@datagrok-libraries/bio 5.38.10 → 5.38.12

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Files changed (9) 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/units-handler.d.ts +1 -1
  7. package/src/utils/units-handler.d.ts.map +1 -1
  8. package/src/viewers/vd-regions.d.ts +2 -1
  9. package/src/viewers/vd-regions.d.ts.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": "5.38.10",
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+ "version": "5.38.12",
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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/units-handler.d.ts CHANGED
@@ -126,7 +126,7 @@ export declare class UnitsHandler {
126
126
  * @param {string | null} tgtSeparator Possible separator
127
127
  * @return {DG.Column} Converted column
128
128
  */
129
- convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column;
129
+ convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column<string>;
130
130
  /**
131
131
  * @param name
132
132
  * @param startIdx Start position index of the region (0-based)
package/src/utils/units-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/src/viewers/vd-regions.d.ts CHANGED
@@ -36,7 +36,8 @@ export type VdRegionsProps = Required<typeof VdRegionsPropsDefault>;
36
36
  /** Interface for VdRegionsViewer from @datagrok/bio to unbind dependency to Bio package */
37
37
  export interface IVdRegionsViewer extends VdRegionsProps, IViewer {
38
38
  init(): Promise<void>;
39
- setData(mlbDf: DG.DataFrame, regions: VdRegion[]): void;
39
+ /** List of regions referencing the column with sequences by {@link VdRegion.sequenceColumnName }. */
40
+ setData(regions: VdRegion[]): void;
40
41
  }
41
42
  declare module 'datagrok-api/dg' {
42
43
  interface DataFramePlotHelper {
package/src/viewers/vd-regions.d.ts.map CHANGED
@@ -1 +1 @@
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