@datagrok-libraries/bio 5.38.9 → 5.38.11

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Files changed (12) hide show
  1. package/package.json +2 -2
  2. package/src/monomer-works/monomer-utils.d.ts +9 -0
  3. package/src/monomer-works/monomer-utils.d.ts.map +1 -1
  4. package/src/monomer-works/monomer-utils.js +21 -0
  5. package/src/monomer-works/monomer-utils.js.map +1 -1
  6. package/src/utils/const.d.ts +4 -0
  7. package/src/utils/const.d.ts.map +1 -1
  8. package/src/utils/const.js +4 -0
  9. package/src/utils/const.js.map +1 -1
  10. package/src/utils/units-handler.d.ts.map +1 -1
  11. package/src/utils/units-handler.js +7 -8
  12. package/src/utils/units-handler.js.map +1 -1
package/package.json CHANGED
@@ -8,12 +8,12 @@
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  "access": "public"
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  },
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  "friendlyName": "Datagrok bio library",
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- "version": "5.38.9",
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+ "version": "5.38.11",
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  "description": "",
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  "dependencies": {
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  "@datagrok-libraries/gridext": "^1.3.64",
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  "@datagrok-libraries/utils": "^4.1.0",
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- "@datagrok-libraries/ml": "^6.3.28",
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+ "@datagrok-libraries/ml": "^6.3.48",
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  "@deck.gl/core": "8.8.12",
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  "cash-dom": "latest",
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  "datagrok-api": "^1.13.3",
package/src/monomer-works/monomer-utils.d.ts CHANGED
@@ -30,4 +30,13 @@ export declare function getMonomerLibHelper(): Promise<IMonomerLibHelper>;
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  * @returns {Promise<DG.Column<number>>} Column with similarity values. */
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  export declare function sequenceChemSimilarity(sequenceCol: DG.Column<string>, referenceSequence: ISeqSplitted): Promise<DG.Column<number>>;
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  export declare function sequenceChemSimilarity(positionColumns: DG.Column<string>[], referenceSequence: ISeqSplitted): Promise<DG.Column<number>>;
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+ /** Calculates chemical similarity between each pair of monomers.
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+ * @param {string[]} monomerSet Set of unique monomers.
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+ * @returns {Promise<{scoringMatrix: number[][], alphabetIndexes: {[monomerId: string]: number}}>} Ojbect containing similarity scoring matrix and monomer to index mapping. */
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+ export declare function calculateMonomerSimilarity(monomerSet: string[]): Promise<{
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+ scoringMatrix: number[][];
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+ alphabetIndexes: {
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+ [monomerId: string]: number;
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+ };
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+ }>;
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  //# sourceMappingURL=monomer-utils.d.ts.map
package/src/monomer-works/monomer-utils.d.ts.map CHANGED
@@ -1 +1 @@
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1
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package/src/monomer-works/monomer-utils.js CHANGED
@@ -222,4 +222,25 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
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  const similarityCol = DG.Column.fromFloat32Array('Similarity', totalSimilarity);
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  return similarityCol;
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  }
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+ /** Calculates chemical similarity between each pair of monomers.
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+ * @param {string[]} monomerSet Set of unique monomers.
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+ * @returns {Promise<{scoringMatrix: number[][], alphabetIndexes: {[monomerId: string]: number}}>} Ojbect containing similarity scoring matrix and monomer to index mapping. */
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+ export async function calculateMonomerSimilarity(monomerSet) {
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+ const libHelper = await getMonomerLibHelper();
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+ const monomerLib = libHelper.getBioLib();
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+ const scoringMatrix = [];
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+ const alphabetIndexes = {};
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+ const monomerMolecules = monomerSet.map((monomer) => monomerLib.getMonomer('PEPTIDE', monomer)?.smiles ?? '');
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+ const monomerMoleculesCol = DG.Column.fromStrings('smiles', monomerMolecules);
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+ for (let monomerIndex = 0; monomerIndex < monomerMolecules.length; ++monomerIndex) {
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+ const monomer = monomerSet[monomerIndex];
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+ alphabetIndexes[monomer] = monomerIndex;
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+ const monomerMol = monomerMolecules[monomerIndex];
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+ const similarityScores = monomerMol === '' ? new Array(monomerMolecules.length).fill(0) :
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+ (await grok.chem.getSimilarities(monomerMoleculesCol, monomerMol)).getRawData();
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+ similarityScores[monomerIndex] = 1;
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+ scoringMatrix[monomerIndex] = Array.from(similarityScores);
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+ }
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+ return { scoringMatrix, alphabetIndexes };
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+ }
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  //# sourceMappingURL=monomer-utils.js.map
package/src/monomer-works/monomer-utils.js.map CHANGED
@@ -1 +1 @@
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package/src/utils/const.d.ts CHANGED
@@ -89,4 +89,8 @@ export declare const dummyMonomer: {
89
89
  };
90
90
  export declare const MONOMER_ENCODE_MIN = 256;
91
91
  export declare const MONOMER_ENCODE_MAX = 1034;
92
+ export declare const RIBOSE_SYMBOL = "r";
93
+ export declare const DEOXYRIBOSE_SYMBOL = "d";
94
+ export declare const PHOSPHATE_SYMBOL = "p";
95
+ export declare const HELM_WRAPPERS_REGEXP: RegExp;
92
96
  //# sourceMappingURL=const.d.ts.map
package/src/utils/const.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/src/utils/const.js CHANGED
@@ -60,4 +60,8 @@ export const dummyMonomer = {
60
60
  // range of hex nubers used in PepSea library to endode monomers
61
61
  export const MONOMER_ENCODE_MIN = 0x100;
62
62
  export const MONOMER_ENCODE_MAX = 0x40A;
63
+ export const RIBOSE_SYMBOL = 'r';
64
+ export const DEOXYRIBOSE_SYMBOL = 'd';
65
+ export const PHOSPHATE_SYMBOL = 'p';
66
+ export const HELM_WRAPPERS_REGEXP = new RegExp(`[${RIBOSE_SYMBOL}${DEOXYRIBOSE_SYMBOL}]\\((\\w)\\)${PHOSPHATE_SYMBOL}?`, 'g');
63
67
  //# sourceMappingURL=const.js.map
package/src/utils/const.js.map CHANGED
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package/src/utils/units-handler.d.ts.map CHANGED
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package/src/utils/units-handler.js CHANGED
@@ -4,6 +4,7 @@ import { NOTATION, candidateAlphabets, positionSeparator } from './macromolecule
4
4
  import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator, splitterAsFasta, splitterAsFastaSimple, splitterAsHelm } from './macromolecule/utils';
5
5
  import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
6
6
  import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
7
+ import { HELM_WRAPPERS_REGEXP, PHOSPHATE_SYMBOL } from './const';
7
8
  export const Tags = new class {
8
9
  constructor() {
9
10
  /** Column's temp slot name for a UnitsHandler object */
@@ -399,15 +400,14 @@ export class UnitsHandler {
399
400
  }
400
401
  if (!tgtSeparator)
401
402
  tgtSeparator = (this.toFasta(tgtNotation)) ? '' : this.separator;
402
- const helmWrappersRe = /(R\(|D\(|\)|P)/g;
403
- const isNucleotide = helmPolymer.startsWith('DNA') || helmPolymer.startsWith('RNA');
403
+ const isNucleotide = helmPolymer.startsWith('RNA');
404
404
  // items can be monomers or helms
405
405
  const helmItemsArray = this.splitter(helmPolymer);
406
406
  const tgtMonomersArray = [];
407
407
  for (let i = 0; i < helmItemsArray.length; i++) {
408
408
  let item = helmItemsArray[i];
409
409
  if (isNucleotide)
410
- item = item.replace(helmWrappersRe, '');
410
+ item = item.replace(HELM_WRAPPERS_REGEXP, '');
411
411
  if (item === GapSymbols[NOTATION.HELM])
412
412
  tgtMonomersArray.push(tgtGapSymbol);
413
413
  else if (this.toFasta(tgtNotation) && item.length > 1) {
@@ -557,13 +557,12 @@ export class UnitsHandler {
557
557
  return col.temp[Tags.uhTemp];
558
558
  }
559
559
  }
560
- const helmWrappersRe = /[RD]\((\w)\)P?/g;
561
560
  function joinToFasta(srcUh, seqS) {
562
561
  const resMList = new Array(seqS.length);
563
562
  for (const [srcM, mI] of wu.enumerate(seqS)) {
564
563
  let m = srcM;
565
564
  if (srcUh.isHelm())
566
- m = srcM.replace(helmWrappersRe, '$1');
565
+ m = srcM.replace(HELM_WRAPPERS_REGEXP, '$1');
567
566
  if (srcUh.isGap(m))
568
567
  m = GapSymbols[NOTATION.FASTA];
569
568
  else if (m.length > 1)
@@ -597,7 +596,7 @@ function joinToHelm(srcUh, seqS, isDnaOrRna) {
597
596
  if (srcUh.isGap(m))
598
597
  m = GapSymbols[NOTATION.HELM];
599
598
  else if (isDnaOrRna)
600
- m = m.replace(helmWrappersRe, '$1');
599
+ m = m.replace(HELM_WRAPPERS_REGEXP, '$1');
601
600
  else
602
601
  m = srcM.length == 1 ? `${leftWrapper}${srcM}${rightWrapper}` : `${leftWrapper}[${srcM}]${rightWrapper}`;
603
602
  return m;
@@ -618,8 +617,8 @@ function splitterAsHelmNucl(srcUh, src) {
618
617
  for (const [srcM, mI] of wu.enumerate(srcMList)) {
619
618
  let m = srcM;
620
619
  if (isDna || isRna) {
621
- m = m.replace(helmWrappersRe, '$1');
622
- m = m === 'P' ? null : m;
620
+ m = m.replace(HELM_WRAPPERS_REGEXP, '$1');
621
+ m = m === PHOSPHATE_SYMBOL ? null : m;
623
622
  }
624
623
  tgtMList[mI] = m;
625
624
  }
package/src/utils/units-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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