npm - @datagrok-libraries/bio - Versions diffs - 5.63.6 → 5.64.0 - Mend

@datagrok-libraries/bio 5.63.6 → 5.64.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (36) hide show

package/CLAUDE.md +0 -13
package/package.json +1 -1
package/src/monomer-works/monomer-hover.js +1 -1
package/src/monomer-works/monomer-hover.js.map +1 -1
package/src/monomer-works/seq-to-molfile-worker.js +3 -2
package/src/monomer-works/seq-to-molfile-worker.js.map +1 -1
package/src/monomer-works/seq-to-molfile.d.ts +2 -2
package/src/monomer-works/seq-to-molfile.d.ts.map +1 -1
package/src/monomer-works/seq-to-molfile.js +2 -2
package/src/monomer-works/seq-to-molfile.js.map +1 -1
package/src/monomer-works/to-atomic-level-utils.d.ts +7 -5
package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level-utils.js +195 -46
package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
package/src/monomer-works/to-atomic-level.d.ts +7 -5
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +156 -36
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/monomer-works/types.d.ts +10 -0
package/src/monomer-works/types.d.ts.map +1 -1
package/src/monomer-works/types.js +7 -0
package/src/monomer-works/types.js.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts +3 -0
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +71 -10
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/macromolecule/utils.d.ts +2 -0
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +19 -3
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/macromolecule-highlight.d.ts +87 -0
package/src/utils/macromolecule-highlight.d.ts.map +1 -0
package/src/utils/macromolecule-highlight.js +87 -0
package/src/utils/macromolecule-highlight.js.map +1 -0
package/src/utils/monomer-selection-dialog.js +1 -1
package/src/utils/monomer-selection-dialog.js.map +1 -1

package/CLAUDE.md CHANGED Viewed

@@ -1,24 +1,11 @@
 # CLAUDE.md
-This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
 ## Overview
 **@datagrok-libraries/bio** is the core shared library for all bioinformatics functionality in the Datagrok platform. It provides types, utilities, renderers, and service interfaces for working with macromolecules (peptides, DNA, RNA, HELM), 3D molecular structures (PDB/PDBQT/mmCIF), phylogenetic trees, and monomer libraries.
 This is a **library** (not a package) — it has no `package.ts`, no webpack, no platform registration. It is compiled with `tsc` to `.js`/`.d.ts` and consumed by multiple packages (`Bio`, `Helm`, `Peptides`, `BiostructureViewer`, `Dendrogram`, `HitTriage`, etc.).
-## Build Commands
-```bash
-npm install
-npm run build              # grok check --soft && tsc
-npm run build-all          # Builds chem-meta → js-api → gridext → utils → ml → this library
-npm run lint               # eslint "./src/**/*.ts"
-npm run lint-fix
-npm run link-all           # Links chem-meta, datagrok-api, gridext, utils, ml
-```
 ## Key Dependencies
 - `datagrok-api` — platform API (`DG`, `grok`, `ui`)

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.63.6",
+  "version": "5.64.0",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

package/src/monomer-works/monomer-hover.js CHANGED Viewed

@@ -46,7 +46,7 @@ export async function buildMonomerHoverLink(seqCol, molCol, monomerLib, seqHelpe
                 .toArray();
             const alphabet = seqSH.alphabet;
             const polymerType = alphabet == ALPHABET.RNA || alphabet == ALPHABET.DNA ? "RNA" /* PolymerTypes.RNA */ : "PEPTIDE" /* PolymerTypes.PEPTIDE */;
-            const monomersDict = getMonomersDictFromLib([seqMList], polymerType, alphabet, monomerLib, rdKitModule);
+            const monomersDict = getMonomersDictFromLib([seqMList], [undefined], polymerType, alphabet, monomerLib, rdKitModule);
             // Call seq-to-molfile worker core directly
             const molWM = monomerSeqToMolfile(seqMList, monomersDict, alphabet, polymerType);
             return molWM.monomers;

package/src/monomer-works/monomer-hover.js.map CHANGED Viewed

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1	+ 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package/src/monomer-works/seq-to-molfile-worker.js CHANGED Viewed

@@ -1,12 +1,13 @@
 import { monomerSeqToMolfile } from './to-atomic-level-utils';
 onmessage = (event) => {
-    const { seqList, monomersDict, alphabet, polymerType, start, end } = event.data;
+    const { seqList, rolesList, monomersDict, alphabet, polymerType, start, end } = event.data;
     const resMolList = new Array(end - start);
     const molfileWarningList = new Array(0);
     for (let rowI = start; rowI < end; ++rowI) {
         try {
             const seq = seqList[rowI];
-            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType);
+            const roles = rolesList ? rolesList[rowI] : undefined;
+            resMolList[rowI - start] = monomerSeqToMolfile(seq, monomersDict, alphabet, polymerType, roles);
         }
         catch (err) {
             const errMsg = err instanceof Error ? err.message : err.toString();

package/src/monomer-works/seq-to-molfile-worker.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"seq-to-molfile-worker.js","sourceRoot":"","sources":["seq-to-molfile-worker.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AAG5D,SAAS,GAAG,CAAC,KAAK,EAAE,EAAE;IACpB,MAAM,EAAC,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAAC,GAA2B,KAAK,CAAC,IAAI,CAAC;~~IACtG~~,MAAM,UAAU,GAAqB,IAAI,KAAK,CAAiB,GAAG,GAAG,KAAK,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GAAG,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC;IAChD,KAAK,IAAI,IAAI,GAAG,KAAK,EAAE,IAAI,GAAG,GAAG,EAAE,EAAE,IAAI,EAAE,CAAC;QAC1C,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;YAC1B,UAAU,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,mBAAmB,CAAC,GAAG,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAC;~~QAC3F~~,CAAC;QAAC,OAAO,GAAQ,EAAE,CAAC;YAClB,MAAM,MAAM,GAAW,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC;YAC3E,MAAM,GAAG,GAAW,8BAA8B,IAAI,KAAK,MAAM,GAAG,CAAC;YACrE,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC/B,CAAC;IACH,CAAC;IACD,WAAW,CAAC,EAAC,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,kBAAkB,EAA0B,CAAC,CAAC;AAC7F,CAAC,CAAC"}
1	+ {"version":3,"file":"seq-to-molfile-worker.js","sourceRoot":"","sources":["seq-to-molfile-worker.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AAG5D,SAAS,GAAG,CAAC,KAAK,EAAE,EAAE;IACpB,MAAM,EAAC,OAAO,EAAE,SAAS,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAAC,GAA2B,KAAK,CAAC,IAAI,CAAC;IACjH,MAAM,UAAU,GAAqB,IAAI,KAAK,CAAiB,GAAG,GAAG,KAAK,CAAC,CAAC;IAC5E,MAAM,kBAAkB,GAAG,IAAI,KAAK,CAAS,CAAC,CAAC,CAAC;IAChD,KAAK,IAAI,IAAI,GAAG,KAAK,EAAE,IAAI,GAAG,GAAG,EAAE,EAAE,IAAI,EAAE,CAAC;QAC1C,IAAI,CAAC;YACH,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;YAC1B,MAAM,KAAK,GAAG,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;YACtD,UAAU,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,mBAAmB,CAAC,GAAG,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;QAClG,CAAC;QAAC,OAAO,GAAQ,EAAE,CAAC;YAClB,MAAM,MAAM,GAAW,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC;YAC3E,MAAM,GAAG,GAAW,8BAA8B,IAAI,KAAK,MAAM,GAAG,CAAC;YACrE,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;QAC/B,CAAC;IACH,CAAC;IACD,WAAW,CAAC,EAAC,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,kBAAkB,EAA0B,CAAC,CAAC;AAC7F,CAAC,CAAC"}

package/src/monomer-works/seq-to-molfile.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import { RDModule } from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import { ALPHABET } from '../utils/macromolecule';
-import { MonomerMap, MonomerMapValue, MonomerMolGraphMap } from './types';
+import { MonomerMap, MonomerMapValue, MonomerMolGraphMap, NucleotideRole } from './types';
 import { ISeqHelper, ToAtomicLevelRes } from '../utils/seq-helper';
 import { IMonomerLib, IMonomerLibBase } from '../types/monomer-library';
 import { PolymerType } from '../helm/types';
@@ -13,6 +13,6 @@ export type SeqToMolfileResult = {
     }[];
     warnings: string[];
 };
-export declare function seqToMolFileWorker(seqCol: DG.Column<string>, monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule): Promise<ToAtomicLevelRes>;
+export declare function seqToMolFileWorker(seqCol: DG.Column<string>, monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, monomerLib: IMonomerLib, seqHelper: ISeqHelper, rdKitModule: RDModule, rolesList?: (NucleotideRole[] | undefined)[]): Promise<ToAtomicLevelRes>;
 export declare function getMolHighlight(monomerMaps: Iterable<MonomerMapValue>, monomerLib: IMonomerLibBase): ISubstruct;
 //# sourceMappingURL=seq-to-molfile.d.ts.map

package/src/monomer-works/seq-to-molfile.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"seq-to-molfile.d.ts","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,QAAQ,EAAC,MAAM,6CAA6C,CAAC;AAGrE,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAChD,OAAO,EACqB,UAAU,EAAE,eAAe,EAAE,kBAAkB,EAAE,cAAc,EAE1F,MAAM,SAAS,CAAC;AACjB,OAAO,EAAC,UAAU,EAAE,gBAAgB,EAAC,MAAM,qBAAqB,CAAC;AAEjE,OAAO,EAAC,WAAW,EAAE,eAAe,EAAC,MAAM,0BAA0B,CAAC;AACtE,OAAO,EAAc,WAAW,EAAC,MAAM,eAAe,CAAC;AAEvD,OAAO,EAAC,UAAU,EAAC,MAAM,yCAAyC,CAAC;AAGnE,MAAM,MAAM,kBAAkB,GAAG;IAC/B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM,CAAC;QAChB,QAAQ,EAAE,UAAU,CAAA;KACrB,EAAE,CAAC;IACJ,QAAQ,EAAE,MAAM,EAAE,CAAA;CACnB,CAAA;AAED,wBAAsB,kBAAkB,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,YAAY,EAAE,kBAAkB,EAClG,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,EAC5C,UAAU,EAAE,WAAW,EAAE,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,EACrE,SAAS,CAAC,EAAE,CAAC,cAAc,EAAE,GAAG,SAAS,CAAC,EAAE,GAC3C,OAAO,CAAC,gBAAgB,CAAC,CAsD3B;AAED,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,CAAC,eAAe,CAAC,EAAE,UAAU,EAAE,eAAe,GAAG,UAAU,CAuB/G"}

package/src/monomer-works/seq-to-molfile.js CHANGED Viewed

@@ -2,7 +2,7 @@ import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { getMolColName, hexToPercentRgb } from './utils';
 import { HelmTypes } from '../helm/consts';
-export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule) {
+export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule, rolesList) {
     const srcColLength = seqCol.length;
     const df = seqCol.dataFrame;
     const threadCount = Math.max(navigator.hardwareConcurrency - 2, 1);
@@ -29,7 +29,7 @@ export async function seqToMolFileWorker(seqCol, monomersDict, alphabet, polymer
                 resolve(res.data);
             };
         });
-        worker.postMessage({ seqList, monomersDict, alphabet, polymerType, start, end });
+        worker.postMessage({ seqList, rolesList, monomersDict, alphabet, polymerType, start, end });
     }
     const molList = [];
     const warnings = [];

package/src/monomer-works/seq-to-molfile.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"seq-to-molfile.js","sourceRoot":"","sources":["seq-to-molfile.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAWpB,OAAO,EAAC,aAAa,EAAE,eAAe,EAAC,MAAM,SAAS,CAAC;AAGvD,OAAO,EAAC,SAAS,EAAe,MAAM,gBAAgB,CAAC;AAYvD,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,MAAyB,EAAE,YAAgC,EAClG,QAAkB,EAAE,WAAwB,EAC5C,UAAuB,EAAE,SAAqB,EAAE,WAAqB,EACrE,SAA4C;IAE5C,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC;IACnC,MAAM,EAAE,GAA6B,MAAM,CAAC,SAAS,CAAC;IACtD,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,mBAAmB,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC;IACnE,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;SAC9C,GAAG,CAAC,GAAG,EAAE,CAAC,IAAI,MAAM,CAAC,IAAI,GAAG,CAAC,yBAAyB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;IAC9E,MAAM,SAAS,GAAG,YAAY,GAAG,WAAW,CAAC;IAC7C,MAAM,QAAQ,GAAG,IAAI,KAAK,CAAiC,WAAW,CAAC,CAAC;IACxE,MAAM,KAAK,GAAG,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;IAC9C,MAAM,OAAO,GAAG,WAAW,gCAAoB,CAAC,CAAC,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC;IACtF,MAAM,OAAO,GAAoB,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;QAC9E,MAAM,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QACxC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC;aAClC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE;YACd,OAAO,EAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,OAAO,EAAgB,CAAC;QACjG,CAAC,CAAC;aACD,OAAO,EAAE,CAAC;IACf,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC;IACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;QACrC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,SAAS,CAAC,CAAC;QACxC,MAAM,GAAG,GAAG,CAAC,CAAC,KAAK,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC,CAAC;QACrF,QAAQ,CAAC,CAAC,CAAC,GAAG,IAAI,OAAO,CAAwB,CAAC,OAAO,EAAE,EAAE;YAC3D,MAAM,CAAC,SAAS,GAAG,CAAC,GAAoC,EAAQ,EAAE;gBAChE,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;YACpB,CAAC,CAAC;QACJ,CAAC,CAAC,CAAC;QACH,MAAM,CAAC,WAAW,CAAC,EAAC,OAAO,EAAE,SAAS,EAAE,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,EAA2B,CAAC,CAAC;IACtH,CAAC;IAED,MAAM,OAAO,GAAqB,EAAE,CAAC;IACrC,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,MAAM,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,QAAiC,EAAE,EAAE;QACrE,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;YAC/B,OAAO,CAAC,IAAI,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAClC,QAAQ,CAAC,IAAI,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;QACrC,CAAC;IACH,CAAC,CAAC,CAAC;IAEH,+GAA+G;IAE/G,UAAU,CAAC,GAAG,EAAE;QACd,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,EAAE;YACzB,MAAM,CAAC,SAAS,EAAE,CAAC;QACrB,CAAC,CAAC,CAAC;IACL,CAAC,EAAE,CAAC,CAAC,CAAC;IACN,MAAM,UAAU,GAAG,aAAa,CAAC,EAAE,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC;IAClD,MAAM,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC;SAChF,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC,CAAC;IAC9C,MAAM,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,QAAQ,CAAC;IACrC,MAAM,CAAC,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC;IAC/C,MAAM,CAAC,MAAM,sDAA4B,MAAM,CAAC,IAAI,CAAC,CAAC;IAEtD,OAAO,EAAC,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAC,CAAC;AAC9C,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,WAAsC,EAAE,UAA2B;IACjG,MAAM,OAAO,GAAgC,EAAE,CAAC;IAChD,MAAM,OAAO,GAAgC,EAAE,CAAC;IAEhD,KAAK,MAAM,eAAe,IAAI,WAAW,EAAE,CAAC;QAC1C,MAAM,GAAG,GAAG,UAAU,CAAC,mBAAmB,CAAC,eAAe,CAAC,OAAO,EAAE,eAAe,CAAC,MAAM,CAAE,CAAC;QAC7F,MAAM,SAAS,GAAG,GAAG,CAAC,eAAe,CAAC;QACtC,mDAAmD;QACnD,MAAM,OAAO,GAAG,eAAe,CAAC,SAAS,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;QAC7G,KAAK,MAAM,KAAK,IAAI,eAAe,CAAC,KAAK;YACvC,OAAO,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;QAC3B,KAAK,MAAM,KAAK,IAAI,eAAe,CAAC,KAAK;YACvC,OAAO,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;IAC7B,CAAC;IAED,MAAM,YAAY,GAAe;QAC/B,KAAK,EAAE,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnD,KAAK,EAAE,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnD,mBAAmB,EAAE,OAAO;QAC5B,mBAAmB,EAAE,OAAO;KAC7B,CAAC;IAEF,OAAO,YAAY,CAAC;AACtB,CAAC"}

package/src/monomer-works/to-atomic-level-utils.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { MolfileWithMap, MonomerMolGraphMap } from './types';
+import { MolfileWithMap, MonomerMolGraphMap, NucleotideRole } from './types';
 import { ALPHABET } from '../utils/macromolecule/consts';
 import { IMonomerLibBase } from '../types/monomer-library';
 import { ISeqMonomer, PolymerType } from '../helm/types';
@@ -9,12 +9,14 @@ import { ISeqMonomer, PolymerType } from '../helm/types';
  * @return {Map<string, any>} - Mapping of peptide symbols to HELM monomer library objects with selected fields*/
 export declare function getFormattedMonomerLib(monomerLib: IMonomerLibBase, polymerType: PolymerType, alphabet: ALPHABET): Map<string, any>;
 /** Translate a sequence of monomer symbols into Molfile V3000
- * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)
- * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects
+ * @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)
+ * @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects
  * @param {ALPHABET} alphabet - Alphabet of the column
  * @param {PolymerType} polymerType - Polymer type
- * @return {string} - Molfile V3000*/
-export declare function monomerSeqToMolfile(monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType): MolfileWithMap;
+ * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly
+ *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).
+ * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */
+export declare function monomerSeqToMolfile(monomerSeq: ISeqMonomer[], monomersDict: MonomerMolGraphMap, alphabet: ALPHABET, polymerType: PolymerType, roles?: NucleotideRole[]): MolfileWithMap;
 /** Keep precision upon floating point operations over atom coordinates
  * @param {number}x - the floating point number
  * @return {number} - the floating point number with the same precision

package/src/monomer-works/to-atomic-level-utils.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AAEA,OAAO,EAA4C,cAAc,EAAwB,kBAAkB,EACzG,cAAc,EAAC,MAAM,SAAS,CAAC;AAEjC,OAAO,EAAC,QAAQ,EAAa,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAAC,eAAe,EAAU,MAAM,0BAA0B,CAAC;AAClE,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AAIvD;;;;iHAIiH;AACjH,wBAAgB,sBAAsB,CACpC,UAAU,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,QAAQ,EAAE,QAAQ,GACxE,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,CAuBlB;AAED;;;;;;;+EAO+E;AAC/E,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,WAAW,EAAE,EAAE,YAAY,EAAE,kBAAkB,EAC3D,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,EAC5C,KAAK,CAAC,EAAE,cAAc,EAAE,GACvB,cAAc,CA2HhB;AA6YD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C"}

package/src/monomer-works/to-atomic-level-utils.js CHANGED Viewed

@@ -13,11 +13,13 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
     const map = new Map();
     for (const monomerSymbol of monomerLib.getMonomerSymbolsByType(polymerType)) {
         const it = monomerLib.getMonomer(polymerType, monomerSymbol);
-        if (polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ &&
+        if (
+        // RNA: all branch monomers (bases) and all backbone monomers (sugars +
+        // phosphates, including modified ones). Modifications are looked up by
+        // symbol at assembly time, so they MUST be present in the formatted lib.
+        polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ &&
             (it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] === "Branch" /* HELM_MONOMER_TYPE.BRANCH */ ||
-                alphabet === ALPHABET.DNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.DEOXYRIBOSE.symbol ||
-                alphabet === ALPHABET.RNA && it["symbol" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE.symbol ||
-                it["symbol" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE.symbol) ||
+                it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] === "Backbone" /* HELM_MONOMER_TYPE.BACKBONE */) ||
             polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */ &&
                 it["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] !== "Branch" /* HELM_MONOMER_TYPE.BRANCH */) {
             const monomerObject = {};
@@ -31,19 +33,25 @@ export function getFormattedMonomerLib(monomerLib, polymerType, alphabet) {
     return map;
 }
 /** Translate a sequence of monomer symbols into Molfile V3000
- * @param {string[]} monomerSeq - Sequence of monomer symbols (canonical)
- * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects
+ * @param {ISeqMonomer[]} monomerSeq - Sequence of monomer symbols (canonical)
+ * @param {MonomerMolGraphMap} monomersDict - Mapping of monomer symbols to MolGraph objects
  * @param {ALPHABET} alphabet - Alphabet of the column
  * @param {PolymerType} polymerType - Polymer type
- * @return {string} - Molfile V3000*/
-export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType) {
+ * @param {Array} roles - Optional per-position NucleotideRole tags. When set, RNA assembly
+ *   uses per-position sugars/phosphates from monomerSeq directly (HELM triples mode).
+ * @return {MolfileWithMap} - Molfile V3000 + per-position monomer index map */
+export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerType, roles) {
     if (monomerSeq.length === 0) {
         // throw new Error('monomerSeq is empty');
         return MolfileWithMap.createEmpty();
     }
+    // Triples mode is on only when (a) caller flagged the row with roles, and
+    // (b) the row's length is a positive multiple of 3 (sugar/base/phosphate triples).
+    // in edge cases, terminal phosphate may be missing, so we also allow length % 3 === 2, but only if roles are present to disambiguate the monomers.
+    const triplesMode = polymerType === "RNA" /* HELM_POLYMER_TYPE.RNA */ && !!roles &&
+        roles.length === monomerSeq.length && (monomerSeq.length % 3 === 0 || monomerSeq.length % 3 === 2);
     // define atom and bond counts, taking into account the bond type
-    const getAtomAndBondCounts = getResultingAtomBondCounts;
-    const { atomCount, bondCount, needsCapping } = getAtomAndBondCounts(monomerSeq, monomersDict, alphabet, polymerType);
+    const { atomCount, bondCount, needsCapping } = getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode);
     // create arrays to store lines of the resulting molfile
     const molfileAtomBlock = new Array(atomCount);
     const molfileBondBlock = new Array(bondCount);
@@ -54,8 +62,12 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
         addMonomerToMolblock = addAminoAcidToMolblock;
     else { // nucleotides
         addMonomerToMolblock = addNucleotideToMolblock;
-        sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);
-        phosphate = getMolGraph(monomersDict, C.PHOSPHATE);
+        // Default sugar/phosphate are only consulted in bases-only mode. In
+        // triples mode, every nucleotide carries its own.
+        if (!triplesMode) {
+            sugar = (alphabet === ALPHABET.DNA) ? getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);
+            phosphate = getMolGraph(monomersDict, C.PHOSPHATE);
+        }
     }
     const v = {
         i: 0,
@@ -70,7 +82,8 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     const LC = {
         sugar: sugar,
         phosphate: phosphate,
-        seqLength: monomerSeq.length,
+        // In triples mode, the "logical" sequence length is the nucleotide count.
+        seqLength: triplesMode ? Math.ceil(monomerSeq.length / 3) : monomerSeq.length,
         atomCount: atomCount,
         bondCount: bondCount,
     };
@@ -78,31 +91,36 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     const steabsCollection = [];
     let nAtoms = 0;
     let lastMonomerCappingAtom = undefined;
-    for (v.i = 0; v.i < LC.seqLength; ++v.i) {
-        const seqMonomer = monomerSeq[v.i];
-        if (seqMonomer.symbol === GAP_SYMBOL)
-            continue;
-        const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });
-        lastMonomerCappingAtom = monomer.terminalR2Atom;
-        const mAtomFirst = v.nodeShift;
-        const mBondFirst = v.bondShift;
-        addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);
-        //adding stereo atoms to array for further STEABS block generation
-        monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));
-        nAtoms += monomer.atoms.x.length;
-        const mAtomCount = v.nodeShift - mAtomFirst;
-        const mAtomList = new Array(mAtomCount);
-        for (let maI = 0; maI < mAtomCount; ++maI)
-            mAtomList[maI] = mAtomFirst + maI;
-        const mBondCount = v.bondShift - mBondFirst;
-        const mBondList = new Array(mBondCount);
-        for (let mbI = 0; mbI < mBondCount; ++mbI)
-            mBondList[mbI] = mBondFirst + mbI;
-        monomers.set(v.i, {
-            biotype: seqMonomer.biotype,
-            symbol: seqMonomer.symbol,
-            atoms: mAtomList, bonds: mBondList
-        });
+    if (triplesMode) {
+        runTriplesAssembly(monomerSeq, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, (a) => { nAtoms += a; }, () => nAtoms);
+    }
+    else {
+        for (v.i = 0; v.i < LC.seqLength; ++v.i) {
+            const seqMonomer = monomerSeq[v.i];
+            if (seqMonomer.symbol === GAP_SYMBOL)
+                continue;
+            const monomer = getMolGraph(monomersDict, { symbol: seqMonomer.symbol, polymerType: helmTypeToPolymerType(seqMonomer.biotype) });
+            lastMonomerCappingAtom = monomer.terminalR2Atom;
+            const mAtomFirst = v.nodeShift;
+            const mBondFirst = v.bondShift;
+            addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);
+            //adding stereo atoms to array for further STEABS block generation
+            monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));
+            nAtoms += monomer.atoms.x.length;
+            const mAtomCount = v.nodeShift - mAtomFirst;
+            const mAtomList = new Array(mAtomCount);
+            for (let maI = 0; maI < mAtomCount; ++maI)
+                mAtomList[maI] = mAtomFirst + maI;
+            const mBondCount = v.bondShift - mBondFirst;
+            const mBondList = new Array(mBondCount);
+            for (let mbI = 0; mbI < mBondCount; ++mbI)
+                mBondList[mbI] = mBondFirst + mbI;
+            monomers.set(v.i, {
+                biotype: seqMonomer.biotype,
+                symbol: seqMonomer.symbol,
+                atoms: mAtomList, bonds: mBondList
+            });
+        }
     }
     // if the last monomer needs to be capped, add the terminal OH to the resulting molfile
     if (needsCapping)
@@ -282,19 +300,22 @@ function fillBackboneToBranchBond(branchMonomer, molfileBondBlock, v) {
 }
 /** Compute the atom/bond counts for the resulting molfile, depending on the
  * type of polymer (peptide/nucleotide)
- * @param {string[]}monomerSeq - the sequence of monomers
- * @param {Map<string, MolGraph>}monomersDict - the dictionary of monomers
- * @param {ALPHABET}alphabet - the alphabet of the monomers
- * @param {HELM_POLYMER_TYPE}polymerType - the type of polymer
- * @return {{atomCount: number, bondCount: number}} - the atom/bond counts*/
-function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType) {
+ * @param {ISeqMonomer[]} monomerSeq - the sequence of monomers
+ * @param {MonomerMolGraphMap} monomersDict - the dictionary of monomers
+ * @param {ALPHABET} alphabet - the alphabet of the monomers
+ * @param {PolymerType} polymerType - the type of polymer
+ * @param {boolean} triplesMode - true when monomerSeq is a flat list of HELM RNA triples
+ * @return {Object} the atom/bond counts plus needsCapping flag */
+function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerType, triplesMode) {
     let atomCount = 0;
     let bondCount = 0;
     let monomerCount = 0;
     let needsCapping = true;
     let lastMonomerGraph = null;
+    let lastPhosphateGraph = null;
     // sum up all the atoms/nodes provided by the sequence
-    for (const seqMonomer of monomerSeq) {
+    for (let i = 0; i < monomerSeq.length; ++i) {
+        const seqMonomer = monomerSeq[i];
         if (seqMonomer.symbol === GAP_SYMBOL)
             continue; // Skip for gap/empty monomer in MSA
         if (seqMonomer.symbol == '*')
@@ -303,6 +324,10 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
         atomCount += lastMonomerGraph.atoms.x.length;
         bondCount += lastMonomerGraph.bonds.bondTypes.length;
         monomerCount++;
+        // In triples mode, every 3rd entry (index 2 mod 3) is a phosphate. Track
+        // the LAST one — its atoms/bonds are dropped at the 3'-terminus.
+        if (triplesMode && i % 3 === 2)
+            lastPhosphateGraph = lastMonomerGraph;
     }
     // add extra values depending on the polymer type
     if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
@@ -321,7 +346,19 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
             }
         }
     }
-    else { // nucleotides
+    else if (triplesMode) { // nucleotides — HELM triples (per-position sugar/base/phosphate)
+        void lastPhosphateGraph; // kept for symmetry; trailing P is now retained when HELM wrote it
+        // Per-monomer-loop already summed sugars + bases + phosphates for every
+        // entry in monomerSeq. Reservation: each backbone (sugar/phosphate)
+        // reserves +1 bond slot for the chain-extending bond, each branch (base)
+        // reserves +1 for its branch bond. Total reservations = monomerCount.
+        //   length === 3N      → trailing P emitted, monomerCount = 3N.
+        //   length === 3N - 1  → trailing P absent, monomerCount = 3N - 1.
+        // Either way, bondCount = sum_bonds + monomerCount.
+        atomCount += 1; // OH cap atom (rides on trailing P or on last sugar's R2)
+        bondCount += monomerCount;
+    }
+    else { // nucleotides — bases-only legacy path with default sugar/phosphate
         const sugar = (alphabet === ALPHABET.DNA) ?
             getMolGraph(monomersDict, C.DEOXYRIBOSE) : getMolGraph(monomersDict, C.RIBOSE);
         const phosphate = getMolGraph(monomersDict, C.PHOSPHATE);
@@ -342,6 +379,118 @@ function getResultingAtomBondCounts(monomerSeq, monomersDict, alphabet, polymerT
     }
     return { atomCount, bondCount, needsCapping };
 }
+/** Triples-mode RNA assembly. Iterate by NUCLEOTIDE; each nucleotide normally
+ * contributes 3 entries from monomerSeq in order [sugar, base, phosphate].
+ * The LAST nucleotide may omit its trailing phosphate (length === 3N - 1) —
+ * in that case HELM specified an unphosphorylated 3'-end and we cap on the
+ * last sugar's R2 instead of on a final phosphate.
+ *
+ * @param {ISeqMonomer[]} monomerSeq - flat sugar/base/[phosphate] entries
+ * @param {MonomerMolGraphMap} monomersDict - monomer dictionary
+ * @param {string[]} molfileAtomBlock - output atom block buffer
+ * @param {string[]} molfileBondBlock - output bond block buffer
+ * @param {LoopVariables} v - mutable loop variables
+ * @param {LoopConstants} LC - loop constants (seqLength = nucleotide count)
+ * @param {MonomerMap} monomers - per-position monomer index map (filled in)
+ * @param {number[]} steabsCollection - stereo atoms collected for STEABS block
+ * @param {Function} addAtoms - callback to bump per-row atom counter for stereo offsets
+ * @param {Function} getAtoms - callback to read current atom counter */
+function runTriplesAssembly(monomerSeq, monomersDict, molfileAtomBlock, molfileBondBlock, v, LC, monomers, steabsCollection, addAtoms, getAtoms) {
+    const N = LC.seqLength;
+    // length === 3N → trailing P present. length === 3N-1 → trailing P absent.
+    const hasTrailingP = monomerSeq.length === 3 * N;
+    for (let n = 0; n < N; ++n) {
+        v.i = n;
+        const sugarSm = monomerSeq[3 * n];
+        const baseSm = monomerSeq[3 * n + 1];
+        const sugarG = getMolGraph(monomersDict, { symbol: sugarSm.symbol, polymerType: helmTypeToPolymerType(sugarSm.biotype) });
+        const baseG = getMolGraph(monomersDict, { symbol: baseSm.symbol, polymerType: helmTypeToPolymerType(baseSm.biotype) });
+        // The previous nucleotide's trailing phosphate is the linker into THIS
+        // nucleotide's sugar. It always exists for n >= 1 because only the
+        // very LAST nucleotide is permitted to omit its phosphate.
+        const prevPhosG = (n === 0) ? null :
+            getMolGraph(monomersDict, { symbol: monomerSeq[3 * (n - 1) + 2].symbol,
+                polymerType: helmTypeToPolymerType(monomerSeq[3 * (n - 1) + 2].biotype) });
+        // emit prevPhosphate (chain linker), then sugar, then base
+        const seqStartIdx = 3 * n; // for keying the per-row monomer map by HELM splitter index
+        if (prevPhosG) {
+            const prevAtomFirst = v.nodeShift;
+            const prevBondFirst = v.bondShift;
+            addBackboneMonomerToMolblock(prevPhosG, molfileAtomBlock, molfileBondBlock, v);
+            prevPhosG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));
+            addAtoms(prevPhosG.atoms.x.length);
+            // The phosphate "belongs to" nucleotide n-1's HELM index (3*(n-1)+2).
+            const prevPhosKey = 3 * (n - 1) + 2;
+            const aList = [];
+            for (let a = prevAtomFirst; a < v.nodeShift; ++a)
+                aList.push(a);
+            const bList = [];
+            for (let b = prevBondFirst; b < v.bondShift; ++b)
+                bList.push(b);
+            monomers.set(prevPhosKey, {
+                biotype: monomerSeq[prevPhosKey].biotype,
+                symbol: monomerSeq[prevPhosKey].symbol,
+                atoms: aList, bonds: bList,
+            });
+        }
+        const sugarAtomFirst = v.nodeShift;
+        const sugarBondFirst = v.bondShift;
+        addBackboneMonomerToMolblock(sugarG, molfileAtomBlock, molfileBondBlock, v);
+        sugarG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));
+        addAtoms(sugarG.atoms.x.length);
+        const sAList = [];
+        for (let a = sugarAtomFirst; a < v.nodeShift; ++a)
+            sAList.push(a);
+        const sBList = [];
+        for (let b = sugarBondFirst; b < v.bondShift; ++b)
+            sBList.push(b);
+        monomers.set(seqStartIdx, {
+            biotype: sugarSm.biotype, symbol: sugarSm.symbol,
+            atoms: sAList, bonds: sBList,
+        });
+        const baseAtomFirst = v.nodeShift;
+        const baseBondFirst = v.bondShift;
+        addBranchMonomerToMolblock(baseG, molfileAtomBlock, molfileBondBlock, v);
+        baseG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));
+        addAtoms(baseG.atoms.x.length);
+        const bAList = [];
+        for (let a = baseAtomFirst; a < v.nodeShift; ++a)
+            bAList.push(a);
+        const bBList = [];
+        for (let b = baseBondFirst; b < v.bondShift; ++b)
+            bBList.push(b);
+        monomers.set(seqStartIdx + 1, {
+            biotype: baseSm.biotype, symbol: baseSm.symbol,
+            atoms: bAList, bonds: bBList,
+        });
+    }
+    // Emit the trailing phosphate (the LAST nucleotide's P) as the final
+    // backbone monomer ONLY if HELM explicitly wrote it. The OH cap then
+    // rides on its free oxygen (3'-phosphate-OH terminus). If HELM omitted
+    // the trailing phosphate, the cap rides on the last sugar's R2 — that
+    // requires no extra emission here, since v.backboneAttachNode already
+    // points at the last sugar's R2 attach.
+    if (hasTrailingP) {
+        const lastPhosKey = 3 * (N - 1) + 2;
+        const lastPhosSm = monomerSeq[lastPhosKey];
+        const lastPhosG = getMolGraph(monomersDict, { symbol: lastPhosSm.symbol, polymerType: helmTypeToPolymerType(lastPhosSm.biotype) });
+        const trailAtomFirst = v.nodeShift;
+        const trailBondFirst = v.bondShift;
+        addBackboneMonomerToMolblock(lastPhosG, molfileAtomBlock, molfileBondBlock, v);
+        lastPhosG.stereoAtoms?.forEach((i) => steabsCollection.push(i + getAtoms()));
+        addAtoms(lastPhosG.atoms.x.length);
+        const tAList = [];
+        for (let a = trailAtomFirst; a < v.nodeShift; ++a)
+            tAList.push(a);
+        const tBList = [];
+        for (let b = trailBondFirst; b < v.bondShift; ++b)
+            tBList.push(b);
+        monomers.set(lastPhosKey, {
+            biotype: lastPhosSm.biotype, symbol: lastPhosSm.symbol,
+            atoms: tAList, bonds: tBList,
+        });
+    }
+}
 /** Keep precision upon floating point operations over atom coordinates
  * @param {number}x - the floating point number
  * @return {number} - the floating point number with the same precision

package/src/monomer-works/to-atomic-level-utils.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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