npm - @datagrok-libraries/bio - Versions diffs - 5.34.3 → 5.36.0 - Mend

@datagrok-libraries/bio 5.34.3 → 5.36.0

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Files changed (42) hide show

package/.eslintrc.json +4 -3
package/CHANGELOG.md +18 -9
package/package.json +1 -1
package/src/monomer-works/monomer-utils.d.ts +9 -0
package/src/monomer-works/monomer-utils.d.ts.map +1 -1
package/src/monomer-works/monomer-utils.js +58 -13
package/src/monomer-works/monomer-utils.js.map +1 -1
package/src/monomer-works/to-atomic-level.d.ts +1 -1
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +7 -8
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 +7 -8
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/cell-renderer.d.ts +3 -2
package/src/utils/cell-renderer.d.ts.map +1 -1
package/src/utils/cell-renderer.js +1 -1
package/src/utils/cell-renderer.js.map +1 -1
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js +1 -1
package/src/utils/macromolecule/consts.js.map +1 -1
package/src/utils/macromolecule/index.d.ts +1 -1
package/src/utils/macromolecule/index.d.ts.map +1 -1
package/src/utils/macromolecule/index.js +1 -1
package/src/utils/macromolecule/index.js.map +1 -1
package/src/utils/macromolecule/types.d.ts +5 -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 +1 -7
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +18 -31
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/notation-converter.d.ts.map +1 -1
package/src/utils/notation-converter.js +5 -7
package/src/utils/notation-converter.js.map +1 -1
package/src/utils/splitter.d.ts.map +1 -1
package/src/utils/splitter.js +3 -2
package/src/utils/splitter.js.map +1 -1
package/src/utils/units-handler.d.ts +3 -3
package/src/utils/units-handler.d.ts.map +1 -1
package/src/utils/units-handler.js +26 -18
package/src/utils/units-handler.js.map +1 -1

package/.eslintrc.json CHANGED Viewed

@@ -18,15 +18,16 @@
     "indent": ["error", 2, {"SwitchCase": 1}],
     "max-len": ["error", 120],
     "no-unused-vars": "off",
-    "@typescript-eslint/no-unused-vars": ["warn", { "varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}],
+    "@typescript-eslint/no-unused-vars": [
+      "warn", {"varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}
+    ],
     "require-jsdoc": "off",
     "valid-jsdoc": "warn",
     "spaced-comment": "off",
     "linebreak-style": "off",
     "curly": [
       "error",
-      "multi-or-nest",
-      "consistent"
+      "multi-or-nest"
     ],
     "brace-style": [
       "error",

package/CHANGELOG.md CHANGED Viewed

@@ -1,29 +1,38 @@
 # bio changelog
-## 5.35.0 (WIP)
+## 5.36.0 (2023-08-10)
-Add WebLogo property showPositionLabels
+This release introduces chemical sequence similarity functionality.
 ### Features
-* Add WebLogo property showPositionLabels
+* Added `sequenceChemSimilarity` function.
-## 5.34.1 (2023-08-01)
+## 5.35.0 (2023-08-06)
+Optimize with splitterAsFastaSimple returning ISeqSplitted allowing to speed up processing of
+single character alphabets.
+## Breaking changes
-Patch release for a small fix for Macromolecule cell renderer
+* SplitterFunc now returns `ISeqSplitted` instead of `string[]`.
+### Features
-*Dependency: datgarok-api >= 1.10.2*
+* Add WebLogo property showPositionLabels.
+## 5.34.1 (2023-08-01)
+Patch release for a small fix for the Macromolecule cell renderer.
 ### Bug fixes
-* GROK-13659: Bio | Tools: Fix MaxMonomerLength Macromolecule cell renderer
+* GROK-13659: Bio | Tools: Fix MaxMonomerLength Macromolecule cell renderer.
 ## 5.34.0 (2023-07-21)
 This release focuses on improving usability.
-*Dependency: datgarok-api >= 1.10.2*
 ### Features
 * Added `NotationConverter.getConverter()` getting a function to convert a single value.

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.34.3",
+  "version": "5.36.0",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.64",

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

@@ -1,5 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { IMonomerLib } from '../types/index';
+import { ISeqSplitted } from '../utils/macromolecule/types';
 export declare function encodeMonomers(col: DG.Column): DG.Column | null;
 export declare function getMolfilesFromSeq(col: DG.Column, monomersLibObject: any[]): any[][] | null;
 export declare function getMolfilesFromSingleSeq(cell: DG.Cell, monomersLibObject: any[]): any[][] | null;
@@ -18,4 +19,12 @@ export interface IMonomerLibHelper {
     readLibrary(path: string, fileName: string): Promise<IMonomerLib>;
 }
 export declare function getMonomerLibHelper(): Promise<IMonomerLibHelper>;
+/** Calculates chemical similarity between reference sequence and list of sequences.
+ * Similarity is computed as a sum of monomer similarities on corresponding positions. Monomer similarity is calculated
+ * based on Morgan fingerprints.
+ * @param {DG.Column<string>[]} positionColumns List of position columns containing monomers.
+ * @param {string[]} referenceSequence Reference sequence.
+ * @returns {Promise<DG.Column<number>>} Column with similarity values. */
+export declare function sequenceChemSimilarity(sequenceCol: DG.Column<string>, referenceSequence: ISeqSplitted): Promise<DG.Column<number>>;
+export declare function sequenceChemSimilarity(positionColumns: DG.Column<string>[], referenceSequence: ISeqSplitted): Promise<DG.Column<number>>;
 //# sourceMappingURL=monomer-utils.d.ts.map

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

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package/src/monomer-works/monomer-utils.js CHANGED Viewed

@@ -2,18 +2,18 @@
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
 import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME } from '../utils/const';
-import { getSplitter } from '../utils/macromolecule/utils';
+import { UnitsHandler } from '../utils/units-handler';
+import { splitAlignedSequences } from '../utils/splitter';
 export function encodeMonomers(col) {
     let encodeSymbol = MONOMER_ENCODE_MIN;
     const monomerSymbolDict = {};
-    const units = col.tags[DG.TAGS.UNITS];
-    const sep = col.getTag("separator" /* TAGS.separator */);
-    const splitterFunc = getSplitter(units, sep);
+    const uh = UnitsHandler.getOrCreate(col);
+    const splitterFunc = uh.getSplitter();
     const encodedStringArray = [];
     for (let i = 0; i < col.length; ++i) {
         let encodedMonomerStr = '';
         const monomers = splitterFunc(col.get(i));
-        monomers.forEach((m) => {
+        for (const m of monomers) {
             if (!monomerSymbolDict[m]) {
                 if (encodeSymbol > MONOMER_ENCODE_MAX) {
                     grok.shell.error(`Not enough symbols to encode monomers`);
@@ -23,20 +23,19 @@ export function encodeMonomers(col) {
                 encodeSymbol++;
             }
             encodedMonomerStr += String.fromCodePoint(monomerSymbolDict[m]);
-        });
+        }
         encodedStringArray.push(encodedMonomerStr);
     }
     return DG.Column.fromStrings('encodedMolecules', encodedStringArray);
 }
 export function getMolfilesFromSeq(col, monomersLibObject) {
-    const units = col.tags[DG.TAGS.UNITS];
-    const sep = col.getTag('separator');
-    const splitterFunc = getSplitter(units, sep);
+    const uh = UnitsHandler.getOrCreate(col);
+    const splitter = uh.getSplitter();
     const monomersDict = createMomomersMolDict(monomersLibObject);
     const molFiles = [];
     for (let i = 0; i < col.length; ++i) {
         const macroMolecule = col.get(i);
-        const monomers = splitterFunc(macroMolecule);
+        const monomers = splitter(macroMolecule);
         const molFilesForSeq = [];
         for (let j = 0; j < monomers.length; ++j) {
             if (monomers[j]) {
@@ -53,9 +52,8 @@ export function getMolfilesFromSeq(col, monomersLibObject) {
     return molFiles;
 }
 export function getMolfilesFromSingleSeq(cell, monomersLibObject) {
-    const units = cell.column.tags[DG.TAGS.UNITS];
-    const sep = cell.column.getTag('separator');
-    const splitterFunc = getSplitter(units, sep);
+    const uh = UnitsHandler.getOrCreate(cell.column);
+    const splitterFunc = uh.getSplitter();
     const monomersDict = createMomomersMolDict(monomersLibObject);
     const molFiles = [];
     const macroMolecule = cell.value;
@@ -126,4 +124,51 @@ export async function getMonomerLibHelper() {
     const res = (await funcList[0].prepare().call()).getOutputParamValue();
     return res;
 }
+export async function sequenceChemSimilarity(positionColumns, referenceSequence) {
+    if (positionColumns instanceof DG.Column)
+        positionColumns = splitAlignedSequences(positionColumns).columns.toList();
+    const libHelper = await getMonomerLibHelper();
+    const monomerLib = libHelper.getBioLib();
+    // const smilesCols: DG.Column<string>[] = new Array(monomerCols.length);
+    const rawCols = new Array(positionColumns.length);
+    const rowCount = positionColumns[0].length;
+    const totalSimilarity = new Float32Array(rowCount);
+    // Calculate base similarity
+    for (let position = 0; position < positionColumns.length; ++position) {
+        const referenceMonomer = referenceSequence[position];
+        const referenceMol = monomerLib.getMonomer('PEPTIDE', referenceMonomer)?.smiles ?? '';
+        const monomerCol = positionColumns[position];
+        const monomerColData = monomerCol.getRawData();
+        const monomerColCategories = monomerCol.categories;
+        const emptyCategoryIdx = monomerColCategories.indexOf('');
+        rawCols[position] = { categories: monomerColCategories, data: monomerColData, emptyIndex: emptyCategoryIdx };
+        if (typeof referenceMonomer === 'undefined')
+            continue;
+        // Calculating similarity for
+        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();
+        for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
+            const monomerCategoryIdx = monomerColData[rowIdx];
+            totalSimilarity[rowIdx] += referenceMonomer !== '' && monomerCategoryIdx !== emptyCategoryIdx ?
+                similarityColData[monomerCategoryIdx] :
+                referenceMonomer === '' && monomerCategoryIdx === emptyCategoryIdx ? 1 : 0;
+        }
+    }
+    for (let similarityIndex = 0; similarityIndex < totalSimilarity.length; ++similarityIndex) {
+        let updatedSimilarity = totalSimilarity[similarityIndex] / referenceSequence.length;
+        for (let position = 0; position < positionColumns.length; ++position) {
+            const currentRawCol = rawCols[position];
+            if ((position >= referenceSequence.length && currentRawCol.data[similarityIndex] !== currentRawCol.emptyIndex) ||
+                (currentRawCol.data[similarityIndex] === currentRawCol.emptyIndex && position < referenceSequence.length)) {
+                updatedSimilarity = DG.FLOAT_NULL;
+                break;
+            }
+        }
+        totalSimilarity[similarityIndex] = updatedSimilarity;
+    }
+    const similarityCol = DG.Column.fromFloat32Array('Similarity', totalSimilarity);
+    return similarityCol;
+}
 //# sourceMappingURL=monomer-utils.js.map

package/src/monomer-works/monomer-utils.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/src/monomer-works/to-atomic-level.d.ts CHANGED Viewed

@@ -7,7 +7,7 @@ import { Bonds, MolGraph } from './types';
  * @param {DG.DataFrame} df - DataFrame containing the column to be converted
  * @param {DG.Column} seqCol - Column containing the macromolecule sequence
  * @param {IMonomerLib} monomerLib - Monomer library
-*/
+ */
 export declare function _toAtomicLevel(df: DG.DataFrame, seqCol: DG.Column<string>, monomerLib: IMonomerLib): Promise<{
     col: DG.Column | null;
     warnings: string[];

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

@@ -1,20 +1,20 @@
 /* Do not change these import lines to match external modules in webpack configuration */
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
+import wu from 'wu';
+import { errorToConsole } from '@datagrok-libraries/utils';
 import { NOTATION } from '../utils/macromolecule/consts';
 import { NotationConverter } from '../utils/notation-converter';
 import { UnitsHandler } from '../utils/units-handler';
 import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
 import { seqToMolFileWorker } from './seq-to-molfile';
 import { monomerWorksConsts as C } from './consts';
-import { errorToConsole } from '@datagrok-libraries/utils';
-import { getSplitter } from '../utils/macromolecule';
 // todo: verify that all functions have return types
 /** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
  * @param {DG.DataFrame} df - DataFrame containing the column to be converted
  * @param {DG.Column} seqCol - Column containing the macromolecule sequence
  * @param {IMonomerLib} monomerLib - Monomer library
-*/
+ */
 export async function _toAtomicLevel(df, seqCol, monomerLib) {
     // todo: remove this from the library
     if (DG.Func.find({ package: 'Chem', name: 'getRdKitModule' }).length === 0) {
@@ -70,13 +70,12 @@ export function getMonomerSequencesArray(macroMolCol) {
     const columnLength = macroMolCol.length;
     const result = new Array(columnLength);
     // split the string into monomers
-    const colUnits = macroMolCol.getTag(DG.TAGS.UNITS);
-    const separator = macroMolCol.getTag("separator" /* TAGS.separator */);
-    const splitterFunc = getSplitter(colUnits, separator);
+    const uh = UnitsHandler.getOrCreate(macroMolCol);
+    const splitter = uh.getSplitter();
     for (let row = 0; row < columnLength; ++row) {
         const macroMolecule = macroMolCol.get(row);
-        // todo: handle the exception case when macroMolecule is null
-        result[row] = macroMolecule ? splitterFunc(macroMolecule).filter((monomerCode) => monomerCode !== '') : [];
+        result[row] = macroMolecule ? wu(splitter(macroMolecule))
+            .filter((monomerCode) => monomerCode !== '').toArray() : [];
     }
     return result;
 }

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

	@@ -1 +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

@@ -1,5 +1,6 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
+import wu from 'wu';
 import { getSplitterForColumn } from './macromolecule';
 const polymerTypeMap = {
     ["DNA" /* ALPHABET.DNA */]: "RNA" /* HELM_POLYMER_TYPE.RNA */,
@@ -60,7 +61,7 @@ export class MonomerPlacer {
         if (res === null) {
             const seqMonList = this.getSeqMonList(rowIdx);
             res = this._monomerLengthList[rowIdx] = new Array(seqMonList.length);
-            for (const [seqMonI, seqMonLabel] of seqMonList.entries()) {
+            for (const [seqMonLabel, seqMonI] of wu.enumerate(seqMonList)) {
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.props.monomerLengthLimit);
                 const separatorWidth = this.props.unitsHandler.isSeparator() ? this.separatorWidth : this.props.separatorWidth;
                 const seqMonWidth = separatorWidth + shortMon.length * this.props.monomerCharWidth;
@@ -86,7 +87,7 @@ export class MonomerPlacer {
             const seqMonList = this.getSeqMonList(seqIdx);
             if (seqMonList.length > res.length)
                 res.push(...new Array(seqMonList.length - res.length).fill(0));
-            for (const [seqMonI, seqMonLabel] of seqMonList.entries()) {
+            for (const [seqMonLabel, seqMonI] of wu.enumerate(seqMonList)) {
                 const shortMon = this.props.monomerToShort(seqMonLabel, this.props.monomerLengthLimit);
                 const seqMonWidth = this.props.separatorWidth + shortMon.length * this.props.monomerCharWidth;
                 res[seqMonI] = Math.max(res[seqMonI] ?? 0, seqMonWidth);
@@ -99,7 +100,7 @@ export class MonomerPlacer {
     getPosition(rowIdx, x) {
         const [monomerMaxLengthList, monomerMaxLengthSumList] = this.getCellMonomerLengths(rowIdx);
         const seq = this.col.get(rowIdx);
-        const seqMonList = this._splitter(seq);
+        const seqMonList = wu(this._splitter(seq)).toArray();
         let iterationCount = 100;
         let left = null;
         let right = seqMonList.length;
@@ -112,12 +113,10 @@ export class MonomerPlacer {
                     left = mid;
                     found = true;
                 }
-                else if (x < monomerMaxLengthSumList[mid]) {
+                else if (x < monomerMaxLengthSumList[mid])
                     right = mid - 1;
-                }
-                else if (x > monomerMaxLengthSumList[mid + 1]) {
+                else if (x > monomerMaxLengthSumList[mid + 1])
                     left = mid + 1;
-                }
                 if (left == right)
                     found = true;
                 if (--iterationCount <= 0) {
@@ -130,7 +129,7 @@ export class MonomerPlacer {
     }
     getSeqMonList(rowIdx) {
         const seq = this.col.get(rowIdx);
-        return seq ? this._splitter(seq) : [];
+        return seq ? wu(this._splitter(seq)).toArray() : [];
     }
     getMonomer(symbol) {
         const alphabet = this.props.unitsHandler.alphabet ?? "UN" /* ALPHABET.UN */;

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

@@ -1,4 +1,5 @@
 import * as DG from 'datagrok-api/dg';
+import { ISeqSplitted } from './macromolecule/types';
 export declare enum DrawStyle {
     MSA = "MSA",
     classic = "classic"
@@ -20,11 +21,11 @@ export declare enum DrawStyle {
  * @param {number[]}maxWord {{[pos: number]: number}}  Max word lengths per position.
  * @param {number}wordIdx Is index of word we currently draw.
  * @param {DG.GridCell}gridCell Is grid cell.
- * @param {string[]}referenceSequence Is reference sequence for diff mode.
+ * @param {ISeqSplitted}referenceSequence Is reference sequence for diff mode.
  * @param {number}maxLengthOfMonomer Is max length of monomer.
  * @param {{[key: string]: TextMetrics}}monomerTextSizeMap Is map of monomer text sizes.
  * @return {number} x coordinate to start printing at.*/
-export declare function printLeftOrCentered(x: number, y: number, w: number, h: number, g: CanvasRenderingContext2D, s: string, color?: string, pivot?: number, left?: boolean, transparencyRate?: number, separator?: string, last?: boolean, drawStyle?: DrawStyle, maxWord?: number[], wordIdx?: number, gridCell?: DG.GridCell | null, referenceSequence?: string[], maxLengthOfMonomer?: number | null, monomerTextSizeMap?: {
+export declare function printLeftOrCentered(x: number, y: number, w: number, h: number, g: CanvasRenderingContext2D, s: string, color?: string, pivot?: number, left?: boolean, transparencyRate?: number, separator?: string, last?: boolean, drawStyle?: DrawStyle, maxWord?: number[], wordIdx?: number, gridCell?: DG.GridCell | null, referenceSequence?: ISeqSplitted, maxLengthOfMonomer?: number | null, monomerTextSizeMap?: {
     [key: string]: TextMetrics;
 }): number;
 //# sourceMappingURL=cell-renderer.d.ts.map