npm - @datagrok-libraries/bio - Versions diffs - 5.54.8 → 5.55.0 - Mend

@datagrok-libraries/bio 5.54.8 → 5.55.0

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

Files changed (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-async-base.d.ts +2 -0
package/src/utils/cell-renderer-async-base.d.ts.map +1 -1
package/src/utils/cell-renderer-async-base.js +10 -3
package/src/utils/cell-renderer-async-base.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/macromolecule/consts.d.ts +2 -1
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js +2 -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 +14 -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 +24 -1
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +167 -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": "5.54.8",
+  "version": "5.55.0",
   "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-async-base.d.ts CHANGED Viewed

@@ -64,6 +64,8 @@ export declare abstract class CellRendererBackAsyncBase<TProps extends PropsBase
     readonly cacheEnabled: boolean;
     protected readonly taskQueueMap: Map<string, RenderTask<TProps, TAux>>;
     protected imageCache: LRUCache<string, ImageData, unknown>;
+    protected get minWidth(): number;
+    protected get minHeight(): number;
     /** Consumer identifier of the render service */
     protected consumerId: number | null;
     protected constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column, logger: ILogger, cacheEnabled?: boolean);

package/src/utils/cell-renderer-async-base.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/cell-renderer-async-base.js CHANGED Viewed

@@ -217,11 +217,13 @@ export class RenderServiceBase {
 }
 RenderServiceBase.viewerCounter = -1;
 export class CellRendererBackAsyncBase extends CellRendererBackBase {
+    get minWidth() { return 25; }
+    get minHeight() { return 25; }
     constructor(gridCol, tableCol, logger, cacheEnabled = true) {
         super(gridCol, tableCol, logger);
         this.cacheEnabled = cacheEnabled;
         this.taskQueueMap = new Map;
-        this.imageCache = new LRUCache({ max: 100 });
+        this.imageCache = new LRUCache({ max: 300 });
         /** Consumer identifier of the render service */
         this.consumerId = null;
     }
@@ -277,9 +279,14 @@ export class CellRendererBackAsyncBase extends CellRendererBackBase {
                 gridCellHeight = h * dpr - 2;
                 backColor = DG.Color.argb(0, 0, 0, 0);
             }
+            if (gridCellWidth < this.minWidth * dpr || gridCellHeight < this.minHeight * dpr) {
+                this.logger.debug('PdbRenderer.render(), skip too small cell ' +
+                    `rowIdx=${rowIdx}, width=${gridCellWidth}, height=${gridCellHeight}`);
+                return;
+            }
             if (!this.cacheEnabled || !cellImageData ||
-                Math.abs(cellImageData.width / dpr - gridCellWidth) > 0.5 ||
-                Math.abs(cellImageData.height / dpr - gridCellHeight) > 0.5) {
+                Math.abs(cellImageData.width - gridCellWidth) > 1 ||
+                Math.abs(cellImageData.height - gridCellHeight) > 1) {
                 let toUpdate = true;
                 if (cellImageData)
                     toUpdate = this.renderCellImageData(g, bd, gridCell, cellImageData);

package/src/utils/cell-renderer-async-base.js.map CHANGED Viewed

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

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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/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",

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

	@@ -1 +1 @@
1	- {"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;IACmB,MAAM,WAAW;~~CAClD~~;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,oBAAY,QAAQ;IAClB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;IACtC,aAAa,mBAAmB;IAChC,cAAc,oBAAoB;IAClC,OAAO,aAAa;IACpB,aAAa,mBAAmB;IAChC,gBAAgB,sBAAsB;CACvC;AAED,OAAO,EAAC,IAAI,IAAI,OAAO,EAAC,CAAC;AAEzB,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAE9C,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,MAAM,EAAE,MAA0C,CAAC;AAChE,eAAO,MAAM,SAAS,EAAE,MAAyB,CAAC;AAElD,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC;AAEF,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,eAAO,MAAM,YAAY,EAAE;IACzB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;~~CAKxB~~,CAAC;AAEF,eAAO,MAAM,sBAAsB,QAAQ,CAAC"}
1	+ {"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;IACmB,MAAM,WAAW;IACjB,IAAI,SAAS;CAC9C;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,oBAAY,QAAQ;IAClB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,oBAAY,IAAI;IACd,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;IACvB,gBAAgB,sBAAsB;IACtC,aAAa,mBAAmB;IAChC,cAAc,oBAAoB;IAClC,OAAO,aAAa;IACpB,aAAa,mBAAmB;IAChC,gBAAgB,sBAAsB;CACvC;AAED,OAAO,EAAC,IAAI,IAAI,OAAO,EAAC,CAAC;AAEzB,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAE9C,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,MAAM,EAAE,MAA0C,CAAC;AAChE,eAAO,MAAM,SAAS,EAAE,MAAyB,CAAC;AAElD,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC;AAEF,2BAA2B;AAC3B,eAAO,MAAM,UAAU,EAAE,MAAW,CAAC;AAErC,eAAO,MAAM,YAAY,EAAE;IACzB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAA;CAMxB,CAAC;AAEF,eAAO,MAAM,sBAAsB,QAAQ,CAAC"}

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) {
@@ -57,6 +58,7 @@ 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

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

@@ -2,7 +2,21 @@ import * as DG from 'datagrok-api/dg';
 import { CellRendererBackBase } from '../cell-renderer-back-base';
 import { ISeqHandler } from './seq-handler';
 export type SeqSplittedBase = ArrayLike<string> & Iterable<string>;
+export interface ISeqConnection {
+    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[];
+    disjointSeqStarts: number[];
+}
 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

@@ -1,5 +1,5 @@
 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';
@@ -7,6 +7,7 @@ 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 +17,26 @@ 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;
+    constructor(mListSeparated: string[][], // list of lists of monomers (separated by | in helm notation
+    connections: string, // string part of helm defining connections between monomers
+    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 +70,13 @@ 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)

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

@@ -11,6 +11,10 @@ import { UnknownSeqPalettes } from '../../unknown';
 import { cleanupHelmSymbol } from '../../helm/utils';
 export class StringListSeqSplitted {
     get length() { return this.mList.length; }
+    get graphInfo() {
+        return undefined;
+    }
+    ;
     isGap(posIdx) {
         return this.getOriginal(posIdx) === this.gapOriginalMonomer;
     }
@@ -47,6 +51,137 @@ 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
+    gapOriginalMonomer) {
+        super(mListSeparated.flat(), gapOriginalMonomer);
+        this.mListSeparated = mListSeparated;
+        this.connections = connections;
+        this._graphInfo = undefined;
+    }
+    get graphInfo() {
+        this._graphInfo ?? (this._graphInfo = this.parseConnections());
+        return this._graphInfo;
+    }
+    parseConnections() {
+        const graphInfo = {
+            connections: [],
+            disjointSeqStarts: []
+        };
+        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)\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].substring(7)) - 1;
+                const seq2 = parseInt(cpParts[1].substring(7)) - 1;
+                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({
+                    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, '', 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 = /\(\d{1,2},\d{1,2}\)$/.exec(cmRes)?.[0];
+                    cmRes = cmRes.replace(re, '');
+                    if (con != null) {
+                        const nums = con.substring(1, con.length - 1).split(',').map((s) => parseInt(s, 10));
+                        if (nums.length !== 2 || nums.some((n) => n == null || Number.isNaN(n)))
+                            continue; // this should never happen, but just in case
+                        const bondId = nums[0].toString();
+                        const rGroup = nums[1];
+                        if (bondId in connectionStorage) {
+                            // there is already a monomer with this bondId
+                            const prev = connectionStorage[bondId];
+                            graphInfo.connections.push({
+                                seqIndex1: prev.seqIndex,
+                                seqIndex2: i,
+                                monomerIndex1: prev.monomerIndex,
+                                monomerIndex2: j,
+                                rGroup1: prev.rGroup,
+                                rGroup2: rGroup
+                            });
+                            delete connectionStorage[bondId];
+                        }
+                        else
+                            connectionStorage[bondId] = { seqIndex: i, monomerIndex: j, rGroup: rGroup }; // store for later
+                    }
+                }
+            }
+        }
+        return graphInfo;
+    }
+}
 export class FastaSimpleSeqSplitted {
     get length() { return this.seqS.length; }
     isGap(posIdx) {
@@ -150,7 +285,7 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
         else {
             let mmList;
             const mRe = new RegExp(`(?<=^|\\${separator})("-"|'-'|[^\\${separator}]*)(?=\\${separator}|$)`, 'g'); // depends on separator args
-            if (limit !== undefined) {
+            if (limit != undefined) {
                 mRe.lastIndex = 0;
                 mmList = wu(seq.matchAll(mRe)).take(limit).map((ea) => ea[0]).toArray();
             }
@@ -162,6 +297,7 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
 }
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
+ * EG byciclic helm: PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$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 +305,36 @@ 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 res = new HelmSplitted(mListSplit, helmParts[1] ?? '', 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 +348,8 @@ 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

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

	@@ -1 +1 @@
1	- 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