@datagrok/helm 2.13.0 → 2.13.2

package/CHANGELOG.md

@@ -1,5 +1,9 @@
 # Helm changelog
 
+## 2.13.1 (2025-10-31)
+
+Polifill for 1.25
+
 ## 2.13.0 (2025-10-29)
 
 * CHEMS and SMILES support in HELM

package/CLAUDE.md

@@ -0,0 +1,186 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## 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.
+
+Category: **Bioinformatics**.
+
+## Build Commands
+
+```bash
+npm install
+npm run build              # grok api && grok check --soft && webpack
+npm run test               # grok test
+npm run lint               # eslint src --ext .ts
+npm run lint-fix
+npm run build-all          # Builds chem-meta → js-api → utils → bio → this package
+```
+
+## 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
+- `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
+
+**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
+
+### Package Utilities — `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
+
+### HELM Helper — `src/helm-helper.ts`
+
+`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 Web Editor Wrapper — `src/helm-web-editor.ts`
+
+`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
+
+## 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` |
+
+## 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 |
+
+## 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
+- `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.
+
+## Tests (`src/tests/`)
+
+Test entry point: `src/package-test.ts` — imports all test files, exports `test()` and `initAutoTests()`.
+
+| File | What it tests |
+|---|---|
+| `_first-tests.ts` | Package import sanity check |
+| `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-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 |
+
+## 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
+
+## 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
+- `cash-dom` — jQuery-like DOM manipulation
+- `lru-cache` — LRU caching for editors and rendered images
+- `wu` — lazy iteration
+- `rxjs` — reactive subscriptions
+
+## Quick Lookups
+
+| 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` |
+| 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` |
+| Auto-generated function wrappers | `src/package.g.ts` / `src/package-api.ts` |
+| Autostart / input polyfill | `detectors.js` |
+| Test entry point | `src/package-test.ts` |
+| Sample data | `files/samples/`, `files/tests/` |

package/detectors.js

@@ -7,7 +7,7 @@
 class HelmPackageDetectors extends DG.Package {
 
   //name: autostart
-  //tags: autostart
+  //meta.role: autostart
   //description: Helm bootstrap
   autostart() {
     this.logger.debug('Helm: detectors.js: autostart()');

package/dist/455.js

@@ -1,2 +1,2 @@
-var helm;(()=>{"use strict";const t={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:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"};function o(t,o){return t[o.polymerType]?.[o.symbol]}class n extends Map{constructor(t){super(t)}}class e{constructor(t,o){this.molfile=t,this.monomers=o}static createEmpty(){return new e("",new n(null))}}new RegExp("[rd]\\((\\w)\\)p?","g");class a{constructor(t,o,n){this.name=t,this.alphabet=o,this.cutoff=n}}var s,i,r,l;!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(s||(s={})),(l=i||(i={})).DNA="DNA",l.RNA="RNA",l.PT="PT",l.UN="UN",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"}(r||(r={}));const c=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"])}}};var h;function E(t){let o;switch(t){case h.BASE:case h.SUGAR:case 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s=a.bondShift,i=a.branchAttachNode,r=o.meta.terminalNodes[0]+a.nodeShift;e[s-1]=t.V3K_BEGIN_DATA_LINE+s+" 1 "+i+" "+r+"\n",a.bondShift+=o.bonds.atomPairs.length+1,a.nodeShift+=o.atoms.atomTypes.length}(o,n,e,a)}function m(o,n,e){for(let a=0;a<o.bonds.atomPairs.length;++a){const s=e.bondShift+a+1,i=o.bonds.atomPairs[a][0]+e.nodeShift,r=o.bonds.atomPairs[a][1]+e.nodeShift;let l="";if(o.bonds.bondConfiguration.has(a)){let t=o.bonds.bondConfiguration.get(a);e.flipFactor<0&&(t=1===t?3:1),l=" CFG="+t}const c=o.bonds.kwargs.has(a)?" "+o.bonds.kwargs.get(a):"";n[e.bondShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+o.bonds.bondTypes[a]+" "+i+" "+r+l+c+"\n"}}function A(n,e,a,s){let r=0,l=0,c=0,h=!0,N=null;for(const t of n)if(""!==t.symbol){if("*"==t.symbol)throw new Error("Gap canonical symbol is '', not '*");N=o(e,{symbol:t.symbol,polymerType:E(t.biotype)}),r+=N.atoms.x.length,l+=N.bonds.bondTypes.length,c++}if("PEPTIDE"===s)r+=1,l+=c,c>0&&((N?.meta?.rNodes?.length??0)<2||N?.terminalR2Atom?.toLowerCase()===t.HYDROGEN.toLowerCase())&&(h=!1,r-=1,l-=1);else{const s=a===i.DNA?o(e,t.DEOXYRIBOSE):o(e,t.RIBOSE),c=o(e,t.PHOSPHATE);r+=(n.length-1)*c.atoms.x.length,r+=n.length*s.atoms.x.length,r+=1,l+=(n.length-1)*c.bonds.bondTypes.length,l+=n.length*s.bonds.bondTypes.length,l-=1,l+=3*n.length}return{atomCount:r,bondCount:l,needsCapping:h}}function S(o){return Math.round(t.PRECISION_FACTOR*o)/t.PRECISION_FACTOR}new a(i.PT,c.fasta.peptide,.5),new a(i.DNA,c.fasta.dna,.55),new a(i.RNA,c.fasta.rna,.55),s.FASTA,s.SEPARATOR,s.HELM,s.BILN,function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(h||(h={})),onmessage=t=>{const{seqList:o,monomersDict:n,alphabet:e,polymerType:a,start:s,end:i}=t.data,r=new Array(i-s),l=new Array(0);for(let t=s;t<i;++t)try{const i=o[t];r[t-s]=N(i,n,e,a)}catch(o){const n=`Cannot get molfile of row #${t}: ${o instanceof Error?o.message:o.toString()}.`;l.push(n)}postMessage({molfiles:r,warnings:l})},helm={}})();
+var helm;(()=>{"use strict";const t={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:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"};function n(t,n){return t[n.polymerType]?.[n.symbol]}class o extends Map{constructor(t){super(t)}}class e{constructor(t,n){this.molfile=t,this.monomers=n}static createEmpty(){return new e("",new o(null))}}new RegExp("[rd]\\((\\w)\\)p?","g");class a{constructor(t,n,o){this.name=t,this.alphabet=n,this.cutoff=o}}var s,i,r,l;!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm",t.CUSTOM="custom",t.BILN="biln"}(s||(s={})),(l=i||(i={})).DNA="DNA",l.RNA="RNA",l.PT="PT",l.UN="UN",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"}(r||(r={}));const c=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"])}}};var h;function E(t){let n;switch(t){case h.BASE:case h.SUGAR:case h.LINKER:case h.NUCLEOTIDE:case"nucleotide":n="RNA";break;case h.AA:n="PEPTIDE";break;case h.CHEM:n="CHEM";break;case h.BLOB:n="BLOB";break;default:n="PEPTIDE",console.warn(`Unexpected HelmType '${t}'`)}return n}function N(a,s,r,l){if(0===a.length)return e.createEmpty();const c=A,{atomCount:h,bondCount:N,needsCapping:f}=c(a,s,r,l),_=new Array(h),d=new Array(N);let p,T=null,I=null;"PEPTIDE"===l?p=m:(p=b,T=r===i.DNA?n(s,t.DEOXYRIBOSE):n(s,t.RIBOSE),I=n(s,t.PHOSPHATE));const O={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},u={sugar:T,phosphate:I,seqLength:a.length,atomCount:h,bondCount:N},C=new o,B=[];let L,y=0;for(O.i=0;O.i<u.seqLength;++O.i){const t=a[O.i];if(""===t.symbol)continue;const o=n(s,{symbol:t.symbol,polymerType:E(t.biotype)});L=o.terminalR2Atom;const e=O.nodeShift,i=O.bondShift;p(o,_,d,O,u),o.stereoAtoms?.forEach(t=>B.push(t+y)),y+=o.atoms.x.length;const r=O.nodeShift-e,l=new Array(r);for(let t=0;t<r;++t)l[t]=e+t;const c=O.bondShift-i,h=new Array(c);for(let t=0;t<c;++t)h[t]=i+t;C.set(O.i,{biotype:t.biotype,symbol:t.symbol,atoms:l,bonds:h})}f&&function(n,o,e,a,s=t.OXYGEN){const i=e.nodeShift+1;n[a.atomCount]=t.V3K_BEGIN_DATA_LINE+i+" "+(s??t.OXYGEN)+" "+S(e.backbonePositionShift[0])+" "+e.flipFactor*S(e.backbonePositionShift[1])+" 0.000000 0\n";const r=e.backboneAttachNode,l=i;o[a.bondCount]=t.V3K_BEGIN_DATA_LINE+e.bondShift+" 1 "+r+" "+l+"\n"}(_,d,O,u,L??t.OXYGEN);const D=t.V3K_BEGIN_COUNTS_LINE+h+" "+N+t.V3K_COUNTS_LINE_ENDING;let g="";return g+=t.V3K_HEADER_FIRST_LINE,g+=t.V3K_HEADER_SECOND_LINE,g+=t.V3K_BEGIN_CTAB_BLOCK,g+=D,g+=t.V3K_BEGIN_ATOM_BLOCK,g+=_.join(""),g+=t.V3K_END_ATOM_BLOCK,g+=t.V3K_BEGIN_BOND_BLOCK,g+=d.join(""),g+=t.V3K_END_BOND_BLOCK,B.length>0&&(g+=function(t){const n=[];let o=`M  V30 MDLV30/STEABS ATOMS=(${t.length}`;for(let e=0;e<t.length;e++){const a=`${o} ${t[e]}`;a.length>76?(n.push(`${o} -\n`),o=`M  V30 ${t[e]}`):o=a,e===t.length-1&&n.push(`${o})\n`)}return`M  V30 BEGIN COLLECTION\n${n.join("")}M  V30 END COLLECTION\n`}(B)),g+=t.V3K_END_CTAB_BLOCK,g+=t.V3K_END,{molfile:g,monomers:C}}function m(t,n,o,e){e.flipFactor=(-1)**(e.i%2),f(t,n,o,e)}function f(n,o,e,a){!function(n,o,e){for(let a=0;a<n.atoms.atomTypes.length;++a){const s=e.nodeShift+a+1;o[e.nodeShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+n.atoms.atomTypes[a]+" "+S(e.backbonePositionShift[0]+n.atoms.x[a])+" "+S(e.backbonePositionShift[1]+e.flipFactor*n.atoms.y[a])+" "+n.atoms.kwargs[a]}}(n,o,a),_(n,e,a),function(n,o,e){if(0!==e.backboneAttachNode){const a=e.bondShift,s=e.backboneAttachNode,i=n.meta.terminalNodes[0]+e.nodeShift;o[e.bondShift-1]=t.V3K_BEGIN_DATA_LINE+a+" 1 "+s+" "+i+"\n"}}(n,e,a),null!==n.meta.branchShift&&n.meta.terminalNodes.length>2&&function(t,n){n.branchAttachNode=n.nodeShift+t.meta.terminalNodes[2];for(let o=0;o<2;++o)n.branchPositionShift[o]=n.backbonePositionShift[o]+t.meta.branchShift[o]}(n,a),function(t,n){n.backboneAttachNode=n.nodeShift+t.meta.terminalNodes[1],n.bondShift+=t.bonds.atomPairs.length+1,n.nodeShift+=t.atoms.atomTypes.length,n.backbonePositionShift[0]+=t.meta.backboneShift?.[0]??0,n.backbonePositionShift[1]+=n.flipFactor*(t.meta.backboneShift?.[1]??0)}(n,a)}function b(n,o,e,a,s){if(0===a.i)f(s.sugar,o,e,a);else for(const t of[s.phosphate,s.sugar])f(t,o,e,a);!function(n,o,e,a){(function(n,o,e){for(let a=0;a<n.atoms.atomTypes.length;++a){const s=e.nodeShift+a+1;o[e.nodeShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+n.atoms.atomTypes[a]+" "+S(e.branchPositionShift[0]+n.atoms.x[a])+" "+S(e.branchPositionShift[1]+e.flipFactor*n.atoms.y[a])+" "+n.atoms.kwargs[a]}})(n,o,a),_(n,e,a),function(n,o,e){const a=e.bondShift,s=e.branchAttachNode,i=n.meta.terminalNodes[0]+e.nodeShift;o[a-1]=t.V3K_BEGIN_DATA_LINE+a+" 1 "+s+" "+i+"\n"}(n,e,a);const s=a.bondShift,i=a.branchAttachNode,r=n.meta.terminalNodes[0]+a.nodeShift;e[s-1]=t.V3K_BEGIN_DATA_LINE+s+" 1 "+i+" "+r+"\n",a.bondShift+=n.bonds.atomPairs.length+1,a.nodeShift+=n.atoms.atomTypes.length}(n,o,e,a)}function _(n,o,e){for(let a=0;a<n.bonds.atomPairs.length;++a){const s=e.bondShift+a+1,i=n.bonds.atomPairs[a][0]+e.nodeShift,r=n.bonds.atomPairs[a][1]+e.nodeShift;let l="";if(n.bonds.bondConfiguration.has(a)){let t=n.bonds.bondConfiguration.get(a);e.flipFactor<0&&(t=1===t?3:1),l=" CFG="+t}const c=n.bonds.kwargs.has(a)?" "+n.bonds.kwargs.get(a):"";o[e.bondShift+a]=t.V3K_BEGIN_DATA_LINE+s+" "+n.bonds.bondTypes[a]+" "+i+" "+r+l+c+"\n"}}function A(o,e,a,s){let r=0,l=0,c=0,h=!0,N=null;for(const t of o)if(""!==t.symbol){if("*"==t.symbol)throw new Error("Gap canonical symbol is '', not '*");N=n(e,{symbol:t.symbol,polymerType:E(t.biotype)}),r+=N.atoms.x.length,l+=N.bonds.bondTypes.length,c++}if("PEPTIDE"===s)r+=1,l+=c,c>0&&((N?.meta?.rNodes?.length??0)<2||N?.terminalR2Atom?.toLowerCase()===t.HYDROGEN.toLowerCase())&&(h=!1,r-=1,l-=1);else{const s=a===i.DNA?n(e,t.DEOXYRIBOSE):n(e,t.RIBOSE),c=n(e,t.PHOSPHATE);r+=(o.length-1)*c.atoms.x.length,r+=o.length*s.atoms.x.length,r+=1,l+=(o.length-1)*c.bonds.bondTypes.length,l+=o.length*s.bonds.bondTypes.length,l-=1,l+=3*o.length}return{atomCount:r,bondCount:l,needsCapping:h}}function S(n){return Math.round(t.PRECISION_FACTOR*n)/t.PRECISION_FACTOR}new a(i.PT,c.fasta.peptide,.5),new a(i.DNA,c.fasta.dna,.55),new a(i.RNA,c.fasta.rna,.55),s.FASTA,s.SEPARATOR,s.HELM,s.BILN,function(t){t.BASE="HELM_BASE",t.SUGAR="HELM_SUGAR",t.LINKER="HELM_LINKER",t.AA="HELM_AA",t.CHEM="HELM_CHEM",t.BLOB="HELM_BLOB",t.NUCLEOTIDE="HELM_NUCLETIDE"}(h||(h={})),onmessage=t=>{const{seqList:n,monomersDict:o,alphabet:e,polymerType:a,start:s,end:i}=t.data,r=new Array(i-s),l=new Array(0);for(let t=s;t<i;++t)try{const i=n[t];r[t-s]=N(i,o,e,a)}catch(n){const o=`Cannot get molfile of row #${t}: ${n instanceof Error?n.message:n.toString()}.`;l.push(o)}postMessage({molfiles:r,warnings:l})},helm={}})();
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package/dist/455.js.map

@@ -1 +1 @@
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/macromolecule/types.js","webpack://helm/./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/consts.js","webpack://helm/./node_modules/@datagrok-libraries/js-draw-lite/src/types/org.js","webpack://helm/./node_modules/@datagrok-libraries/bio/src/monomer-works/monomer-works.js","webpack://helm/./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js","webpack://helm/./node_modules/@datagrok-libraries/bio/src/monomer-works/seq-to-molfile-worker.js"],"sourcesContent":["export const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'd' },\n    RIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'r' },\n    PHOSPHATE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null, // -> Backbone\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\n                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n            ]),\n            dna: new Set(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\n    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\n//# sourceMappingURL=consts.js.map","export var HelmTypes;\n(function (HelmTypes) {\n    HelmTypes[\"BASE\"] = \"HELM_BASE\";\n    HelmTypes[\"SUGAR\"] = \"HELM_SUGAR\";\n    HelmTypes[\"LINKER\"] = \"HELM_LINKER\";\n    HelmTypes[\"AA\"] = \"HELM_AA\";\n    HelmTypes[\"CHEM\"] = \"HELM_CHEM\";\n    HelmTypes[\"BLOB\"] = \"HELM_BLOB\";\n    HelmTypes[\"NUCLEOTIDE\"] = \"HELM_NUCLETIDE\";\n})(HelmTypes || (HelmTypes = {}));\n//# sourceMappingURL=org.js.map","import { HelmTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\n        // TODO: Check type of monomerType arg\n        const monomer = this.monomerLib.getMonomer(monomerType, monomerName);\n        if (monomer)\n            return monomer.molfile; //TODO cap\n        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = undefined;\n    switch (helmType) {\n        case HelmTypes.BASE:\n        case HelmTypes.SUGAR: // r - ribose, d - deoxyribose\n        case HelmTypes.LINKER: // p - phosphate\n        case HelmTypes.NUCLEOTIDE:\n        // @ts-ignore\n        case 'nucleotide':\n            polymerType = \"RNA\" /* PolymerTypes.RNA */;\n            break;\n        case HelmTypes.AA:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = \"CHEM\" /* PolymerTypes.CHEM */;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = \"BLOB\" /* PolymerTypes.BLOB */;\n            break;\n        default:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap } from './types';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                alphabet === ALPHABET.DNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE.symbol ||\n                alphabet === ALPHABET.RNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE.symbol ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE.symbol) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(monomerSymbol, monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @return {string} - Molfile V3000*/\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount, needsCapping } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */)\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        seqLength: monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const seqMonomer = monomerSeq[v.i];\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue;\n        const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        lastMonomerCappingAtom = monomer.terminalR2Atom;\n        const mAtomFirst = v.nodeShift;\n        const mBondFirst = v.bondShift;\n        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n        //adding stereo atoms to array for further STEABS block generation\n        monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n        nAtoms += monomer.atoms.x.length;\n        const mAtomCount = v.nodeShift - mAtomFirst;\n        const mAtomList = new Array(mAtomCount);\n        for (let maI = 0; maI < mAtomCount; ++maI)\n            mAtomList[maI] = mAtomFirst + maI;\n        const mBondCount = v.bondShift - mBondFirst;\n        const mBondList = new Array(mBondCount);\n        for (let mbI = 0; mbI < mBondCount; ++mbI)\n            mBondList[mbI] = mBondFirst + mbI;\n        monomers.set(v.i, {\n            biotype: seqMonomer.biotype,\n            symbol: seqMonomer.symbol,\n            atoms: mAtomList, bonds: mBondList\n        });\n    }\n    // if the last monomer needs to be capped, add the terminal OH to the resulting molfile\n    if (needsCapping)\n        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? C.OXYGEN);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (steabsCollection.length > 0)\n        result += getCollectionBlock(steabsCollection);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\n    //one row in STEABS block can be no longer than 80 symbols\n    //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n    const maxSymbols = 76;\n    const rowsArray = [];\n    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n    for (let i = 0; i < collection.length; i++) {\n        const updatedRow = `${newCollectionRow} ${collection[i]}`;\n        if (updatedRow.length > maxSymbols) {\n            rowsArray.push(`${newCollectionRow} -\\n`);\n            newCollectionRow = `M  V30 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        (cappingAtomType ?? C.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0)\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {string[]}monomerSeq - the sequence of monomers\n * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers\n * @param {ALPHABET}alphabet - the alphabet of the monomers\n * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer\n * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (const seqMonomer of monomerSeq) {\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue; // Skip for gap/empty monomer in MSA\n        if (seqMonomer.symbol == '*')\n            throw new Error(`Gap canonical symbol is '', not '*`);\n        lastMonomerGraph = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        atomCount += lastMonomerGraph.atoms.x.length;\n        bondCount += lastMonomerGraph.bonds.bondTypes.length;\n        monomerCount++;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerCount;\n        // if the last monomer is something like NH2, which only has R1, there is no need to cap it\n        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen\n        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted\n        if (monomerCount > 0) {\n            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === C.HYDROGEN.toLowerCase()) {\n                needsCapping = false;\n                atomCount -= 1; // remove the last atom (the terminal 'O')\n                bondCount -= 1; // remove the last bond (the terminal C-OH)\n            }\n        }\n    }\n    else { // nucleotides\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n */\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const seq = seqList[rowI];\n            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? 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pack://helm/./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/types.js","webpack://helm/./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/consts.js","webpack://helm/./node_modules/@datagrok-libraries/js-draw-lite/src/types/org.js","webpack://helm/./node_modules/@datagrok-libraries/bio/src/monomer-works/monomer-works.js","webpack://helm/./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js","webpack://helm/./node_modules/@datagrok-libraries/bio/src/monomer-works/seq-to-molfile-worker.js"],"sourcesContent":["export const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'd' },\n    RIBOSE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'r' },\n    PHOSPHATE: { polymerType: \"RNA\" /* PolymerTypes.RNA */, symbol: 'p' },\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","export function getMolGraph(dict, libKey) {\n    return dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function hasMolGraph(dict, libKey) {\n    return !!dict[libKey.polymerType]?.[libKey.symbol];\n}\nexport function setMolGraph(dict, libKey, value) {\n    let pt = dict[libKey.polymerType];\n    if (!pt)\n        pt = dict[libKey.polymerType] = {};\n    pt[libKey.symbol] = value;\n}\nexport class MonomerMap extends Map {\n    constructor(entries) {\n        super(entries);\n    }\n}\n/** @property monomers key - helm seq position, */\nexport class MolfileWithMap {\n    constructor(molfile, monomers) {\n        this.molfile = molfile;\n        this.monomers = monomers;\n    }\n    static createEmpty() { return new MolfileWithMap('', new MonomerMap(null)); }\n}\n//# sourceMappingURL=types.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null, // -> Backbone\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","import { NOTATION_PROVIDER_CONSTRUCTOR_ROLE } from './consts';\nexport class NotationProviderBase {\n    /** Name of the custom notation */\n    static get notationName() {\n        return 'Custom';\n    }\n    ;\n    /** flag to let bio know if this provider implements method for converting helm to it */\n    static get implementsFromHelm() {\n        return false;\n    }\n    ;\n    /** Method for converting HELM to this notation */\n    static convertFromHelm(helm, options) {\n        throw new Error(`Method convertFromHelm not implemented for this notation provider`);\n    }\n    ;\n    static async getProviderConstructors() {\n        // this is terrible, I know, but otherwise this gets put in webworkers and fails due to DG resolution)))\n        // @ts-ignore\n        if (window?.DG) {\n            // @ts-ignore\n            const constFuncs = window.DG.Func.find({ meta: { role: NOTATION_PROVIDER_CONSTRUCTOR_ROLE } });\n            return Promise.all(constFuncs.map((f) => f.apply({})));\n        }\n        return [];\n    }\n}\n/** Alphabet candidate type */\nexport class CandidateType {\n    constructor(name, alphabet, cutoff) {\n        this.name = name;\n        this.alphabet = alphabet;\n        this.cutoff = cutoff;\n    }\n}\n/** Alphabet candidate similarity type */\nexport class CandidateSimType extends CandidateType {\n    constructor(candidate, freq, similarity) {\n        super(candidate.name, candidate.alphabet, candidate.cutoff);\n        this.freq = freq;\n        this.similarity = similarity;\n    }\n}\n//# sourceMappingURL=types.js.map","import { CandidateType } from './types';\n/** enum type to simplify setting \"user-friendly\" notation if necessary */\nexport var NOTATION;\n(function (NOTATION) {\n    NOTATION[\"FASTA\"] = \"fasta\";\n    NOTATION[\"SEPARATOR\"] = \"separator\";\n    NOTATION[\"HELM\"] = \"helm\";\n    /* Requires notation handler */ NOTATION[\"CUSTOM\"] = \"custom\";\n    /* Requires notation handler */ NOTATION[\"BILN\"] = \"biln\";\n})(NOTATION || (NOTATION = {}));\nexport var ALPHABET;\n(function (ALPHABET) {\n    ALPHABET[\"DNA\"] = \"DNA\";\n    ALPHABET[\"RNA\"] = \"RNA\";\n    ALPHABET[\"PT\"] = \"PT\";\n    /** Unknown */\n    ALPHABET[\"UN\"] = \"UN\";\n})(ALPHABET || (ALPHABET = {}));\nexport var TAGS;\n(function (TAGS) {\n    TAGS[\"aligned\"] = \"aligned\";\n    TAGS[\"alphabet\"] = \"alphabet\";\n    TAGS[\"alphabetSize\"] = \".alphabetSize\";\n    TAGS[\"alphabetIsMultichar\"] = \".alphabetIsMultichar\";\n    TAGS[\"separator\"] = \"separator\";\n    TAGS[\"isHelmCompatible\"] = \".isHelmCompatible\";\n    TAGS[\"positionNames\"] = \".positionNames\";\n    TAGS[\"positionLabels\"] = \".positionLabels\";\n    TAGS[\"regions\"] = \".regions\";\n    TAGS[\"positionShift\"] = \".positionShift\";\n    TAGS[\"selectedPosition\"] = \".selectedPosition\";\n    TAGS[\"polymerTypeColumnName\"] = \".polymerTypeColumnName\";\n    TAGS[\"annotations\"] = \".annotations\";\n    TAGS[\"numberingScheme\"] = \".numberingScheme\";\n    TAGS[\"annotationColumnName\"] = \".annotationColumnName\";\n})(TAGS || (TAGS = {}));\nexport { TAGS as BioTags };\nexport const positionSeparator = ', ';\nexport const monomerRe = /(?:\\[([A-Za-z0-9_\\-,()]+)\\])|([A-Za-z\\-])/g;\nexport const helmRe = /(PEPTIDE1|DNA1|RNA1)\\{([^}]+)}/g;\nexport const helmPp1Re = /\\[([^\\[\\]]+)]/g;\nexport const Alphabets = new class {\n    constructor() {\n        this.fasta = {\n            peptide: new Set([\n                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',\n                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',\n            ]),\n            dna: new Set(['A', 'C', 'G', 'T']),\n            rna: new Set(['A', 'C', 'G', 'U']),\n        };\n    }\n}();\nexport const candidateAlphabets = [\n    new CandidateType(ALPHABET.PT, Alphabets.fasta.peptide, 0.50),\n    new CandidateType(ALPHABET.DNA, Alphabets.fasta.dna, 0.55),\n    new CandidateType(ALPHABET.RNA, Alphabets.fasta.rna, 0.55),\n];\n/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\nexport const GapOriginals = {\n    [NOTATION.FASTA]: '-',\n    [NOTATION.SEPARATOR]: '',\n    [NOTATION.HELM]: '*',\n    [NOTATION.BILN]: '',\n};\nexport const MONOMER_MOTIF_SPLITTER = ' , ';\nexport const NOTATION_PROVIDER_CONSTRUCTOR_ROLE = 'notationProviderConstructor';\n//# sourceMappingURL=consts.js.map","export var HelmTypes;\n(function (HelmTypes) {\n    HelmTypes[\"BASE\"] = \"HELM_BASE\";\n    HelmTypes[\"SUGAR\"] = \"HELM_SUGAR\";\n    HelmTypes[\"LINKER\"] = \"HELM_LINKER\";\n    HelmTypes[\"AA\"] = \"HELM_AA\";\n    HelmTypes[\"CHEM\"] = \"HELM_CHEM\";\n    HelmTypes[\"BLOB\"] = \"HELM_BLOB\";\n    HelmTypes[\"NUCLEOTIDE\"] = \"HELM_NUCLETIDE\";\n})(HelmTypes || (HelmTypes = {}));\n//# sourceMappingURL=org.js.map","import { HelmTypes } from '../helm/consts';\nexport class MonomerWorks {\n    //private molfileConverter: IMolfileConverter;\n    constructor(monomerLib /*, molfileConverter: IMolfileConverter*/) {\n        this.monomerLib = monomerLib;\n        //this.molfileConverter = molfileConverter;\n    }\n    //types according to Monomer possible\n    getCappedRotatedMonomer(monomerType, monomerName) {\n        // TODO: Check type of monomerType arg\n        const monomer = this.monomerLib.getMonomer(monomerType, monomerName);\n        if (monomer)\n            return monomer.molfile; //TODO cap\n        return null;\n    }\n}\nexport function helmTypeToPolymerType(helmType) {\n    let polymerType = undefined;\n    switch (helmType) {\n        case HelmTypes.BASE:\n        case HelmTypes.SUGAR: // r - ribose, d - deoxyribose\n        case HelmTypes.LINKER: // p - phosphate\n        case HelmTypes.NUCLEOTIDE:\n        // @ts-ignore\n        case 'nucleotide':\n            polymerType = \"RNA\" /* PolymerTypes.RNA */;\n            break;\n        case HelmTypes.AA:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            break;\n        case HelmTypes.CHEM:\n            polymerType = \"CHEM\" /* PolymerTypes.CHEM */;\n            break;\n        case HelmTypes.BLOB:\n            polymerType = \"BLOB\" /* PolymerTypes.BLOB */;\n            break;\n        default:\n            polymerType = \"PEPTIDE\" /* PolymerTypes.PEPTIDE */;\n            console.warn(`Unexpected HelmType '${helmType}'`);\n    }\n    return polymerType;\n}\n//# sourceMappingURL=monomer-works.js.map","/* eslint-disable max-len */\nimport { monomerWorksConsts as C } from './consts';\nimport { getMolGraph, MolfileWithMap, MonomerMap } from './types';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET, GAP_SYMBOL } from '../utils/macromolecule/consts';\nimport { helmTypeToPolymerType } from './monomer-works';\n/** Get a mapping of peptide symbols to HELM monomer library objects with selected fields.\n * @param {IMonomerLib} monomerLib - Monomer library\n * @param {HELM_POLYMER_TYPE} polymerType - Polymer type\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/\nexport function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {\n    const map = new Map();\n    for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {\n        const it = monomerLib.getMonomer(polymerType, monomerSymbol);\n        if (polymerType === \"RNA\" /* HELM_POLYMER_TYPE.RNA */ &&\n            (it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] === \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */ ||\n                alphabet === ALPHABET.DNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE.symbol ||\n                alphabet === ALPHABET.RNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE.symbol ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE.symbol) ||\n            polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */ &&\n                it[\"monomerType\" /* HELM_FIELDS.MONOMER_TYPE */] !== \"Branch\" /* HELM_MONOMER_TYPE.BRANCH */) {\n            const monomerObject = {};\n            HELM_CORE_FIELDS.forEach((field) => {\n                //@ts-ignore\n                monomerObject[field] = it[field];\n            });\n            map.set(monomerSymbol, monomerObject);\n        }\n    }\n    return map;\n}\n/** Translate a sequence of monomer symbols into Molfile V3000\n * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {PolymerType} polymerType - Polymer type\n * @return {string} - Molfile V3000*/\nexport function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {\n    if (monomerSeq.length === 0) {\n        // throw new Error('monomerSeq is empty');\n        return MolfileWithMap.createEmpty();\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount, needsCapping } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);\n    // create arrays to store lines of the resulting molfile\n    const molfileAtomBlock = new Array(atomCount);\n    const molfileBondBlock = new Array(bondCount);\n    let addMonomerToMolblock;\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */)\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n    }\n    const v = {\n        i: 0,\n        nodeShift: 0,\n        bondShift: 0,\n        backbonePositionShift: new Array(2).fill(0),\n        branchPositionShift: new Array(2).fill(0),\n        backboneAttachNode: 0,\n        branchAttachNode: 0,\n        flipFactor: 1,\n    };\n    const LC = {\n        sugar: sugar,\n        phosphate: phosphate,\n        seqLength: monomerSeq.length,\n        atomCount: atomCount,\n        bondCount: bondCount,\n    };\n    const monomers = new MonomerMap();\n    const steabsCollection = [];\n    let nAtoms = 0;\n    let lastMonomerCappingAtom = undefined;\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const seqMonomer = monomerSeq[v.i];\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue;\n        const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        lastMonomerCappingAtom = monomer.terminalR2Atom;\n        const mAtomFirst = v.nodeShift;\n        const mBondFirst = v.bondShift;\n        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);\n        //adding stereo atoms to array for further STEABS block generation\n        monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));\n        nAtoms += monomer.atoms.x.length;\n        const mAtomCount = v.nodeShift - mAtomFirst;\n        const mAtomList = new Array(mAtomCount);\n        for (let maI = 0; maI < mAtomCount; ++maI)\n            mAtomList[maI] = mAtomFirst + maI;\n        const mBondCount = v.bondShift - mBondFirst;\n        const mBondList = new Array(mBondCount);\n        for (let mbI = 0; mbI < mBondCount; ++mbI)\n            mBondList[mbI] = mBondFirst + mbI;\n        monomers.set(v.i, {\n            biotype: seqMonomer.biotype,\n            symbol: seqMonomer.symbol,\n            atoms: mAtomList, bonds: mBondList\n        });\n    }\n    // if the last monomer needs to be capped, add the terminal OH to the resulting molfile\n    if (needsCapping)\n        capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, lastMonomerCappingAtom ?? C.OXYGEN);\n    const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;\n    // todo: possible optimization may be achieved by replacing .join('') with +=\n    // since counterintuitively joining an array into a new string is reportedly\n    // slower than using += as below\n    let result = '';\n    result += C.V3K_HEADER_FIRST_LINE;\n    result += C.V3K_HEADER_SECOND_LINE;\n    result += C.V3K_BEGIN_CTAB_BLOCK;\n    result += molfileCountsLine;\n    result += C.V3K_BEGIN_ATOM_BLOCK;\n    result += molfileAtomBlock.join('');\n    result += C.V3K_END_ATOM_BLOCK;\n    result += C.V3K_BEGIN_BOND_BLOCK;\n    result += molfileBondBlock.join('');\n    result += C.V3K_END_BOND_BLOCK;\n    if (steabsCollection.length > 0)\n        result += getCollectionBlock(steabsCollection);\n    result += C.V3K_END_CTAB_BLOCK;\n    result += C.V3K_END;\n    // return molfileParts.join('');\n    return { molfile: result, monomers: monomers };\n}\nfunction getCollectionBlock(collection) {\n    //one row in STEABS block can be no longer than 80 symbols\n    //maxSymbols = 80 symbols minus ' -\\n' (4 symbols)\n    const maxSymbols = 76;\n    const rowsArray = [];\n    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;\n    for (let i = 0; i < collection.length; i++) {\n        const updatedRow = `${newCollectionRow} ${collection[i]}`;\n        if (updatedRow.length > maxSymbols) {\n            rowsArray.push(`${newCollectionRow} -\\n`);\n            newCollectionRow = `M  V30 ${collection[i]}`;\n        }\n        else\n            newCollectionRow = updatedRow;\n        //in case last atom was added - close the block\n        if (i === collection.length - 1)\n            rowsArray.push(`${newCollectionRow})\\n`);\n    }\n    return `M  V30 BEGIN COLLECTION\\n${rowsArray.join('')}M  V30 END COLLECTION\\n`;\n}\n/** Cap the resulting (after sewing up all the monomers) molfile with 'O'\n * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block\n * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block\n * @param {LoopVariables} v - Loop variables\n * @param {LoopConstants} LC - Loop constants*/\nfunction capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC, cappingAtomType = C.OXYGEN) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        (cappingAtomType ?? C.OXYGEN) + ' ' + keepPrecision(v.backbonePositionShift[0]) + ' ' +\n        v.flipFactor * keepPrecision(v.backbonePositionShift[1]) + ' ' + '0.000000 0' + '\\n';\n    // add terminal bond\n    const firstAtom = v.backboneAttachNode;\n    const secondAtom = atomIdx;\n    molfileBondBlock[LC.bondCount] = C.V3K_BEGIN_DATA_LINE + v.bondShift + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\nfunction addAminoAcidToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    v.flipFactor = (-1) ** (v.i % 2); // to flip every even monomer over OX\n    addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    // todo: remove these comments to the docstrings of the corr. functions\n    // construnct the lines of V3K molfile atom block\n    fillAtomLines(monomer, molfileAtomBlock, v);\n    // construct the lines of V3K molfile bond block\n    fillBondLines(monomer, molfileBondBlock, v);\n    // peptide bond\n    fillChainExtendingBond(monomer, molfileBondBlock, v);\n    // update branch variables if necessary\n    if (monomer.meta.branchShift !== null && monomer.meta.terminalNodes.length > 2)\n        updateBranchVariables(monomer, v);\n    // update loop variables\n    updateChainExtendingVariables(monomer, v);\n}\nfunction addNucleotideToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v, LC) {\n    // construnct the lines of V3K molfile atom block corresponding to phosphate\n    // and sugar\n    if (v.i === 0)\n        addBackboneMonomerToMolblock(LC.sugar, molfileAtomBlock, molfileBondBlock, v);\n    else {\n        for (const monomer of [LC.phosphate, LC.sugar])\n            addBackboneMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v);\n    }\n    addBranchMonomerToMolblock(nucleobase, molfileAtomBlock, molfileBondBlock, v);\n}\nfunction addBranchMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v) {\n    fillBranchAtomLines(monomer, molfileAtomBlock, v);\n    fillBondLines(monomer, molfileBondBlock, v);\n    fillBackboneToBranchBond(monomer, molfileBondBlock, v);\n    // C-N bond\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    // update loop variables\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n}\nfunction updateChainExtendingVariables(monomer, v) {\n    v.backboneAttachNode = v.nodeShift + monomer.meta.terminalNodes[1];\n    v.bondShift += monomer.bonds.atomPairs.length + 1;\n    v.nodeShift += monomer.atoms.atomTypes.length;\n    v.backbonePositionShift[0] += monomer.meta.backboneShift?.[0] ?? 0; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * (monomer.meta.backboneShift?.[1] ?? 0);\n}\nfunction updateBranchVariables(monomer, v) {\n    v.branchAttachNode = v.nodeShift + monomer.meta.terminalNodes[2];\n    for (let i = 0; i < 2; ++i)\n        v.branchPositionShift[i] = v.backbonePositionShift[i] + monomer.meta.branchShift[i];\n}\nfunction fillAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.backbonePositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.backbonePositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\n// todo: remove as quickfix\nfunction fillBranchAtomLines(monomer, molfileAtomBlock, v) {\n    for (let j = 0; j < monomer.atoms.atomTypes.length; ++j) {\n        const atomIdx = v.nodeShift + j + 1;\n        molfileAtomBlock[v.nodeShift + j] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n            monomer.atoms.atomTypes[j] + ' ' +\n            keepPrecision(v.branchPositionShift[0] + monomer.atoms.x[j]) + ' ' +\n            keepPrecision(v.branchPositionShift[1] + v.flipFactor * monomer.atoms.y[j]) +\n            ' ' + monomer.atoms.kwargs[j];\n    }\n}\nfunction fillBondLines(monomer, molfileBondBlock, v) {\n    // construct the lines of V3K molfile bond block\n    for (let j = 0; j < monomer.bonds.atomPairs.length; ++j) {\n        const bondIdx = v.bondShift + j + 1;\n        const firstAtom = monomer.bonds.atomPairs[j][0] + v.nodeShift;\n        const secondAtom = monomer.bonds.atomPairs[j][1] + v.nodeShift;\n        let bondCfg = '';\n        if (monomer.bonds.bondConfiguration.has(j)) {\n            // flip orientation when necessary\n            let orientation = monomer.bonds.bondConfiguration.get(j);\n            if (v.flipFactor < 0)\n                orientation = (orientation === 1) ? 3 : 1;\n            bondCfg = ' CFG=' + orientation;\n        }\n        const kwargs = monomer.bonds.kwargs.has(j) ?\n            ' ' + monomer.bonds.kwargs.get(j) : '';\n        molfileBondBlock[v.bondShift + j] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            monomer.bonds.bondTypes[j] + ' ' +\n            firstAtom + ' ' + secondAtom + bondCfg + kwargs + '\\n';\n    }\n}\nfunction fillChainExtendingBond(monomer, molfileBondBlock, v) {\n    if (v.backboneAttachNode !== 0) {\n        const bondIdx = v.bondShift;\n        const firstAtom = v.backboneAttachNode;\n        const secondAtom = monomer.meta.terminalNodes[0] + v.nodeShift;\n        molfileBondBlock[v.bondShift - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n            1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n    }\n}\n// todo: remove\nfunction fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {\n    const bondIdx = v.bondShift;\n    const firstAtom = v.branchAttachNode;\n    const secondAtom = branchMonomer.meta.terminalNodes[0] + v.nodeShift;\n    molfileBondBlock[bondIdx - 1] = C.V3K_BEGIN_DATA_LINE + bondIdx + ' ' +\n        1 + ' ' + firstAtom + ' ' + secondAtom + '\\n';\n}\n/** Compute the atom/bond counts for the resulting molfile, depending on the\n * type of polymer (peptide/nucleotide)\n * @param {string[]}monomerSeq - the sequence of monomers\n * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers\n * @param {ALPHABET}alphabet - the alphabet of the monomers\n * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer\n * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/\nfunction getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {\n    let atomCount = 0;\n    let bondCount = 0;\n    let monomerCount = 0;\n    let needsCapping = true;\n    let lastMonomerGraph = null;\n    // sum up all the atoms/nodes provided by the sequence\n    for (const seqMonomer of monomerSeq) {\n        if (seqMonomer.symbol === GAP_SYMBOL)\n            continue; // Skip for gap/empty monomer in MSA\n        if (seqMonomer.symbol == '*')\n            throw new Error(`Gap canonical symbol is '', not '*`);\n        lastMonomerGraph = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });\n        atomCount += lastMonomerGraph.atoms.x.length;\n        bondCount += lastMonomerGraph.bonds.bondTypes.length;\n        monomerCount++;\n    }\n    // add extra values depending on the polymer type\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        // add the rightmost/terminating cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add chain-extending bonds (C-NH per each monomer pair and terminal C-OH)\n        bondCount += monomerCount;\n        // if the last monomer is something like NH2, which only has R1, there is no need to cap it\n        // although, this should never happen, but hey... in other bits of code, there is a chunk that adds pseudo-R2 as hydrogen\n        // we should also check, if the R2 of the last monomer is not hydrogen, that case should also be omitted\n        if (monomerCount > 0) {\n            if ((lastMonomerGraph?.meta?.rNodes?.length ?? 0) < 2 || lastMonomerGraph?.terminalR2Atom?.toLowerCase() === C.HYDROGEN.toLowerCase()) {\n                needsCapping = false;\n                atomCount -= 1; // remove the last atom (the terminal 'O')\n                bondCount -= 1; // remove the last bond (the terminal C-OH)\n            }\n        }\n    }\n    else { // nucleotides\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);\n        const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);\n        // add phosphate per each pair of nucleobase symbols\n        atomCount += (monomerSeq.length - 1) * phosphate.atoms.x.length;\n        // add sugar per each nucleobase symbol\n        atomCount += monomerSeq.length * sugar.atoms.x.length;\n        // add the leftmost cap group 'OH' (i.e. 'O')\n        atomCount += 1;\n        // add bonds from phosphate monomers\n        bondCount += (monomerSeq.length - 1) * phosphate.bonds.bondTypes.length;\n        // add bonds from sugar monomers\n        bondCount += monomerSeq.length * sugar.bonds.bondTypes.length;\n        // exclude the first chain-extending bond O-P (absent, no 'leftmost' phosphate)\n        bondCount -= 1;\n        // add chain-extending and branch bonds (O-P, C-O and C-N per each nucleotide)\n        bondCount += monomerSeq.length * 3;\n    }\n    return { atomCount, bondCount, needsCapping };\n}\n/** Keep precision upon floating point operations over atom coordinates\n * @param {number}x - the floating point number\n * @return {number} - the floating point number with the same precision\n */\nexport function keepPrecision(x) {\n    return Math.round(C.PRECISION_FACTOR * x) / C.PRECISION_FACTOR;\n}\n//# sourceMappingURL=to-atomic-level-utils.js.map","import { monomerSeqToMolfile } from './to-atomic-level-utils';\nonmessage = (event) => {\n    const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const resMolList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const seq = seqList[rowI];\n            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType);\n        }\n        catch (err) {\n            const errMsg = err instanceof Error ? err.message : err.toString();\n            const msg = `Cannot get molfile of row #${rowI}: ${errMsg}.`;\n            molfileWarningList.push(msg);\n        }\n    }\n    postMessage({ molfiles: resMolList, warnings: molfileWarningList });\n};\n//# sourceMappingURL=seq-to-molfile-worker.js.map"],"names":["monomerWorksConsts","V2K_RGP_SHIFT","V2K_RGP_LINE","V2K_A_LINE","V3K_COUNTS_SHIFT","V3K_IDX_SHIFT","V3K_HEADER_FIRST_LINE","V3K_HEADER_SECOND_LINE","V3K_BEGIN_CTAB_BLOCK","V3K_END_CTAB_BLOCK","V3K_BEGIN_COUNTS_LINE","V3K_COUNTS_LINE_ENDING","V3K_BEGIN_ATOM_BLOCK","V3K_END_ATOM_BLOCK","V3K_BEGIN_BOND_BLOCK","V3K_END_BOND_BLOCK","V3K_BOND_CONFIG","V3K_BEGIN_DATA_LINE","V3K_END","PRECISION_FACTOR","DEOXYRIBOSE","polymerType","symbol","RIBOSE","PHOSPHATE","OXYGEN","HYDROGEN","getMolGraph","dict","libKey","MonomerMap","Map","constructor","entries","super","MolfileWithMap","molfile","monomers","this","createEmpty","RegExp","CandidateType","name","alphabet","cutoff","NOTATION","TAGS","ALPHABET","Alphabets","fasta","peptide","Set","dna","rna","HelmTypes","helmTypeToPolymerType","helmType","BASE","SUGAR","LINKER","NUCLEOTIDE","AA","CHEM","BLOB","console","warn","monomerSeqToMolfile","monomerSeq","monomersDict","length","getAtomAndBondCounts","getResultingAtomBondCounts","atomCount","bondCount","needsCapping","molfileAtomBlock","Array","molfileBondBlock","addMonomerToMolblock","sugar","phosphate","addAminoAcidToMolblock","addNucleotideToMolblock","DNA","v","i","nodeShift","bondShift","backbonePositionShift","fill","branchPositionShift","backboneAttachNode","branchAttachNode","flipFactor","LC","seqLength","steabsCollection","lastMonomerCappingAtom","nAtoms","seqMonomer","monomer","biotype","terminalR2Atom","mAtomFirst","mBondFirst","stereoAtoms","forEach","push","atoms","x","mAtomCount","mAtomList","maI","mBondCount","mBondList","mbI","set","bonds","cappingAtomType","atomIdx","keepPrecision","firstAtom","secondAtom","capResultingMolblock","molfileCountsLine","result","join","collection","rowsArray","newCollectionRow","updatedRow","getCollectionBlock","addBackboneMonomerToMolblock","j","atomTypes","y","kwargs","fillAtomLines","fillBondLines","bondIdx","meta","terminalNodes","fillChainExtendingBond","branchShift","updateBranchVariables","atomPairs","backboneShift","updateChainExtendingVariables","nucleobase","fillBranchAtomLines","branchMonomer","fillBackboneToBranchBond","addBranchMonomerToMolblock","bondCfg","bondConfiguration","has","orientation","get","bondTypes","monomerCount","lastMonomerGraph","Error","rNodes","toLowerCase","Math","round","PT","RNA","FASTA","SEPARATOR","HELM","BILN","onmessage","event","seqList","start","end","data","resMolList","molfileWarningList","rowI","seq","err","msg","message","toString","postMessage","molfiles","warnings"],"sourceRoot":""}