npm - @datagrok-libraries/bio - Versions diffs - 5.42.4 → 5.42.5 - Mend

@datagrok-libraries/bio 5.42.4 → 5.42.5

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 (26) hide show

package/CHANGELOG.md +10 -0
package/package.json +4 -4
package/src/helm/helm-helper.d.ts +21 -2
package/src/helm/helm-helper.d.ts.map +1 -1
package/src/helm/helm-helper.js +4 -0
package/src/helm/helm-helper.js.map +1 -1
package/src/helm/types.d.ts +4 -0
package/src/helm/types.d.ts.map +1 -1
package/src/monomer-works/monomer-utils.d.ts.map +1 -1
package/src/monomer-works/monomer-utils.js +9 -5
package/src/monomer-works/monomer-utils.js.map +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/fasta-handler.js +1 -1
package/src/utils/fasta-handler.js.map +1 -1
package/src/utils/generator.js +2 -2
package/src/utils/generator.js.map +1 -1
package/src/utils/macromolecule/scoring.d.ts.map +1 -1
package/src/utils/macromolecule/scoring.js +6 -3
package/src/utils/macromolecule/scoring.js.map +1 -1
package/src/utils/macromolecule/utils.js +1 -1
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/seq-handler.js +10 -10
package/src/utils/seq-handler.js.map +1 -1
package/src/utils/units-handler-base.js +1 -1
package/src/utils/units-handler-base.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,15 @@
 # bio changelog
+## 5.42.5 (WIP)
+### Features
+* Add IHelmHelper.createHelmInput, ui.input.helmAsync
+### Bug fixes
+* Fix identity scoring for seqs of different lengths
 ## 5.42.4 (2024-07-02)
 Fix types ISeqMonomer from Helm

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.4",
+  "version": "5.42.5",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",
@@ -16,7 +16,7 @@
     "@datagrok-libraries/utils": "^4.2.11",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "latest",
-    "datagrok-api": "^1.18.6",
+    "datagrok-api": "^1.20.0",
     "dayjs": "latest",
     "fastest-levenshtein": "^1.0.16",
     "js-base64": "^3.7.5",
@@ -26,8 +26,8 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.5",
-    "@datagrok-libraries/js-draw-lite": "^0.0.3",
+    "@datagrok-libraries/helm-web-editor": "^1.1.6",
+    "@datagrok-libraries/js-draw-lite": "^0.0.4",
     "@types/signals": "1.0.1",
     "@types/three": "^0.159.0",
     "@types/uuid": "^9.0.1",

package/src/helm/helm-helper.d.ts CHANGED Viewed

@@ -1,9 +1,20 @@
+import * as DG from 'datagrok-api/dg';
 import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
-import { IHelmWebEditor } from './types';
+import { HelmMol, IHelmWebEditor } from './types';
 import { IMonomerLib } from '../types/index';
 import { GetMonomerFunc } from '../helm/types';
+export interface IInputInitOptions<T = any> {
+    value?: T;
+    property?: DG.Property;
+    nullable?: boolean;
+    elementOptions?: DG.ElementOptions;
+    tooltipText?: string;
+    onCreated?: (input: DG.InputBase<T>) => void;
+    onValueChanged?: (input: DG.InputBase<T>) => void;
+}
 export interface IHelmHelper {
-    createHelmWebEditor(): IHelmWebEditor;
+    createHelmInput(name: string, options?: IInputInitOptions<HelmMol>): DG.InputBase<HelmMol>;
+    createHelmWebEditor(host?: HTMLElement): IHelmWebEditor;
     createWebEditorApp(host: HTMLDivElement, helm?: string): App;
     get originalGetMonomer(): GetMonomerFunc | null;
     buildGetMonomerFromLib(monomerLib: IMonomerLib): GetMonomerFunc;
@@ -11,4 +22,12 @@ export interface IHelmHelper {
     revertOriginalGetMonomer(): GetMonomerFunc;
 }
 export declare function getHelmHelper(): Promise<IHelmHelper>;
+declare module 'datagrok-api/ui' {
+    namespace input {
+        /** To create HelmInput synchronously, get the {@link IHelmHelper} object
+         * via {@link getHelmHelper} in advance, and call {@link IHelmHelper.createHelmInput}.
+         */
+        function helmAsync(name: string, options?: IInputInitOptions<HelmMol>): Promise<DG.InputBase<HelmMol>>;
+    }
+}
 //# sourceMappingURL=helm-helper.d.ts.map

package/src/helm/helm-helper.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/helm/helm-helper.js CHANGED Viewed

@@ -1,3 +1,4 @@
+import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 export async function getHelmHelper() {
     const packageName = 'Helm';
@@ -7,4 +8,7 @@ export async function getHelmHelper() {
     const res = (await funcList[0].prepare().call()).getOutputParamValue();
     return res;
 }
+ui.input.helmAsync = async function (name, options) {
+    return (await getHelmHelper()).createHelmInput(name, options);
+};
 //# sourceMappingURL=helm-helper.js.map

package/src/helm/helm-helper.js.map CHANGED Viewed

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

@@ -13,6 +13,10 @@ import type { Monomers } from '@datagrok-libraries/helm-web-editor/helm/Monomers
 import type { DojoType, DojoxType } from '@datagrok-libraries/js-draw-lite/src/types/dojo';
 export { HelmType, PolymerType, MonomerType, WebEditorRGroups };
 export { Atom, IJsAtom, Bond, Mol, Editor };
+export type HelmString = string;
+export type HelmAtom = Atom<HelmType>;
+export type HelmBond = Bond<HelmType>;
+export type HelmMol = Mol<HelmType>;
 export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, App, Monomers, GetMonomerFunc, GetMonomerResType };
 export { DojoType, DojoxType };
 export { HweWindow, ScilModuleType, JSDraw2ModuleType, OrgType };

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

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package/src/monomer-works/monomer-utils.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/monomer-works/monomer-utils.js CHANGED Viewed

@@ -143,7 +143,8 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
     const totalSimilarity = new Float32Array(rowCount);
     // Calculate base similarity
     for (let position = 0; position < positionColumns.length; ++position) {
-        const referenceMonomerCanonical = referenceSequence.getCanonical(position);
+        const referenceMonomerCanonical = position < referenceSequence.length ?
+            referenceSequence.getCanonical(position) : GAP_SYMBOL;
         const referenceMol = monomerLib.getMonomer('PEPTIDE', referenceMonomerCanonical)?.smiles ?? '';
         const monomerCol = positionColumns[position];
         const monomerColData = monomerCol.getRawData();
@@ -156,12 +157,15 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
         const molCol = DG.Column.fromStrings('smiles', monomerColCategories.map((cat) => monomerLib.getMonomer('PEPTIDE', cat)?.smiles ?? ''));
         const _df = DG.DataFrame.fromColumns([molCol]); // getSimilarities expects that column is in dataframe
         const similarityCol = (await grok.chem.getSimilarities(molCol, referenceMol));
-        const similarityColData = similarityCol.getRawData();
+        const similarityColData = similarityCol ? similarityCol.getRawData() : null;
         for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
             const monomerCategoryIdx = monomerColData[rowIdx];
-            totalSimilarity[rowIdx] += referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx ?
-                similarityColData[monomerCategoryIdx] :
-                referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx ? 1 : 0;
+            if (referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx) {
+                totalSimilarity[rowIdx] += similarityColData[monomerCategoryIdx];
+            }
+            else if (referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx) {
+                totalSimilarity[rowIdx] += 1;
+            } // Do not increase similarity on mismatch score/penalty equals 0;
         }
     }
     for (let similarityIndex = 0; similarityIndex < totalSimilarity.length; ++similarityIndex) {

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

@@ -55,7 +55,7 @@ export async function _toAtomicLevel(df, seqCol, monomerLib) {
     const resColName = df.columns.getUnusedName(name);
     const resCol = DG.Column.fromStrings(resColName, molfileList);
     resCol.semType = DG.SEMTYPE.MOLECULE;
-    resCol.setTag(DG.TAGS.UNITS, DG.UNITS.Molecule.MOLBLOCK);
+    resCol.meta.units = DG.UNITS.Molecule.MOLBLOCK;
     return { col: resCol, warnings: molfileWarningList };
 }
 /** Get jagged array of monomer symbols for the dataframe

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

	@@ -1 +1 @@
1	- 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package/src/utils/fasta-handler.js CHANGED Viewed

@@ -43,7 +43,7 @@ export class FastaFileHandler {
         const descriptionsArrayCol = DG.Column.fromStrings('description', this.descriptionsArray);
         const sequenceCol = DG.Column.fromStrings('sequence', this.sequencesArray);
         sequenceCol.semType = DG.SEMTYPE.MACROMOLECULE;
-        sequenceCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+        sequenceCol.meta.units = NOTATION.FASTA;
         // here should go the code from units handler
         const sh = SeqHandler.forColumn(sequenceCol);
         return [DG.DataFrame.fromColumns([

package/src/utils/fasta-handler.js.map CHANGED Viewed

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

@@ -14,7 +14,7 @@ export function generateLongSequence(length = 10 ** 5) {
     const longSequence = `meI/hHis/Aca/N//dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe`.repeat(Math.ceil(length / 10)).slice(0, -1);
     const msaCol = DG.Column.fromList(DG.COLUMN_TYPE.STRING, 'MSA', new Array(10 ** 2).fill(longSequence));
     msaCol.semType = DG.SEMTYPE.MACROMOLECULE;
-    msaCol.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
+    msaCol.meta.units = NOTATION.SEPARATOR;
     msaCol.setTag(TAGS.separator, '/');
     msaCol.setTag(TAGS.alphabet, ALPHABET.UN);
     msaCol.setTag(TAGS.alphabetIsMultichar, 'true');
@@ -29,7 +29,7 @@ export function generateLongSequence2(notation = NOTATION.SEPARATOR, alphabet =
     const alphabetSize = alphabetSet.length;
     const col = DG.Column.fromType(DG.COLUMN_TYPE.STRING, colName, rowCount);
     col.semType = DG.SEMTYPE.MACROMOLECULE;
-    col.setTag(DG.TAGS.UNITS, notation);
+    col.meta.units = notation;
     col.setTag(TAGS.alphabet, alphabet);
     if (notation == NOTATION.SEPARATOR)
         col.setTag(TAGS.separator, separator);

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

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

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

@@ -1,5 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { sequenceChemSimilarity } from '../../monomer-works/monomer-utils';
+import { GAP_SYMBOL } from '../../utils/macromolecule/types';
 import { splitAlignedSequences } from '../splitter';
 import { SeqHandler } from '../seq-handler';
 export var SCORE;
@@ -22,7 +23,7 @@ export async function calculateScores(table, col, ref, scoring) {
     const scoresCol = scoring === SCORE.IDENTITY ? calculateIdentity(refSplitted, splitSeqDf) :
         scoring === SCORE.SIMILARITY ? await calculateSimilarity(refSplitted, splitSeqDf) : null;
     if (scoresCol === null)
-        throw new Error(`In bio library: Unkown sequence scoring method: ${scoring}`);
+        throw new Error(`In bio library: Unknown sequence scoring method: ${scoring}`);
     scoresCol.name = table.columns.getUnusedName(scoresCol.name);
     table.columns.add(scoresCol);
     return scoresCol;
@@ -40,14 +41,16 @@ export function calculateIdentity(reference, positionsDf) {
         const posCol = positionsDf.columns.byIndex(posIdx);
         positionCols[posIdx] = posCol.getRawData();
         positionEmptyCategories[posIdx] = posCol.categories.indexOf('');
-        categoryIndexesTemplate[posIdx] = posCol.categories.indexOf(reference.getOriginal(posIdx) ?? '');
+        const refM = posIdx < reference.length ? reference.getOriginal(posIdx) : GAP_SYMBOL;
+        categoryIndexesTemplate[posIdx] = posCol.categories.indexOf(refM);
     }
     const identityScoresCol = DG.Column.float('Identity', positionsDf.rowCount);
     const identityScoresData = identityScoresCol.getRawData();
     for (let rowIndex = 0; rowIndex < positionsDf.rowCount; ++rowIndex) {
         identityScoresData[rowIndex] = 0;
         for (let posIdx = 0; posIdx < reference.length; ++posIdx) {
-            const categoryIndex = positionCols[posIdx][rowIndex];
+            const positionCol = positionCols[posIdx];
+            const categoryIndex = positionCol ? positionCols[posIdx][rowIndex] : 0;
             if (categoryIndex === categoryIndexesTemplate[posIdx])
                 ++identityScoresData[rowIndex];
         }

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

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

@@ -265,7 +265,7 @@ export function getPaletteByType(paletteType) {
 export function pickUpSeqCol(df) {
     const semTypeColList = df.columns.bySemTypeAll(DG.SEMTYPE.MACROMOLECULE);
     let resCol = semTypeColList.find((col) => {
-        const units = col.getTag(DG.TAGS.UNITS);
+        const units = col.meta.units;
         return units ? units.indexOf('MSA') !== -1 : false;
     }) ?? null;
     if (!resCol && semTypeColList.length > 0)

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

	@@ -1 +1 @@
1	- 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package/src/utils/seq-handler.js CHANGED Viewed

@@ -34,7 +34,7 @@ export class SeqHandler {
         if (col.type !== DG.TYPE.STRING)
             throw new Error(`Unexpected column type '${col.type}', must be '${DG.TYPE.STRING}'.`);
         this._column = col;
-        const units = this._column.getTag(DG.TAGS.UNITS);
+        const units = this._column.meta.units;
         if (units !== null && units !== undefined)
             this._units = units;
         else
@@ -56,7 +56,7 @@ export class SeqHandler {
             else if (this.isHelm())
                 SeqHandler.setUnitsToHelmColumn(this);
             else
-                throw new Error(`Unexpected units '${this.column.getTag(DG.TAGS.UNITS)}'.`);
+                throw new Error(`Unexpected units '${this.column.meta.units}'.`);
         }
         // if (!this.column.tags.has(TAGS.alphabetSize)) {
         //   if (this.isHelm())
@@ -78,29 +78,29 @@ export class SeqHandler {
         this.columnVersion = this.column.version;
     }
     static setUnitsToFastaColumn(uh) {
-        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== NOTATION.FASTA)
+        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.meta.units !== NOTATION.FASTA)
             throw new Error(`The column of notation '${NOTATION.FASTA}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
-        uh.column.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+        uh.column.meta.units = NOTATION.FASTA;
         SeqHandler.setTags(uh);
     }
     static setUnitsToSeparatorColumn(uh, separator) {
-        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== NOTATION.SEPARATOR)
+        if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.meta.units !== NOTATION.SEPARATOR)
             throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must be '${DG.SEMTYPE.MACROMOLECULE}'.`);
         if (!separator)
             throw new Error(`The column of notation '${NOTATION.SEPARATOR}' must have the separator tag.`);
-        uh.column.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
+        uh.column.meta.units = NOTATION.SEPARATOR;
         uh.column.setTag(TAGS.separator, separator);
         SeqHandler.setTags(uh);
     }
     static setUnitsToHelmColumn(uh) {
         if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE)
             throw new Error(`The column of notation '${NOTATION.HELM}' must be '${DG.SEMTYPE.MACROMOLECULE}'`);
-        uh.column.setTag(DG.TAGS.UNITS, NOTATION.HELM);
+        uh.column.meta.units = NOTATION.HELM;
         SeqHandler.setTags(uh);
     }
     /** From detectMacromolecule */
     static setTags(uh) {
-        const units = uh.column.getTag(DG.TAGS.UNITS);
+        const units = uh.column.meta.units;
         if ([NOTATION.FASTA, NOTATION.SEPARATOR].includes(units)) {
             // Empty monomer alphabet is allowed, only if alphabet tag is annotated
             if (!uh.column.getTag(TAGS.alphabet) && Object.keys(uh.stats.freq).length === 0)
@@ -317,7 +317,7 @@ export class SeqHandler {
         const newColName = colName ?? col.dataFrame.columns.getUnusedName(name);
         const newColumn = DG.Column.fromList('string', newColName, data ?? new Array(this.column.length).fill(''));
         newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
-        newColumn.setTag(DG.TAGS.UNITS, tgtNotation);
+        newColumn.meta.units = tgtNotation;
         if (tgtNotation === NOTATION.SEPARATOR) {
             if (!tgtSeparator)
                 throw new Error(`Notation \'${NOTATION.SEPARATOR}\' requires separator value.`);
@@ -390,7 +390,7 @@ export class SeqHandler {
             throw new Error('Invalid format of \'units\' parameter');
         const newColumn = DG.Column.fromList('string', name, new Array(len).fill(''));
         newColumn.semType = DG.SEMTYPE.MACROMOLECULE;
-        newColumn.setTag(DG.TAGS.UNITS, units);
+        newColumn.meta.units = units;
         return newColumn;
     }
     /** Gets function to split seq value to monomers */

package/src/utils/seq-handler.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/src/utils/units-handler-base.js CHANGED Viewed

@@ -14,7 +14,7 @@ export class UnitsHandlerBase {
             throw new Error(`Invalid semantic type '${this.column.semType} of column '${this.column.name}', ` +
                 `expected '${requiredSemType}'.`);
         }
-        this.units = this.column.getTag(DG.TAGS.UNITS);
+        this.units = this.column.meta.units;
         if (!this.units)
             throw new Error(`Units not specified in column '${this.column.name}'.`);
     }

package/src/utils/units-handler-base.js.map CHANGED Viewed

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