npm - @datagrok-libraries/bio - Versions diffs - 5.54.9 → 5.55.1 - Mend

@datagrok-libraries/bio 5.54.9 → 5.55.1

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 (24) hide show

package/CHANGELOG.md +4 -0
package/package.json +1 -1
package/src/monomer-works/to-atomic-level.js +1 -1
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +5 -2
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/composition-table.d.ts +3 -1
package/src/utils/composition-table.d.ts.map +1 -1
package/src/utils/composition-table.js +3 -2
package/src/utils/composition-table.js.map +1 -1
package/src/utils/macromolecule/consts.d.ts +4 -2
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js +3 -0
package/src/utils/macromolecule/consts.js.map +1 -1
package/src/utils/macromolecule/seq-handler.d.ts +2 -1
package/src/utils/macromolecule/seq-handler.d.ts.map +1 -1
package/src/utils/macromolecule/types.d.ts +20 -0
package/src/utils/macromolecule/types.d.ts.map +1 -1
package/src/utils/macromolecule/types.js.map +1 -1
package/src/utils/macromolecule/utils.d.ts +29 -1
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +193 -5
package/src/utils/macromolecule/utils.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,9 @@
 # bio changelog
+## 5.55.0 (2025-10-03)
+* Full BILN support: conversion to/from HELM/separator/fasta/molecular form, parsing, rendering, monomer library handling.
 ## 5.54.1 (2025-06-25)
 * To Atomic Level: Handling of terminal monomers with 1 R group, wrongly configured r-groups, and incorrect notations.

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.54.9",
+  "version": "5.55.1",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

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

@@ -25,7 +25,7 @@ export async function _toAtomicLevel(df, seqCol, monomerLib, seqHelper, rdKitMod
     let srcCol = seqCol;
     const seqUh = seqHelper.getSeqHandler(seqCol);
     // convert 'helm' to 'separator' units
-    if (seqUh.notation !== NOTATION.SEPARATOR) {
+    if (seqUh.notation !== NOTATION.SEPARATOR && seqUh.notation !== NOTATION.BILN) {
         srcCol = seqUh.convert(NOTATION.SEPARATOR, '.');
         srcCol.name = seqCol.name; // Replace converted col name 'separator(<original>)' to '<original>';
     }

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

	@@ -1 +1 @@
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package/src/utils/cell-renderer-monomer-placer.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-monomer-placer.js CHANGED Viewed

@@ -469,7 +469,7 @@ export class MonomerPlacer extends CellRendererBackBase {
                             isMultiLineContext: true,
                             transparencyRate: transparencyRate,
                             selectedPosition: isNaN(selectedPosition) || selectedPosition < 1 ? undefined : selectedPosition,
-                            wordIdx: monomerIndex
+                            wordIdx: monomerIndex,
                         });
                     }
                 }
@@ -491,9 +491,12 @@ export class MonomerPlacer extends CellRendererBackBase {
                     if (this.getMonomerLib())
                         color = this.getMonomerLib().getMonomerTextColor(sh.defaultBiotype, cm);
                     const last = posIdx === subParts.length - 1;
+                    // here, the first index of disjointSeqStarts is always 0, so we check from position 1, and also, next index
+                    // will show where the next disjoint sequence starts, so we check posIdx + 1
+                    const drawnSeparator = (subParts?.graphInfo?.disjointSeqStarts?.indexOf(posIdx + 1) ?? 0) > 0 ? '|' : separator;
                     const opts = {
                         color: color, pivot: 0, left: true, transparencyRate: 0.0,
-                        separator: separator, last: last,
+                        separator: drawnSeparator, last: last,
                         drawStyle: drawStyle, maxWord: maxLengthWordsSum, wordIdx: posIdx - positionShift, gridCell: gridCell,
                         referenceSequence: referenceSequence, maxLengthOfMonomer: maxLengthOfMonomer,
                         monomerTextSizeMap: this._monomerLengthMap, logger: this.logger,

package/src/utils/cell-renderer-monomer-placer.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/composition-table.d.ts CHANGED Viewed

@@ -2,5 +2,7 @@ import { IMonomerLibBase } from './../types';
 import { HelmType } from './../helm/types';
 export declare function buildCompositionTable(counts: {
     [m: string]: number;
-}, biotype: HelmType, monomerLib: IMonomerLibBase): HTMLTableElement;
+}, biotype: HelmType, monomerLib: IMonomerLibBase, monomerBioTypes?: {
+    [m: string]: HelmType;
+}): HTMLTableElement;
 //# sourceMappingURL=composition-table.d.ts.map

package/src/utils/composition-table.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"composition-table.d.ts","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,eAAe,EAAC,MAAM,YAAY,CAAC;AAC3C,OAAO,EAAC,QAAQ,EAAC,MAAM,iBAAiB,CAAC;AAEzC,wBAAgB,qBAAqB,CACnC,MAAM,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,eAAe,~~GAC9E~~,gBAAgB,~~CA0ClB~~"}
1	+ {"version":3,"file":"composition-table.d.ts","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,eAAe,EAAC,MAAM,YAAY,CAAC;AAC3C,OAAO,EAAC,QAAQ,EAAC,MAAM,iBAAiB,CAAC;AAEzC,wBAAgB,qBAAqB,CACnC,MAAM,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,eAAe,EAC/E,eAAe,CAAC,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,QAAQ,CAAA;CAAE,GAC1C,gBAAgB,CA2ClB"}

package/src/utils/composition-table.js CHANGED Viewed

@@ -1,7 +1,7 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import { GAP_SYMBOL } from './macromolecule/consts';
-export function buildCompositionTable(counts, biotype, monomerLib) {
+export function buildCompositionTable(counts, biotype, monomerLib, monomerBioTypes) {
     let sumValue = 0;
     let maxValue = null;
     for (const value of Object.values(counts)) {
@@ -15,7 +15,8 @@ export function buildCompositionTable(counts, biotype, monomerLib) {
         const ratio = value / sumValue;
         let color;
         try {
-            const colors = monomerLib.getMonomerColors(biotype, cm);
+            const actBioType = monomerBioTypes ? (monomerBioTypes[cm] || biotype) : biotype;
+            const colors = monomerLib.getMonomerColors(actBioType, cm);
             color = colors?.backgroundcolor || '#CCCCCC';
         }
         catch (error) {

package/src/utils/composition-table.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/consts.d.ts CHANGED Viewed

@@ -4,7 +4,8 @@ export declare enum NOTATION {
     FASTA = "fasta",
     SEPARATOR = "separator",
     HELM = "helm",
-    CUSTOM = "custom"
+    CUSTOM = "custom",
+    BILN = "biln"
 }
 export declare const enum ALIGNMENT {
     SEQ_MSA = "SEQ.MSA",
@@ -28,7 +29,8 @@ export declare enum TAGS {
     positionLabels = ".positionLabels",
     regions = ".regions",
     positionShift = ".positionShift",
-    selectedPosition = ".selectedPosition"
+    selectedPosition = ".selectedPosition",
+    polymerTypeColumnName = ".polymerTypeColumnName"
 }
 export { TAGS as BioTags };
 export declare const positionSeparator: string;

package/src/utils/macromolecule/consts.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/consts.js CHANGED Viewed

@@ -6,6 +6,7 @@ export var NOTATION;
     NOTATION["SEPARATOR"] = "separator";
     NOTATION["HELM"] = "helm";
     /* Requires notation handler */ NOTATION["CUSTOM"] = "custom";
+    /* Requires notation handler */ NOTATION["BILN"] = "biln";
 })(NOTATION || (NOTATION = {}));
 export var ALPHABET;
 (function (ALPHABET) {
@@ -28,6 +29,7 @@ export var TAGS;
     TAGS["regions"] = ".regions";
     TAGS["positionShift"] = ".positionShift";
     TAGS["selectedPosition"] = ".selectedPosition";
+    TAGS["polymerTypeColumnName"] = ".polymerTypeColumnName";
 })(TAGS || (TAGS = {}));
 export { TAGS as BioTags };
 export const positionSeparator = ', ';
@@ -57,6 +59,7 @@ export const GapOriginals = {
     [NOTATION.FASTA]: '-',
     [NOTATION.SEPARATOR]: '',
     [NOTATION.HELM]: '*',
+    [NOTATION.BILN]: '',
 };
 export const MONOMER_MOTIF_SPLITTER = ' , ';
 //# sourceMappingURL=consts.js.map

package/src/utils/macromolecule/consts.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/seq-handler.d.ts CHANGED Viewed

@@ -27,6 +27,7 @@ export declare class SeqValueBase extends DG.SemanticValue<string> {
 }
 export interface ISeqHandler {
     get column(): DG.Column<string>;
+    get refinerPromise(): Promise<void>;
     get alphabet(): string;
     get notation(): NOTATION;
     get separator(): string | undefined;
@@ -62,6 +63,6 @@ export interface ISeqHandler {
     }): JoinerFunc;
     getDistanceFunctionName(): MmDistanceFunctionsNames;
     getConverter(tgtUnits: NOTATION, tgtSeparator?: string): ConvertFunc;
-    getRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string>;
+    getRendererBack(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>): CellRendererBackBase<string> | null;
 }
 //# sourceMappingURL=seq-handler.d.ts.map

package/src/utils/macromolecule/seq-handler.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/types.d.ts CHANGED Viewed

@@ -1,8 +1,28 @@
 import * as DG from 'datagrok-api/dg';
 import { CellRendererBackBase } from '../cell-renderer-back-base';
 import { ISeqHandler } from './seq-handler';
+import { PolymerType } from '../../helm/types';
 export type SeqSplittedBase = ArrayLike<string> & Iterable<string>;
+export interface ISeqConnection {
+    seq1Type: PolymerType;
+    seq2Type: PolymerType;
+    seqIndex1: number;
+    seqIndex2: number;
+    monomerIndex1: number;
+    monomerIndex2: number;
+    rGroup1: number;
+    rGroup2: number;
+}
+export interface ISeqGraphInfo {
+    /**  Connections between monomers with numbers - note that monomer numbers are 0-based*/
+    connections: ISeqConnection[];
+    /** Start positions of disjoint sequence parts in the original sequence */
+    disjointSeqStarts: number[];
+    /** Polimer types same as the indexes. only applicapble to helm */
+    polymerTypes?: PolymerType[];
+}
 export interface ISeqSplitted {
+    graphInfo?: ISeqGraphInfo;
     isGap(posIdx: number): boolean;
     /** */
     getCanonical(posIdx: number): string;

package/src/utils/macromolecule/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/utils.d.ts CHANGED Viewed

@@ -1,12 +1,15 @@
 import * as DG from 'datagrok-api/dg';
-import { CandidateType, ISeqSplitted, MonomerFreqs, SeqColStats, SeqSplittedBase, SplitterFunc } from './types';
+import { CandidateType, ISeqGraphInfo, ISeqSplitted, MonomerFreqs, SeqColStats, SeqSplittedBase, SplitterFunc } from './types';
 import { ALPHABET } from './consts';
 import { SeqPalette } from '../../seq-palettes';
 import { ISeqHelper } from '../seq-helper';
+import { PolymerTypes } from '../../helm/consts';
+import { HelmType, PolymerType } from '../../helm/types';
 export declare class StringListSeqSplitted implements ISeqSplitted {
     private readonly mList;
     private readonly gapOriginalMonomer;
     get length(): number;
+    get graphInfo(): ISeqGraphInfo | undefined;
     isGap(posIdx: number): boolean;
     /** @param {number} posIdx monomer position 0-based index */
     getCanonical(posIdx: number): string;
@@ -16,6 +19,28 @@ export declare class StringListSeqSplitted implements ISeqSplitted {
     get gapOriginal(): string;
     constructor(mList: SeqSplittedBase, gapOriginalMonomer: string);
 }
+/** Same as string list splitted, but for helm will also encode the graph info, and define a getter for it
+ *
+ */
+export declare class HelmSplitted extends StringListSeqSplitted {
+    protected mListSeparated: string[][];
+    private readonly connections;
+    private polymerTypes;
+    constructor(mListSeparated: string[][], // list of lists of monomers (separated by | in helm notation
+    connections: string, // string part of helm defining connections between monomers
+    polymerTypes: PolymerTypes[], // polymer types for each disjoint sequence part
+    gapOriginalMonomer: string);
+    protected _graphInfo: ISeqGraphInfo | undefined;
+    get graphInfo(): ISeqGraphInfo;
+    protected parseConnections(): ISeqGraphInfo;
+}
+/** Gets canonical monomers for original ones with cyclization marks */
+export declare class BilnSeqSplitted extends HelmSplitted {
+    getCanonical(posIdx: number): string;
+    getOriginal(posIdx: number): string;
+    constructor(seqListSplit: string[][], gapOriginalMonomer: string);
+    protected parseConnections(): ISeqGraphInfo;
+}
 export declare class FastaSimpleSeqSplitted implements ISeqSplitted {
     private readonly seqS;
     get length(): number;
@@ -49,11 +74,13 @@ export declare const splitterAsFastaSimple: SplitterFunc;
 export declare function getSplitterWithSeparator(separator: string, limit?: number | undefined): SplitterFunc;
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
+ * EG byciclic helm: PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0
  * @param {string} seq Source string of HELM notation
  * @param {ISeqSource} src Source of the {@link seq} string
  * @return {string[]}
  */
 export declare const splitterAsHelm: SplitterFunc;
+export declare function splitterAsBiln(seq: string): ISeqSplitted;
 /** Func type to shorten a {@link monomerLabel} with length {@link limit} */
 export type MonomerToShortFunc = (monomerLabel: string, limit: number) => string;
 /** Get splitter method to split sequences to monomers (required for MacromoleculeDifferenceCellRenderer)
@@ -85,4 +112,5 @@ export declare function detectHelmAlphabet(freq: MonomerFreqs, candidates: Candi
 export declare function pickUpPalette(seqCol: DG.Column, seqHelper: ISeqHelper, minLength?: number): SeqPalette;
 export declare function getPaletteByType(paletteType: string): SeqPalette;
 export declare function pickUpSeqCol(df: DG.DataFrame): DG.Column<string> | null;
+export declare function polymerTypeToHelmType(pt: PolymerType): HelmType;
 //# sourceMappingURL=utils.d.ts.map

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package/src/utils/macromolecule/utils.js CHANGED Viewed

@@ -9,8 +9,13 @@ import { AminoacidsPalettes } from '../../aminoacids';
 import { NucleotidesPalettes } from '../../nucleotides';
 import { UnknownSeqPalettes } from '../../unknown';
 import { cleanupHelmSymbol } from '../../helm/utils';
+import { HelmTypes } from '../../helm/consts';
 export class StringListSeqSplitted {
     get length() { return this.mList.length; }
+    get graphInfo() {
+        return undefined;
+    }
+    ;
     isGap(posIdx) {
         return this.getOriginal(posIdx) === this.gapOriginalMonomer;
     }
@@ -47,6 +52,146 @@ export class StringListSeqSplitted {
         this.gapOriginalMonomer = gapOriginalMonomer;
     }
 }
+/** Same as string list splitted, but for helm will also encode the graph info, and define a getter for it
+ *
+ */
+export class HelmSplitted extends StringListSeqSplitted {
+    constructor(mListSeparated, // list of lists of monomers (separated by | in helm notation
+    connections, // string part of helm defining connections between monomers
+    polymerTypes, // polymer types for each disjoint sequence part
+    gapOriginalMonomer) {
+        super(mListSeparated.flat(), gapOriginalMonomer);
+        this.mListSeparated = mListSeparated;
+        this.connections = connections;
+        this._graphInfo = undefined;
+        this.polymerTypes = mListSeparated.map((n, i) => new Array(n.length).fill(polymerTypes[i])).flat();
+    }
+    get graphInfo() {
+        this._graphInfo ?? (this._graphInfo = this.parseConnections());
+        return this._graphInfo;
+    }
+    parseConnections() {
+        const graphInfo = {
+            connections: [],
+            disjointSeqStarts: [],
+            polymerTypes: this.polymerTypes
+        };
+        if ((this.connections?.length ?? 0) > 0) {
+            // parse helm connections
+            let seqStart = 0;
+            for (let i = 0; i < this.mListSeparated.length; ++i) {
+                graphInfo.disjointSeqStarts.push(seqStart);
+                seqStart += this.mListSeparated[i].length;
+            }
+            ;
+            // parse connections like PEPTIDE2,PEPTIDE2,16:R2-1:R1
+            const connectionParts = (this.connections ?? '').split('|').filter((cp) => (cp?.length ?? 0) > 0);
+            const sequenceConSeqIdxRe = /^(PEPTIDE|RNA|BLOB|CHEM)\d{1,2}$/;
+            const sequenceConRe = /^\d{1,2}:R\d{1}-\d{1,2}:R\d{1}$/;
+            for (const cp of connectionParts) {
+                const cpParts = cp.split(',');
+                if (cpParts.length !== 3 || !sequenceConRe.test(cpParts[2]) || !sequenceConSeqIdxRe.test(cpParts[0]) || !sequenceConSeqIdxRe.test(cpParts[1]))
+                    continue;
+                const seq1 = parseInt(cpParts[0].replace(/^(PEPTIDE|RNA|BLOB|CHEM)/, '')) - 1;
+                const seq2 = parseInt(cpParts[1].replace(/^(PEPTIDE|RNA|BLOB|CHEM)/, '')) - 1;
+                const seq1Type = cpParts[0].replace(/\d{1,2}$/, '');
+                const seq2Type = cpParts[1].replace(/\d{1,2}$/, '');
+                if (seq1 < 0 || seq1 >= this.mListSeparated.length || seq2 < 0 || seq2 >= this.mListSeparated.length)
+                    continue;
+                const conParts = cpParts[2].split('-');
+                if (conParts.length !== 2)
+                    continue;
+                const con1Parts = conParts[0].split(':');
+                const con2Parts = conParts[1].split(':');
+                if (con1Parts.length !== 2 || con2Parts.length !== 2)
+                    continue;
+                const con1 = parseInt(con1Parts[0]) - 1;
+                const con2 = parseInt(con2Parts[0]) - 1;
+                if (con1 < 0 || con1 >= this.mListSeparated[seq1].length || con2 < 0 || con2 >= this.mListSeparated[seq2].length)
+                    continue;
+                graphInfo.connections.push({
+                    seq1Type: seq1Type,
+                    seq2Type: seq2Type,
+                    seqIndex1: seq1,
+                    seqIndex2: seq2,
+                    monomerIndex1: con1,
+                    monomerIndex2: con2,
+                    rGroup1: parseInt(con1Parts[1].substring(1)),
+                    rGroup2: parseInt(con2Parts[1].substring(1)),
+                });
+            }
+        }
+        return graphInfo;
+    }
+}
+/** Gets canonical monomers for original ones with cyclization marks */
+export class BilnSeqSplitted extends HelmSplitted {
+    getCanonical(posIdx) {
+        if (this.isGap(posIdx))
+            return GAP_SYMBOL;
+        const om = this.getOriginal(posIdx);
+        let cmRes = om;
+        const re = /\(\d{1,2},\d{1,2}\)$/; // there can be multiple cyclization marks
+        while (re.test(cmRes))
+            cmRes = cmRes.replace(re, '');
+        return cmRes;
+    }
+    getOriginal(posIdx) {
+        const om = super.getOriginal(posIdx);
+        // replace [] with '' for biln
+        return om.replace(/^\[(.*)\]/, '$1');
+    }
+    constructor(seqListSplit, gapOriginalMonomer) {
+        super(seqListSplit, '', seqListSplit.map(() => "PEPTIDE" /* PolymerTypes.PEPTIDE */), gapOriginalMonomer);
+    }
+    parseConnections() {
+        // create graph info for cyclization marks
+        // EG: A(1,2).G(1,1)(2,2).C(2,1) -> first number is the bond identifier, second is the R group (1-based)
+        // . is used as separator between different sequences
+        const graphInfo = { connections: [], disjointSeqStarts: [] };
+        const connectionStorage = {};
+        let seqLengthCounter = 0;
+        for (let i = 0; i < this.mListSeparated.length; i++) {
+            const ss = this.mListSeparated[i];
+            graphInfo.disjointSeqStarts.push(seqLengthCounter);
+            seqLengthCounter += ss.length;
+            for (let j = 0; j < ss.length; j++) {
+                const om = ss[j];
+                const re = /\(\d{1,2},\d{1,2}\)$/; // there can be multiple cyclization marks
+                let cmRes = om;
+                while (re.test(cmRes)) {
+                    const con = /\(\d{1,2},\d{1,2}\)$/.exec(cmRes)?.[0];
+                    cmRes = cmRes.replace(re, '');
+                    if (con != null) {
+                        const nums = con.substring(1, con.length - 1).split(',').map((s) => parseInt(s, 10));
+                        if (nums.length !== 2 || nums.some((n) => n == null || Number.isNaN(n)))
+                            continue; // this should never happen, but just in case
+                        const bondId = nums[0].toString();
+                        const rGroup = nums[1];
+                        if (bondId in connectionStorage) {
+                            // there is already a monomer with this bondId
+                            const prev = connectionStorage[bondId];
+                            graphInfo.connections.push({
+                                seq1Type: "PEPTIDE" /* PolymerTypes.PEPTIDE */, // for biln, its always peptides
+                                seq2Type: "PEPTIDE" /* PolymerTypes.PEPTIDE */,
+                                seqIndex1: prev.seqIndex,
+                                seqIndex2: i,
+                                monomerIndex1: prev.monomerIndex,
+                                monomerIndex2: j,
+                                rGroup1: prev.rGroup,
+                                rGroup2: rGroup
+                            });
+                            delete connectionStorage[bondId];
+                        }
+                        else
+                            connectionStorage[bondId] = { seqIndex: i, monomerIndex: j, rGroup: rGroup }; // store for later
+                    }
+                }
+            }
+        }
+        return graphInfo;
+    }
+}
 export class FastaSimpleSeqSplitted {
     get length() { return this.seqS.length; }
     isGap(posIdx) {
@@ -150,7 +295,7 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
         else {
             let mmList;
             const mRe = new RegExp(`(?<=^|\\${separator})("-"|'-'|[^\\${separator}]*)(?=\\${separator}|$)`, 'g'); // depends on separator args
-            if (limit !== undefined) {
+            if (limit != undefined) {
                 mRe.lastIndex = 0;
                 mmList = wu(seq.matchAll(mRe)).take(limit).map((ea) => ea[0]).toArray();
             }
@@ -162,6 +307,7 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
 }
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
+ * EG byciclic helm: PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0
  * @param {string} seq Source string of HELM notation
  * @param {ISeqSource} src Source of the {@link seq} string
  * @return {string[]}
@@ -169,12 +315,37 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
 export const splitterAsHelm = (seq) => {
     const helmParts = seq.split('$');
     const spList = helmParts[0].split('|');
-    const mList = wu(spList
+    const mListSplit = spList
         .map((sp) => (sp.match(/(?<=\{).+(?=})/)?.[0]?.split('.') ?? [])
-        .map((m) => cleanupHelmSymbol(m))))
-        .flatten().toArray();
-    return new StringListSeqSplitted(mList, GapOriginals[NOTATION.HELM]);
+        .map((m) => cleanupHelmSymbol(m)));
+    const polymerTypes = spList.map((sp) => sp.replace(/\d{1,2}\{.+\}/, ''));
+    const res = new HelmSplitted(mListSplit, helmParts[1] ?? '', polymerTypes, GapOriginals[NOTATION.HELM]);
+    return res;
 };
+export function splitterAsBiln(seq) {
+    const disjointPartsRaw = seq.split('.')
+        .map((ds) => ds.replaceAll('\"-\"', '').replaceAll('\'-\'', ''));
+    // some monomers might contain '-', and need to be enclosed in [], e.g. A-[D-Arg]-C
+    // replace all separators inside [] with some temporary string, then split by separator, then restore
+    const tempSep = '___TEMP___';
+    for (let i = 0; i < disjointPartsRaw.length; i++) {
+        const re = /\[([^\]]+)\]/g;
+        let match;
+        let dp = disjointPartsRaw[i];
+        while ((match = re.exec(disjointPartsRaw[i])) !== null) {
+            const inside = match[1];
+            const replaced = inside.replaceAll('-', tempSep);
+            dp = dp.replace(inside, replaced);
+        }
+        disjointPartsRaw[i] = dp;
+    }
+    const disjointParts = disjointPartsRaw
+        .map((ds) => ds.split('-')
+        .map((m) => m.replaceAll(tempSep, '-')));
+    //const totalLength = disjointParts.reduce((acc, ss) => acc + ss.length, 0);
+    const res = new BilnSeqSplitted(disjointParts, GapOriginals[NOTATION.SEPARATOR]);
+    return res;
+}
 /** Get splitter method to split sequences to monomers (required for MacromoleculeDifferenceCellRenderer)
  * @param {string} units
  * @param {string} separator
@@ -188,6 +359,8 @@ export function getSplitter(units, separator, limit = undefined) {
         return getSplitterWithSeparator(separator, limit);
     else if (units.toLowerCase().startsWith(NOTATION.HELM))
         return splitterAsHelm;
+    else if (units.toLowerCase().startsWith(NOTATION.BILN))
+        return splitterAsBiln;
     else
         throw new Error(`Unexpected units ${units} .`);
     // TODO: Splitter for HELM
@@ -250,6 +423,7 @@ export function detectAlphabet(freq, candidates, gapSymbol = '-') {
     }
     else
         alphabetName = ALPHABET.UN;
+    console.log(maxSim, alphabetName);
     return alphabetName;
 }
 export function detectHelmAlphabet(freq, candidates, gapSymbol = '-') {
@@ -308,4 +482,18 @@ export function pickUpSeqCol(df) {
         resCol = semTypeColList[0];
     return resCol;
 }
+export function polymerTypeToHelmType(pt) {
+    switch (pt) {
+        case "PEPTIDE" /* PolymerTypes.PEPTIDE */:
+            return HelmTypes.AA;
+        case "RNA" /* PolymerTypes.RNA */:
+            return HelmTypes.NUCLEOTIDE;
+        case "CHEM" /* PolymerTypes.CHEM */:
+            return HelmTypes.CHEM;
+        case "BLOB" /* PolymerTypes.BLOB */:
+            return HelmTypes.BLOB;
+        default:
+            return HelmTypes.AA;
+    }
+}
 //# sourceMappingURL=utils.js.map

package/src/utils/macromolecule/utils.js.map CHANGED Viewed

	@@ -1 +1 @@
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