@datagrok/bio 2.15.2 → 2.15.5

package/src/utils/monomer-lib/web-editor-monomer-dummy.ts

@@ -0,0 +1,121 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {
+  HelmType, PolymerType, MonomerType,
+  IWebEditorMonomer, WebEditorRGroups
+} from '@datagrok-libraries/bio/src/helm/types';
+
+/* eslint-disable camelcase */
+export abstract class WebEditorMonomerDummy implements IWebEditorMonomer {
+  //@formatter:off
+  public abstract get backgroundcolor(): string | undefined;
+  public abstract get linecolor(): string | undefined;
+  public abstract get textcolor(): string | undefined;
+  //@formatter:on
+
+  get issmiles(): boolean { return !!this.smiles; }
+
+  /** R-Group index os single digit only is allowed in Pistoia code */
+  public readonly at: WebEditorRGroups = {
+    R1: 'H', R2: 'H', R3: 'H', R4: 'H', R5: 'H', R6: 'H', R7: 'H', R8: 'H', R9: 'H'
+  };
+
+  public get rs(): number { return Object.keys(this.at).length; }
+
+  protected constructor(
+    public readonly biotype: string,
+    /** symbol */ public readonly id: string,
+    /** name */ public readonly n: string | undefined = 'missing',
+    /** molfile */ public readonly m: string | undefined = undefined,
+    /* Pistoia.HELM deletes .type and .mt in Monomers.addOneMonomer() */
+    /** polymer type */ public readonly type: PolymerType | undefined = undefined,
+    /** monomer type */ public readonly mt: MonomerType | undefined = undefined,
+    public readonly smiles?: string,
+  ) {
+    if (!this.id)
+      throw new Error('Invalid arg undefined [id].');
+
+    // return new Proxy(this, {
+    //   get: (target: any, prop: string | symbol, _receiver: any) => {
+    //     const logPrefix = `${this.toLog()}.proxy.get( '${String(prop)}' )`;
+    //     switch (prop) {
+    //     case 'id':
+    //     case 'at':
+    //     case 'na':
+    //     case 'nature':
+    //     case 'backgroundcolor':
+    //     case 'linecolor':
+    //     case 'textcolor': {
+    //       // these attributes are known and handled
+    //       return target[prop];
+    //     }
+    //     case 'rs': {
+    //       /* R-Group count (?), 2 is default for monomer "?" */
+    //       throw new Error('Not supported get "rs" attribute.');
+    //     }
+    //     default:
+    //       // Unexpected attribute requested
+    //       _package.logger.warning(`${logPrefix}`);
+    //       return target[prop];
+    //     }
+    //   },
+    //   set: (target, prop, value: any, _receiver: any): boolean => {
+    //     throw new Error(`Not supported set '${String(prop)}' attribute, any.`);
+    //   },
+    //   apply: (target: any, thisArg: any, argArray: any[]): any | undefined => {
+    //     throw new Error(`Not supported call (apply) '${thisArg.toString()}' method, any.`);
+    //   }
+    // });
+  }
+
+  private static objCounter: number = -1;
+  private readonly objId: number = ++WebEditorMonomerDummy.objCounter;
+
+  private readonly className: string = 'WebEditorMonomerDummy';
+
+  protected toLog(): string {
+    return `Helm: ${this.className}<${this.objId}>`;
+  }
+}
+
+export class GapWebEditorMonomer extends WebEditorMonomerDummy {
+  public readonly backgroundcolor: string = '#FFFFFF';
+  public readonly linecolor: string = '#808080';
+  public readonly textcolor: string = '#808080';
+
+  constructor(biotype: string, id: string) {
+    super(biotype, id, 'gap');
+  }
+}
+
+export class AmbiguousWebEditorMonomer extends WebEditorMonomerDummy {
+  public readonly backgroundcolor: string = '#808080';
+  public readonly linecolor: string = '#000000';
+  public readonly textcolor: string = '#000000';
+
+  constructor(biotype: string, id: string) {
+    super(biotype, id, 'ambiguous');
+  }
+}
+
+export class MissingWebEditorMonomer extends WebEditorMonomerDummy {
+  public readonly backgroundcolor: string = '#FF4444';
+  public readonly linecolor: string = '#800000';
+  public readonly textcolor: string = '#FFFFFF';
+
+  constructor(biotype: string, id: string) {
+    super(biotype, id, 'missing');
+  }
+}
+
+export class BrokenWebEditorMonomer extends WebEditorMonomerDummy {
+  public readonly backgroundcolor: string = '#FFFF44';
+  public readonly linecolor: string = '#800000';
+  public readonly textcolor: string = '#000000';
+
+  constructor(biotype: string, id: string) {
+    super(biotype, id, 'broken');
+  }
+}

package/src/utils/monomer-lib/web-editor-monomer-of-library.ts

@@ -0,0 +1,102 @@
+import * as grok from 'datagrok-api/grok';
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+
+import {HelmType, IMonomerColors, IWebEditorMonomer, MonomerType, PolymerType, WebEditorRGroups} from '@datagrok-libraries/bio/src/helm/types';
+import {IMonomerLibBase, Monomer} from '@datagrok-libraries/bio/src/types/index';
+import {HELM_OPTIONAL_FIELDS as OPT, HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP} from '@datagrok-libraries/bio/src/utils/const';
+
+import {BrokenWebEditorMonomer, MissingWebEditorMonomer} from './web-editor-monomer-dummy';
+import {naturalMonomerColors} from './monomer-colors';
+
+export class LibraryWebEditorMonomer implements IWebEditorMonomer {
+  public get rs(): number { return Object.keys(this.at).length; }
+
+  public get issmiles(): boolean { return !!this.smiles; }
+
+  public linecolor?: string;
+  public backgroundcolor?: string;
+  public textcolor?: string;
+
+  /* eslint-disable max-params */
+  protected constructor(
+    public readonly id: string,
+    public readonly m: string,
+    public readonly n: string,
+    public readonly na: string | undefined,
+    public readonly type: PolymerType,
+    public readonly mt: MonomerType,
+    public readonly at: WebEditorRGroups,
+    public readonly smiles?: string,
+  ) /* eslint-enable max-params */ {}
+
+  static fromMonomer(biotype: HelmType, monomer: Monomer, monomerLib: IMonomerLibBase): IWebEditorMonomer {
+    let at: WebEditorRGroups = {};
+    const symbol = monomer[REQ.SYMBOL];
+    const smiles = monomer[REQ.SMILES];
+    if (monomer.rgroups.length > 0) {
+      monomer.rgroups.forEach((it) => {
+        at[it[RGP.LABEL]] = it[RGP.CAP_GROUP_NAME];
+      });
+    } else if (smiles) {
+      // Generate R-Groups from SMILES
+      at = monomerLib.getRS(smiles);
+    } else if (!monomer.lib) {
+      // missing
+      return new MissingWebEditorMonomer(biotype, symbol);
+    } else {
+      // broken
+      return new BrokenWebEditorMonomer(biotype, symbol);
+    }
+
+    const res = new LibraryWebEditorMonomer(
+      monomer[REQ.SYMBOL],
+      monomer[REQ.MOLFILE],
+      monomer[REQ.NAME],
+      monomer[OPT.NATURAL_ANALOG],
+      monomer[REQ.POLYMER_TYPE],
+      monomer[REQ.MONOMER_TYPE],
+      at);
+
+    const colors = getMonomerColors(biotype, monomer);
+    if (colors) {
+      res.textcolor = colors?.textcolor;
+      res.linecolor = colors?.linecolor;
+      res.backgroundcolor = colors?.backgroundcolor;
+    }
+
+    return res;
+  }
+}
+
+function getMonomerColors(biotype: HelmType, monomer: Monomer): IMonomerColors | null {
+  const currentMonomerSchema = 'default';
+  let monomerSchema: string = currentMonomerSchema;
+
+  let res: any;
+  if (monomer.meta && monomer.meta.colors) {
+    const monomerColors: { [colorSchemaName: string]: any } = monomer.meta.colors;
+    if (!(currentMonomerSchema in monomerColors)) monomerSchema = 'default';
+    let res = monomerColors[monomerSchema];
+  }
+
+  if (!res) {
+    const biotypeColors: { [symbol: string]: string } | undefined = naturalMonomerColors[biotype];
+    const nColor = biotypeColors?.[monomer.symbol];
+    if (nColor)
+      res = {textColor: "#000000", lineColor: "#000000", backgroundColor: nColor};
+  }
+
+  const na = monomer[OPT.NATURAL_ANALOG];
+  if (!res && na) {
+    const biotypeColors: { [symbol: string]: string } | undefined = naturalMonomerColors[biotype];
+    const naColor = biotypeColors?.[na];
+    res = {textColor: "#000000", lineColor: "#000000", backgroundColor: naColor ?? "#FFFFFF",};
+  }
+
+  return !res ? null : {
+    textcolor: res.text ?? res.textColor,
+    linecolor: res.line ?? res.lineColor,
+    backgroundcolor: res.background ?? res.backgroundColor
+  } as IMonomerColors;
+}

package/src/utils/save-as-fasta.ts

@@ -105,7 +105,7 @@ export function wrapSequence(srcSS: ISeqSplitted, lineWidth: number = FASTA_LINE
   const seqLineList: string[] = [];
   while (seqPos < seqLength) {
     /* join sliced monomer into line */
-    const seqLine = wu(srcSS.originals).slice(seqPos, seqPos + lineWidth).toArray();
+    const seqLine = wu.count(seqPos).take(Math.min(srcSS.length - seqPos, lineWidth)).map((p) => srcSS.getOriginal(p)).toArray();
     const seqLineTxt: string = seqLine.map((om) => om.length > 1 ? `[${om}]` : om)
       .reduce((a, b) => a + b, '');
     seqLineList.push(seqLineTxt);

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

@@ -4,18 +4,20 @@ import * as DG from 'datagrok-api/dg';
 
 import wu from 'wu';
 
-import {ISeqHelper, ISubstruct, SUBSTRUCT_COL, ToAtomicLevelResType} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {ISeqHelper, ToAtomicLevelRes} from '@datagrok-libraries/bio/src/utils/seq-helper';
 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 {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
+import {MolfileWithMap} from '@datagrok-libraries/bio/src/monomer-works/types';
+import {getMolColName, hexToPercentRgb} 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';
-import {Column, DataFrame} from 'datagrok-api/dg';
-import {MolfileWithMap, MonomerMap} from '../helm-to-molfile/converter/types';
+import {MonomerLibManager} from '../monomer-lib/lib-manager';
 
 import {_package, getMonomerLibHelper} from '../../package';
-import {MonomerLibManager} from '../monomer-lib/lib-manager';
 
 type SeqHelperWindowType = Window & { $seqHelperPromise?: Promise<SeqHelper> };
 declare const window: SeqHelperWindowType;
@@ -27,27 +29,23 @@ export class SeqHelper implements ISeqHelper {
     private readonly rdKitModule: RDModule
   ) {}
 
-  getHelmToMolfileConverter(df: DataFrame, helmCol: Column<string>) {
-    return new HelmToMolfileConverter(helmCol, df, this.libHelper, this.helmHelper);
+  getHelmToMolfileConverter(monomerLib: IMonomerLibBase): HelmToMolfileConverter {
+    return new HelmToMolfileConverter(this.helmHelper, this.rdKitModule, monomerLib);
   }
 
   async helmToAtomicLevel(
-    helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean
-  ): Promise<ToAtomicLevelResType> {
-    const getUnusedName = (df: DG.DataFrame | undefined, colName: string): string => {
-      if (!df) return colName;
-      return df.columns.getUnusedName(colName);
-    };
+    helmCol: DG.Column<string>, chiralityEngine?: boolean, highlight?: boolean, overrideMonomerLib?: IMonomerLibBase
+  ): Promise<ToAtomicLevelRes> {
+    const monomerLib: IMonomerLibBase = overrideMonomerLib ?? this.libHelper.getMonomerLib();
 
     const df: DG.DataFrame = helmCol.dataFrame;
-    const molColName: string = getUnusedName(df, `molfile(${helmCol})`);
-    const molHlColName: string = getUnusedName(df, `~${molColName}-hl`);
+    const molColName: string = getMolColName(df, helmCol.name);
 
-    const converter = this.getHelmToMolfileConverter(df, helmCol);
+    const converter = this.getHelmToMolfileConverter(monomerLib);
 
     //#region From HelmToMolfileConverter.convertToRdKitBeautifiedMolfileColumn
 
-    const molfilesV3K = converter.convertToMolfileV3K(this.rdKitModule);
+    const molfilesV3K = converter.convertToMolfileV3K(helmCol, this.rdKitModule, monomerLib);
 
     const beautifiedMolList: (RDMol | null)[] = molfilesV3K.map((item) => {
       const molfile = item.molfile;
@@ -78,41 +76,14 @@ export class SeqHelper implements ISeqHelper {
 
     //#endregion From HelmToMolfileConverter
 
-    const molHlList = molfilesV3K.map((item: MolfileWithMap) => {
-      const mmList: MonomerMap[] = item.monomers;
-
-      const hlAtoms: { [key: number]: number[] } = {};
-      const hlBonds: { [key: number]: number[] } = {};
-
-      for (const [mm, mmI] of wu.enumerate(mmList)) {
-        if (mmI >= 2) continue;
-
-        const mmColor = [Math.random(), Math.random(), Math.random(), 0.3]; // green color
-        for (const mAtom of mm.atoms) {
-          hlAtoms[mAtom] = mmColor;
-        }
-        for (const mBond of mm.bonds) {
-          hlBonds[mBond] = mmColor;
-        }
-      }
-
-      let resSubstruct: ISubstruct = {
-        atoms: Object.keys(hlAtoms).map((k) => parseInt(k)),
-        bonds: Object.keys(hlBonds).map((k) => parseInt(k)),
-        highlightAtomColors: hlAtoms,
-        highlightBondColors: hlBonds,
-      };
-
-      return resSubstruct;
-    });
+    const molHlList = molfilesV3K.map((item: MolfileWithMap) => getMolHighlight(item.monomers.values(), monomerLib));
 
     const molCol = DG.Column.fromStrings(molColName, molList);
-    molCol.semType = 'Molecule';
-    molCol.temp[SUBSTRUCT_COL] = molHlColName;
-    const molHlCol = DG.Column.fromList(DG.COLUMN_TYPE.OBJECT, molHlColName, molHlList);
-    molHlCol.semType = 'Molecule-substruct';
+    molCol.semType = DG.SEMTYPE.MOLECULE;
+    molCol.meta.units = DG.UNITS.Molecule.MOLBLOCK;
+    molCol.setTag(ChemTags.SEQUENCE_SRC_COL, helmCol.name);
 
-    return {molCol: molCol, molHighlightCol: molHlCol};
+    return {molCol: molCol, warnings: []};
   }
 
   static getInstance(): Promise<SeqHelper> {

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

@@ -6,30 +6,23 @@ import {_toAtomicLevel} from '@datagrok-libraries/bio/src/monomer-works/to-atomi
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {getRdKitModule} from '@datagrok-libraries/bio/src/chem/rdkit-module';
-import {getSeqHelper, ToAtomicLevelResType} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {getSeqHelper, ToAtomicLevelRes} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {RDModule} from '@datagrok-libraries/chem-meta/src/rdkit-api';
+import {ChemTags, ChemTemps} from '@datagrok-libraries/chem-meta/src/consts';
+import {buildMonomerHoverLink} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
 
 import {checkInputColumnUI} from './check-input-column';
+import {getMolColName} from '@datagrok-libraries/bio/src/monomer-works/utils';
 
 export async function sequenceToMolfile(
-  df: DG.DataFrame, macroMolecule: DG.Column, nonlinear: boolean, monomerLib: IMonomerLib
-): Promise<DG.Column<string> | null> {
-  let rdKitModule: RDModule;
-  try {
-    rdKitModule = await getRdKitModule();
-  } catch (ex: any) {
-    grok.shell.warning('Transformation to atomic level requires package "Chem" installed.');
-    return null;
-  }
-
-  let resCol: DG.Column<string> | null = null;
+  df: DG.DataFrame, macroMolecule: DG.Column, nonlinear: boolean, highlight: boolean,
+  monomerLib: IMonomerLib, rdKitModule: RDModule
+): Promise<ToAtomicLevelRes> {
+  let res: ToAtomicLevelRes;
   if (nonlinear) {
     const seqHelper = await getSeqHelper();
     const seqSh = SeqHandler.forColumn(macroMolecule);
 
-    let atomicLevelRes: ToAtomicLevelResType;
-
     let helmCol: DG.Column<string>;
     let seqColName!: string;
     if (seqSh.isHelm())
@@ -42,25 +35,28 @@ export async function sequenceToMolfile(
       df.columns.add(helmCol, false);
     }
     try {
-      atomicLevelRes = await seqHelper.helmToAtomicLevel(helmCol, true, true);
+      res = await seqHelper.helmToAtomicLevel(helmCol, true, true);
     } finally {
       if (helmCol !== macroMolecule) {
         df.columns.remove(helmCol.name);
         macroMolecule.name = seqColName;
       }
     }
-    df.columns.add(atomicLevelRes.molCol);
-    df.columns.add(atomicLevelRes.molHighlightCol);
-    resCol = atomicLevelRes.molCol;
-  } else {
+  } else { // linear
     if (!checkInputColumnUI(macroMolecule, 'To Atomic Level'))
-      return null;
-    const atomicLevelRes = await _toAtomicLevel(df, macroMolecule, monomerLib);
-    if (atomicLevelRes.col !== null) {
-      df.columns.add(atomicLevelRes.col, true);
-      resCol = atomicLevelRes.col;
-    }
+      return {molCol: null, warnings: ['Column is not suitable']};
+
+    res = await _toAtomicLevel(df, macroMolecule, monomerLib, rdKitModule);
+  }
+
+  if (res.molCol) {
+    const molColName = getMolColName(df, macroMolecule.name);
+    res.molCol.name = molColName;
+    df.columns.add(res.molCol, true);
+
+    buildMonomerHoverLink(macroMolecule, res.molCol, monomerLib, rdKitModule);
+    res.molCol.setTag(ChemTags.SEQUENCE_SRC_HL_MONOMERS, String(highlight));
+    await grok.data.detectSemanticTypes(df);
   }
-  if (resCol) await grok.data.detectSemanticTypes(df);
-  return resCol;
+  return res;
 }

package/src/viewers/web-logo-viewer.ts

@@ -17,9 +17,10 @@ import {
 } from '@datagrok-libraries/bio/src/viewers/web-logo';
 import {errorToConsole} from '@datagrok-libraries/utils/src/to-console';
 import {intToHtmlA} from '@datagrok-libraries/utils/src/color';
-import {GAP_SYMBOL, ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {testEvent} from '@datagrok-libraries/utils/src/test';
 import {PromiseSyncer} from '@datagrok-libraries/bio/src/utils/syncer';
+import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 
 import {AggFunc, getAgg} from '../utils/agg';
 import {buildCompositionTable} from '../widgets/composition-analysis-widget';

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

@@ -9,7 +9,7 @@ import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
 import '../../css/composition-analysis.css';
 import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
-import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/consts';
 
 
 export function getCompositionAnalysisWidget(val: DG.SemanticValue): DG.Widget {
@@ -32,8 +32,9 @@ export function getCompositionAnalysisWidget(val: DG.SemanticValue): DG.Widget {
   const counts: { [m: string]: number } = {};
   const sh = SeqHandler.forColumn(val.cell.column as DG.Column<string>);
   const rowIdx = val.cell.rowIndex;
-  const parts = sh.getSplitted(rowIdx);
-  wu(parts.canonicals).filter((cm) => cm !== GAP_SYMBOL).forEach((cm) => {
+  const seqSS = sh.getSplitted(rowIdx);
+  wu.count(0).take(seqSS.length).filter((posIdx) => !seqSS.isGap(posIdx)).forEach((posIdx) => {
+    const cm = seqSS.getCanonical(posIdx);
     const count = counts[cm] || 0;
     counts[cm] = count + 1;
   });

package/src/widgets/representations.ts

@@ -5,9 +5,7 @@ import * as DG from 'datagrok-api/dg';
 import {getMolfilesFromSingleSeq} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {TAGS as mmcrTAGS} from '@datagrok-libraries/bio/src/utils/cell-renderer';
 
-import {
-  Temps as mmcrTemps, rendererSettingsChangedState, Temps
-} from '../utils/cell-renderer-consts';
+import {MmcrTemps, rendererSettingsChangedState} from '@datagrok-libraries/bio/src/utils/cell-renderer-consts';
 
 import {_package} from '../package';
 import {max} from 'rxjs/operators';
@@ -30,8 +28,8 @@ export function getMacromoleculeColumnPropertyPanel(col: DG.Column): DG.Widget {
     const v = parseInt(col.getTag(mmcrTAGS.maxMonomerLength));
     maxMonomerLength = !isNaN(v) ? v : maxMonomerLength;
   }
-  if (Temps.maxMonomerLength in col.temp) {
-    const v = parseInt(col.temp[Temps.maxMonomerLength]);
+  if (MmcrTemps.maxMonomerLength in col.temp) {
+    const v = parseInt(col.temp[MmcrTemps.maxMonomerLength]);
     maxMonomerLength = !isNaN(v) ? v : maxMonomerLength;
   }
   const maxMonomerLengthInput = ui.input.int('Max Monomer Length', {
@@ -43,8 +41,8 @@ export function getMacromoleculeColumnPropertyPanel(col: DG.Column): DG.Widget {
       else {
         const newValue = value ?? '';
         const tagValue = newValue == null ? '' : newValue.toString();
-        col.temp[Temps.maxMonomerLength] = tagValue;
-        col.temp[Temps.rendererSettingsChanged] = rendererSettingsChangedState.true;
+        col.temp[MmcrTemps.maxMonomerLength] = tagValue;
+        col.temp[MmcrTemps.rendererSettingsChanged] = rendererSettingsChangedState.true;
         col.dataFrame.fireValuesChanged();
       }
     },
@@ -52,10 +50,10 @@ export function getMacromoleculeColumnPropertyPanel(col: DG.Column): DG.Widget {
   });
 
   const gapLengthInput = ui.input.int('Monomer Margin', {
-    value: col.temp[mmcrTemps.gapLength] ?? 0,
+    value: col.temp[MmcrTemps.gapLength] ?? 0,
     onValueChanged: (value) => {
-      col.temp[mmcrTemps.gapLength] = value;
-      col.temp[mmcrTemps.rendererSettingsChanged] = rendererSettingsChangedState.true;
+      col.temp[MmcrTemps.gapLength] = value;
+      col.temp[MmcrTemps.rendererSettingsChanged] = rendererSettingsChangedState.true;
       col.dataFrame.fireValuesChanged();
     },
     tooltipText: 'The size of margin between monomers (in pixels)'

package/dist/248.js

@@ -1,2 +0,0 @@
-var bio;(()=>{"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:"d",RIBOSE:"r",PHOSPHATE:"p",OXYGEN:"O",HYDROGEN:"H"};new RegExp("[rd]\\((\\w)\\)p?","g");class n{constructor(t,n,o){this.name=t,this.alphabet=n,this.cutoff=o}}var o,e,a,i;!function(t){t.FASTA="fasta",t.SEPARATOR="separator",t.HELM="helm"}(o||(o={})),(i=e||(e={})).DNA="DNA",i.RNA="RNA",i.PT="PT",i.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"}(a||(a={}));const s=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}};function h(n,o,a,i){if(0===n.length)return"";const s=f,{atomCount:h,bondCount:r}=s(n,o,a,i),c=new Array(h),E=new Array(r);let b,S=null,A=null;"PEPTIDE"===i?b=N:(b=_,S=a===e.DNA?o.get(t.DEOXYRIBOSE):o.get(t.RIBOSE),A=o.get(t.PHOSPHATE));const d={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},m={sugar:S,phosphate:A,seqLength:n.length,atomCount:h,bondCount:r},I=[];let g=0;for(d.i=0;d.i<m.seqLength;++d.i){const t=o.get(n[d.i]);b(t,c,E,d,m),t.stereoAtoms?.forEach((t=>I.push(t+g))),g+=t.atoms.x.length}!function(n,o,e,a){const i=e.nodeShift+1;n[a.atomCount]=t.V3K_BEGIN_DATA_LINE+i+" "+t.OXYGEN+" "+l(e.backbonePositionShift[0])+" "+e.flipFactor*l(e.backbonePositionShift[1])+" 0.000000 0\n";const s=e.backboneAttachNode,h=i;o[a.bondCount]=t.V3K_BEGIN_DATA_LINE+e.bondShift+" 1 "+s+" "+h+"\n"}(c,E,d,m);const O=t.V3K_BEGIN_COUNTS_LINE+h+" "+r+t.V3K_COUNTS_LINE_ENDING;let T="";return T+=t.V3K_HEADER_FIRST_LINE,T+=t.V3K_HEADER_SECOND_LINE,T+=t.V3K_BEGIN_CTAB_BLOCK,T+=O,T+=t.V3K_BEGIN_ATOM_BLOCK,T+=c.join(""),T+=t.V3K_END_ATOM_BLOCK,T+=t.V3K_BEGIN_BOND_BLOCK,T+=E.join(""),T+=t.V3K_END_BOND_BLOCK,I.length>0&&(T+=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`}(I)),T+=t.V3K_END_CTAB_BLOCK,T+=t.V3K_END,T}function N(t,n,o,e){e.flipFactor=(-1)**(e.i%2),r(t,n,o,e)}function r(n,o,e,a){!function(n,o,e){for(let a=0;a<n.atoms.atomTypes.length;++a){const i=e.nodeShift+a+1;o[e.nodeShift+a]=t.V3K_BEGIN_DATA_LINE+i+" "+n.atoms.atomTypes[a]+" "+l(e.backbonePositionShift[0]+n.atoms.x[a])+" "+l(e.backbonePositionShift[1]+e.flipFactor*n.atoms.y[a])+" "+n.atoms.kwargs[a]}}(n,o,a),c(n,e,a),function(n,o,e){if(0!==e.backboneAttachNode){const a=e.bondShift,i=e.backboneAttachNode,s=n.meta.terminalNodes[0]+e.nodeShift;o[e.bondShift-1]=t.V3K_BEGIN_DATA_LINE+a+" 1 "+i+" "+s+"\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],n.backbonePositionShift[1]+=n.flipFactor*t.meta.backboneShift[1]}(n,a)}function _(n,o,e,a,i){if(0===a.i)r(i.sugar,o,e,a);else for(const t of[i.phosphate,i.sugar])r(t,o,e,a);!function(n,o,e,a){(function(n,o,e){for(let a=0;a<n.atoms.atomTypes.length;++a){const i=e.nodeShift+a+1;o[e.nodeShift+a]=t.V3K_BEGIN_DATA_LINE+i+" "+n.atoms.atomTypes[a]+" "+l(e.branchPositionShift[0]+n.atoms.x[a])+" "+l(e.branchPositionShift[1]+e.flipFactor*n.atoms.y[a])+" "+n.atoms.kwargs[a]}})(n,o,a),c(n,e,a),function(n,o,e){const a=e.bondShift,i=e.branchAttachNode,s=n.meta.terminalNodes[0]+e.nodeShift;o[a-1]=t.V3K_BEGIN_DATA_LINE+a+" 1 "+i+" "+s+"\n"}(n,e,a);const i=a.bondShift,s=a.branchAttachNode,h=n.meta.terminalNodes[0]+a.nodeShift;e[i-1]=t.V3K_BEGIN_DATA_LINE+i+" 1 "+s+" "+h+"\n",a.bondShift+=n.bonds.atomPairs.length+1,a.nodeShift+=n.atoms.atomTypes.length}(n,o,e,a)}function c(n,o,e){for(let a=0;a<n.bonds.atomPairs.length;++a){const i=e.bondShift+a+1,s=n.bonds.atomPairs[a][0]+e.nodeShift,h=n.bonds.atomPairs[a][1]+e.nodeShift;let N="";if(n.bonds.bondConfiguration.has(a)){let t=n.bonds.bondConfiguration.get(a);e.flipFactor<0&&(t=1===t?3:1),N=" CFG="+t}const r=n.bonds.kwargs.has(a)?" "+n.bonds.kwargs.get(a):"";o[e.bondShift+a]=t.V3K_BEGIN_DATA_LINE+i+" "+n.bonds.bondTypes[a]+" "+s+" "+h+N+r+"\n"}}function f(n,o,a,i){let s=0,h=0;for(const t of n){if(""===t)continue;const n=o.get(t);s+=n.atoms.x.length,h+=n.bonds.bondTypes.length}if("PEPTIDE"===i)s+=1,h+=n.length;else{const i=a===e.DNA?o.get(t.DEOXYRIBOSE):o.get(t.RIBOSE),N=o.get(t.PHOSPHATE);s+=(n.length-1)*N.atoms.x.length,s+=n.length*i.atoms.x.length,s+=1,h+=(n.length-1)*N.bonds.bondTypes.length,h+=n.length*i.bonds.bondTypes.length,h-=1,h+=3*n.length}return{atomCount:s,bondCount:h}}function l(n){return Math.round(t.PRECISION_FACTOR*n)/t.PRECISION_FACTOR}new n(e.PT,s.fasta.peptide,.5),new n(e.DNA,s.fasta.dna,.55),new n(e.RNA,s.fasta.rna,.55),onmessage=t=>{const{monomerSequencesArray:n,monomersDict:o,alphabet:e,polymerType:a,start:i,end:s}=t.data,N=new Array(s-i),r=new Array(0);for(let t=i;t<s;++t)try{const s=n[t];N[t-i]=h(s,o,e,a)}catch(n){const o=`Cannot get molfile of row #${t}: ${n instanceof Error?n.message:n.toString()}.`;r.push(o)}postMessage({molfileList:N,molfileWarningList:r})},bio={}})();
-//# sourceMappingURL=248.js.map

package/dist/248.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"248.js","mappings":"2BAAO,MAAMA,EAAqB,CAE9BC,cAAe,EACfC,aAAc,SACdC,WAAY,MAEZC,iBAAkB,GAClBC,cAAe,EACfC,sBAAuB,uCACvBC,uBAAwB,4CACxBC,qBAAsB,sBACtBC,mBAAoB,oBACpBC,sBAAuB,iBACvBC,uBAAwB,WACxBC,qBAAsB,sBACtBC,mBAAoB,oBACpBC,qBAAsB,sBACtBC,mBAAoB,oBACpBC,gBAAiB,QACjBC,oBAAqB,UACrBC,QAAS,SACTC,iBAAkB,IAElBC,YAAa,IACbC,OAAQ,IACRC,UAAW,IACXC,OAAQ,IACRC,SAAU,KCgBsB,IAAIC,OAAO,oBAA0E,KCxClH,MAAMC,EACT,WAAAC,CAAYC,EAAMC,EAAUC,GACxBC,KAAKH,KAAOA,EACZG,KAAKF,SAAWA,EAChBE,KAAKD,OAASA,CAClB,ECNG,IAAIE,EAMA,EAQAC,EAPAC,GANX,SAAWF,GACPA,EAAgB,MAAI,QACpBA,EAAoB,UAAI,YACxBA,EAAe,KAAI,MACtB,CAJD,CAIGA,IAAaA,EAAW,CAAC,KAEjBE,EAMR,IAAa,EAAW,CAAC,IALV,IAAI,MAClBA,EAAc,IAAI,MAClBA,EAAa,GAAI,KAEjBA,EAAa,GAAI,KAGrB,SAAWD,GACPA,EAAc,QAAI,UAClBA,EAAe,SAAI,WACnBA,EAAmB,aAAI,gBACvBA,EAA0B,oBAAI,uBAC9BA,EAAgB,UAAI,YACpBA,EAAuB,iBAAI,oBAC3BA,EAAoB,cAAI,iBACxBA,EAAqB,eAAI,kBACzBA,EAAc,QAAI,UACrB,CAVD,CAUGA,IAASA,EAAO,CAAC,IACb,MAIME,EAAY,IAAI,MACzB,WAAAR,GACII,KAAKK,MAAQ,CACTC,QAAS,IAAIC,IAAI,CACb,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,IAC7C,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,IAAK,MAEjDC,IAAK,IAAID,IAAI,CAAC,IAAK,IAAK,IAAK,MAC7BE,IAAK,IAAIF,IAAI,CAAC,IAAK,IAAK,IAAK,MAErC,GCPG,SAASG,EAAoBC,EAAYC,EAAcd,EAAUe,GACpE,GAA0B,IAAtBF,EAAWG,OAEX,MAAO,GAGX,MAAMC,EAAuBC,GACvB,UAAEC,EAAS,UAAEC,GAAcH,EAAqBJ,EAAYC,EAAcd,EAAUe,GAEpFM,EAAmB,IAAIC,MAAMH,GAC7BI,EAAmB,IAAID,MAAMF,GACnC,IAAII,EACAC,EAAQ,KACRC,EAAY,KACI,YAAhBX,EACAS,EAAuBG,GAGvBH,EAAuBI,EACvBH,EAASzB,IAAa,EAAS6B,IAAOf,EAAagB,IAAI,EAAEvC,aAAeuB,EAAagB,IAAI,EAAEtC,QAC3FkC,EAAYZ,EAAagB,IAAI,EAAErC,YAEnC,MAAMsC,EAAI,CACNC,EAAG,EACHC,UAAW,EACXC,UAAW,EACXC,sBAAuB,IAAIb,MAAM,GAAGc,KAAK,GACzCC,oBAAqB,IAAIf,MAAM,GAAGc,KAAK,GACvCE,mBAAoB,EACpBC,iBAAkB,EAClBC,WAAY,GAEVC,EAAK,CACPhB,MAAOA,EACPC,UAAWA,EACXgB,UAAW7B,EAAWG,OACtBG,UAAWA,EACXC,UAAWA,GAETuB,EAAmB,GACzB,IAAIC,EAAS,EACb,IAAKb,EAAEC,EAAI,EAAGD,EAAEC,EAAIS,EAAGC,YAAaX,EAAEC,EAAG,CACrC,MAAMa,EAAU/B,EAAagB,IAAIjB,EAAWkB,EAAEC,IAC9CR,EAAqBqB,EAASxB,EAAkBE,EAAkBQ,EAAGU,GAErEI,EAAQC,aAAaC,SAASf,GAAMW,EAAiBK,KAAKhB,EAAIY,KAC9DA,GAAUC,EAAQI,MAAMC,EAAElC,MAC9B,EAiDJ,SAA8BK,EAAkBE,EAAkBQ,EAAGU,GAEjE,MAAMU,EAAUpB,EAAEE,UAAY,EAC9BZ,EAAiBoB,EAAGtB,WAAa,EAAE/B,oBAAsB+D,EAAU,IAC/D,EAAEzD,OAAS,IAAM0D,EAAcrB,EAAEI,sBAAsB,IAAM,IAC7DJ,EAAES,WAAaY,EAAcrB,EAAEI,sBAAsB,IAFxB,gBAIjC,MAAMkB,EAAYtB,EAAEO,mBACdgB,EAAaH,EACnB5B,EAAiBkB,EAAGrB,WAAa,EAAEhC,oBAAsB2C,EAAEG,UAA1B,MACnBmB,EAAY,IAAMC,EAAa,IACjD,CA3DIC,CAAqBlC,EAAkBE,EAAkBQ,EAAGU,GAC5D,MAAMe,EAAoB,EAAE3E,sBAAwBsC,EAAY,IAAMC,EAAY,EAAEtC,uBAIpF,IAAI2E,EAAS,GAgBb,OAfAA,GAAU,EAAEhF,sBACZgF,GAAU,EAAE/E,uBACZ+E,GAAU,EAAE9E,qBACZ8E,GAAUD,EACVC,GAAU,EAAE1E,qBACZ0E,GAAUpC,EAAiBqC,KAAK,IAChCD,GAAU,EAAEzE,mBACZyE,GAAU,EAAExE,qBACZwE,GAAUlC,EAAiBmC,KAAK,IAChCD,GAAU,EAAEvE,mBACRyD,EAAiB3B,OAAS,IAC1ByC,GAMR,SAA4BE,GAGxB,MACMC,EAAY,GAClB,IAAIC,EAAmB,+BAA+BF,EAAW3C,SACjE,IAAK,IAAIgB,EAAI,EAAGA,EAAI2B,EAAW3C,OAAQgB,IAAK,CACxC,MAAM8B,EAAa,GAAGD,KAAoBF,EAAW3B,KACjD8B,EAAW9C,OALA,IAMX4C,EAAUZ,KAAK,GAAGa,SAClBA,EAAmB,UAAUF,EAAW3B,MAGxC6B,EAAmBC,EAEnB9B,IAAM2B,EAAW3C,OAAS,GAC1B4C,EAAUZ,KAAK,GAAGa,OAC1B,CACA,MAAO,4BAA4BD,EAAUF,KAAK,4BACtD,CAzBkBK,CAAmBpB,IACjCc,GAAU,EAAE7E,mBACZ6E,GAAU,EAAEpE,QAELoE,CACX,CAsCA,SAAS9B,EAAuBkB,EAASxB,EAAkBE,EAAkBQ,GACzEA,EAAES,aAAe,KAAOT,EAAEC,EAAI,GAC9BgC,EAA6BnB,EAASxB,EAAkBE,EAAkBQ,EAC9E,CACA,SAASiC,EAA6BnB,EAASxB,EAAkBE,EAAkBQ,IAoDnF,SAAuBc,EAASxB,EAAkBU,GAC9C,IAAK,IAAIkC,EAAI,EAAGA,EAAIpB,EAAQI,MAAMiB,UAAUlD,SAAUiD,EAAG,CACrD,MAAMd,EAAUpB,EAAEE,UAAYgC,EAAI,EAClC5C,EAAiBU,EAAEE,UAAYgC,GAAK,EAAE7E,oBAAsB+D,EAAU,IAClEN,EAAQI,MAAMiB,UAAUD,GAAK,IAC7Bb,EAAcrB,EAAEI,sBAAsB,GAAKU,EAAQI,MAAMC,EAAEe,IAAM,IACjEb,EAAcrB,EAAEI,sBAAsB,GAAKJ,EAAES,WAAaK,EAAQI,MAAMkB,EAAEF,IAC1E,IAAMpB,EAAQI,MAAMmB,OAAOH,EACnC,CACJ,CA1DII,CAAcxB,EAASxB,EAAkBU,GAEzCuC,EAAczB,EAAStB,EAAkBQ,GAyF7C,SAAgCc,EAAStB,EAAkBQ,GACvD,GAA6B,IAAzBA,EAAEO,mBAA0B,CAC5B,MAAMiC,EAAUxC,EAAEG,UACZmB,EAAYtB,EAAEO,mBACdgB,EAAaT,EAAQ2B,KAAKC,cAAc,GAAK1C,EAAEE,UACrDV,EAAiBQ,EAAEG,UAAY,GAAK,EAAE9C,oBAAsBmF,EAAxB,MACtBlB,EAAY,IAAMC,EAAa,IACjD,CACJ,CA/FIoB,CAAuB7B,EAAStB,EAAkBQ,GAEjB,OAA7Bc,EAAQ2B,KAAKG,aAAwB9B,EAAQ2B,KAAKC,cAAczD,OAAS,GAsCjF,SAA+B6B,EAASd,GACpCA,EAAEQ,iBAAmBR,EAAEE,UAAYY,EAAQ2B,KAAKC,cAAc,GAC9D,IAAK,IAAIzC,EAAI,EAAGA,EAAI,IAAKA,EACrBD,EAAEM,oBAAoBL,GAAKD,EAAEI,sBAAsBH,GAAKa,EAAQ2B,KAAKG,YAAY3C,EACzF,CAzCQ4C,CAAsB/B,EAASd,GA8BvC,SAAuCc,EAASd,GAC5CA,EAAEO,mBAAqBP,EAAEE,UAAYY,EAAQ2B,KAAKC,cAAc,GAChE1C,EAAEG,WAAaW,EAAQgC,MAAMC,UAAU9D,OAAS,EAChDe,EAAEE,WAAaY,EAAQI,MAAMiB,UAAUlD,OACvCe,EAAEI,sBAAsB,IAAMU,EAAQ2B,KAAKO,cAAc,GACzDhD,EAAEI,sBAAsB,IAAMJ,EAAES,WAAaK,EAAQ2B,KAAKO,cAAc,EAC5E,CAlCIC,CAA8BnC,EAASd,EAC3C,CACA,SAASH,EAAwBqD,EAAY5D,EAAkBE,EAAkBQ,EAAGU,GAGhF,GAAY,IAARV,EAAEC,EACFgC,EAA6BvB,EAAGhB,MAAOJ,EAAkBE,EAAkBQ,QAG3E,IAAK,MAAMc,IAAW,CAACJ,EAAGf,UAAWe,EAAGhB,OACpCuC,EAA6BnB,EAASxB,EAAkBE,EAAkBQ,IAItF,SAAoCc,EAASxB,EAAkBE,EAAkBQ,IAqCjF,SAA6Bc,EAASxB,EAAkBU,GACpD,IAAK,IAAIkC,EAAI,EAAGA,EAAIpB,EAAQI,MAAMiB,UAAUlD,SAAUiD,EAAG,CACrD,MAAMd,EAAUpB,EAAEE,UAAYgC,EAAI,EAClC5C,EAAiBU,EAAEE,UAAYgC,GAAK,EAAE7E,oBAAsB+D,EAAU,IAClEN,EAAQI,MAAMiB,UAAUD,GAAK,IAC7Bb,EAAcrB,EAAEM,oBAAoB,GAAKQ,EAAQI,MAAMC,EAAEe,IAAM,IAC/Db,EAAcrB,EAAEM,oBAAoB,GAAKN,EAAES,WAAaK,EAAQI,MAAMkB,EAAEF,IACxE,IAAMpB,EAAQI,MAAMmB,OAAOH,EACnC,CACJ,EA7CIiB,CAAoBrC,EAASxB,EAAkBU,GAC/CuC,EAAczB,EAAStB,EAAkBQ,GA4E7C,SAAkCoD,EAAe5D,EAAkBQ,GAC/D,MAAMwC,EAAUxC,EAAEG,UACZmB,EAAYtB,EAAEQ,iBACde,EAAa6B,EAAcX,KAAKC,cAAc,GAAK1C,EAAEE,UAC3DV,EAAiBgD,EAAU,GAAK,EAAEnF,oBAAsBmF,EAAxB,MAClBlB,EAAY,IAAMC,EAAa,IACjD,CAjFI8B,CAAyBvC,EAAStB,EAAkBQ,GAEpD,MAAMwC,EAAUxC,EAAEG,UACZmB,EAAYtB,EAAEQ,iBACde,EAAaT,EAAQ2B,KAAKC,cAAc,GAAK1C,EAAEE,UACrDV,EAAiBgD,EAAU,GAAK,EAAEnF,oBAAsBmF,EAAxB,MAClBlB,EAAY,IAAMC,EAAa,KAE7CvB,EAAEG,WAAaW,EAAQgC,MAAMC,UAAU9D,OAAS,EAChDe,EAAEE,WAAaY,EAAQI,MAAMiB,UAAUlD,MAC3C,CAfIqE,CAA2BJ,EAAY5D,EAAkBE,EAAkBQ,EAC/E,CAgDA,SAASuC,EAAczB,EAAStB,EAAkBQ,GAE9C,IAAK,IAAIkC,EAAI,EAAGA,EAAIpB,EAAQgC,MAAMC,UAAU9D,SAAUiD,EAAG,CACrD,MAAMM,EAAUxC,EAAEG,UAAY+B,EAAI,EAC5BZ,EAAYR,EAAQgC,MAAMC,UAAUb,GAAG,GAAKlC,EAAEE,UAC9CqB,EAAaT,EAAQgC,MAAMC,UAAUb,GAAG,GAAKlC,EAAEE,UACrD,IAAIqD,EAAU,GACd,GAAIzC,EAAQgC,MAAMU,kBAAkBC,IAAIvB,GAAI,CAExC,IAAIwB,EAAc5C,EAAQgC,MAAMU,kBAAkBzD,IAAImC,GAClDlC,EAAES,WAAa,IACfiD,EAA+B,IAAhBA,EAAqB,EAAI,GAC5CH,EAAU,QAAUG,CACxB,CACA,MAAMrB,EAASvB,EAAQgC,MAAMT,OAAOoB,IAAIvB,GACpC,IAAMpB,EAAQgC,MAAMT,OAAOtC,IAAImC,GAAK,GACxC1C,EAAiBQ,EAAEG,UAAY+B,GAAK,EAAE7E,oBAAsBmF,EAAU,IAClE1B,EAAQgC,MAAMa,UAAUzB,GAAK,IAC7BZ,EAAY,IAAMC,EAAagC,EAAUlB,EAAS,IAC1D,CACJ,CAyBA,SAASlD,EAA2BL,EAAYC,EAAcd,EAAUe,GACpE,IAAII,EAAY,EACZC,EAAY,EAEhB,IAAK,MAAMuE,KAAiB9E,EAAY,CACpC,GAAsB,KAAlB8E,EACA,SACJ,MAAM9C,EAAU/B,EAAagB,IAAI6D,GACjCxE,GAAa0B,EAAQI,MAAMC,EAAElC,OAC7BI,GAAayB,EAAQgC,MAAMa,UAAU1E,MACzC,CAEA,GAAoB,YAAhBD,EAEAI,GAAa,EAEbC,GAAaP,EAAWG,WAEvB,CACD,MAAMS,EAASzB,IAAa,EAAS6B,IACjCf,EAAagB,IAAI,EAAEvC,aAAeuB,EAAagB,IAAI,EAAEtC,QACnDkC,EAAYZ,EAAagB,IAAI,EAAErC,WAErC0B,IAAcN,EAAWG,OAAS,GAAKU,EAAUuB,MAAMC,EAAElC,OAEzDG,GAAaN,EAAWG,OAASS,EAAMwB,MAAMC,EAAElC,OAE/CG,GAAa,EAEbC,IAAcP,EAAWG,OAAS,GAAKU,EAAUmD,MAAMa,UAAU1E,OAEjEI,GAAaP,EAAWG,OAASS,EAAMoD,MAAMa,UAAU1E,OAEvDI,GAAa,EAEbA,GAAiC,EAApBP,EAAWG,MAC5B,CACA,MAAO,CAAEG,YAAWC,YACxB,CAKO,SAASgC,EAAcF,GAC1B,OAAO0C,KAAKC,MAAM,EAAEvG,iBAAmB4D,GAAK,EAAE5D,gBAClD,CDzQI,IAAIO,EAAc,EAASiG,GAAIxF,EAAUC,MAAMC,QAAS,IACxD,IAAIX,EAAc,EAASgC,IAAKvB,EAAUC,MAAMG,IAAK,KACrD,IAAIb,EAAc,EAASkG,IAAKzF,EAAUC,MAAMI,IAAK,KE9CzDqF,UAAaC,IACT,MAAM,sBAAEC,EAAqB,aAAEpF,EAAY,SAAEd,EAAQ,YAAEe,EAAW,MAAEoF,EAAK,IAAEC,GAAQH,EAAMI,KACnFC,EAAc,IAAIhF,MAAM8E,EAAMD,GAC9BI,EAAqB,IAAIjF,MAAM,GACrC,IAAK,IAAIkF,EAAOL,EAAOK,EAAOJ,IAAOI,EACjC,IACI,MAAM3F,EAAaqF,EAAsBM,GACzCF,EAAYE,EAAOL,GAASvF,EAAoBC,EAAYC,EAAcd,EAAUe,EACxF,CACA,MAAO0F,GACH,MACMC,EAAM,8BAA8BF,MAD3BC,aAAeE,MAAQF,EAAIG,QAAUH,EAAII,cAExDN,EAAmBvD,KAAK0D,EAC5B,CAEJI,YAAY,CAAER,cAAaC,sBAAqB,E","sources":["webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/consts.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/utils/const.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/types.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/utils/macromolecule/consts.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/to-atomic-level-utils.js","webpack://bio/./node_modules/@datagrok-libraries/bio/src/monomer-works/seq-to-molfile-worker.js"],"sourcesContent":["export const monomerWorksConsts = {\n    // constants for parsing molfile V2000\n    V2K_RGP_SHIFT: 8,\n    V2K_RGP_LINE: 'M  RGP',\n    V2K_A_LINE: 'A  ',\n    // constants for parsing/reconstruction of molfile V3000\n    V3K_COUNTS_SHIFT: 14,\n    V3K_IDX_SHIFT: 7,\n    V3K_HEADER_FIRST_LINE: '\\nDatagrok macromolecule handler\\n\\n',\n    V3K_HEADER_SECOND_LINE: '  0  0  0  0  0  0            999 V3000\\n',\n    V3K_BEGIN_CTAB_BLOCK: 'M  V30 BEGIN CTAB\\n',\n    V3K_END_CTAB_BLOCK: 'M  V30 END CTAB\\n',\n    V3K_BEGIN_COUNTS_LINE: 'M  V30 COUNTS ',\n    V3K_COUNTS_LINE_ENDING: ' 0 0 0\\n',\n    V3K_BEGIN_ATOM_BLOCK: 'M  V30 BEGIN ATOM\\n',\n    V3K_END_ATOM_BLOCK: 'M  V30 END ATOM\\n',\n    V3K_BEGIN_BOND_BLOCK: 'M  V30 BEGIN BOND\\n',\n    V3K_END_BOND_BLOCK: 'M  V30 END BOND\\n',\n    V3K_BOND_CONFIG: ' CFG=',\n    V3K_BEGIN_DATA_LINE: 'M  V30 ',\n    V3K_END: 'M  END',\n    PRECISION_FACTOR: 10000, // HELMCoreLibrary has 4 significant digits after decimal point in atom coordinates\n    // symbols for the corresponding monomers in HELM library\n    DEOXYRIBOSE: 'd',\n    RIBOSE: 'r',\n    PHOSPHATE: 'p',\n    OXYGEN: 'O',\n    HYDROGEN: 'H',\n};\n//# sourceMappingURL=consts.js.map","// core fields of HELM library object used in toAtomicLevel function\nexport const HELM_CORE_FIELDS = [\n    \"symbol\" /* HELM_FIELDS.SYMBOL */,\n    \"molfile\" /* HELM_FIELDS.MOLFILE */,\n    \"rgroups\" /* HELM_FIELDS.RGROUPS */,\n    \"name\" /* HELM_FIELDS.NAME */,\n    // HELM_FIELDS.MONOMER_TYPE, // add if terminal monomers for PEPTIDEs to be\n    // supported\n];\nexport const SDF_MONOMER_NAME = 'MonomerName';\n// todo: ideally, keys should be expressed via constants\nexport const jsonSdfMonomerLibDict = {\n    'monomerType': null, // -> Backbone\n    'smiles': null,\n    'name': 'Name',\n    'author': null,\n    'molfile': 'molecule',\n    'naturalAnalog': 'MonomerNaturalAnalogCode',\n    'rgroups': 'MonomerCaps',\n    'createDate': null,\n    'id': null,\n    'polymerType': 'MonomerType',\n    'symbol': 'MonomerName'\n};\nexport const DUMMY_MONOMER = {\n    'monomerType': 'Backbone',\n    'smiles': '',\n    'name': '',\n    'author': 'Datagrok',\n    'molfile': '',\n    'naturalAnalog': '',\n    'rgroups': [],\n    'createDate': null,\n    'id': 0,\n    'polymerType': 'PEPTIDE',\n    'symbol': ''\n};\n// range of hex nubers used in PepSea library to endode monomers\nexport const MONOMER_ENCODE_MIN = 0x100;\nexport const MONOMER_ENCODE_MAX = 0x40A;\nexport const RIBOSE_SYMBOL = 'r';\nexport const DEOXYRIBOSE_SYMBOL = 'd';\nexport const PHOSPHATE_SYMBOL = 'p';\nexport const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\\\((\\\\w)\\\\)${PHOSPHATE_SYMBOL}?`, 'g');\n//# sourceMappingURL=const.js.map","/** Canonical gap symbol */\nexport const GAP_SYMBOL = '';\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})(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 || (TAGS = {}));\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//# sourceMappingURL=consts.js.map","import { monomerWorksConsts as C } from './consts';\nimport { HELM_CORE_FIELDS, } from '../utils/const';\nimport { ALPHABET } from '../utils/macromolecule/consts';\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 ||\n                alphabet === ALPHABET.RNA && it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.RIBOSE ||\n                it[\"symbol\" /* HELM_FIELDS.SYMBOL */] === C.PHOSPHATE) ||\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(it[\"symbol\" /* HELM_FIELDS.SYMBOL */], 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\n * @param {Map<string, MolGraph>} monomersDict - Mapping of monomer symbols to MolGraph objects\n * @param {ALPHABET} alphabet - Alphabet of the column\n * @param {HELM_POLYMER_TYPE} 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 '';\n    }\n    // define atom and bond counts, taking into account the bond type\n    const getAtomAndBondCounts = getResultingAtomBondCounts;\n    const { atomCount, bondCount } = 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; // todo: types?\n    let sugar = null;\n    let phosphate = null;\n    if (polymerType === \"PEPTIDE\" /* HELM_POLYMER_TYPE.PEPTIDE */) {\n        addMonomerToMolblock = addAminoAcidToMolblock;\n    }\n    else { // nucleotides\n        addMonomerToMolblock = addNucleotideToMolblock;\n        sugar = (alphabet === ALPHABET.DNA) ? monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);\n        phosphate = monomersDict.get(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 steabsCollection = [];\n    let nAtoms = 0;\n    for (v.i = 0; v.i < LC.seqLength; ++v.i) {\n        const monomer = monomersDict.get(monomerSeq[v.i]);\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    }\n    capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC);\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 result;\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) {\n    // add terminal oxygen\n    const atomIdx = v.nodeShift + 1;\n    molfileAtomBlock[LC.atomCount] = C.V3K_BEGIN_DATA_LINE + atomIdx + ' ' +\n        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    }\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]; // todo: non-null check\n    v.backbonePositionShift[1] += v.flipFactor * monomer.meta.backboneShift[1];\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    // sum up all the atoms/nodes provided by the sequence\n    for (const monomerSymbol of monomerSeq) {\n        if (monomerSymbol === '')\n            continue; // Skip for gap/empty monomer in MSA\n        const monomer = monomersDict.get(monomerSymbol);\n        atomCount += monomer.atoms.x.length;\n        bondCount += monomer.bonds.bondTypes.length;\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 += monomerSeq.length;\n    }\n    else { // nucleotides\n        const sugar = (alphabet === ALPHABET.DNA) ?\n            monomersDict.get(C.DEOXYRIBOSE) : monomersDict.get(C.RIBOSE);\n        const phosphate = monomersDict.get(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 };\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 { monomerSequencesArray, monomersDict, alphabet, polymerType, start, end } = event.data;\n    const molfileList = new Array(end - start);\n    const molfileWarningList = new Array(0);\n    for (let rowI = start; rowI < end; ++rowI) {\n        try {\n            const monomerSeq = monomerSequencesArray[rowI];\n            molfileList[rowI - start] = monomerSeqToMolfile(monomerSeq, 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({ molfileList, 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","RIBOSE","PHOSPHATE","OXYGEN","HYDROGEN","RegExp","CandidateType","constructor","name","alphabet","cutoff","this","NOTATION","TAGS","ALPHABET","Alphabets","fasta","peptide","Set","dna","rna","monomerSeqToMolfile","monomerSeq","monomersDict","polymerType","length","getAtomAndBondCounts","getResultingAtomBondCounts","atomCount","bondCount","molfileAtomBlock","Array","molfileBondBlock","addMonomerToMolblock","sugar","phosphate","addAminoAcidToMolblock","addNucleotideToMolblock","DNA","get","v","i","nodeShift","bondShift","backbonePositionShift","fill","branchPositionShift","backboneAttachNode","branchAttachNode","flipFactor","LC","seqLength","steabsCollection","nAtoms","monomer","stereoAtoms","forEach","push","atoms","x","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","bonds","atomPairs","backboneShift","updateChainExtendingVariables","nucleobase","fillBranchAtomLines","branchMonomer","fillBackboneToBranchBond","addBranchMonomerToMolblock","bondCfg","bondConfiguration","has","orientation","bondTypes","monomerSymbol","Math","round","PT","RNA","onmessage","event","monomerSequencesArray","start","end","data","molfileList","molfileWarningList","rowI","err","msg","Error","message","toString","postMessage"],"sourceRoot":""}

package/src/utils/cell-renderer-consts.ts

@@ -1,31 +0,0 @@
-import * as grok from 'datagrok-api/grok';
-import * as ui from 'datagrok-api/ui';
-import * as DG from 'datagrok-api/dg';
-
-export const rendererSettingsChangedState = {
-  true: '1',
-  false: '0',
-};
-
-export const enum Temps {
-  maxMonomerLength = '.mm.cellRenderer.maxMonomerLength',
-  colorCode = '.mm.cellRenderer.colorCode',
-  compareWithCurrent = '.mm.cellRenderer.compareWithCurrent',
-  highlightDifference = '.mm.cellRenderer.highlightDifference',
-  gapLength = '.mm.cellRenderer.gapLength',
-  monomerPlacer = '.mm.cellRenderer.monomerPlacer',
-
-  rendererSettingsChanged = '.mm.cellRenderer.settingsChanged',
-}
-
-export const enum tempTAGS {
-  referenceSequence = 'reference-sequence',
-  currentWord = 'current-word',
-}
-
-// export const MacromoleculeCellRendererDefaults = new class {
-//   monomerWidth: MonomerWidthMode = MonomerWidthMode.short;
-//   maxMonomerLength: number = 3;
-//   colorCode: boolean = true;
-//   compareWithCurrent: boolean = true;
-// }();