npm - @datagrok-libraries/bio - Versions diffs - 5.44.4 → 5.45.0 - Mend

@datagrok-libraries/bio 5.44.4 → 5.45.0

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Files changed (84) hide show

package/CHANGELOG.md +9 -0
package/package.json +6 -6
package/src/helm/consts.d.ts +2 -2
package/src/helm/consts.d.ts.map +1 -1
package/src/helm/consts.js.map +1 -1
package/src/helm/helm-helper.d.ts +5 -5
package/src/helm/helm-helper.d.ts.map +1 -1
package/src/helm/types.d.ts +4 -3
package/src/helm/types.d.ts.map +1 -1
package/src/monomer-works/monomer-hover.d.ts +3 -2
package/src/monomer-works/monomer-hover.d.ts.map +1 -1
package/src/monomer-works/monomer-hover.js +4 -3
package/src/monomer-works/monomer-hover.js.map +1 -1
package/src/monomer-works/monomer-utils.d.ts +6 -5
package/src/monomer-works/monomer-utils.d.ts.map +1 -1
package/src/monomer-works/monomer-utils.js +10 -11
package/src/monomer-works/monomer-utils.js.map +1 -1
package/src/monomer-works/seq-to-molfile.d.ts +2 -2
package/src/monomer-works/seq-to-molfile.d.ts.map +1 -1
package/src/monomer-works/seq-to-molfile.js +2 -3
package/src/monomer-works/seq-to-molfile.js.map +1 -1
package/src/monomer-works/to-atomic-level-utils.d.ts +2 -2
package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
package/src/monomer-works/to-atomic-level.d.ts +5 -5
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +17 -14
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/types/index.d.ts +6 -4
package/src/types/index.d.ts.map +1 -1
package/src/unknown.d.ts.map +1 -1
package/src/unknown.js +2 -2
package/src/unknown.js.map +1 -1
package/src/utils/cell-renderer-async-base.d.ts +1 -1
package/src/utils/cell-renderer-async-base.d.ts.map +1 -1
package/src/utils/cell-renderer-async-base.js +5 -3
package/src/utils/cell-renderer-async-base.js.map +1 -1
package/src/utils/cell-renderer-consts.d.ts +2 -1
package/src/utils/cell-renderer-consts.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts +6 -4
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +59 -47
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/fasta-handler.d.ts.map +1 -1
package/src/utils/fasta-handler.js +0 -3
package/src/utils/fasta-handler.js.map +1 -1
package/src/utils/generator.d.ts +2 -1
package/src/utils/generator.d.ts.map +1 -1
package/src/utils/generator.js +2 -3
package/src/utils/generator.js.map +1 -1
package/src/utils/macromolecule/consts.d.ts +1 -0
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js +1 -0
package/src/utils/macromolecule/consts.js.map +1 -1
package/src/utils/macromolecule/scoring.d.ts +4 -2
package/src/utils/macromolecule/scoring.d.ts.map +1 -1
package/src/utils/macromolecule/scoring.js +8 -8
package/src/utils/macromolecule/scoring.js.map +1 -1
package/src/utils/macromolecule/seq-handler.d.ts +47 -0
package/src/utils/macromolecule/seq-handler.d.ts.map +1 -0
package/src/utils/macromolecule/seq-handler.js +8 -0
package/src/utils/macromolecule/seq-handler.js.map +1 -0
package/src/utils/macromolecule/types.d.ts +2 -1
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 +2 -1
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +4 -5
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/seq-helper.d.ts +2 -0
package/src/utils/seq-helper.d.ts.map +1 -1
package/src/utils/seq-helper.js.map +1 -1
package/src/utils/splitter.d.ts +2 -1
package/src/utils/splitter.d.ts.map +1 -1
package/src/utils/splitter.js +2 -3
package/src/utils/splitter.js.map +1 -1
package/src/viewers/helm-service.d.ts +3 -1
package/src/viewers/helm-service.d.ts.map +1 -1
package/src/viewers/helm-service.js +2 -1
package/src/viewers/helm-service.js.map +1 -1
package/src/utils/seq-handler.d.ts +0 -167
package/src/utils/seq-handler.d.ts.map +0 -1
package/src/utils/seq-handler.js +0 -748
package/src/utils/seq-handler.js.map +0 -1

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

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

@@ -3,7 +3,6 @@ import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { ALPHABET, NOTATION } from '../utils/macromolecule/consts';
-import { SeqHandler } from '../utils/seq-handler';
 import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
 import { seqToMolFileWorker } from './seq-to-molfile';
 import { hasMolGraph, setMolGraph } from './types';
@@ -16,14 +15,14 @@ import { monomerWorksConsts as C } from './consts';
  * @param {DG.Column} seqCol - Column containing the macromolecule sequence
  * @param {IMonomerLib} monomerLib - Monomer library
  */
-export async function _toAtomicLevel(df, seqCol, monomerLib, rdKitModule) {
+export async function _toAtomicLevel(df, seqCol, monomerLib, seqHelper, rdKitModule) {
     if (seqCol.semType !== DG.SEMTYPE.MACROMOLECULE) {
         const msg = `Only the ${DG.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, ` +
             `the chosen column has semType '${seqCol.semType}'`;
         return { molCol: null, warnings: [msg] };
     }
     let srcCol = seqCol;
-    const seqUh = SeqHandler.forColumn(seqCol);
+    const seqUh = seqHelper.getSeqHandler(seqCol);
     // convert 'helm' to 'separator' units
     if (seqUh.notation !== NOTATION.SEPARATOR) {
         srcCol = seqUh.convert(NOTATION.SEPARATOR, '.');
@@ -32,7 +31,7 @@ export async function _toAtomicLevel(df, seqCol, monomerLib, rdKitModule) {
     let polymerType;
     let alphabet;
     try {
-        const srcSh = SeqHandler.forColumn(srcCol);
+        const srcSh = seqHelper.getSeqHandler(srcCol);
         alphabet = srcSh.alphabet;
         polymerType = alphabetToPolymerType(alphabet);
     }
@@ -40,10 +39,10 @@ export async function _toAtomicLevel(df, seqCol, monomerLib, rdKitModule) {
         const [errMsg, _errStack] = errInfo(err);
         return { molCol: null, warnings: [errMsg] };
     }
-    const monomerSequencesArray = getMonomerSequencesArray(srcCol);
+    const monomerSequencesArray = getMonomerSequencesArray(srcCol, seqHelper);
     const monomersDict = getMonomersDictFromLib(monomerSequencesArray, polymerType, alphabet, monomerLib, rdKitModule);
     const srcColLength = srcCol.length;
-    const res = await seqToMolFileWorker(srcCol, monomersDict, alphabet, polymerType, monomerLib, rdKitModule);
+    const res = await seqToMolFileWorker(srcCol, monomersDict, alphabet, polymerType, monomerLib, seqHelper, rdKitModule);
     if (res.warnings.length > 0.05 * srcColLength)
         throw new Error('Too many errors getting molfiles.');
     return res;
@@ -51,11 +50,11 @@ export async function _toAtomicLevel(df, seqCol, monomerLib, rdKitModule) {
 /** Get jagged array of monomer symbols for the dataframe
  * @param {DG.Column} macroMolCol - Column with macro-molecules
  * @return {string[]} - Jagged array of monomer symbols for the dataframe */
-export function getMonomerSequencesArray(macroMolCol) {
+export function getMonomerSequencesArray(macroMolCol, seqHelper) {
     const rowCount = macroMolCol.length;
     const result = new Array(rowCount);
     // split the string into monomers
-    const sh = SeqHandler.forColumn(macroMolCol);
+    const sh = seqHelper.getSeqHandler(macroMolCol);
     let containsEmptyValues = false;
     const biotype = sh.defaultBiotype;
     for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
@@ -615,10 +614,12 @@ function adjustPeptideMonomerGraph(monomer) {
     if (x[monomer.meta.rNodes[1] - 1] < 0)
         flipMonomerAroundOY(monomer);
     const doubleBondedOxygen = findDoubleBondedCarbonylOxygen(monomer);
-    // flip carboxyl and R if necessary
-    flipCarboxylAndRadical(monomer, doubleBondedOxygen);
-    // flip hydroxyl group with double-bound O inside carboxyl group if necessary
-    flipHydroxilGroup(monomer, doubleBondedOxygen);
+    if (doubleBondedOxygen != null) {
+        // flip carboxyl and R if necessary
+        flipCarboxylAndRadical(monomer, doubleBondedOxygen);
+        // flip hydroxyl group with double-bound O inside carboxyl group if necessary
+        flipHydroxilGroup(monomer, doubleBondedOxygen);
+    }
 }
 function adjustPhosphateMonomerGraph(monomer) {
     const centeredNode = monomer.meta.terminalNodes[0] - 1; // Phosphorus
@@ -802,8 +803,10 @@ function findDoubleBondedCarbonylOxygen(monomer) {
         if (monomer.atoms.atomTypes[node - 1] === C.OXYGEN && node !== monomer.meta.rNodes[1])
             doubleBondedOxygen = node;
         i++;
-        if (i > sentinel)
-            throw new Error(`Search for double-bonded Oxygen in ${monomer} has exceeded the limit of ${sentinel}`);
+        if (i > sentinel) {
+            // throw new Error(`Search for double-bonded Oxygen in ${monomer} has exceeded the limit of ${sentinel}`);
+            return null;
+        }
     }
     return doubleBondedOxygen;
 }

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

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

@@ -1,7 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import { Observable } from 'rxjs';
 import { HelmAtom } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
-import { HelmType, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
+import { HelmType, IMonomerColors, IWebEditorMonomer, MonomerSetType, MonomerType, PolymerType } from '../helm/types';
 import { HELM_REQUIRED_FIELD as REQ, HELM_RGROUP_FIELDS as RGP, HELM_OPTIONAL_FIELDS as OPT } from '../utils/const';
 export type RGroup = {
     [RGP.CAP_GROUP_SMILES]: string;
@@ -59,8 +59,10 @@ export type MonomerLibData = {
     };
 };
 export interface IMonomerLibBase {
+    get source(): string;
     get isEmpty(): boolean;
     get onChanged(): Observable<any>;
+    getMonomerSymbolsByType(polymerType: PolymerType): string[];
     addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer;
     getMonomer(polymerType: PolymerType | null, monomerSymbol: string): Monomer | null;
     /** HELMWebEditor expects null for HelmTypes.LINKER and R-Group count != 2 */
@@ -69,15 +71,15 @@ export interface IMonomerLibBase {
         [r: string]: string;
     };
     getTooltip(biotype: HelmType, monomerSymbol: string): HTMLElement;
+    getMonomerColors(biotype: HelmType, symbol: string): IMonomerColors;
+    getMonomerTextColor(biotype: HelmType, symbol: string): string;
 }
 export interface IMonomerLib extends IMonomerLibBase {
-    get source(): string | undefined;
     get error(): string | undefined;
     getMonomerMolsByPolymerType(polymerType: PolymerType): {
         [monomerSymbol: string]: string;
     } | null;
     getMonomerSymbolsByRGroup(rGroupNumber: number, polymerType: PolymerType, element?: string): string[];
-    getMonomerSymbolsByType(polymerType: PolymerType): string[];
     getPolymerTypes(): PolymerType[];
     toJSON(): Monomer[];
     /** Summary string with lib monomer count by type
@@ -88,6 +90,6 @@ export interface IMonomerLib extends IMonomerLibBase {
     /** Gets dataframe with columns 'polymerType', 'count'. */
     getSummaryDf(): DG.DataFrame;
     getMonomerSet(biotype: HelmType): MonomerSetType | null;
-    override(overrideData: MonomerLibData): IMonomerLibBase;
+    override(overrideData: MonomerLibData, source: string): IMonomerLibBase;
 }
 //# sourceMappingURL=index.d.ts.map

package/src/types/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/unknown.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/unknown.js CHANGED Viewed

@@ -48,7 +48,7 @@ export class GrayAllPalette extends UnknownSeqPalette {
 export class UnknownColorPalette extends UnknownSeqPalette {
     static buildPalette() {
         getMonomerLibHelper().then((lh) => {
-            lh.awaitLoaded().then(() => {
+            lh.awaitLoaded(Infinity).then(() => {
                 const monLib = lh.getMonomerLib();
                 monLib.onChanged.subscribe(() => {
                     UnknownColorPalette.customMonomerColors = {};
@@ -82,7 +82,7 @@ export class UnknownColorPalette extends UnknownSeqPalette {
     }
 }
 UnknownColorPalette.palette = UnknownColorPalette.buildPalette();
-// this way is just more futureproof, when we start distinguishing
+// this way is just more future-proof, when we start distinguishing
 // between different polymer types for coloring of non natural aa's or nucleotides
 UnknownColorPalette.customMonomerColors = {};
 UnknownColorPalette.polymerTypes = [];

package/src/unknown.js.map CHANGED Viewed

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

@@ -67,7 +67,7 @@ export declare abstract class CellRendererBackAsyncBase<TProps extends PropsBase
     protected consumerId: number | null;
     protected constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column, logger: ILogger, cacheEnabled?: boolean);
     protected reset(): void;
-    protected abstract getRenderService(): RenderServiceBase<TProps, TAux>;
+    protected abstract getRenderService(): RenderServiceBase<TProps, TAux> | null;
     protected abstract getRenderTaskProps(gridCell: DG.GridCell, backColor: number, width: number, height: number): TProps;
     render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell, cellStyle: DG.GridCellStyle): void;
     /** Renders cell from image data (cache)

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

@@ -233,6 +233,11 @@ export class CellRendererBackAsyncBase extends CellRendererBackBase {
         super.reset();
     }
     render(g, x, y, w, h, gridCell, cellStyle) {
+        if (gridCell.tableRowIndex == null)
+            return;
+        const service = this.getRenderService();
+        if (!service)
+            return;
         if (this.dirty) {
             try {
                 this.reset();
@@ -243,9 +248,6 @@ export class CellRendererBackAsyncBase extends CellRendererBackBase {
             }
         }
         const dpr = window.devicePixelRatio;
-        const service = this.getRenderService();
-        if (gridCell.tableRowIndex == null)
-            return;
         const rowIdx = gridCell.tableRowIndex;
         this.logger.debug('PdbRenderer.render() start ' + `rowIdx=${rowIdx}`);
         g.save();

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

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

@@ -10,7 +10,8 @@ export declare const enum MmcrTemps {
     highlightDifference = ".mm.cellRenderer.highlightDifference",
     gapLength = ".mm.cellRenderer.gapLength",
     monomerPlacer = ".mm.cellRenderer.monomerPlacer",
-    rendererSettingsChanged = ".mm.cellRenderer.settingsChanged"
+    rendererSettingsChanged = ".mm.cellRenderer.settingsChanged",
+    overriddenLibrary = ".mm.cellRenderer.overriddenLibrary"
 }
 export declare const enum tempTAGS {
     referenceSequence = "reference-sequence",

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"cell-renderer-consts.d.ts","sourceRoot":"","sources":["cell-renderer-consts.ts"],"names":[],"mappings":"AAIA,eAAO,MAAM,4BAA4B;;;CAGxC,CAAC;AAEF,kDAAkD;AAClD,0BAAkB,SAAS;IACzB,gBAAgB,sCAAsC;IACtD,SAAS,+BAA+B;IACxC,kBAAkB,wCAAwC;IAC1D,mBAAmB,yCAAyC;IAC5D,SAAS,+BAA+B;IACxC,aAAa,mCAAmC;IAEhD,uBAAuB,qCAAqC;IAC5D,iBAAiB,uCAAuC;CACzD;AAED,0BAAkB,QAAQ;IACxB,iBAAiB,uBAAuB;IACxC,WAAW,iBAAiB;CAC7B"}

package/src/utils/cell-renderer-monomer-placer.d.ts CHANGED Viewed

@@ -1,10 +1,9 @@
 import * as DG from 'datagrok-api/dg';
-import { SeqHandler } from './seq-handler';
 import { MonomerToShortFunc } from './macromolecule';
 import { CellRendererBackBase } from './cell-renderer-back-base';
 import { ILogger } from './logger';
+import { IMonomerLibBase } from '../types/index';
 type MonomerPlacerProps = {
-    seqHandler: SeqHandler;
     monomerCharWidth: number;
     separatorWidth: number;
     monomerToShort: MonomerToShortFunc;
@@ -26,10 +25,14 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
     _monomerStructureMap: {
         [key: string]: HTMLElement;
     };
-    private monomerLib;
+    private seqHelper;
+    private sysMonomerLib;
     /** View is required to subscribe and handle for data frame changes */
     constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>, logger: ILogger, monomerLengthLimit: number, propsProvider: () => MonomerPlacerProps);
+    init(): Promise<void>;
+    protected getMonomerLib(): IMonomerLibBase | null;
     protected reset(): void;
+    protected invalidateGrid(): void;
     /** Returns monomers lengths of the {@link rowIdx} and cumulative sums for borders, monomer places */
     getCellMonomerLengths(rowIdx: number, newWidth: number): [number[], number[]];
     private getCellMonomerLengthsForSeq;
@@ -38,7 +41,6 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
     getPosition(rowIdx: number, x: number, width: number): number | null;
     setMonomerLengthLimit(value: number): void;
     setSeparatorWidth(value: number): void;
-    isMsa(): boolean;
     private padding;
     render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell, _cellStyle: DG.GridCellStyle): void;
     onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void;

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

	@@ -1 +1 @@
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