@datagrok-libraries/bio 5.39.13 → 5.39.14
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.
package/package.json
CHANGED
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@@ -36,4 +36,10 @@ export declare function calculateMonomerSimilarity(monomerSet: string[]): Promis
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[monomerId: string]: number;
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37
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};
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38
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}>;
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39
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+
export declare function getMonomerSubstitutionMatrix(monomerSet: string[], fingerprintType?: string): Promise<{
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40
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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
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAC,YAAY,EAAe,MAAM,8BAA8B,CAAC;
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1
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{"version":3,"file":"monomer-utils.d.ts","sourceRoot":"","sources":["monomer-utils.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAOtC,OAAO,EAAC,WAAW,EAAC,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAAC,YAAY,EAAe,MAAM,8BAA8B,CAAC;AAMxE,wBAAgB,cAAc,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM,GAAG,IAAI,CAuB/D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAsB3F;AAED,wBAAgB,wBAAwB,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,iBAAiB,EAAE,GAAG,EAAE,GAAG,GAAG,EAAE,EAAE,GAAG,IAAI,CAmBhG;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG;IAAE,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,GAAG,GAAG,CAAA;CAAE,CAYjF;AAGD,wBAAgB,2BAA2B,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,GAAG,GAAG,CA8BpE;AAED,MAAM,WAAW,iBAAiB;IAChC,gCAAgC;IAChC,SAAS,IAAI,WAAW,CAAC;IAEzB;;OAEG;IACH,aAAa,CAAC,MAAM,CAAC,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;IAE/C,6DAA6D;IAC7D,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC;CACnE;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,iBAAiB,CAAC,CAOtE;AAED;;;;;0EAK0E;AAC1E,wBAAsB,sBAAsB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AAC1I,wBAAsB,sBAAsB,CAAC,eAAe,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,GAAG,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;AA0DhJ;;+KAE+K;AAC/K,wBAAsB,0BAA0B,CAAC,UAAU,EAAE,MAAM,EAAE,GAClE,OAAO,CAAC;IAAC,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAC,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAC,CAAA;CAAC,CAAC,CAoBtF;AAED,wBAAsB,4BAA4B,CAAC,UAAU,EAAE,MAAM,EAAE,EAAE,eAAe,GAAE,MAAiB,GACxG,OAAO,CAAC;IAAC,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAAC,eAAe,EAAE;QAAC,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAAA;KAAC,CAAA;CAAC,CAAC,CAmCtF"}
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@@ -4,6 +4,7 @@ import * as grok from 'datagrok-api/grok';
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import { HELM_CORE_FIELDS, jsonSdfMonomerLibDict, MONOMER_ENCODE_MAX, MONOMER_ENCODE_MIN, SDF_MONOMER_NAME, } from '../utils/const';
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import { UnitsHandler } from '../utils/units-handler';
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import { splitAlignedSequences } from '../utils/splitter';
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import { tanimotoSimilarity } from '@datagrok-libraries/ml/src/distance-metrics-methods';
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export function encodeMonomers(col) {
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let encodeSymbol = MONOMER_ENCODE_MIN;
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const monomerSymbolDict = {};
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@@ -192,4 +193,38 @@ export async function calculateMonomerSimilarity(monomerSet) {
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}
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return { scoringMatrix, alphabetIndexes };
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}
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export async function getMonomerSubstitutionMatrix(monomerSet, fingerprintType = 'Morgan') {
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const libHelper = await getMonomerLibHelper();
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const monomerLib = libHelper.getBioLib();
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const scoringMatrix = new Array(monomerSet.length).fill(0).map(() => new Array(monomerSet.length).fill(0));
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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 fingerprintsFunc = DG.Func.find({ package: 'Chem', name: 'getFingerprints' })[0];
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if (!fingerprintsFunc) {
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console.warn('Function "Chem:getFingerprints" is not found in chem package. falling back to Morgan fingerprints');
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return await calculateMonomerSimilarity(monomerSet);
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}
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const monomerMoleculesCol = DG.Column.fromStrings('smiles', monomerMolecules);
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// needed for function to work
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const _unusedMolDf = DG.DataFrame.fromColumns([monomerMoleculesCol]);
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const fingerPrints = (await fingerprintsFunc.apply({ col: monomerMoleculesCol, fingerprintType: fingerprintType }))?.entries;
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if (!fingerPrints) {
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console.warn(`${fingerprintType} Fingerprints could not be calculated for monomers from chem package.
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falling back to Morgan fingerprints`);
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return await calculateMonomerSimilarity(monomerSet);
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}
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for (let i = 0; i < fingerPrints.length; ++i) {
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scoringMatrix[i][i] = 1;
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alphabetIndexes[monomerSet[i]] = i;
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if (!fingerPrints[i])
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continue;
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for (let j = i + 1; j < fingerPrints.length; ++j) {
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if (!fingerPrints[j])
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continue;
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scoringMatrix[i][j] = scoringMatrix[j][i] = tanimotoSimilarity(fingerPrints[i], fingerPrints[j]);
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}
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}
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return { scoringMatrix, alphabetIndexes };
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}
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;
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//# sourceMappingURL=monomer-utils.js.map
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@@ -1 +1 @@
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1
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-
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