@datagrok/bio 2.18.3 → 2.19.0

package/files/tests/to-atomic-level-pt-fasta-2.mol

@@ -5,41 +5,41 @@ Datagrok macromolecule handler
 M  V30 BEGIN CTAB
 M  V30 COUNTS 17 16 0 0 0
 M  V30 BEGIN ATOM
-M  V30 1 C 0.7144 -1.2375  0.000000 0
-M  V30 2 C 0.7144 -0.4125  0.000000 0
+M  V30 1 C 1.2991 -2.25  0.000000 0
+M  V30 2 C 1.2991 -0.75  0.000000 0
 M  V30 3 N 0 0  0.000000 0
-M  V30 4 C 1.4289 0  0.000000 0
-M  V30 5 O 2.1434 -0.4126  0.000000 0
-M  V30 6 N 4.2867 4.9501  0.000000 0
-M  V30 7 C 3.5722 4.5376  0.000000 0
-M  V30 8 N 2.8578 4.95  0.000000 0
-M  V30 9 N 3.5723 3.7126  0.000000 0
-M  V30 10 C 2.8578 3.3001  0.000000 0
-M  V30 11 C 2.8578 2.475  0.000000 0
-M  V30 12 C 2.1433 2.0626  0.000000 0
-M  V30 13 C 2.1433 1.2375  0.000000 0
-M  V30 14 N 1.4289 0.825  0.000000 0
-M  V30 15 C 2.8578 0.8251  0.000000 0
-M  V30 16 O 3.5723 1.2376  0.000000 0
-M  V30 17 O 2.8578 0 0.000000 0
+M  V30 4 C 2.5981 0  0.000000 0
+M  V30 5 O 3.8971 -0.75  0.000000 0
+M  V30 6 N 7.7941 9  0.000000 0
+M  V30 7 C 6.4951 8.2501  0.000000 0
+M  V30 8 N 5.196 9  0.000000 0
+M  V30 9 N 6.4951 6.7501  0.000000 0
+M  V30 10 C 5.1961 6  0.000000 0
+M  V30 11 C 5.1961 4.5  0.000000 0
+M  V30 12 C 3.8971 3.75  0.000000 0
+M  V30 13 C 3.8971 2.25  0.000000 0
+M  V30 14 N 2.5981 1.5  0.000000 0
+M  V30 15 C 5.1962 1.5  0.000000 0
+M  V30 16 O 6.4952 2.25  0.000000 0
+M  V30 17 O 5.1962 -0.0001 0.000000 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
-M  V30 1 1 2 1 CFG=3
-M  V30 2 1 2 3
+M  V30 1 1 2 1 CFG=3 
+M  V30 2 1 2 3 
 M  V30 3 1 2 4
-M  V30 4 2 4 5
+M  V30 4 2 4 5 
 M  V30 5 1 4 14
-M  V30 6 1 6 7
-M  V30 7 2 7 8
-M  V30 8 1 7 9
-M  V30 9 1 9 10
-M  V30 10 1 10 11
-M  V30 11 1 11 12
-M  V30 12 1 13 12 CFG=1
-M  V30 13 1 13 14
+M  V30 6 2 6 7 
+M  V30 7 1 7 8 
+M  V30 8 1 7 9 
+M  V30 9 1 9 10 
+M  V30 10 1 10 11 
+M  V30 11 1 11 12 
+M  V30 12 1 13 12 CFG=1 
+M  V30 13 1 13 14 
 M  V30 14 1 13 15
-M  V30 15 2 15 16
+M  V30 15 2 15 16 
 M  V30 16 1 15 17
 M  V30 END BOND
 M  V30 END CTAB
-M  END
+M  END

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.18.3",
+  "version": "2.19.0",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -44,13 +44,13 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.48.1",
+    "@datagrok-libraries/bio": "^5.50.1",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/math": "^1.2.4",
     "@datagrok-libraries/ml": "^6.7.6",
     "@datagrok-libraries/tutorials": "^1.4.3",
     "@datagrok-libraries/utils": "^4.4.0",
-    "datagrok-api": "^1.23.0",
+    "datagrok-api": "^1.24.0",
     "@webgpu/types": "^0.1.40",
     "ajv": "^8.12.0",
     "ajv-errors": "^3.0.0",

package/src/analysis/sequence-search-base-viewer.ts

@@ -70,7 +70,7 @@ export class SequenceSearchBaseViewer extends DG.JsViewer {
     this.render();
   }
 
-  /** For tests */ public computeRequested: boolean;
+  /** For tests */ public computeRequested: boolean = false;
   public renderPromise: Promise<void> = Promise.resolve();
 
   protected render(computeData = true): void {

package/src/package.ts

@@ -422,7 +422,7 @@ export function getRegion(
     start ?? null, end ?? null, name ?? null);
 }
 
-//top-menu: Bio | Convert | Get Region...
+//top-menu: Bio | Calculate | Get Region...
 //name: Get Region Top Menu
 //description: Get sequences for a region specified from a Macromolecule
 //input: dataframe table                           [Input data table]
@@ -607,14 +607,13 @@ export async function sequenceSpaceTopMenu(table: DG.DataFrame, molecules: DG.Co
   return res;
 }
 
-//top-menu: Bio | Convert | To Atomic Level...
+//top-menu: Bio | Transform | To Atomic Level...
 //name: To Atomic Level
 //description: Converts sequences to molblocks
 //input: dataframe table [Input data table]
 //input: column seqCol {caption: Sequence; semType: Macromolecule}
 //input: bool nonlinear =false {caption: Non-linear; description: Slower mode for cycling/branching HELM structures}
 //input: bool highlight =false {caption: Highlight monomers; description: Highlight monomers' substructures of the molecule }
-//output:
 export async function toAtomicLevel(
   table: DG.DataFrame, seqCol: DG.Column, nonlinear: boolean, highlight: boolean = false
 ): Promise<void> {
@@ -630,6 +629,17 @@ export async function toAtomicLevel(
   }
 }
 
+//name: To Atomic Level...
+//input: column seqCol {semType: Macromolecule}
+//meta.action: to atomic level
+export async function toAtomicLevelAction(seqCol: DG.Column) {
+  if (!seqCol?.dataFrame)
+    throw new Error('Sequence column is not found or its data frame is not empty');
+  const func = DG.Func.find({name: 'toAtomicLevel', package: 'Bio'})[0];
+  if (!func) throw new Error('To Atomic level Function not found');
+  func.prepare({table: seqCol.dataFrame, seqCol: seqCol}).edit();
+}
+
 //top-menu: Bio | Analyze | MSA...
 //name: MSA
 //description: Performs multiple sequence alignment
@@ -743,38 +753,20 @@ export function importBam(fileContent: string): DG.DataFrame [] {
   return [];
 }
 
-//top-menu: Bio | Convert | Notation...
+//top-menu: Bio | Transform | Convert Notation...
 //name: convertDialog
 export function convertDialog() {
   const col: DG.Column<string> | undefined = getMacromoleculeColumns()[0];
   convert(col, _package.seqHelper);
 }
 
-//top-menu: Bio | Convert | TestConvert
-//name: convertSeqNotation
-//description: RDKit-based conversion for SMILES, SMARTS, InChi, Molfile V2000 and Molfile V3000
-//input: string sequence {semType: Macromolecule}
-//input: string targetNotation
-//input: string separator
-//output: string result
-export async function convertSeqNotation(sequence: string, targetNotation: NOTATION, separator?: string): Promise<string | undefined | null> {
-  try {
-    const col = DG.Column.fromStrings('sequence', [sequence]);
-    const _df = DG.DataFrame.fromColumns([col]);
-    const semType = await grok.functions.call('Bio:detectMacromolecule', {col: col});
-    if (semType)
-      col.semType = semType;
-    const converterSh = _package.seqHelper.getSeqHandler(col);
-    const newColumn = converterSh.convert(targetNotation, separator);
-    return newColumn.get(0);
-  } catch (err: any) {
-    const [errMsg, errStack] = errInfo(err);
-    _package.logger.error(errMsg, undefined, errStack);
-    throw err;
-  }
+//name: Convert Notation...
+//input: column col {semType: Macromolecule}
+//meta.action: Convert Notation...
+export function convertColumnAction(col: DG.Column) {
+  convert(col, _package.seqHelper);
 }
 
-
 //name: monomerCellRenderer
 //tags: cellRenderer
 //meta.cellType: Monomer
@@ -835,7 +827,7 @@ export async function testDetectMacromolecule(path: string): Promise<DG.DataFram
   return resDf;
 }
 
-//top-menu: Bio | Convert | Split to Monomers...
+//top-menu: Bio | Transform | Split to Monomers...
 //name: Split to Monomers
 //input: dataframe table
 //input: column sequence { semType: Macromolecule }
@@ -979,7 +971,8 @@ export async function manageLibrariesApp(): Promise<DG.View> {
 export async function manageLibrariesAppTreeBrowser(treeNode: DG.TreeViewGroup, browseView: DG.BrowseView) {
   const libraries = (await (await MonomerLibManager.getInstance()).getFileManager()).getValidLibraryPaths();
   libraries.forEach((libName) => {
-    const libNode = treeNode.item(libName);
+    const nodeName = libName.endsWith('.json') ? libName.substring(0, libName.length - 5) : libName;
+    const libNode = treeNode.item(nodeName);
     // eslint-disable-next-line rxjs/no-ignored-subscription, rxjs/no-async-subscribe
     libNode.onSelected.subscribe(async () => {
       const monomerManager = await MonomerManager.getNewInstance();

package/src/tests/scoring.ts

@@ -21,8 +21,8 @@ category('Scoring', () => {
   /* eslint-disable max-len */
   const table = DG.DataFrame.fromCsv(`${sequence},${expectedSimilarity},${expectedIdentity}
 PEPTIDE1{Aca.Orn.gGlu.Pqa.D-His_1Bn.dH.hHis.4Abz.D-Tic.D-Dap.Y.Iva.meS.F.P.F.D-1Nal}$$$$,1.0,1.0
-PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC}$$$$,0.68,0.53
-PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal]}$$$$V2.0,0.34,0.0`
+PEPTIDE1{Iva.Gly_allyl.gGlu.Pqa.D-Dip.dH.hHis.4Abz.D-aHyp.D-Dap.Y.Iva.I.Tyr_26diMe.P.Asu.meC}$$$$,0.691,0.53
+PEPTIDE1{[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal].[1Nal]}$$$$V2.0,0.37,0.0`
   );
   const seqCol: DG.Column<string> = table.getCol(sequence);
   seqCol.meta.units = NOTATION.HELM;

package/src/tests/seq-handler-get-region-tests.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-lines-per-function */
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
@@ -68,7 +69,7 @@ PEPTIDE1{N.T.[dE].[Thr_PO3H2]}$$$$
 PEPTIDE1{[Cys_SEt].T.[dK].[Thr_PO3H2]}$$$$
 PEPTIDE1{[Cys_SEt].T.*.*}$$$$`,
       units: NOTATION.HELM,
-      alphabet: null,
+      alphabet: ALPHABET.UN,
 
       positionNames: {tag: null, start: '4', end: '7'}
     }

package/src/utils/helm-to-molfile/converter/converter.ts

@@ -4,9 +4,8 @@ import * as OCL from 'openchemlib/full';
 
 import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
-import {IMonomerLib, IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
-import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
-import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
+import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
+import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {MolfileWithMap, MonomerMap} from '@datagrok-libraries/bio/src/monomer-works/types';
 
 import {Polymer} from './polymer';
@@ -14,9 +13,10 @@ import {GlobalMonomerPositionHandler} from './position-handler';
 
 import {_package} from '../../../package';
 import {getUnusedColName} from '@datagrok-libraries/bio/src/monomer-works/utils';
+import {IHelmToMolfileConverter} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 
-export class HelmToMolfileConverter {
+export class HelmToMolfileConverter implements IHelmToMolfileConverter {
   constructor(
     private readonly helmHelper: IHelmHelper,
     private readonly rdKitModule: RDModule,
@@ -41,6 +41,20 @@ export class HelmToMolfileConverter {
     return smiles;
   }
 
+  public molV3KtoMolV3KOCL(molV3k: string): string {
+    try {
+      if (!molV3k)
+        return '';
+      const oclMolecule = OCL.Molecule.fromMolfile(molV3k);
+      const molV3000 = oclMolecule.toMolfileV3();
+      return molV3000.replace('STERAC1', 'STEABS');
+    } catch (err) {
+      const [errMsg, errStack] = errInfo(err);
+      _package.logger.error(errMsg, undefined, errStack);
+      return '';
+    }
+  }
+
   public getMolV3000ViaOCL(beautifiedMols: (RDMol | null)[], columnName: string): DG.Column<string> {
     const beautifiedMolV2000 = beautifiedMols.map((mol) => {
       if (mol === null)
@@ -52,9 +66,7 @@ export class HelmToMolfileConverter {
     const molv3000Arr = new Array<string>(beautifiedMolV2000.length);
     const chiralityPb = DG.TaskBarProgressIndicator.create(`Handling chirality...`);
     for (let i = 0; i < beautifiedMolV2000.length; i++) {
-      const oclMolecule = OCL.Molecule.fromMolfile(beautifiedMolV2000[i]);
-      const molV3000 = oclMolecule.toMolfileV3();
-      molv3000Arr[i] = molV3000.replace('STERAC1', 'STEABS');
+      molv3000Arr[i] = this.molV3KtoMolV3KOCL(beautifiedMolV2000[i]);
       const progress = i / beautifiedMolV2000.length * 100;
       chiralityPb.update(progress, `${progress?.toFixed(2)}% of molecules completed`);
     }
@@ -136,9 +148,9 @@ export class HelmToMolfileConverter {
     const woGapsRes = this.helmHelper.removeGaps(helm);
     const woGapsHelm = woGapsRes.resHelm;
     const woGapsReverseMap = new Map<number, number>();
-    for (const [orgPosIdx, woGapsPosIdx] of (woGapsRes.monomerMap?.entries() ?? [])) {
+    for (const [orgPosIdx, woGapsPosIdx] of (woGapsRes.monomerMap?.entries() ?? []))
       woGapsReverseMap.set(woGapsPosIdx, orgPosIdx);
-    }
+
     const pseudoMolfile = this.helmHelper.getMolfiles([woGapsHelm])[0];
     const globalPositionHandler = new GlobalMonomerPositionHandler(pseudoMolfile);
     const woGapsPolymer = new Polymer(woGapsHelm, this.rdKitModule, this.monomerLib);

package/src/utils/helm-to-molfile/converter/simple-polymer.ts

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import {HELM_MONOMER_TYPE, HELM_POLYMER_TYPE} from '@datagrok-libraries/bio/src/utils/const';
 import {cleanupHelmSymbol} from '@datagrok-libraries/bio/src/helm/utils';
 
@@ -5,8 +6,10 @@ import {Bond} from './types';
 
 /** Wrapper over simple polymer substring of HELM, like RNA1{d(A)p}  */
 export class SimplePolymer {
+  private isNucleotideSequence = false;
   constructor(private simplePolymer: string) {
     this.polymerType = this.getPolymerType();
+    this.isNucleotideSequence = this.polymerType === HELM_POLYMER_TYPE.RNA;
     this.idx = this.getIdx();
     const {monomers, monomerTypes} = this.getMonomerSymbolsAndTypes();
     this.monomers = monomers;
@@ -49,17 +52,23 @@ export class SimplePolymer {
     const monomerList: string[] = [];
     const monomerTypeList: HELM_MONOMER_TYPE[] = [];
     monomerGroups.forEach((monomerGroup) => {
-      // const splitted = monomerGroup.split(/\(|\)/).map((el) => el.replace(/[\[\]]/g, ''));
-      // monomerList.push(...splitted);
-      // WARNING: only the groups of the form r(A)p, as in RNA, are supported
+      if (!this.isNucleotideSequence) {
+        // const splitted = monomerGroup.split(/\(|\)/).map((el) => el.replace(/[\[\]]/g, ''));
+        // monomerList.push(...splitted);
+        // WARNING: only the groups of the form r(A)p, as in RNA, are supported
 
-      monomerList.push(cleanupHelmSymbol(monomerGroup));
-      // const monomerTypes = splitted.map(
-      //   (_, idx) => (idx % 2 === 0) ? HELM_MONOMER_TYPE.BACKBONE : HELM_MONOMER_TYPE.BRANCH
-      // );
+        monomerList.push(cleanupHelmSymbol(monomerGroup));
+        // const monomerTypes = splitted.map(
+        //   (_, idx) => (idx % 2 === 0) ? HELM_MONOMER_TYPE.BACKBONE : HELM_MONOMER_TYPE.BRANCH
+        // );
 
-      // monomerTypeList.push(...monomerTypes);
-      monomerTypeList.push(HELM_MONOMER_TYPE.BACKBONE);
+        // monomerTypeList.push(...monomerTypes);
+        monomerTypeList.push(HELM_MONOMER_TYPE.BACKBONE);
+      } else {
+        const splitted = monomerGroup.split(/\(|\)/).filter((el) => !!el).map((el) => cleanupHelmSymbol(el));
+        monomerList.push(...splitted);
+        splitted.forEach((_, i) => monomerTypeList.push(i % 3 === 1 ? HELM_MONOMER_TYPE.BRANCH : HELM_MONOMER_TYPE.BACKBONE));
+      }
     });
     return {monomers: monomerList, monomerTypes: monomerTypeList};
   }

package/src/utils/monomer-lib/monomer-lib-base.ts

@@ -177,13 +177,13 @@ export class MonomerLibBase implements IMonomerLibBase {
       // Symbol & Name
       const symbol = monomer[REQ.SYMBOL];
       const _name = monomer[REQ.NAME];
-
-      const htmlColor = wem.backgroundcolor;
+      const [color, backgroundColor, lineColor] =
+        wem ? [wem.textcolor, wem.backgroundcolor, wem.linecolor] : ['#202020', '#A0A0A0', '#202020'];
       res.append(ui.divH([
         ui.div([symbol], {
           style: {
             /* fontWeight: 'bolder', */ textWrap: 'nowrap', marginLeft: '4px', marginRight: '4px',
-            color: wem.textcolor, backgroundColor: wem.backgroundcolor, borderColor: wem.linecolor,
+            color: color, backgroundColor: backgroundColor, borderColor: lineColor,
             borderWidth: '1px', borderStyle: 'solid', borderRadius: '2px', padding: '3px',
             minWidth: '24px', textAlign: 'center',
           }
@@ -192,7 +192,7 @@ export class MonomerLibBase implements IMonomerLibBase {
       ], {style: {display: 'flex', flexDirection: 'row', justifyContent: 'left'}}));
 
       // Structure
-      const chemOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
+      //const chemOptions = {autoCrop: true, autoCropMargin: 0, suppressChiralText: true};
       let structureEl: HTMLElement;
       if (monomer.molfile)
         structureEl = drawMoleculeCall(monomer.molfile);

package/src/utils/monomer-lib/monomer-manager/monomer-manager.ts

@@ -1028,6 +1028,7 @@ function getCorrectedMolBlock(molBlock: string) {
   // 2. RGP field is present in the correct format
   // 3. R group labels are written as R# and not just R
   // 4. there is no ISO field in the molblock. if there is, it needs to be substituted with RGP field and thats it.
+  // 5. make sure that R groups have no metadata in the atomblocks
 
   const lines = molBlock.split('\n');
 
@@ -1055,7 +1056,7 @@ function getCorrectedMolBlock(molBlock: string) {
       rgroupLineNumbers[atomI - molStartIdx] = rgroupNum;
   }
 
-  const rgroupLineNums = Object.values(rgroupLineNumbers);
+  const rgroupLineNums = Object.keys(rgroupLineNumbers);
   // find and possibly add rgp field
 
   const rgpLineIdx = lines.findIndex((line) => line.startsWith('M') && line.includes('RGP'));
@@ -1066,6 +1067,23 @@ function getCorrectedMolBlock(molBlock: string) {
     const mEndIdx = lines.findIndex((line) => line.startsWith('M') && line.includes('END'));
     lines.splice(mEndIdx, 0, rgpLine);
   }
+
+  //make sure that R# lines do not have any metadata that can be interpreted as isotopes or anything else
+  //for example, following line could be interpreted as isotope with mass 2 in some cases
+  //"    3.9970    0.3462    0.0000 R#  0  0  0  0  0  1  0  0  0  0  2  0"
+  const rGroupActualLines = rgroupLineNums.filter((rLine) => !!Number.parseInt(rLine)).map((atomLine) => Number.parseInt(atomLine) + molStartIdx);
+  rGroupActualLines.forEach((lineIdx) => {
+    const splitLine = lines[lineIdx].split(' ');
+    const rIdx = splitLine.findIndex((s) => s === 'R#');
+    if (rIdx === -1)
+      return;
+    for (let i = rIdx + 1; i < splitLine.length; i++) {
+      if (!!splitLine[i] && splitLine[i].length == 1 && (Number.parseInt(splitLine[i]) ?? 0) > 0)
+        splitLine[i] = '0';
+    }
+    lines[lineIdx] = splitLine.join(' ');
+  });
+
   return lines.join('\n');
 }
 

package/src/utils/seq-helper/seq-handler.ts

@@ -1,3 +1,5 @@
+/* eslint-disable max-lines */
+/* eslint-disable @typescript-eslint/no-unused-vars */
 import * as DG from 'datagrok-api/dg';
 
 import wu from 'wu';
@@ -5,7 +7,7 @@ import wu from 'wu';
 /* eslint-disable max-len */
 import {ALIGNMENT, ALPHABET, candidateAlphabets, getSplitterWithSeparator, NOTATION, positionSeparator, splitterAsFasta, splitterAsHelm, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule/index';
 import {INotationProvider, ISeqSplitted, SeqColStats, SplitterFunc,} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
-import {detectAlphabet, splitterAsFastaSimple, StringListSeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
+import {detectAlphabet, detectHelmAlphabet, splitterAsFastaSimple, StringListSeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
 import {mmDistanceFunctions, MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import {mmDistanceFunctionType} from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
@@ -123,6 +125,12 @@ export class SeqHandler implements ISeqHandler {
         uh.column.setTag(TAGS.alphabetSize, alphabetSize.toString());
         uh.column.setTag(TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
       }
+    } else if (units === NOTATION.HELM) {
+      let alphabet = uh.column.getTag(TAGS.alphabet);
+      if (alphabet === null) {
+        alphabet = detectHelmAlphabet(uh.stats.freq, candidateAlphabets, uh.defaultGapOriginal);
+        uh.column.setTag(TAGS.alphabet, alphabet);
+      }
     }
   }
 
@@ -539,6 +547,7 @@ export class SeqHandler implements ISeqHandler {
     // convert the peptides list to a set for faster lookup
     const peptidesSet = new Set(peptides);
     // get splitter for given separator and check if all monomers are in the lib
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
     const splitterFunc = getSplitterWithSeparator(this.separator!);
     // iterate over the columns, split them and check if all monomers are in the lib
     //TODO maybe add missing threshold so that if there are not too many missing monomers
@@ -596,12 +605,12 @@ export class SeqHandler implements ISeqHandler {
 
     const isNucleotide = srcSeq.startsWith('RNA');
     // items can be monomers or helms
-    const helmItemsArray = this.splitter(srcSeq);
+    const helmItemsArray = splitterAsHelm(srcSeq);
     const tgtMonomersArray: string[] = [];
     for (let posIdx = 0; posIdx < helmItemsArray.length; ++posIdx) {
       let om: string = helmItemsArray.getOriginal(posIdx);
       if (isNucleotide)
-        om = om.replace(HELM_WRAPPERS_REGEXP, '');
+        om = om.replace(HELM_WRAPPERS_REGEXP, '$1');
       if (om === GapOriginals[NOTATION.HELM])
         tgtMonomersArray.push(tgtGapOriginal);
       else if (this.toFasta(tgtNotation as NOTATION) && om.length > 1) {

package/src/utils/seq-helper/seq-helper.ts

@@ -9,9 +9,8 @@ import {RDModule, RDMol} from '@datagrok-libraries/chem-meta/src/rdkit-api';
 import {IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {getHelmHelper, IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 import {MolfileWithMap} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {getMolColName, hexToPercentRgb} from '@datagrok-libraries/bio/src/monomer-works/utils';
+import {getMolColName} from '@datagrok-libraries/bio/src/monomer-works/utils';
 import {ChemTags} from '@datagrok-libraries/chem-meta/src/consts';
-import {getMolHighlight} from '@datagrok-libraries/bio/src/monomer-works/seq-to-molfile';
 import {IMonomerLibBase} from '@datagrok-libraries/bio/src/types/index';
 
 import {HelmToMolfileConverter} from '../helm-to-molfile/converter';
@@ -19,6 +18,8 @@ import {ISeqHandler} from '@datagrok-libraries/bio/src/utils/macromolecule/seq-h
 import {SeqHandler} from './seq-handler';
 import {Column} from 'datagrok-api/dg';
 import {NOTATION, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
+import {_package} from '../../package';
 
 type SeqHelperWindowType = Window & { $seqHelperPromise?: Promise<SeqHelper> };
 declare const window: SeqHelperWindowType;
@@ -44,6 +45,37 @@ export class SeqHelper implements ISeqHelper {
     return new HelmToMolfileConverter(helmHelper, this.rdKitModule, monomerLib);
   }
 
+  helmToAtomicLevelSingle(
+    helm: string, converter: HelmToMolfileConverter, chiralityEngine?: boolean, beautifyMol: boolean = true) {
+    if (!helm)
+      return MolfileWithMap.createEmpty();
+    const molfileV3k = converter.convertToMolfileV3K([helm])[0];
+    if (!molfileV3k || !molfileV3k.molfile)
+      return MolfileWithMap.createEmpty();
+    let mol: RDMol | null = null;
+    try {
+      let v3k = molfileV3k.molfile;
+      if (beautifyMol) {
+        mol = this.rdKitModule.get_mol(v3k);
+        if (!mol)
+          return MolfileWithMap.createEmpty();
+        mol.set_new_coords();
+        mol.normalize_depiction(1);
+        mol.straighten_depiction(true);
+        v3k = mol.get_v3Kmolblock();
+      }
+      if (chiralityEngine)
+        v3k = converter.molV3KtoMolV3KOCL(v3k);
+      return new MolfileWithMap(v3k, molfileV3k.monomers);
+    } catch (err) {
+      const [errMsg, errStack] = errInfo(err);
+      _package.logger.error(errMsg, undefined, errStack);
+      return MolfileWithMap.createEmpty();
+    } finally {
+      mol?.delete();
+    }
+  }
+
   async helmToAtomicLevel(
     helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean, overrideMonomerLib?: IMonomerLibBase
   ): Promise<ToAtomicLevelRes> {
@@ -54,40 +86,44 @@ export class SeqHelper implements ISeqHelper {
 
     const converter = await this.getHelmToMolfileConverter(monomerLib);
 
-    //#region From HelmToMolfileConverter.convertToRdKitBeautifiedMolfileColumn
-
-    const molfilesV3K = converter.convertToMolfileV3K(helmCol.toList());
-
-    const beautifiedMolList: (RDMol | null)[] = molfilesV3K.map((item) => {
-      const molfile = item.molfile;
-      if (molfile === '')
-        return null;
-      const mol = this.rdKitModule.get_mol(molfile);
-      if (!mol)
-        return null;
-      mol.set_new_coords();
-      mol.normalize_depiction(1);
-      mol.straighten_depiction(true);
-      return mol;
-    });
-
-    let molList: string[];
-    if (chiralityEngine) {
-      molList = converter.getMolV3000ViaOCL(beautifiedMolList, molColName).toList();
-      // TODO: Cleanup mol objects
-    } else {
-      molList = beautifiedMolList.map((mol) => {
-        if (mol === null)
-          return '';
-        const molBlock = mol.get_v3Kmolblock();
-        mol!.delete();
-        return molBlock;
-      });
-    }
+    // //#region From HelmToMolfileConverter.convertToRdKitBeautifiedMolfileColumn
+
+    // const molfilesV3K = converter.convertToMolfileV3K(helmCol.toList());
+
+    // const beautifiedMolList: (RDMol | null)[] = molfilesV3K.map((item) => {
+    //   const molfile = item.molfile;
+    //   if (molfile === '')
+    //     return null;
+    //   const mol = this.rdKitModule.get_mol(molfile);
+    //   if (!mol)
+    //     return null;
+    //   mol.set_new_coords();
+    //   mol.normalize_depiction(1);
+    //   mol.straighten_depiction(true);
+    //   return mol;
+    // });
+
+    // let molList: string[];
+    // if (chiralityEngine)// also creates progress indicator
+    //   molList = converter.getMolV3000ViaOCL(beautifiedMolList, molColName).toList();
+    //   // TODO: Cleanup mol objects
+    // else {
+    //   molList = beautifiedMolList.map((mol) => {
+    //     if (mol === null)
+    //       return '';
+    //     const molBlock = mol.get_v3Kmolblock();
+    //     mol!.delete();
+    //     return molBlock;
+    //   });
+    // }
 
     //#endregion From HelmToMolfileConverter
+    const helmList = helmCol.toList();
+    const molList = new Array<string>(helmCol.length);
+    for (let i = 0; i < helmCol.length; i++)
+      molList[i] = (await this.helmToAtomicLevelSingle(helmList[i], converter, chiralityEngine)).molfile;
 
-    const molHlList = molfilesV3K.map((item: MolfileWithMap) => getMolHighlight(item.monomers.values(), monomerLib));
+    //const molHlList = molfilesV3K.map((item: MolfileWithMap) => getMolHighlight(item.monomers.values(), monomerLib));
 
     const molCol = DG.Column.fromStrings(molColName, molList);
     molCol.semType = DG.SEMTYPE.MOLECULE;

package/src/utils/sequence-to-mol.ts

@@ -53,7 +53,7 @@ export async function sequenceToMolfile(
     res.molCol.name = molColName;
     df.columns.add(res.molCol, true);
 
-    buildMonomerHoverLink(macroMolecule, res.molCol, monomerLib, seqHelper, rdKitModule);
+    await buildMonomerHoverLink(macroMolecule, res.molCol, monomerLib, seqHelper, rdKitModule, nonlinear);
     res.molCol.setTag(ChemTags.SEQUENCE_SRC_HL_MONOMERS, String(highlight));
     await grok.data.detectSemanticTypes(df);
   }

package/src/widgets/composition-analysis-widget.ts

@@ -26,7 +26,9 @@ export function getCompositionAnalysisWidget(
   const rowIdx = val.cell.rowIndex;
   const seqSS = sh.getSplitted(rowIdx);
   wu.count(0).take(seqSS.length).filter((posIdx) => !seqSS.isGap(posIdx)).forEach((posIdx) => {
-    const cm = seqSS.getCanonical(posIdx);
+    let cm = seqSS.getCanonical(posIdx);
+    if (biotype === HelmTypes.NUCLEOTIDE && sh.isHelm() && cm[1] === '(' && cm[cm.length - 2] === ')')
+      cm = cm.substring(2, cm.length - 2);
     const count = counts[cm] || 0;
     counts[cm] = count + 1;
   });