if(0===r.length&&0===s.length){let e=ot(this._doc,"div",{class:"hw-palette__placeholder","data-testid":"palette-favorites-empty"},["No favorites yet — click the ☆ on any tile to add one."]);return void t.appendChild(e)}for(let[e,i]of this._groupByPolymerAndType(r))t.appendChild(this._renderGroup(e,i));s.length>0&&t.appendChild(this._renderTripletGroup("RNA · Triplets",s,e))}_groupByPolymerAndType(t){let e=new Map;for(let i of t){let t=i.polymerType,r=i.monomerType??"Undefined",s=`${t}|${r}`,l=e.get(s);void 0===l&&(l={pt:t,mt:r,list:[]},e.set(s,l)),l.list.push(i)}let i=t=>{let e=It.indexOf(t);return e<0?99:e},r={Backbone:0,Branch:1,Terminal:2,Undefined:3};return Array.from(e.values()).sort((t,e)=>i(t.pt)-i(e.pt)||(r[t.mt]??9)-(r[e.mt]??9)||t.mt.localeCompare(e.mt)).map(t=>[`${this._polymerLabel(t.pt)} · ${t.mt}`,t.list])}_polymerLabel(t){return Mt[t]??t}_renderTripletGroup(t,e,i){let r=ot(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),s=ot(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),l=ot(this._doc,"div",{class:"hw-triplet-chips","data-testid":"palette-triplet-favorites"});for(let t of e)l.appendChild(this._renderTripletChip(t,i));return r.appendChild(s),r.appendChild(l),r}_renderTripletChip(t,e){let i=mt(t.sugar,t.base,t.linker),r=e.getMonomerSet(l).get(t.base)??null,s=F(r,l,this._theme().colorTheme),o=this.isFavoriteTriplet(t.sugar,t.base,t.linker),n=void 0!==r?.name&&""!==r.name?`${i} — ${r.name}`:i,{root:a}=function(t,e){let i=!1!==e.showStar,r=ot(t,"span",{class:"hw-triplet-chip__star"},[e.favorite?"★":"☆"]),s=ot(t,"span",{class:"hw-triplet-chip__label"},[e.label]),l=["hw-triplet-chip"];e.favorite&&l.push("hw-triplet-chip--favorite");let o=i?[r,s]:[s];return{root:ot(t,"div",{class:l.join(" "),role:"button",tabindex:"0","aria-label":e.title,"data-sugar":e.sugar,"data-base":e.base,"data-linker":e.linker,"data-triplet":e.label,"data-testid":`palette-triplet-${e.label}`,title:e.title,style:`background:${e.background};color:${e.textColor};`},o),star:r}}(this._doc,{sugar:t.sugar,base:t.base,linker:t.linker,label:i,title:n,background:v(s.background),textColor:s.text,favorite:o,showStar:this._opts.allowFavorites});return this._wireTripletChip(a,t),a}_wireTripletChip(t,e){t.addEventListener("mouseenter",t=>{let i=t,r=at(this._doc,"palette-triplet-tooltip","hw-palette-tooltip hw-triplet-tooltip");(function(t,e,i){for(;null!==e.firstChild;)e.removeChild(e.firstChild);e.appendChild(ot(t,"div",{class:"hw-tooltip__symbol"},[i.title]));let r=ot(t,"div",{class:"hw-tooltip__triplet"});for(let e of i.parts){let s=ot(t,"div",{class:"hw-tooltip__triplet-part"});if(s.appendChild(ot(t,"div",{class:"hw-tooltip__triplet-role"},[`${e.role}: ${e.symbol}`])),void 0!==e.name&&""!==e.name&&e.name!==e.symbol&&s.appendChild(ot(t,"div",{class:"hw-tooltip__name"},[e.name])),void 0!==e.rdkitSvg&&null!==e.rdkitSvg&&""!==e.rdkitSvg){let r={class:"hw-tooltip__rdkit"};void 0!==i.rdkitTestid&&(r["data-testid"]=i.rdkitTestid);let l=ot(t,"div",r);l.innerHTML=e.rdkitSvg,s.appendChild(l)}r.appendChild(s)}e.appendChild(r),void 0!==i.hint&&""!==i.hint&&e.appendChild(ot(t,"div",{class:"hw-tooltip__hint"},[i.hint]))})(this._doc,r,{title:mt(e.sugar,e.base,e.linker),parts:this._tripletTooltipParts(e),hint:"Click to add this triplet",rdkitTestid:"palette-triplet-tooltip-rdkit-svg"}),dt(r,"number"==typeof i.clientX?i.clientX:0,"number"==typeof i.clientY?i.clientY:0)}),t.addEventListener("mouseleave",()=>{ut(this._doc.body.querySelector('[data-testid="palette-triplet-tooltip"]'))}),t.addEventListener("click",t=>{let i=t.target;if(this._opts.allowFavorites&&!0===i?.classList?.contains("hw-triplet-chip__star"))return this.setFavoriteTriplet(e.sugar,e.base,e.linker,!this.isFavoriteTriplet(e.sugar,e.base,e.linker)),void t.stopPropagation();this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)}),t.addEventListener("keydown",t=>{let i=t;("Enter"===i.key||" "===i.key)&&this._editor.placeRnaTriplet(e.sugar,e.base,e.linker)})}_buildRnaDefaultChips(e){let i=this._pickSymbol(e.getMonomerSet(s),["r","R"]),r=this._pickSymbol(e.getMonomerSet(o),["p","P"]),n=e.getMonomerSet(l);if(null===i||null===r)return null;let a=t._DEFAULT_TRIPLET_BASES.filter(t=>n.has(t));if(0===a.length)return null;let h=ot(this._doc,"div",{class:"hw-triplet-chips hw-triplet-chips--defaults","data-testid":"rna-default-triplets"});for(let t of a)h.appendChild(this._renderTripletChip({sugar:i,base:t,linker:r},e));return h}_tripletTooltipParts(t){let e=this._editor.getService().monomerLib,i=(t,i,r)=>{let s=e.getMonomerSet(i).get(r)??null;return{role:t,symbol:r,...void 0!==s?.name?{name:s.name}:{},rdkitSvg:null===s?null:this._paletteRdkitSvg(s)}};return[i("Sugar",s,t.sugar),i("Base",l,t.base),i("Linker",o,t.linker)]}_pickSymbol(t,e){for(let i of e)if(t.has(i))return i;let i=t.keys().next();return!0===i.done?null:i.value}_restoreRnaSelection(){let t=this._pendingRnaSelection;if(this._pendingRnaSelection=null,null===t||null===this._rnaBuilder)return;let e=this._editor.getService().monomerLib;""!==t.sugar&&e.getMonomerSet(s).has(t.sugar)&&this._rnaBuilder.setField("sugar",t.sugar),""!==t.base&&e.getMonomerSet(l).has(t.base)&&this._rnaBuilder.setField("base",t.base),""!==t.linker&&e.getMonomerSet(o).has(t.linker)&&this._rnaBuilder.setField("linker",t.linker)}_resolveFavoriteMonomers(t){let e=[];for(let i of this._favorites){let r=this._findMonomer(t,i);null!==r&&e.push(r)}return e}_findMonomer(t,e){for(let i of t.getPolymerTypes()){let r=t.getMonomer(i,e);if(null!==r)return r}return null}_buildPolymerPane(t,e,i,r){let s=e,l=this._monomersForPolymer(s,i);if(0===l.length)return;if(s===d.RNA){this._rnaBuilder=new kt(t,this._editor,{documentImpl:this._doc,paletteHooks:this._buildPaletteFilterHooks(),favoriteHooks:this._opts.allowFavorites?{isFavoriteTriplet:(t,e,i)=>this.isFavoriteTriplet(t,e,i),toggleFavoriteTriplet:(t,e,i)=>this.setFavoriteTriplet(t,e,i,!this.isFavoriteTriplet(t,e,i))}:null}),this._restoreRnaSelection();let e=this._buildRnaDefaultChips(i);null!==e&&t.appendChild(e);let r=this._groupRna(l);for(let[e,i]of r)0!==i.length&&t.appendChild(this._renderGroup(e,i));return}if(s===d.PEPTIDE&&this._opts.groupByNaturalAnalog){let e=this._groupByAnalog(l);for(let[i,r]of e){let e=""===i?"Other":i;t.appendChild(this._renderGroup(e,r))}return}let o=ot(this._doc,"div",{class:"hw-palette__group-tiles"}),n=this._editor.getNextAddSymbol(),a=this._sortByColor(l);for(let t of a){let e=this._biotype(t,s);o.appendChild(this._renderTile(t,e,n))}t.appendChild(o)}_renderGroup(t,e){let i=ot(this._doc,"div",{class:"hw-palette__group","data-natural-analog":t}),r=ot(this._doc,"div",{class:"hw-palette__group-header","data-testid":`palette-group-${t}`},[t]),s=ot(this._doc,"div",{class:"hw-palette__group-tiles"}),l=this._editor.getNextAddSymbol(),o=this._sortByColor(e);for(let t of o){let e=this._biotype(t,t.polymerType);s.appendChild(this._renderTile(t,e,l))}return i.appendChild(r),i.appendChild(s),i}_sortByColor(t){let e=this._theme(),i=t.map((t,i)=>{let r=function(t){let e=_(t);if(null===e)return{h:0,s:0,l:0};let[i,r,s]=m(e[0],e[1],e[2]);return{h:i,s:r,l:s}}(F(t,this._biotype(t,t.polymerType),e.colorTheme).background),s=0===r.s?1:0;return{m:t,idx:i,h:r.h,s:r.s,l:r.l,isGrey:s}});return i.sort((t,e)=>t.isGrey!==e.isGrey?t.isGrey-e.isGrey:t.h!==e.h?t.h-e.h:t.s!==e.s?t.s-e.s:t.l!==e.l?t.l-e.l:t.idx-e.idx),i.map(t=>t.m)}_monomersForPolymer(t,e){let i=e.getMonomerSymbolsByType(t),r=[];for(let s of i){let i=e.getMonomer(t,s);null!==i&&r.push(i)}return r.sort((t,e)=>t.symbol.localeCompare(e.symbol)),r}_groupByAnalog(t){let e=new Map;for(let i of t){let t=i.naturalAnalog??"",r=e.get(t);void 0===r&&(r=[],e.set(t,r)),r.push(i)}let i=[],r=Array.from(e.keys()).sort((t,e)=>""===t&&""!==e?1:""===e&&""!==t?-1:t.localeCompare(e));for(let t of r)i.push([t,e.get(t)]);return new Map(i)}_groupRna(t){let e=[],i=[],r=[],n=[];for(let a of t){let t=$(a);t===s?e.push(a):t===l?i.push(a):t===o?r.push(a):n.push(a)}let a=new Map;return a.set("Backbones",e),a.set("Bases",i),a.set("Linkers",r),n.length>0&&a.set("Other",n),a}_renderTile(t,e,i){let r=this._favorites.has(t.symbol),s=null!==i&&i.symbol===t.symbol&&i.biotype===e,{root:l,star:o}=function(t,e){let i=F(e.monomer,e.biotype,e.theme.colorTheme),r=v(i.background),s=i.text,l=function(t,e){let i=w(t),r=w(e);return(Math.max(i,r)+.05)/(Math.min(i,r)+.05)}(s,r)<5,o=e.monomer.symbol,n=function(t){return t<=3?14:t<=6?11:t<=9?9:8}(o.length),a=`font-size:${n}px;${o.length>=10?"line-height:1.1;letter-spacing:-0.02em;":""}white-space:nowrap;overflow:hidden;text-overflow:ellipsis;max-width:80px;display:inline-block;`,h=ot(t,"span",{class:"hw-palette__star"},[e.favorite?"★":"☆"]),d=ot(t,"span",{class:"hw-palette__label",style:a},[o]),u=["hw-palette__tile"];e.primed&&u.push("hw-palette__tile--primed"),e.favorite&&u.push("hw-palette__tile--favorite"),l&&u.push("hw-palette__tile--low-contrast");let c=void 0!==e.monomer.name?`${o} — ${e.monomer.name}`:o,p=`background:${r};color:${s};width:100%;min-width:48px;padding:4px 6px;height:40px;box-sizing:border-box;overflow:hidden;text-overflow:ellipsis;`;return{root:ot(t,"div",{class:u.join(" "),draggable:"true",role:"button","aria-pressed":e.primed?"true":"false","aria-label":c,"data-symbol":o,"data-biotype":e.biotype,"data-bg":r,"data-raw-bg":i.background,"data-testid":`palette-tile-${o}`,title:c,style:p},[h,d]),star:h}}(this._doc,{monomer:t,biotype:e,theme:this._theme(),favorite:r,primed:s});return this._wireTile(l,o,t,e),l}_rdkit(){let t=this._editor.getService().options?.rdkitModule;return t??null}_paletteRdkitSvg(e){let i=e.smiles;if(void 0===i||""===i)return null;let r=this._rdkit();if(null===r)return null;let s=`${e.polymerType}:${e.symbol}`;if(this._paletteRdkitCache.has(s))return this._paletteRdkitCache.get(s)??null;let l=nt(r,i,220,140);if(this._paletteRdkitCache.size>=t._PALETTE_RDKIT_CACHE_LIMIT){let t=this._paletteRdkitCache.keys().next().value;void 0!==t&&this._paletteRdkitCache.delete(t)}return this._paletteRdkitCache.set(s,l),l}_wireTile(t,e,i,r){t.addEventListener("mouseenter",t=>{let e=t,r=at(this._doc,"palette-tooltip","hw-palette-tooltip");ht(this._doc,r,{symbol:i.symbol,name:i.name??"",rdkitSvg:this._paletteRdkitSvg(i),rdkitTestid:"palette-tooltip-rdkit-svg"}),dt(r,"number"==typeof e.clientX?e.clientX:0,"number"==typeof e.clientY?e.clientY:0)}),t.addEventListener("mouseleave",()=>{ut(this._doc.body.querySelector('[data-testid="palette-tooltip"]'))}),t.addEventListener("click",t=>{let e=t.target;if(this._opts.allowFavorites&&void 0!==e&&!0===e?.classList?.contains("hw-palette__star"))return this.setFavorite(i.symbol,!this._favorites.has(i.symbol)),void t.stopPropagation();if(null!==this._activeBiotypeFilter&&this._activeBiotypeFilter===r){let e=this._pickResolver;return this._teardownPickMode(),e?.(i.symbol),this._scrollActivePaneToTop(),void t.stopPropagation()}let s=this._editor.getSelection();if(s.atoms.size>0){let e=this._editor.getMol(),l=[];for(let t of s.atoms){let i=e.atoms.find(e=>e.id===t);void 0!==i&&l.push(i)}return l.length>0&&l.every(t=>t.biotype===r)?(this._editor.replaceMonomers(l,i.symbol),void t.stopPropagation()):(this._editor.fire("editor:status",{message:`Cannot bulk-replace ${l.length} selected atom(s) with ${i.symbol}: selection contains incompatible biotypes for ${r}.`,severity:"warn",durationMs:3e3}),void t.stopPropagation())}let l=this._editor.getNextAddSymbol();if(null!==l&&l.symbol===i.symbol&&l.biotype===r)return this._editor.setNextAddSymbol(null),void this._updatePrimedClasses();this._editor.setNextAddSymbol(i.symbol,r),this._updatePrimedClasses()}),t.addEventListener("dragstart",t=>{let e=t.dataTransfer;if(null!=e)try{e.setData("application/x-hwe-monomer",JSON.stringify({symbol:i.symbol,biotype:r})),e.effectAllowed="copy"}catch{}ut(this._doc.body.querySelector('[data-testid="palette-tooltip"]')),this._editor.startPaletteDrag(i.symbol,r)})}_biotype(t,e){let i=$(t);if(null!==i)return i;switch(e){case d.PEPTIDE:return r;case d.RNA:return s;case d.CHEM:return n;case d.BLOB:return a;default:return n}}_theme(){let t=this._editor;return"function"==typeof t._currentTheme?t._currentTheme():this._editor.getService().theme}_applyFilter(){let t=this._filter,e=this._activeBiotypeFilter,i=this.element.querySelector(`.hw-palette__pane[data-tab="${this._activeTab}"]`),r=(i??this.element).querySelectorAll(".hw-palette__tile");for(let i=0;i<r.length;i++){let s=r[i],l=(s.getAttribute("data-symbol")??"").toLowerCase(),o=(s.getAttribute("title")??"").toLowerCase(),n=s.getAttribute("data-biotype")??"",a=(""===t||l.indexOf(t)>=0||o.indexOf(t)>=0)&&(null===e||n===e);s.style.display=a?"":"none"}let s=(i??this.element).querySelectorAll(".hw-triplet-chip");for(let i=0;i<s.length;i++){let r=s[i],l=[r.getAttribute("data-triplet")??"",r.getAttribute("data-sugar")??"",r.getAttribute("data-base")??"",r.getAttribute("data-linker")??""].join(" ").toLowerCase(),o=(""===t||l.indexOf(t)>=0)&&null===e;r.style.display=o?"":"none"}let l=(i??this.element).querySelectorAll(".hw-palette__group");for(let t=0;t<l.length;t++){let e=l[t],i=e.querySelectorAll(".hw-palette__tile, .hw-triplet-chip"),r=!1;for(let t=0;t<i.length;t++)if("none"!==i[t].style.display){r=!0;break}r?(e.removeAttribute("hidden"),e.removeAttribute("data-section-empty")):(e.setAttribute("hidden",""),e.setAttribute("data-section-empty","true"))}}_updatePrimedClasses(){let t=this._editor.getNextAddSymbol(),e=this.element.querySelectorAll(".hw-palette__tile");for(let i=0;i<e.length;i++){let r=e[i],s=r.getAttribute("data-symbol")??"",l=r.getAttribute("data-biotype")??"",o=null!==t&&t.symbol===s&&t.biotype===l,n=(r.getAttribute("class")??"").split(/\s+/).filter(t=>"hw-palette__tile--primed"!==t).join(" ");r.setAttribute("class",o?`${n} hw-palette__tile--primed`:n),r.setAttribute("aria-pressed",o?"true":"false")}}_applyActiveTabClasses(){let t=this.element.querySelectorAll(".hw-palette__tab");for(let e=0;e<t.length;e++){let i=t[e],r=i.getAttribute("data-tab")??"";i.setAttribute("aria-selected",r===this._activeTab?"true":"false")}let e=this.element.querySelectorAll(".hw-palette__pane");for(let t=0;t<e.length;t++){let i=e[t];(i.getAttribute("data-tab")??"")===this._activeTab?i.removeAttribute("hidden"):i.setAttribute("hidden","")}}_localStorage(){if(!this._opts.allowFavorites)return null;let t=this._doc.defaultView;if(null==t)return null;try{return t.localStorage??null}catch{return null}}_resolveInitialTab(t){if(void 0!==t&&It.includes(t))return t;let e=this._localStorage();if(null!==e)try{let t=e.getItem(xt);if(null!==t&&It.includes(t))return t}catch{}return Nt}_persistActiveTab(){let t=this._localStorage();if(null!==t)try{t.setItem(xt,this._activeTab)}catch{}}_loadFavorites(){let t=this._localStorage();if(null!==t){try{let e=t.getItem(Bt);if(null!==e&&""!==e){let t=JSON.parse(e),i=this._extractSymbols(t);for(let t of i)this._favorites.add(t);for(let e of this._extractTriplets(t))this._favoriteTriplets.push(e);return}}catch{}try{let e=t.getItem("hwe.palette.favorites");if(null===e||""===e)return;let i=JSON.parse(e);if(Array.isArray(i)){for(let t of i){if("string"!=typeof t)continue;let e=t.indexOf("|"),i=e>=0?t.slice(e+1):t;""!==i&&this._favorites.add(i)}this._saveFavorites()}}catch{}}}_extractSymbols(t){if(Array.isArray(t)){let e=[];for(let i of t)"string"==typeof i&&e.push(i);return e}if(null!==t&&"object"==typeof t){let e=t;if(Array.isArray(e.symbols)){let t=[];for(let i of e.symbols)"string"==typeof i&&t.push(i);return t}}return[]}_extractTriplets(t){if(null===t||"object"!=typeof t)return[];let e=t;if(!Array.isArray(e.triplets))return[];let i=[];for(let t of e.triplets){if(null===t||"object"!=typeof t)continue;let e=t;"string"==typeof e.sugar&&"string"==typeof e.base&&"string"==typeof e.linker&&i.push({sugar:e.sugar,base:e.base,linker:e.linker})}return i}_saveFavorites(){let t=this._localStorage();if(null!==t)try{let e={symbols:Array.from(this._favorites)};this._favoriteTriplets.length>0&&(e.triplets=this._favoriteTriplets.map(t=>({...t}))),t.setItem(Bt,JSON.stringify(e))}catch{}}};Pt._DEFAULT_TRIPLET_BASES=["A","C","G","U","T"],Pt._PALETTE_RDKIT_CACHE_LIMIT=256;new Set([d.PEPTIDE,d.RNA,d.CHEM,d.BLOB]),new Set(["Backbone","Branch","Terminal","Undefined"]);var Ft,$t;!function(t){t[t.default=0]="default",t[t.continuous=1]="continuous"}(Ft||(Ft={})),function(t){t.Sequence="sequence",t.Helm="notation",t.Properties="properties",t.StructureView="structureview"}($t||($t={}));const Rt={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M  RGP",V2K_A_LINE:"A  ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:"  0  0  0  0  0  0            999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M  V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M  V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M  V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M  V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M  V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M  V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M  V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M  V30 ",V3K_END:"M  END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:d.RNA,symbol:"d"},RIBOSE:{polymerType:d.RNA,symbol:"r"},PHOSPHATE:{polymerType:d.RNA,symbol:"p"},OXYGEN:"O",HYDROGEN:"H"};function Ot(t,e){return t[e.polymerType]?.[e.symbol]}var Dt;!function(t){t[t.SUGAR=0]="SUGAR",t[t.BASE=1]="BASE",t[t.PHOSPHATE=2]="PHOSPHATE",t[t.TERMINAL_5P=3]="TERMINAL_5P",t[t.TERMINAL_3P=4]="TERMINAL_3P"}(Dt||(Dt={}));class Vt extends Map{constructor(t){super(t)}}class Kt{constructor(t,e){this.molfile=t,this.monomers=e}static createEmpty(){return new Kt("",new Vt(null))}}const Ht=d;var Gt,zt,Ut;new RegExp("[rd]\\((\\w)\\)p?","g");class qt{constructor(t,e,i){this.name=t,this.alphabet=e,this.cutoff=i}}!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(Gt||(Gt={})),function(t){t.DNA="DNA",t.RNA="RNA",t.PT="PT",t.UN="UN"}(zt||(zt={})),function(t){t.aligned="aligned",t.alphabet="alphabet",t.alphabetSize=".alphabetSize",t.alphabetIsMultichar=".alphabetIsMultichar",t.separator="separator",t.isHelmCompatible=".isHelmCompatible",t.positionNames=".positionNames",t.positionLabels=".positionLabels",t.regions=".regions",t.positionShift=".positionShift",t.selectedPosition=".selectedPosition",t.polymerTypeColumnName=".polymerTypeColumnName",t.annotations=".annotations",t.numberingScheme=".numberingScheme",t.annotationColumnName=".annotationColumnName"}(Ut||(Ut={}));const jt=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};function Yt(t){let e;switch(t){case l:case s:case o:case h:case"nucleotide":e=d.RNA;break;case r:e=d.PEPTIDE;break;case n:e=d.CHEM;break;case a:e=d.BLOB;break;default:e=d.PEPTIDE,console.warn(`Unexpected HelmType '${t}'`)}return e}function Wt(t,e,i,r,s,l){if(0===t.length)return Kt.createEmpty();if(l&&l.length>1){const o=new Array(l.length);for(let n=0;n<l.length;++n){const a=l[n],h=n+1<l.length?l[n+1]:t.length,d=t.slice(a,h),u=s?s.slice(a,h):void 0;o[n]=Wt(d,e,i,r,u)}return function(t,e){const i=[],r=[],s=[],l=new Vt;let o=0,n=0,a=Number.POSITIVE_INFINITY,h=!1;for(let d=0;d<t.length;++d){const u=t[d];if(!u||!u.molfile)continue;const c=ne(u.molfile);if(0===c.atoms.length)continue;let p=Number.POSITIVE_INFINITY,_=Number.NEGATIVE_INFINITY;for(const t of c.atoms)t.y<p&&(p=t.y),t.y>_&&(_=t.y);const b=h?ie(a-re-_):0;for(let t=0;t<c.atoms.length;++t){const e=c.atoms[t],r=o+t+1,s=ie(e.y+b);i.push(Rt.V3K_BEGIN_DATA_LINE+r+" "+e.type+" "+e.xStr+" "+s+" "+e.tail+"\n")}for(let t=0;t<c.bonds.length;++t){const e=c.bonds[t],i=n+t+1,s=e.tail?" "+e.tail:"";r.push(Rt.V3K_BEGIN_DATA_LINE+i+" "+e.btype+" "+(e.a1+o)+" "+(e.a2+o)+s+"\n")}for(const t of c.steabs)s.push(t+o);const f=e[d]??0;for(const[t,e]of u.monomers)l.set(f+t,{biotype:e.biotype,symbol:e.symbol,atoms:e.atoms.map(t=>t+o),bonds:e.bonds.map(t=>t+n)});const m=ie(p+b);a=h?Math.min(a,m):m,h=!0,o+=c.atoms.length,n+=c.bonds.length}if(!h)return Kt.createEmpty();let d="";return d+=Rt.V3K_HEADER_FIRST_LINE,d+=Rt.V3K_HEADER_SECOND_LINE,d+=Rt.V3K_BEGIN_CTAB_BLOCK,d+=Rt.V3K_BEGIN_COUNTS_LINE+o+" "+n+Rt.V3K_COUNTS_LINE_ENDING,d+=Rt.V3K_BEGIN_ATOM_BLOCK,d+=i.join(""),d+=Rt.V3K_END_ATOM_BLOCK,d+=Rt.V3K_BEGIN_BOND_BLOCK,d+=r.join(""),d+=Rt.V3K_END_BOND_BLOCK,s.length>0&&(d+=Xt(s)),d+=Rt.V3K_END_CTAB_BLOCK,d+=Rt.V3K_END,{molfile:d,monomers:l}}(o,l)}const o=r===Ht.RNA&&!!s&&s.length===t.length,{atomCount:n,bondCount:a,needsCapping:h}=function(t,e,i,r,s,l){let o=0,n=0,a=0,h=!0,d=null,u=null;for(let i=0;i<t.length;++i){const r=t[i];if(""!==r.symbol){if("*"==r.symbol)throw new Error("Gap canonical symbol is '', not '*");d=Ot(e,{symbol:r.symbol,polymerType:Yt(r.biotype)}),o+=d.atoms.x.length,n+=d.bonds.bondTypes.length,a++,s&&i%3==2&&(u=d)}}if(r===Ht.PEPTIDE)o+=1,n+=a,a>0&&((d?.meta?.rNodes?.length??0)<2||d?.terminalR2Atom?.toLowerCase()===Rt.HYDROGEN.toLowerCase())&&(h=!1,o-=1,n-=1);else if(s)n+=a,l&&l.length>0&&l[l.length-1]===Dt.TERMINAL_3P?(h=!1,n-=1):o+=1;else{const r=i===zt.DNA?Ot(e,Rt.DEOXYRIBOSE):Ot(e,Rt.RIBOSE),s=Ot(e,Rt.PHOSPHATE);o+=(t.length-1)*s.atoms.x.length,o+=t.length*r.atoms.x.length,o+=1,n+=(t.length-1)*s.bonds.bondTypes.length,n+=t.length*r.bonds.bondTypes.length,n-=1,n+=3*t.length}return{atomCount:o,bondCount:n,needsCapping:h}}(t,e,i,r,o,s),d=new Array(n),u=new Array(a);let c,p=null,_=null;r===Ht.PEPTIDE?c=Zt:(c=Qt,o||(p=i===zt.DNA?Ot(e,Rt.DEOXYRIBOSE):Ot(e,Rt.RIBOSE),_=Ot(e,Rt.PHOSPHATE)));const b={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},f={sugar:p,phosphate:_,seqLength:o?Math.ceil(t.length/3):t.length,atomCount:n,bondCount:a},m=new Vt,g=[];let y,v=0;if(o)!function(t,e,i,r,s,l,o,n,a,h){for(let o=0;o<t.length;++o){const d=t[o];if(""===d.symbol)continue;const u=e[o],c=Ot(i,{symbol:d.symbol,polymerType:Yt(d.biotype)}),p=l.nodeShift,_=l.bondShift;l.i=o,u===Dt.BASE?te(c,r,s,l):Jt(c,r,s,l),c.stereoAtoms?.forEach(t=>a.push(t+v)),h(c.atoms.x.length);const b=[];for(let t=p;t<l.nodeShift;++t)b.push(t);const f=[];for(let t=_;t<l.bondShift;++t)f.push(t);n.set(o,{biotype:d.biotype,symbol:d.symbol,atoms:b,bonds:f})}}(t,s,e,d,u,b,0,m,g,t=>{v+=t});else for(b.i=0;b.i<f.seqLength;++b.i){const i=t[b.i];if(""===i.symbol)continue;const r=Ot(e,{symbol:i.symbol,polymerType:Yt(i.biotype)});y=r.terminalR2Atom;const s=b.nodeShift,l=b.bondShift;c(r,d,u,b,f),r.stereoAtoms?.forEach(t=>g.push(t+v)),v+=r.atoms.x.length;const o=b.nodeShift-s,n=new Array(o);for(let t=0;t<o;++t)n[t]=s+t;const a=b.bondShift-l,h=new Array(a);for(let t=0;t<a;++t)h[t]=l+t;m.set(b.i,{biotype:i.biotype,symbol:i.symbol,atoms:n,bonds:h})}h&&function(t,e,i,r,s=Rt.OXYGEN){const l=i.nodeShift+1;t[r.atomCount]=Rt.V3K_BEGIN_DATA_LINE+l+" "+(s??Rt.OXYGEN)+" "+ie(i.backbonePositionShift[0])+" "+i.flipFactor*ie(i.backbonePositionShift[1])+" 0.000000 0\n";const o=i.backboneAttachNode,n=l;e[r.bondCount]=Rt.V3K_BEGIN_DATA_LINE+i.bondShift+" 1 "+o+" "+n+"\n"}(d,u,b,f,y??Rt.OXYGEN);const w=Rt.V3K_BEGIN_COUNTS_LINE+n+" "+a+Rt.V3K_COUNTS_LINE_ENDING;let A="";return A+=Rt.V3K_HEADER_FIRST_LINE,A+=Rt.V3K_HEADER_SECOND_LINE,A+=Rt.V3K_BEGIN_CTAB_BLOCK,A+=w,A+=Rt.V3K_BEGIN_ATOM_BLOCK,A+=d.join(""),A+=Rt.V3K_END_ATOM_BLOCK,A+=Rt.V3K_BEGIN_BOND_BLOCK,A+=u.join(""),A+=Rt.V3K_END_BOND_BLOCK,g.length>0&&(A+=Xt(g)),A+=Rt.V3K_END_CTAB_BLOCK,A+=Rt.V3K_END,{molfile:A,monomers:m}}function Xt(t){const e=[];let i=`M  V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let r=0;r<t.length;r++){const s=`${i} ${t[r]}`;s.length>76?(e.push(`${i} -\n`),i=`M  V30 ${t[r]}`):i=s,r===t.length-1&&e.push(`${i})\n`)}return`M  V30 BEGIN COLLECTION\n${e.join("")}M  V30 END COLLECTION\n`}function Zt(t,e,i,r){r.flipFactor=(-1)**(r.i%2),Jt(t,e,i,r)}function Jt(t,e,i,r){!function(t,e,i){for(let r=0;r<t.atoms.atomTypes.length;++r){const s=i.nodeShift+r+1;e[i.nodeShift+r]=Rt.V3K_BEGIN_DATA_LINE+s+" "+t.atoms.atomTypes[r]+" "+ie(i.backbonePositionShift[0]+t.atoms.x[r])+" "+ie(i.backbonePositionShift[1]+i.flipFactor*t.atoms.y[r])+" "+t.atoms.kwargs[r]}}(t,e,r),ee(t,i,r),function(t,e,i){if(0!==i.backboneAttachNode){const r=i.bondShift,s=i.backboneAttachNode,l=t.meta.terminalNodes[0]+i.nodeShift;e[i.bondShift-1]=Rt.V3K_BEGIN_DATA_LINE+r+" 1 "+s+" "+l+"\n"}}(t,i,r),null!==t.meta.branchShift&&t.meta.terminalNodes.length>2&&function(t,e){e.branchAttachNode=e.nodeShift+t.meta.terminalNodes[2];for(let i=0;i<2;++i)e.branchPositionShift[i]=e.backbonePositionShift[i]+t.meta.branchShift[i]}(t,r),function(t,e){e.backboneAttachNode=e.nodeShift+t.meta.terminalNodes[1],e.bondShift+=t.bonds.atomPairs.length+1,e.nodeShift+=t.atoms.atomTypes.length,e.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,e.backbonePositionShift[1]+=e.flipFactor*(t.meta.backboneShift?.[1]??0)}(t,r)}function Qt(t,e,i,r,s){if(0===r.i)Jt(s.sugar,e,i,r);else for(const t of[s.phosphate,s.sugar])Jt(t,e,i,r);te(t,e,i,r)}function te(t,e,i,r){!function(t,e,i){for(let r=0;r<t.atoms.atomTypes.length;++r){const s=i.nodeShift+r+1;e[i.nodeShift+r]=Rt.V3K_BEGIN_DATA_LINE+s+" "+t.atoms.atomTypes[r]+" "+ie(i.branchPositionShift[0]+t.atoms.x[r])+" "+ie(i.branchPositionShift[1]+i.flipFactor*t.atoms.y[r])+" "+t.atoms.kwargs[r]}}(t,e,r),ee(t,i,r),function(t,e,i){const r=i.bondShift,s=i.branchAttachNode,l=t.meta.terminalNodes[0]+i.nodeShift;e[r-1]=Rt.V3K_BEGIN_DATA_LINE+r+" 1 "+s+" "+l+"\n"}(t,i,r);const s=r.bondShift,l=r.branchAttachNode,o=t.meta.terminalNodes[0]+r.nodeShift;i[s-1]=Rt.V3K_BEGIN_DATA_LINE+s+" 1 "+l+" "+o+"\n",r.bondShift+=t.bonds.atomPairs.length+1,r.nodeShift+=t.atoms.atomTypes.length}function ee(t,e,i){for(let r=0;r<t.bonds.atomPairs.length;++r){const s=i.bondShift+r+1,l=t.bonds.atomPairs[r][0]+i.nodeShift,o=t.bonds.atomPairs[r][1]+i.nodeShift;let n="";if(t.bonds.bondConfiguration.has(r)){let e=t.bonds.bondConfiguration.get(r);i.flipFactor<0&&(e=1===e?3:1),n=" CFG="+e}const a=t.bonds.kwargs.has(r)?" "+t.bonds.kwargs.get(r):"";e[i.bondShift+r]=Rt.V3K_BEGIN_DATA_LINE+s+" "+t.bonds.bondTypes[r]+" "+l+" "+o+n+a+"\n"}}function ie(t){return Math.round(Rt.PRECISION_FACTOR*t)/Rt.PRECISION_FACTOR}new qt(zt.PT,jt.fasta.peptide,.5),new qt(zt.DNA,jt.fasta.dna,.55),new qt(zt.RNA,jt.fasta.rna,.55),Gt.FASTA,Gt.SEPARATOR,Gt.HELM,Gt.BILN;const re=3,se="M  V30 MDLV30/STEABS ATOMS=(";function le(t,e){const i=[];let r=t;for(let t=0;t<e;++t){const t=r.indexOf(" ");-1!==t?(i.push(r.substring(0,t)),r=r.substring(t+1)):(i.push(r),r="")}return i.push(r),i}function oe(t,e,i){const r=t.indexOf(e);if(-1===r)return[];const s=t.indexOf("\n",r)+1,l=t.indexOf(i,s);return t.substring(s,-1===l?t.length:l).split("\n").filter(t=>t.startsWith(Rt.V3K_BEGIN_DATA_LINE)).map(t=>t.substring(Rt.V3K_BEGIN_DATA_LINE.length))}function ne(t){const e=[];for(const i of oe(t,Rt.V3K_BEGIN_ATOM_BLOCK,Rt.V3K_END_ATOM_BLOCK)){const t=le(i,4);e.push({type:t[1],xStr:t[2],y:parseFloat(t[3]),tail:t[4]})}const i=[];for(const e of oe(t,Rt.V3K_BEGIN_BOND_BLOCK,Rt.V3K_END_BOND_BLOCK)){const t=le(e,4);i.push({btype:t[1],a1:parseInt(t[2]),a2:parseInt(t[3]),tail:t[4]})}const r=[];let s=t.indexOf(se);for(;-1!==s;){s+=se.length;const e=t.indexOf(")",s);r.push(...t.substring(s,e).split(" ").slice(1).map(t=>parseInt(t)).filter(t=>!Number.isNaN(t))),s=t.indexOf(se,e)}return{atoms:e,bonds:i,steabs:r}}onmessage=t=>{const{seqList:e,rolesList:i,chainStartsList:r,monomersDict:s,alphabet:l,polymerType:o,start:n,end:a}=t.data,h=new Array(a-n),d=new Array(0);for(let t=n;t<a;++t)try{const a=e[t],d=i?i[t]:void 0,u=r?r[t]:void 0;h[t-n]=Wt(a,s,l,o,d,u)}catch(e){const i=`Cannot get molfile of row #${t}: ${e instanceof Error?e.message:e.toString()}.`;d.push(i)}postMessage({molfiles:h,warnings:d})},helm={}})();
+//# sourceMappingURL=489.js.map