nmr-processing 9.3.0-pre.1669214453 → 9.3.1-pre.1669649322
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/lib/assignment/get13CAssignments.d.ts +1 -1
- package/lib/assignment/get1HAssignments.d.ts +1 -1
- package/lib/assignment/getAssignments.d.ts +1 -1
- package/lib/assignment/utils/getAssignment/buildAssignments.d.ts +1 -1
- package/lib/prediction/Prediction1D.d.ts +1 -1
- package/lib/prediction/predictAll.d.ts +1 -1
- package/lib/prediction/predictAll.js +4 -1
- package/lib/prediction/predictAll.js.map +1 -1
- package/lib/prediction/predictAllSpectra.d.ts +1 -1
- package/lib/prediction/predictCOSY.d.ts +1 -1
- package/lib/prediction/predictCarbon.d.ts +5 -1
- package/lib/prediction/predictCarbon.js +5 -4
- package/lib/prediction/predictCarbon.js.map +1 -1
- package/lib/prediction/predictHMBC.d.ts +1 -1
- package/lib/prediction/predictHSQC.d.ts +1 -1
- package/lib/prediction/predictProton.d.ts +5 -1
- package/lib/prediction/predictProton.js +1 -1
- package/lib/prediction/predictProton.js.map +1 -1
- package/lib/prediction/utils/fetchPrediction.d.ts +1 -1
- package/lib/prediction/utils/getFilteredIDiaIDs.d.ts +2 -3
- package/lib/prediction/utils/getFilteredIDiaIDs.js +5 -6
- package/lib/prediction/utils/getFilteredIDiaIDs.js.map +1 -1
- package/lib/prediction/utils/getPredictions.d.ts +1 -1
- package/lib/prediction/utils/predict2D.d.ts +5 -1
- package/lib/prediction/utils/predict2D.js +3 -3
- package/lib/prediction/utils/predict2D.js.map +1 -1
- package/lib-esm/prediction/predictAll.js +4 -1
- package/lib-esm/prediction/predictAll.js.map +1 -1
- package/lib-esm/prediction/predictCarbon.js +5 -4
- package/lib-esm/prediction/predictCarbon.js.map +1 -1
- package/lib-esm/prediction/predictProton.js +1 -1
- package/lib-esm/prediction/predictProton.js.map +1 -1
- package/lib-esm/prediction/utils/getFilteredIDiaIDs.js +6 -7
- package/lib-esm/prediction/utils/getFilteredIDiaIDs.js.map +1 -1
- package/lib-esm/prediction/utils/predict2D.js +4 -4
- package/lib-esm/prediction/utils/predict2D.js.map +1 -1
- package/package.json +2 -2
- package/src/assignment/get13CAssignments.ts +1 -1
- package/src/assignment/get1HAssignments.ts +1 -1
- package/src/assignment/getAssignments.ts +1 -1
- package/src/assignment/utils/getAssignment/buildAssignments.ts +1 -1
- package/src/openchemlib-utils.d.ts +6 -1
- package/src/prediction/Prediction1D.ts +1 -1
- package/src/prediction/predictAll.ts +5 -3
- package/src/prediction/predictAllSpectra.ts +1 -1
- package/src/prediction/predictCOSY.ts +1 -1
- package/src/prediction/predictCarbon.ts +17 -9
- package/src/prediction/predictHMBC.ts +1 -1
- package/src/prediction/predictHSQC.ts +1 -1
- package/src/prediction/predictProton.ts +6 -2
- package/src/prediction/utils/fetchPrediction.ts +1 -1
- package/src/prediction/utils/getFilteredIDiaIDs.ts +13 -13
- package/src/prediction/utils/getPredictions.ts +1 -1
- package/src/prediction/utils/predict2D.ts +12 -6
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@@ -1,4 +1,4 @@
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-
import { Molecule } from 'openchemlib';
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import { Molecule } from 'openchemlib/full';
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import { NMRSignal1D } from '..';
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import type { PredictCarbonOptions } from '../prediction/predictCarbon';
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import type { PredictProtonOptions } from '../prediction/predictProton';
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@@ -1,5 +1,5 @@
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import { Values } from 'nmr-correlation';
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import { Molecule } from 'openchemlib';
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import { Molecule } from 'openchemlib/full';
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import { NMRSignal1D, PredictCarbonOptions, PredictProtonOptions } from '../../..';
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import { MakeMandatory } from '../../../utilities/MakeMandatory';
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import { SpectraDataWithIds } from '../../nmrAssigment';
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@@ -1,6 +1,7 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.predictAll = void 0;
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const openchemlib_utils_1 = require("openchemlib-utils");
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const predictCOSY_1 = require("./predictCOSY");
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const predictCarbon_1 = require("./predictCarbon");
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const predictHMBC_1 = require("./predictHMBC");
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@@ -13,6 +14,8 @@ const getPredictions_1 = require("./utils/getPredictions");
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*/
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async function predictAll(molecule, options = {}) {
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let { from = 'H', to = 'C', predictor = { H: predictProton_1.predictProton, C: predictCarbon_1.predictCarbon }, predictions, joinDistance = { H: 0.05, C: 0.5 }, predictOptions = {}, } = options;
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const diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule);
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console.log('entra correction');
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const xPrediction = await (0, getPredictions_1.getPredictions)(from, molecule, predictOptions, predictor, predictions);
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const yPrediction = await (0, getPredictions_1.getPredictions)(to, molecule, predictOptions, predictor, predictions);
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if (!xPrediction || !yPrediction) {
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@@ -22,7 +25,7 @@ async function predictAll(molecule, options = {}) {
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H: xPrediction,
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C: yPrediction,
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};
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const { molfile
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const { molfile } = xPrediction;
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const spectra = {
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proton: predictions.H,
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carbon: predictions.C,
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@@ -1 +1 @@
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{"version":3,"file":"predictAll.js","sourceRoot":"","sources":["../../src/prediction/predictAll.ts"],"names":[],"mappings":";;;
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{"version":3,"file":"predictAll.js","sourceRoot":"","sources":["../../src/prediction/predictAll.ts"],"names":[],"mappings":";;;AACA,yDAA8F;AAE9F,+CAA4C;AAC5C,mDAAsE;AACtE,+CAA4C;AAC5C,+CAA4C;AAC5C,mDAAsE;AACtE,2DAAwD;AAmDxD;;;GAGG;AAEI,KAAK,UAAU,UAAU,CAC9B,QAAkB,EAClB,UAA6B,EAAE;IAE/B,IAAI,EACF,IAAI,GAAG,GAAG,EACV,EAAE,GAAG,GAAG,EACR,SAAS,GAAG,EAAE,CAAC,EAAE,6BAAa,EAAE,CAAC,EAAE,6BAAa,EAAE,EAClD,WAAW,EACX,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,cAAc,GAAG,EAAE,GACpB,GAAG,OAAO,CAAC;IAEZ,MAAM,MAAM,GAAG,IAAA,4CAAwB,EAAC,QAAQ,CAAC,CAAC;IAClD,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAC,CAAA;IAC/B,MAAM,WAAW,GAAG,MAAM,IAAA,+BAAc,EACtC,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,MAAM,WAAW,GAAG,MAAM,IAAA,+BAAc,EACtC,EAAE,EACF,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;KACnD;IAED,WAAW,GAAG;QACZ,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;KACf,CAAC;IAEF,MAAM,EAAE,OAAO,EAAE,GAAG,WAAW,CAAC;IAEhC,MAAM,OAAO,GAAQ;QACnB,MAAM,EAAE,WAAW,CAAC,CAAC;QACrB,MAAM,EAAE,WAAW,CAAC,CAAC;KACtB,CAAC;IAEF,OAAO,CAAC,IAAI,GAAG,MAAM,IAAA,yBAAW,EAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IACH,OAAO,CAAC,IAAI,GAAG,MAAM,IAAA,yBAAW,EAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IACH,OAAO,CAAC,IAAI,GAAG,MAAM,IAAA,yBAAW,EAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IAEH,KAAK,MAAM,GAAG,IAAI,OAAO,EAAE;QACzB,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC;QAC5B,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC;KAC5B;IAED,OAAO;QACL,OAAO;QACP,MAAM;QACN,GAAG,OAAO;KACX,CAAC;AACJ,CAAC;AAtED,gCAsEC"}
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import { FromTo, PointXY } from 'cheminfo-types';
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import type { Molecule } from 'openchemlib';
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import type { Molecule } from 'openchemlib/full';
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import { PredictAllOptions } from './predictAll';
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/**
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* This function will generate an object compatible with NMR-ium
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/// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
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import { Molecule } from 'openchemlib';
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import { Molecule } from 'openchemlib/full';
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import type { Prediction1D } from './Prediction1D';
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import { PredictProtonOptions } from './predictProton';
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import { Predictor } from './utils/predict2D';
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import type { Molecule } from 'openchemlib';
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import type { Molecule } from 'openchemlib/full';
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import type { Prediction1D } from './Prediction1D';
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import type { DataBaseStructure } from './dataStructure';
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export interface PredictCarbonOptions {
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* @default 'maximum level in the database'
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*/
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maxSphereSize?: number;
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/**
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* diastereotopic atom ids.
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*/
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diaIDs?: string[];
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}
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export type PredictCarbon = typeof predictCarbon;
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/**
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const setIDs_1 = require("../peaks/util/setIDs");
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const signalsToRanges_1 = require("../signals/signalsToRanges");
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const fetchPrediction_1 = require("./utils/fetchPrediction");
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const flatGroupedDiaIDs_1 = require("./utils/flatGroupedDiaIDs");
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const getFilteredIDiaIDs_1 = require("./utils/getFilteredIDiaIDs");
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const queryByHOSE_1 = require("./utils/queryByHOSE");
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const openchemlib_utils_1 = require("openchemlib-utils");
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const cache = {};
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async function loadDB(url = 'https://www.lactame.com/lib/nmr-processing-data/20210711/carbon.js') {
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if (cache[url]) {
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* @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
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*/
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async function predictCarbon(molecule, options = {}) {
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let { url, database, webserviceURL } = options;
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let { url, database, webserviceURL, diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule), } = options;
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if (webserviceURL) {
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return (0, fetchPrediction_1.fetchPrediction)(molecule, { webserviceURL });
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}
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if (maxSphereSize > maxLevel)
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maxSphereSize = maxLevel;
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const {
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const { carbonDiaIDs, molfile } = (0, getFilteredIDiaIDs_1.getFilteredIDiaIDs)(molecule, {
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});
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let predictions = (0, queryByHOSE_1.queryByHose)(carbonDiaIDs, database, {
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return {
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nucleus: '13C',
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ranges: (0, signalsToRanges_1.signalsToRanges)(joinedSignals),
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{"version":3,"file":"predictCarbon.js","sourceRoot":"","sources":["../../src/prediction/predictCarbon.ts"],"names":[],"mappings":";;;;;;AAAA,uCAAgD;AAChD,8DAAgC;AAGhC,iDAA8C;AAE9C,gEAA6D;AAK7D,6DAA0D;
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{"version":3,"file":"predictCarbon.js","sourceRoot":"","sources":["../../src/prediction/predictCarbon.ts"],"names":[],"mappings":";;;;;;AAAA,uCAAgD;AAChD,8DAAgC;AAGhC,iDAA8C;AAE9C,gEAA6D;AAK7D,6DAA0D;AAE1D,mEAAgE;AAChE,qDAA8D;AAC9D,yDAA6D;AAE7D,MAAM,KAAK,GAAyC,EAAE,CAAC;AAEvD,KAAK,UAAU,MAAM,CACnB,GAAG,GAAG,oEAAoE;IAE1E,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE;QACd,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;KACnB;IACD,MAAM,QAAQ,GAAG,MAAM,IAAA,qBAAK,EAAC,GAAG,CAAC,CAAC;IAClC,MAAM,QAAQ,GAAsB,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;IAC1D,KAAK,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAC;IACtB,OAAO,QAAQ,CAAC;AAClB,CAAC;AAkCD,SAAS,mBAAmB,CAC1B,MAAmB;IAEnB,IAAI,CAAC,MAAM,CAAC,KAAK;QAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;IACzD,IAAI,CAAC,MAAM,CAAC,MAAM;QAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;IAC3D,IAAI,CAAC,MAAM,CAAC,OAAO;QAAE,MAAM,IAAI,KAAK,CAAC,sBAAsB,CAAC,CAAC;AAC/D,CAAC;AACD;;;GAGG;AAEI,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,IAAI,EACF,GAAG,EACH,QAAQ,EACR,aAAa,EACb,MAAM,GAAG,IAAA,4CAAwB,EAAC,QAAQ,CAAC,GAC5C,GAAG,OAAO,CAAC;IAEZ,IAAI,aAAa,EAAE;QACjB,OAAO,IAAA,iCAAe,EAAC,QAAQ,EAAE,EAAE,aAAa,EAAE,CAAC,CAAC;KACrD;IAED,IAAI,CAAC,QAAQ;QAAE,QAAQ,GAAG,MAAM,MAAM,CAAC,GAAG,CAAC,CAAC;IAE5C,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;KAC5C;IAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC;IAErC,IAAI,EAAE,aAAa,GAAG,QAAQ,EAAE,GAAG,OAAO,CAAC;IAE3C,IAAI,aAAa,GAAG,QAAQ;QAAE,aAAa,GAAG,QAAQ,CAAC;IAEvD,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,IAAA,uCAAkB,EAAC,QAAQ,EAAE;QAC7D,aAAa;QACb,MAAM;KACP,CAAC,CAAC;IAEH,IAAI,WAAW,GAAG,IAAA,yBAAW,EAAC,YAAY,EAAE,QAAQ,EAAE;QACpD,aAAa;KACd,CAAC,CAAC;IAEH,MAAM,OAAO,GAAG,aAAa,CAAC,WAAW,CAAC,CAAC;IAC3C,MAAM,aAAa,GAAG,iBAAiB,CAAC,OAAO,CAAC,CAAC;IACjD,OAAO;QACL,OAAO;QACP,OAAO,EAAE,KAAK;QACd,MAAM;QACN,aAAa;QACb,OAAO;QACP,MAAM,EAAE,IAAA,iCAAe,EAAC,aAAa,CAAC;QACtC,QAAQ;KACT,CAAC;AACJ,CAAC;AA/CD,sCA+CC;AAED,SAAS,aAAa,CAAC,WAAyB;IAC9C,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE;QACpC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,UAAU,CAAC;QAChE,MAAM,MAAM,GAAG;YACb,EAAE,EAAE,IAAA,SAAU,GAAE;YAChB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,KAAK;YACL,MAAM;YACN,YAAY,EAAE,GAAG;YACjB,OAAO;YACP,SAAS;YACT,EAAE,EAAE,EAAE;SACP,CAAC;QACF,OAAO,CAAC,IAAI,CAAC,MAAqB,CAAC,CAAC;KACrC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,iBAAiB,CAAC,OAAsB;IAC/C,IAAI,aAAa,GAA8C,EAAE,CAAC;IAClE,KAAK,IAAI,MAAM,IAAI,OAAO,EAAE;QAC1B,mBAAmB,CAAC,MAAM,CAAC,CAAC;QAC5B,IAAI,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QAC7B,IAAI,CAAC,aAAa,CAAC,KAAK,CAAC,EAAE;YACzB,aAAa,CAAC,KAAK,CAAC,GAAG,IAAI,CAAC,KAAK,CAC/B,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CACG,CAAC;SAC7B;aAAM;YACL,aAAa,CAAC,KAAK,CAAC,CAAC,OAAO,IAAI,MAAM,CAAC,OAAO,CAAC;YAC/C,aAAa,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;SAClD;KACF;IACD,OAAO,IAAA,eAAM,EAAC,MAAM,CAAC,MAAM,CAAC,aAAa,CAAC,CAAC,CAAC;AAC9C,CAAC"}
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import { Molecule } from 'openchemlib/full';
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import type { PredictCarbonOptions } from './predictCarbon';
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1
|
-
import type { Molecule } from 'openchemlib';
|
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1
|
+
import type { Molecule } from 'openchemlib/full';
|
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2
2
|
import type { Prediction1D } from './Prediction1D';
|
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3
3
|
/**
|
|
4
4
|
* Makes a prediction using proton.
|
|
@@ -9,6 +9,10 @@ export interface PredictProtonOptions {
|
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|
9
9
|
* A callback receiving a molfile and the result
|
|
10
10
|
*/
|
|
11
11
|
cache?: (molfile: string, result?: string) => void | string | undefined;
|
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12
|
+
/**
|
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13
|
+
* diastereotopic atom ids.
|
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14
|
+
*/
|
|
15
|
+
diaIDs?: string[];
|
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12
16
|
}
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13
17
|
export type PredictProton = typeof predictProton;
|
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14
18
|
export declare function predictProton(molecule: Molecule, options?: PredictProtonOptions): Promise<Prediction1D>;
|
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@@ -33,7 +33,7 @@ async function predictProton(molecule, options = {}) {
|
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33
33
|
cache(molfile, result);
|
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34
34
|
}
|
|
35
35
|
}
|
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36
|
-
const diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule);
|
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36
|
+
const { diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule) } = options;
|
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37
37
|
const signals = protonParser(result, molecule, diaIDs);
|
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38
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|
const joinedSignals = (0, signalsJoin_1.signalsJoin)(signals);
|
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|
return {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":";;;;;;AAAA,uCAAgD;AAChD,8DAAgC;AAChC,0DAAiC;AAEjC,yDAI2B;AAG3B,wDAAqD;AACrD,gEAA6D;
|
|
1
|
+
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":";;;;;;AAAA,uCAAgD;AAChD,8DAAgC;AAChC,0DAAiC;AAEjC,yDAI2B;AAG3B,wDAAqD;AACrD,gEAA6D;AAsBtD,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAC1B,QAAQ,GAAG,QAAQ,CAAC,cAAc,EAAE,CAAC;IACrC,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,mBAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACpC,MAAM,QAAQ,GAAG,MAAM,IAAA,qBAAK,EAAC,yCAAyC,EAAE;YACtE,MAAM,EAAE,MAAM;YACd,+DAA+D;YAC/D,IAAI,EAAE,QAAQ;SACf,CAAC,CAAC;QACH,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,IAAI,KAAK,EAAE;YACT,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;SACxB;KACF;IAED,MAAM,EAAE,MAAM,GAAG,IAAA,4CAAwB,EAAC,QAAQ,CAAC,EAAE,GAAG,OAAO,CAAC;IAChE,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;IACvD,MAAM,aAAa,GAAG,IAAA,yBAAW,EAAC,OAAO,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO;QACP,MAAM;QACN,OAAO,EAAE,IAAI;QACb,aAAa;QACb,OAAO;QACP,MAAM,EAAE,IAAA,iCAAe,EAAC,aAAa,CAAC;QACtC,QAAQ;KACT,CAAC;AACJ,CAAC;AAxCD,sCAwCC;AAED,SAAS,YAAY,CACnB,MAAc,EACd,QAAkB,EAClB,MAAgB;IAEhB,IAAI,QAAQ,CAAC,WAAW,EAAE,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAC5C,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE;QAC1B,MAAM,KAAK,CAAC,wBAAwB,MAAM,EAAE,CAAC,CAAC;KAC/C;IACD,IAAI,cAAc,GAAG,IAAA,yCAAqB,EAAC,QAAQ,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC;IAC3E,IAAI,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC;IACtD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,IAAI,IAAI,IAAI,KAAK,EAAE;QACtB,IAAI,MAAM,GAAa,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACxC,IAAI,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAChC,IAAI,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QACjC,IAAI,MAAM,GAAgB;YACxB,EAAE,EAAE,IAAA,SAAU,GAAE;YAChB,KAAK,EAAE,CAAC,IAAI,CAAC;YACb,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;YACtB,OAAO,EAAE,CAAC;YACV,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACxB,EAAE,EAAE,EAAE;SACP,CAAC;QAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;YACd,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;SACvD;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,IAAI,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACtC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;gBACb,QAAQ,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gBAClC,KAAK,EAAE,CAAC,MAAM,CAAC;gBACf,MAAM,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,YAAY,EAAE,GAAG;gBACjB,UAAU,EAAE,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC;aACzC,CAAC,CAAC;YACH,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC;SACnD;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -1,5 +1,4 @@
|
|
|
1
|
-
|
|
2
|
-
import type { Molecule } from 'openchemlib';
|
|
1
|
+
import type { Molecule } from 'openchemlib/full';
|
|
3
2
|
import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
4
3
|
export interface GroupDiaIDsWithHose extends GroupDiastereotopicAtomIDs {
|
|
5
4
|
hose: string[];
|
|
@@ -7,8 +6,8 @@ export interface GroupDiaIDsWithHose extends GroupDiastereotopicAtomIDs {
|
|
|
7
6
|
export type GroupedDiaIDsWithHose = GroupDiaIDsWithHose[];
|
|
8
7
|
export declare function getFilteredIDiaIDs(molecule: Molecule, options: {
|
|
9
8
|
maxSphereSize: number;
|
|
9
|
+
diaIDs: string[];
|
|
10
10
|
}): {
|
|
11
11
|
molfile: string;
|
|
12
12
|
carbonDiaIDs: GroupedDiaIDsWithHose;
|
|
13
|
-
groupedDiaIDs: import("openchemlib-utils").GroupedDiastereotopicAtomIDs;
|
|
14
13
|
};
|
|
@@ -3,15 +3,15 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
3
3
|
exports.getFilteredIDiaIDs = void 0;
|
|
4
4
|
const openchemlib_utils_1 = require("openchemlib-utils");
|
|
5
5
|
function getFilteredIDiaIDs(molecule, options) {
|
|
6
|
-
const { maxSphereSize } = options;
|
|
6
|
+
const { maxSphereSize, diaIDs } = options;
|
|
7
7
|
molecule.addImplicitHydrogens();
|
|
8
8
|
molecule.addMissingChirality();
|
|
9
9
|
(0, openchemlib_utils_1.addDiastereotopicMissingChirality)(molecule);
|
|
10
10
|
const molfile = molecule.toMolfile();
|
|
11
|
-
let groupedDiaIDs = (0, openchemlib_utils_1.
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
11
|
+
let groupedDiaIDs = (0, openchemlib_utils_1.groupDiasterotopicAtomIDs)(diaIDs, molecule, {
|
|
12
|
+
atomLabel: 'C',
|
|
13
|
+
});
|
|
14
|
+
let carbonDiaIDs = groupedDiaIDs.sort((a, b) => {
|
|
15
15
|
if (a.atomLabel === b.atomLabel) {
|
|
16
16
|
return b.counter - a.counter;
|
|
17
17
|
}
|
|
@@ -26,7 +26,6 @@ function getFilteredIDiaIDs(molecule, options) {
|
|
|
26
26
|
let toReturn = {
|
|
27
27
|
molfile,
|
|
28
28
|
carbonDiaIDs: carbonDiaIDs,
|
|
29
|
-
groupedDiaIDs,
|
|
30
29
|
};
|
|
31
30
|
return toReturn;
|
|
32
31
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getFilteredIDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/getFilteredIDiaIDs.ts"],"names":[],"mappings":";;;AACA,
|
|
1
|
+
{"version":3,"file":"getFilteredIDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/getFilteredIDiaIDs.ts"],"names":[],"mappings":";;;AACA,yDAK2B;AAS3B,SAAgB,kBAAkB,CAChC,QAAkB,EAClB,OAAoD;IAEpD,MAAM,EAAE,aAAa,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC;IAE1C,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,QAAQ,CAAC,mBAAmB,EAAE,CAAC;IAC/B,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,aAAa,GAAG,IAAA,6CAAyB,EAAC,MAAM,EAAE,QAAQ,EAAE;QAC9D,SAAS,EAAE,GAAG;KACf,CAAC,CAAC;IAEH,IAAI,YAAY,GAAG,aAAa,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QAC7C,IAAI,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS,EAAE;YAC/B,OAAO,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAAC;SAC9B;QACD,OAAO,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC5C,CAAC,CAAQ,CAAC;IAEV,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC;IAC9B,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE;QAChC,KAAK,CAAC,IAAI,GAAG,IAAA,oDAAgC,EAC3C,GAAG,CAAC,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,KAAK,CAAC,EACpC;YACE,aAAa;SACd,CACF,CAAC;KACH;IAED,IAAI,QAAQ,GAAG;QACb,OAAO;QACP,YAAY,EAAE,YAAqC;KACpD,CAAC;IAEF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAvCD,gDAuCC"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import type { Molecule } from 'openchemlib';
|
|
1
|
+
import type { Molecule } from 'openchemlib/full';
|
|
2
2
|
import type { Prediction1D } from '../Prediction1D';
|
|
3
3
|
import type { Predictions, PredictOptions, Predictors } from './predict2D';
|
|
4
4
|
export declare function getPredictions(key: string, molecule: Molecule, predictOptions: PredictOptions, predictor?: Predictors, predictions?: Predictions): Promise<Prediction1D | undefined>;
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
/// <reference path="../../../src/ml-matrix-peaks-finder.d.ts" />
|
|
2
|
-
import { Molecule } from 'openchemlib';
|
|
2
|
+
import { Molecule } from 'openchemlib/full';
|
|
3
3
|
import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
|
|
4
4
|
import type { Prediction1D } from '../Prediction1D';
|
|
5
5
|
import type { PredictCarbon, PredictCarbonOptions } from '../predictCarbon';
|
|
@@ -63,6 +63,10 @@ export interface Predict2DOptions {
|
|
|
63
63
|
* @default false
|
|
64
64
|
*/
|
|
65
65
|
includeDiagonal?: boolean;
|
|
66
|
+
/**
|
|
67
|
+
* diastereotopic atom ids of the molecule.
|
|
68
|
+
*/
|
|
69
|
+
diaIDs?: string[];
|
|
66
70
|
}
|
|
67
71
|
export interface PredictOptions {
|
|
68
72
|
[key: string]: PredictProtonOptions | PredictCarbonOptions | undefined;
|
|
@@ -15,17 +15,17 @@ function checkFromTo(options) {
|
|
|
15
15
|
}
|
|
16
16
|
async function predict2D(molecule, options = {}) {
|
|
17
17
|
checkFromTo(options);
|
|
18
|
-
let { from, to, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
|
|
19
18
|
molecule.addImplicitHydrogens();
|
|
20
|
-
let diaIDs =
|
|
19
|
+
let { from, to, diaIDs, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
|
|
21
20
|
const pathsInfo = (0, openchemlib_utils_1.getPathsInfo)(molecule, {
|
|
22
21
|
fromLabel: from,
|
|
23
22
|
toLabel: to,
|
|
24
23
|
minLength,
|
|
25
24
|
maxLength,
|
|
26
25
|
});
|
|
26
|
+
const groupedDiaIDS = diaIDs ? (0, openchemlib_utils_1.groupDiasterotopicAtomIDs)(diaIDs, molecule) : (0, openchemlib_utils_1.getGroupedDiastereotopicAtomIDs)(molecule);
|
|
27
27
|
let diaIDswithAtomInfo = [];
|
|
28
|
-
for (let diaID of
|
|
28
|
+
for (let diaID of groupedDiaIDS) {
|
|
29
29
|
diaIDswithAtomInfo.push({
|
|
30
30
|
...diaID,
|
|
31
31
|
pathInfo: JSON.parse(JSON.stringify(pathsInfo[diaID.atoms[0]])),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":";;;AAAA,uCAAgD;AAChD,yCAA2C;AAC3C,yCAAmC;AAEnC,
|
|
1
|
+
{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":";;;AAAA,uCAAgD;AAChD,yCAA2C;AAC3C,yCAAmC;AAEnC,yDAI2B;AAO3B,oDAAiD;AAQjD,2CAAwC;AACxC,qDAAkD;AA0FlD,SAAS,WAAW,CAClB,OAAyB;IAEzB,IAAI,CAAC,OAAO,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;KACtD;AACH,CAAC;AAMM,KAAK,UAAU,SAAS,CAC7B,QAAkB,EAClB,UAA4B,EAAE;IAE9B,WAAW,CAAC,OAAO,CAAC,CAAC;IAErB,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAEhC,IAAI,EACF,IAAI,EACJ,EAAE,EACF,MAAM,EACN,SAAS,GAAG,CAAC,EACb,SAAS,EACT,cAAc,GAAG,EAAE,EACnB,WAAW,EACX,SAAS,EACT,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,eAAe,GAAG,KAAK,GACxB,GAAG,OAAO,CAAC;IAEZ,MAAM,SAAS,GAAG,IAAA,gCAAY,EAAC,QAAQ,EAAE;QACvC,SAAS,EAAE,IAAI;QACf,OAAO,EAAE,EAAE;QACX,SAAS;QACT,SAAS;KACV,CAAC,CAAC;IAEH,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,CAAC,IAAA,6CAAyB,EAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,IAAA,mDAA+B,EAAC,QAAQ,CAAC,CAAA;IAEtH,IAAI,kBAAkB,GAA6C,EAAE,CAAC;IACtE,KAAK,IAAI,KAAK,IAAI,aAAa,EAAE;QAC/B,kBAAkB,CAAC,IAAI,CAAC;YACtB,GAAG,KAAK;YACR,QAAQ,EAAE,IAAI,CAAC,KAAK,CAClB,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAC9B;SACd,CAAC,CAAC;KACJ;IAED,MAAM,WAAW,GAAG,MAAM,IAAA,+BAAc,EACtC,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,MAAM,WAAW,GACf,IAAI,KAAK,EAAE;QACT,CAAC,CAAC,WAAW;QACb,CAAC,CAAC,MAAM,IAAA,+BAAc,EAClB,EAAE,EACF,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAER,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;KACnD;IAED,MAAM,OAAO,GAAoC;QAC/C,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;KACf,CAAC;IAEF,MAAM,cAAc,GAAoB;QACtC,CAAC,EAAE,EAAE;QACL,CAAC,EAAE,EAAE;KACN,CAAC;IACF,KAAK,MAAM,IAAI,IAAI,cAAc,EAAE;QACjC,KAAK,MAAM,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,aAAa,EAAE;YAChD,IAAI,CAAC,MAAM,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;YAC7D,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC;SACjD;KACF;IACD,IAAI,KAAK,GAAmC,EAAE,CAAC;IAC/C,KAAK,MAAM,KAAK,IAAI,kBAAkB,EAAE;QACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;QAChC,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAExC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC;YAAE,SAAS;QAEhD,MAAM,YAAY,GAAG,QAAQ,CAAC,KAAK,CAAC;QACpC,KAAK,MAAM,IAAI,IAAI,YAAY,EAAE;YAC/B,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC;gBAAE,SAAS;YAE1D,IAAI,WAAW,GAAgC;gBAC7C,CAAC,EAAE,QAAQ;gBACX,CAAC,EAAE,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;aACtB,CAAC;YAEF,MAAM,GAAG,GAAG,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,IAAI,WAAW,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC;YAE5D,IAAI,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,IAAI,QAAQ,CAAC,KAAK,EAAE,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE;gBAC/D,SAAS;aACV;YAED,IAAI,IAAI,GAAQ,EAAE,EAAE,EAAE,IAAA,SAAU,GAAE,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC;YAC7C,IAAI,MAAM,GAAQ,EAAE,EAAE,EAAE,IAAA,SAAU,GAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;YACrD,KAAK,IAAI,IAAI,IAAI,WAAW,EAAE;gBAC5B,IAAI,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC;gBACpC,IAAI,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;gBAC/C,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;gBACvD,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;aACxD;YAED,MAAM,CAAC,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC;YACtB,KAAK,CAAC,GAAG,CAAC,GAAG,MAAqB,CAAC;SACpC;KACF;IAED,IAAI,eAAe,EAAE;QACnB,mBAAmB,CAAC,KAAK,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,cAAc,EAAE,CAAC,CAAC;KAClE;IAED,iCAAiC;IACjC,MAAM,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;IAC3C,MAAM,KAAK,GAAG,WAAW,CAAC,aAAa,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC;IAErE,OAAO;QACL,OAAO,EAAE,QAAQ,CAAC,SAAS,EAAE;QAC7B,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,MAAM;QACxB,MAAM,EAAE,IAAA,qBAAS,EAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC;QAC/B,aAAa;QACb,OAAO,EAAE,YAAY,CAAC,aAAa,CAAC;QACpC,KAAK;QACL,QAAQ;KACT,CAAC;AACJ,CAAC;AApID,8BAoIC;AAED,SAAS,YAAY,CAAC,aAA4B;IAChD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,MAAM,MAAM,IAAI,aAAa,EAAE;QAClC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;YACxC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;gBACxC,IAAI,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;gBACnD,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;aACzB;SACF;KACF;IACD,OAAO,IAAA,eAAM,EAAC,OAAO,CAAC,CAAC;AACzB,CAAC;AAMD,SAAS,mBAAmB,CAC1B,KAAqC,EACrC,OAAmC;IAEnC,MAAM,EAAE,KAAK,GAAG,EAAE,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAC/C,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAEpC,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC;QACvB,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,CAAC;YAAE,SAAS;QACvC,IAAI,KAAK,CAAC,GAAG,KAAK,IAAI,KAAK,EAAE,CAAC;YAAE,SAAS;QAEzC,IAAI,MAAM,GAAQ,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;QAEnC,IAAI,IAAI,GAAQ,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC;QACzB,KAAK,IAAI,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE;YAC3B,IAAI,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;YAC/C,MAAM,CAAC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|
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
1
2
|
import { predictCOSY } from './predictCOSY';
|
|
2
3
|
import { predictCarbon } from './predictCarbon';
|
|
3
4
|
import { predictHMBC } from './predictHMBC';
|
|
@@ -10,6 +11,8 @@ import { getPredictions } from './utils/getPredictions';
|
|
|
10
11
|
*/
|
|
11
12
|
export async function predictAll(molecule, options = {}) {
|
|
12
13
|
let { from = 'H', to = 'C', predictor = { H: predictProton, C: predictCarbon }, predictions, joinDistance = { H: 0.05, C: 0.5 }, predictOptions = {}, } = options;
|
|
14
|
+
const diaIDs = getDiastereotopicAtomIDs(molecule);
|
|
15
|
+
console.log('entra correction');
|
|
13
16
|
const xPrediction = await getPredictions(from, molecule, predictOptions, predictor, predictions);
|
|
14
17
|
const yPrediction = await getPredictions(to, molecule, predictOptions, predictor, predictions);
|
|
15
18
|
if (!xPrediction || !yPrediction) {
|
|
@@ -19,7 +22,7 @@ export async function predictAll(molecule, options = {}) {
|
|
|
19
22
|
H: xPrediction,
|
|
20
23
|
C: yPrediction,
|
|
21
24
|
};
|
|
22
|
-
const { molfile
|
|
25
|
+
const { molfile } = xPrediction;
|
|
23
26
|
const spectra = {
|
|
24
27
|
proton: predictions.H,
|
|
25
28
|
carbon: predictions.C,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictAll.js","sourceRoot":"","sources":["../../src/prediction/predictAll.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"predictAll.js","sourceRoot":"","sources":["../../src/prediction/predictAll.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,wBAAwB,EAAmC,MAAM,mBAAmB,CAAC;AAE9F,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,aAAa,EAAwB,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,aAAa,EAAwB,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AAmDxD;;;GAGG;AAEH,MAAM,CAAC,KAAK,UAAU,UAAU,CAC9B,QAAkB,EAClB,UAA6B,EAAE;IAE/B,IAAI,EACF,IAAI,GAAG,GAAG,EACV,EAAE,GAAG,GAAG,EACR,SAAS,GAAG,EAAE,CAAC,EAAE,aAAa,EAAE,CAAC,EAAE,aAAa,EAAE,EAClD,WAAW,EACX,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,cAAc,GAAG,EAAE,GACpB,GAAG,OAAO,CAAC;IAEZ,MAAM,MAAM,GAAG,wBAAwB,CAAC,QAAQ,CAAC,CAAC;IAClD,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAC,CAAA;IAC/B,MAAM,WAAW,GAAG,MAAM,cAAc,CACtC,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,MAAM,WAAW,GAAG,MAAM,cAAc,CACtC,EAAE,EACF,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;KACnD;IAED,WAAW,GAAG;QACZ,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;KACf,CAAC;IAEF,MAAM,EAAE,OAAO,EAAE,GAAG,WAAW,CAAC;IAEhC,MAAM,OAAO,GAAQ;QACnB,MAAM,EAAE,WAAW,CAAC,CAAC;QACrB,MAAM,EAAE,WAAW,CAAC,CAAC;KACtB,CAAC;IAEF,OAAO,CAAC,IAAI,GAAG,MAAM,WAAW,CAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IACH,OAAO,CAAC,IAAI,GAAG,MAAM,WAAW,CAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IACH,OAAO,CAAC,IAAI,GAAG,MAAM,WAAW,CAAC,QAAQ,EAAE;QACzC,WAAW;QACX,YAAY;KACb,CAAC,CAAC;IAEH,KAAK,MAAM,GAAG,IAAI,OAAO,EAAE;QACzB,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC;QAC5B,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC;KAC5B;IAED,OAAO;QACL,OAAO;QACP,MAAM;QACN,GAAG,OAAO;KACX,CAAC;AACJ,CAAC"}
|
|
@@ -3,9 +3,9 @@ import fetch from 'cross-fetch';
|
|
|
3
3
|
import { setIDs } from '../peaks/util/setIDs';
|
|
4
4
|
import { signalsToRanges } from '../signals/signalsToRanges';
|
|
5
5
|
import { fetchPrediction } from './utils/fetchPrediction';
|
|
6
|
-
import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
|
|
7
6
|
import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';
|
|
8
7
|
import { queryByHose } from './utils/queryByHOSE';
|
|
8
|
+
import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
9
9
|
const cache = {};
|
|
10
10
|
async function loadDB(url = 'https://www.lactame.com/lib/nmr-processing-data/20210711/carbon.js') {
|
|
11
11
|
if (cache[url]) {
|
|
@@ -29,7 +29,7 @@ function checkFromPrediction(signal) {
|
|
|
29
29
|
* @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
|
|
30
30
|
*/
|
|
31
31
|
export async function predictCarbon(molecule, options = {}) {
|
|
32
|
-
let { url, database, webserviceURL } = options;
|
|
32
|
+
let { url, database, webserviceURL, diaIDs = getDiastereotopicAtomIDs(molecule), } = options;
|
|
33
33
|
if (webserviceURL) {
|
|
34
34
|
return fetchPrediction(molecule, { webserviceURL });
|
|
35
35
|
}
|
|
@@ -42,8 +42,9 @@ export async function predictCarbon(molecule, options = {}) {
|
|
|
42
42
|
let { maxSphereSize = maxLevel } = options;
|
|
43
43
|
if (maxSphereSize > maxLevel)
|
|
44
44
|
maxSphereSize = maxLevel;
|
|
45
|
-
const {
|
|
45
|
+
const { carbonDiaIDs, molfile } = getFilteredIDiaIDs(molecule, {
|
|
46
46
|
maxSphereSize,
|
|
47
|
+
diaIDs,
|
|
47
48
|
});
|
|
48
49
|
let predictions = queryByHose(carbonDiaIDs, database, {
|
|
49
50
|
maxSphereSize,
|
|
@@ -53,7 +54,7 @@ export async function predictCarbon(molecule, options = {}) {
|
|
|
53
54
|
return {
|
|
54
55
|
molfile,
|
|
55
56
|
nucleus: '13C',
|
|
56
|
-
diaIDs
|
|
57
|
+
diaIDs,
|
|
57
58
|
joinedSignals,
|
|
58
59
|
signals,
|
|
59
60
|
ranges: signalsToRanges(joinedSignals),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictCarbon.js","sourceRoot":"","sources":["../../src/prediction/predictCarbon.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAGhC,OAAO,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAK7D,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;
|
|
1
|
+
{"version":3,"file":"predictCarbon.js","sourceRoot":"","sources":["../../src/prediction/predictCarbon.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAGhC,OAAO,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAK7D,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAE1D,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAChE,OAAO,EAAc,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAC9D,OAAO,EAAE,wBAAwB,EAAE,MAAM,mBAAmB,CAAC;AAE7D,MAAM,KAAK,GAAyC,EAAE,CAAC;AAEvD,KAAK,UAAU,MAAM,CACnB,GAAG,GAAG,oEAAoE;IAE1E,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE;QACd,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;KACnB;IACD,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC;IAClC,MAAM,QAAQ,GAAsB,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;IAC1D,KAAK,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAC;IACtB,OAAO,QAAQ,CAAC;AAClB,CAAC;AAkCD,SAAS,mBAAmB,CAC1B,MAAmB;IAEnB,IAAI,CAAC,MAAM,CAAC,KAAK;QAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;IACzD,IAAI,CAAC,MAAM,CAAC,MAAM;QAAE,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;IAC3D,IAAI,CAAC,MAAM,CAAC,OAAO;QAAE,MAAM,IAAI,KAAK,CAAC,sBAAsB,CAAC,CAAC;AAC/D,CAAC;AACD;;;GAGG;AAEH,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,IAAI,EACF,GAAG,EACH,QAAQ,EACR,aAAa,EACb,MAAM,GAAG,wBAAwB,CAAC,QAAQ,CAAC,GAC5C,GAAG,OAAO,CAAC;IAEZ,IAAI,aAAa,EAAE;QACjB,OAAO,eAAe,CAAC,QAAQ,EAAE,EAAE,aAAa,EAAE,CAAC,CAAC;KACrD;IAED,IAAI,CAAC,QAAQ;QAAE,QAAQ,GAAG,MAAM,MAAM,CAAC,GAAG,CAAC,CAAC;IAE5C,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAC;KAC5C;IAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC;IAErC,IAAI,EAAE,aAAa,GAAG,QAAQ,EAAE,GAAG,OAAO,CAAC;IAE3C,IAAI,aAAa,GAAG,QAAQ;QAAE,aAAa,GAAG,QAAQ,CAAC;IAEvD,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,kBAAkB,CAAC,QAAQ,EAAE;QAC7D,aAAa;QACb,MAAM;KACP,CAAC,CAAC;IAEH,IAAI,WAAW,GAAG,WAAW,CAAC,YAAY,EAAE,QAAQ,EAAE;QACpD,aAAa;KACd,CAAC,CAAC;IAEH,MAAM,OAAO,GAAG,aAAa,CAAC,WAAW,CAAC,CAAC;IAC3C,MAAM,aAAa,GAAG,iBAAiB,CAAC,OAAO,CAAC,CAAC;IACjD,OAAO;QACL,OAAO;QACP,OAAO,EAAE,KAAK;QACd,MAAM;QACN,aAAa;QACb,OAAO;QACP,MAAM,EAAE,eAAe,CAAC,aAAa,CAAC;QACtC,QAAQ;KACT,CAAC;AACJ,CAAC;AAED,SAAS,aAAa,CAAC,WAAyB;IAC9C,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE;QACpC,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,UAAU,CAAC;QAChE,MAAM,MAAM,GAAG;YACb,EAAE,EAAE,UAAU,EAAE;YAChB,KAAK,EAAE,KAAK,IAAI,GAAG;YACnB,KAAK;YACL,MAAM;YACN,YAAY,EAAE,GAAG;YACjB,OAAO;YACP,SAAS;YACT,EAAE,EAAE,EAAE;SACP,CAAC;QACF,OAAO,CAAC,IAAI,CAAC,MAAqB,CAAC,CAAC;KACrC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,iBAAiB,CAAC,OAAsB;IAC/C,IAAI,aAAa,GAA8C,EAAE,CAAC;IAClE,KAAK,IAAI,MAAM,IAAI,OAAO,EAAE;QAC1B,mBAAmB,CAAC,MAAM,CAAC,CAAC;QAC5B,IAAI,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QAC7B,IAAI,CAAC,aAAa,CAAC,KAAK,CAAC,EAAE;YACzB,aAAa,CAAC,KAAK,CAAC,GAAG,IAAI,CAAC,KAAK,CAC/B,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CACG,CAAC;SAC7B;aAAM;YACL,aAAa,CAAC,KAAK,CAAC,CAAC,OAAO,IAAI,MAAM,CAAC,OAAO,CAAC;YAC/C,aAAa,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;SAClD;KACF;IACD,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,aAAa,CAAC,CAAC,CAAC;AAC9C,CAAC"}
|
|
@@ -27,7 +27,7 @@ export async function predictProton(molecule, options = {}) {
|
|
|
27
27
|
cache(molfile, result);
|
|
28
28
|
}
|
|
29
29
|
}
|
|
30
|
-
const diaIDs = getDiastereotopicAtomIDs(molecule);
|
|
30
|
+
const { diaIDs = getDiastereotopicAtomIDs(molecule) } = options;
|
|
31
31
|
const signals = protonParser(result, molecule, diaIDs);
|
|
32
32
|
const joinedSignals = signalsJoin(signals);
|
|
33
33
|
return {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAC;AAEjC,OAAO,EACL,iCAAiC,EACjC,qBAAqB,EACrB,wBAAwB,GACzB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;
|
|
1
|
+
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,KAAK,MAAM,aAAa,CAAC;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAC;AAEjC,OAAO,EACL,iCAAiC,EACjC,qBAAqB,EACrB,wBAAwB,GACzB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAsB7D,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,QAAkB,EAClB,UAAgC,EAAE;IAElC,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAC1B,QAAQ,GAAG,QAAQ,CAAC,cAAc,EAAE,CAAC;IACrC,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;KACzB;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,QAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,yCAAyC,EAAE;YACtE,MAAM,EAAE,MAAM;YACd,+DAA+D;YAC/D,IAAI,EAAE,QAAQ;SACf,CAAC,CAAC;QACH,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,IAAI,KAAK,EAAE;YACT,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;SACxB;KACF;IAED,MAAM,EAAE,MAAM,GAAG,wBAAwB,CAAC,QAAQ,CAAC,EAAE,GAAG,OAAO,CAAC;IAChE,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;IACvD,MAAM,aAAa,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO;QACP,MAAM;QACN,OAAO,EAAE,IAAI;QACb,aAAa;QACb,OAAO;QACP,MAAM,EAAE,eAAe,CAAC,aAAa,CAAC;QACtC,QAAQ;KACT,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CACnB,MAAc,EACd,QAAkB,EAClB,MAAgB;IAEhB,IAAI,QAAQ,CAAC,WAAW,EAAE,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAC5C,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE;QAC1B,MAAM,KAAK,CAAC,wBAAwB,MAAM,EAAE,CAAC,CAAC;KAC/C;IACD,IAAI,cAAc,GAAG,qBAAqB,CAAC,QAAQ,EAAE,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC;IAC3E,IAAI,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC;IACtD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,IAAI,IAAI,IAAI,KAAK,EAAE;QACtB,IAAI,MAAM,GAAa,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QACxC,IAAI,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAChC,IAAI,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QACjC,IAAI,MAAM,GAAgB;YACxB,EAAE,EAAE,UAAU,EAAE;YAChB,KAAK,EAAE,CAAC,IAAI,CAAC;YACb,MAAM,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;YACtB,OAAO,EAAE,CAAC;YACV,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YACxB,EAAE,EAAE,EAAE;SACP,CAAC;QAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;YACd,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAC;SACvD;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,IAAI,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACtC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;gBACb,QAAQ,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;gBAClC,KAAK,EAAE,CAAC,MAAM,CAAC;gBACf,MAAM,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;gBACxB,YAAY,EAAE,GAAG;gBACjB,UAAU,EAAE,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC;aACzC,CAAC,CAAC;YACH,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC;SACnD;QACD,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -1,14 +1,14 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import { getHoseCodesFromDiastereotopicID, addDiastereotopicMissingChirality, groupDiasterotopicAtomIDs, } from 'openchemlib-utils';
|
|
2
2
|
export function getFilteredIDiaIDs(molecule, options) {
|
|
3
|
-
const { maxSphereSize } = options;
|
|
3
|
+
const { maxSphereSize, diaIDs } = options;
|
|
4
4
|
molecule.addImplicitHydrogens();
|
|
5
5
|
molecule.addMissingChirality();
|
|
6
6
|
addDiastereotopicMissingChirality(molecule);
|
|
7
7
|
const molfile = molecule.toMolfile();
|
|
8
|
-
let groupedDiaIDs =
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
8
|
+
let groupedDiaIDs = groupDiasterotopicAtomIDs(diaIDs, molecule, {
|
|
9
|
+
atomLabel: 'C',
|
|
10
|
+
});
|
|
11
|
+
let carbonDiaIDs = groupedDiaIDs.sort((a, b) => {
|
|
12
12
|
if (a.atomLabel === b.atomLabel) {
|
|
13
13
|
return b.counter - a.counter;
|
|
14
14
|
}
|
|
@@ -23,7 +23,6 @@ export function getFilteredIDiaIDs(molecule, options) {
|
|
|
23
23
|
let toReturn = {
|
|
24
24
|
molfile,
|
|
25
25
|
carbonDiaIDs: carbonDiaIDs,
|
|
26
|
-
groupedDiaIDs,
|
|
27
26
|
};
|
|
28
27
|
return toReturn;
|
|
29
28
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getFilteredIDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/getFilteredIDiaIDs.ts"],"names":[],"mappings":"AACA,OAAO,
|
|
1
|
+
{"version":3,"file":"getFilteredIDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/getFilteredIDiaIDs.ts"],"names":[],"mappings":"AACA,OAAO,EAEL,gCAAgC,EAChC,iCAAiC,EACjC,yBAAyB,GAC1B,MAAM,mBAAmB,CAAC;AAS3B,MAAM,UAAU,kBAAkB,CAChC,QAAkB,EAClB,OAAoD;IAEpD,MAAM,EAAE,aAAa,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC;IAE1C,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,QAAQ,CAAC,mBAAmB,EAAE,CAAC;IAC/B,iCAAiC,CAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,QAAQ,CAAC,SAAS,EAAE,CAAC;IAErC,IAAI,aAAa,GAAG,yBAAyB,CAAC,MAAM,EAAE,QAAQ,EAAE;QAC9D,SAAS,EAAE,GAAG;KACf,CAAC,CAAC;IAEH,IAAI,YAAY,GAAG,aAAa,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QAC7C,IAAI,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS,EAAE;YAC/B,OAAO,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAAC;SAC9B;QACD,OAAO,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC5C,CAAC,CAAQ,CAAC;IAEV,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC;IAC9B,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE;QAChC,KAAK,CAAC,IAAI,GAAG,gCAAgC,CAC3C,GAAG,CAAC,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,KAAK,CAAC,EACpC;YACE,aAAa;SACd,CACF,CAAC;KACH;IAED,IAAI,QAAQ,GAAG;QACb,OAAO;QACP,YAAY,EAAE,YAAqC;KACpD,CAAC;IAEF,OAAO,QAAQ,CAAC;AAClB,CAAC"}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
2
|
import { agnes } from 'ml-hclust';
|
|
3
3
|
import { Matrix } from 'ml-matrix';
|
|
4
|
-
import { getGroupedDiastereotopicAtomIDs, getPathsInfo, } from 'openchemlib-utils';
|
|
4
|
+
import { getGroupedDiastereotopicAtomIDs, getPathsInfo, groupDiasterotopicAtomIDs, } from 'openchemlib-utils';
|
|
5
5
|
import { setIDs } from '../../peaks/util/setIDs';
|
|
6
6
|
import { getNuclei } from './getNuclei';
|
|
7
7
|
import { getPredictions } from './getPredictions';
|
|
@@ -12,17 +12,17 @@ function checkFromTo(options) {
|
|
|
12
12
|
}
|
|
13
13
|
export async function predict2D(molecule, options = {}) {
|
|
14
14
|
checkFromTo(options);
|
|
15
|
-
let { from, to, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
|
|
16
15
|
molecule.addImplicitHydrogens();
|
|
17
|
-
let diaIDs =
|
|
16
|
+
let { from, to, diaIDs, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
|
|
18
17
|
const pathsInfo = getPathsInfo(molecule, {
|
|
19
18
|
fromLabel: from,
|
|
20
19
|
toLabel: to,
|
|
21
20
|
minLength,
|
|
22
21
|
maxLength,
|
|
23
22
|
});
|
|
23
|
+
const groupedDiaIDS = diaIDs ? groupDiasterotopicAtomIDs(diaIDs, molecule) : getGroupedDiastereotopicAtomIDs(molecule);
|
|
24
24
|
let diaIDswithAtomInfo = [];
|
|
25
|
-
for (let diaID of
|
|
25
|
+
for (let diaID of groupedDiaIDS) {
|
|
26
26
|
diaIDswithAtomInfo.push({
|
|
27
27
|
...diaID,
|
|
28
28
|
pathInfo: JSON.parse(JSON.stringify(pathsInfo[diaID.atoms[0]])),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,EAAE,KAAK,EAAW,MAAM,WAAW,CAAC;AAC3C,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;AAEnC,OAAO,EACL,+BAA+B,EAC/B,YAAY,
|
|
1
|
+
{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAChD,OAAO,EAAE,KAAK,EAAW,MAAM,WAAW,CAAC;AAC3C,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAC;AAEnC,OAAO,EACL,+BAA+B,EAC/B,YAAY,EACZ,yBAAyB,GAC1B,MAAM,mBAAmB,CAAC;AAO3B,OAAO,EAAE,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAQjD,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAC;AA0FlD,SAAS,WAAW,CAClB,OAAyB;IAEzB,IAAI,CAAC,OAAO,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;KACtD;AACH,CAAC;AAMD,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,QAAkB,EAClB,UAA4B,EAAE;IAE9B,WAAW,CAAC,OAAO,CAAC,CAAC;IAErB,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAEhC,IAAI,EACF,IAAI,EACJ,EAAE,EACF,MAAM,EACN,SAAS,GAAG,CAAC,EACb,SAAS,EACT,cAAc,GAAG,EAAE,EACnB,WAAW,EACX,SAAS,EACT,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,eAAe,GAAG,KAAK,GACxB,GAAG,OAAO,CAAC;IAEZ,MAAM,SAAS,GAAG,YAAY,CAAC,QAAQ,EAAE;QACvC,SAAS,EAAE,IAAI;QACf,OAAO,EAAE,EAAE;QACX,SAAS;QACT,SAAS;KACV,CAAC,CAAC;IAEH,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,CAAC,yBAAyB,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,+BAA+B,CAAC,QAAQ,CAAC,CAAA;IAEtH,IAAI,kBAAkB,GAA6C,EAAE,CAAC;IACtE,KAAK,IAAI,KAAK,IAAI,aAAa,EAAE;QAC/B,kBAAkB,CAAC,IAAI,CAAC;YACtB,GAAG,KAAK;YACR,QAAQ,EAAE,IAAI,CAAC,KAAK,CAClB,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAC9B;SACd,CAAC,CAAC;KACJ;IAED,MAAM,WAAW,GAAG,MAAM,cAAc,CACtC,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,MAAM,WAAW,GACf,IAAI,KAAK,EAAE;QACT,CAAC,CAAC,WAAW;QACb,CAAC,CAAC,MAAM,cAAc,CAClB,EAAE,EACF,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAER,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;KACnD;IAED,MAAM,OAAO,GAAoC;QAC/C,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;KACf,CAAC;IAEF,MAAM,cAAc,GAAoB;QACtC,CAAC,EAAE,EAAE;QACL,CAAC,EAAE,EAAE;KACN,CAAC;IACF,KAAK,MAAM,IAAI,IAAI,cAAc,EAAE;QACjC,KAAK,MAAM,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,aAAa,EAAE;YAChD,IAAI,CAAC,MAAM,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;YAC7D,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC;SACjD;KACF;IACD,IAAI,KAAK,GAAmC,EAAE,CAAC;IAC/C,KAAK,MAAM,KAAK,IAAI,kBAAkB,EAAE;QACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;QAChC,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAExC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC;YAAE,SAAS;QAEhD,MAAM,YAAY,GAAG,QAAQ,CAAC,KAAK,CAAC;QACpC,KAAK,MAAM,IAAI,IAAI,YAAY,EAAE;YAC/B,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC;gBAAE,SAAS;YAE1D,IAAI,WAAW,GAAgC;gBAC7C,CAAC,EAAE,QAAQ;gBACX,CAAC,EAAE,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;aACtB,CAAC;YAEF,MAAM,GAAG,GAAG,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,IAAI,WAAW,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC;YAE5D,IAAI,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,IAAI,QAAQ,CAAC,KAAK,EAAE,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE;gBAC/D,SAAS;aACV;YAED,IAAI,IAAI,GAAQ,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC;YAC7C,IAAI,MAAM,GAAQ,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;YACrD,KAAK,IAAI,IAAI,IAAI,WAAW,EAAE;gBAC5B,IAAI,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC;gBACpC,IAAI,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;gBAC/C,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;gBACvD,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;aACxD;YAED,MAAM,CAAC,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC;YACtB,KAAK,CAAC,GAAG,CAAC,GAAG,MAAqB,CAAC;SACpC;KACF;IAED,IAAI,eAAe,EAAE;QACnB,mBAAmB,CAAC,KAAK,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,cAAc,EAAE,CAAC,CAAC;KAClE;IAED,iCAAiC;IACjC,MAAM,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;IAC3C,MAAM,KAAK,GAAG,WAAW,CAAC,aAAa,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC;IAErE,OAAO;QACL,OAAO,EAAE,QAAQ,CAAC,SAAS,EAAE;QAC7B,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,MAAM;QACxB,MAAM,EAAE,SAAS,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC;QAC/B,aAAa;QACb,OAAO,EAAE,YAAY,CAAC,aAAa,CAAC;QACpC,KAAK;QACL,QAAQ;KACT,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CAAC,aAA4B;IAChD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,MAAM,MAAM,IAAI,aAAa,EAAE;QAClC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;YACxC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;gBACxC,IAAI,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;gBACnD,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;aACzB;SACF;KACF;IACD,OAAO,MAAM,CAAC,OAAO,CAAC,CAAC;AACzB,CAAC;AAMD,SAAS,mBAAmB,CAC1B,KAAqC,EACrC,OAAmC;IAEnC,MAAM,EAAE,KAAK,GAAG,EAAE,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAC/C,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAEpC,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC;QACvB,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,CAAC;YAAE,SAAS;QACvC,IAAI,KAAK,CAAC,GAAG,KAAK,IAAI,KAAK,EAAE,CAAC;YAAE,SAAS;QAEzC,IAAI,MAAM,GAAQ,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;QAEnC,IAAI,IAAI,GAAQ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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "9.3.
|
|
3
|
+
"version": "9.3.1-pre.1669649322",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -77,7 +77,7 @@
|
|
|
77
77
|
"ml-spectra-processing": "^11.14.0",
|
|
78
78
|
"ml-tree-set": "^0.1.1",
|
|
79
79
|
"nmr-correlation": "^2.3.3",
|
|
80
|
-
"openchemlib-utils": "
|
|
80
|
+
"openchemlib-utils": "2.1.1-pre.1669644163",
|
|
81
81
|
"spectrum-generator": "^8.0.6"
|
|
82
82
|
}
|
|
83
83
|
}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
|
-
import { Molecule } from 'openchemlib';
|
|
2
|
+
import { Molecule } from 'openchemlib/full';
|
|
3
3
|
import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
|
|
4
4
|
|
|
5
5
|
import { NMRRange, NMRRangeWithIntegration } from '..';
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
declare module 'openchemlib-utils' {
|
|
2
|
-
import { Molecule } from 'openchemlib';
|
|
2
|
+
import { Molecule } from 'openchemlib/full';
|
|
3
3
|
|
|
4
4
|
export interface GroupDiastereotopicAtomIDs {
|
|
5
5
|
counter: number;
|
|
@@ -7,10 +7,13 @@ declare module 'openchemlib-utils' {
|
|
|
7
7
|
oclID: string;
|
|
8
8
|
atomLabel: string;
|
|
9
9
|
}
|
|
10
|
+
|
|
10
11
|
export type GroupedDiastereotopicAtomIDs = GroupDiastereotopicAtomIDs[];
|
|
11
12
|
function getGroupedDiastereotopicAtomIDs(
|
|
12
13
|
molecule: Molecule,
|
|
14
|
+
options?: { atomLabel: string }
|
|
13
15
|
): GroupedDiastereotopicAtomIDs;
|
|
16
|
+
|
|
14
17
|
interface GetHoseCodesForAtomOptions {
|
|
15
18
|
minSphereSize?: number;
|
|
16
19
|
maxSphereSize?: number;
|
|
@@ -155,4 +158,6 @@ declare module 'openchemlib-utils' {
|
|
|
155
158
|
): number[][] | Float64Array[];
|
|
156
159
|
|
|
157
160
|
function getDiastereotopicAtomIDs(molecule: Molecule): string[];
|
|
161
|
+
|
|
162
|
+
function groupDiasterotopicAtomIDs(diaIDs: string[], molecule: Molecule, options?: { atomLabel: string }): GroupedDiastereotopicAtomIDs
|
|
158
163
|
}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import type { Molecule } from 'openchemlib';
|
|
2
|
-
|
|
1
|
+
import type { Molecule } from 'openchemlib/full';
|
|
2
|
+
import { getDiastereotopicAtomIDs, getGroupedDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
3
3
|
import type { Prediction1D } from './Prediction1D';
|
|
4
4
|
import { predictCOSY } from './predictCOSY';
|
|
5
5
|
import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
|
|
@@ -75,6 +75,8 @@ export async function predictAll(
|
|
|
75
75
|
predictOptions = {},
|
|
76
76
|
} = options;
|
|
77
77
|
|
|
78
|
+
const diaIDs = getDiastereotopicAtomIDs(molecule);
|
|
79
|
+
console.log('entra correction')
|
|
78
80
|
const xPrediction = await getPredictions(
|
|
79
81
|
from,
|
|
80
82
|
molecule,
|
|
@@ -100,7 +102,7 @@ export async function predictAll(
|
|
|
100
102
|
C: yPrediction,
|
|
101
103
|
};
|
|
102
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const { molfile
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const { molfile } = xPrediction;
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const spectra: any = {
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proton: predictions.H,
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@@ -1,5 +1,5 @@
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1
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import { FromTo, PointXY } from 'cheminfo-types';
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-
import type { Molecule } from 'openchemlib';
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+
import type { Molecule } from 'openchemlib/full';
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3
3
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4
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import { signals2DToZ } from '../signals/signals2DToZ';
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import { OptionsSignalsToXY, signalsToXY } from '../signals/signalsToXY';
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@@ -1,6 +1,6 @@
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1
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import { v4 as generateID } from '@lukeed/uuid';
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2
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import fetch from 'cross-fetch';
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-
import type { Molecule } from 'openchemlib';
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+
import type { Molecule } from 'openchemlib/full';
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4
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import { setIDs } from '../peaks/util/setIDs';
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import type { NMRSignal1D } from '../signals/NMRSignal1D';
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@@ -13,6 +13,7 @@ import { fetchPrediction } from './utils/fetchPrediction';
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import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
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import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';
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import { Prediction, queryByHose } from './utils/queryByHOSE';
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import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
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const cache: { [key: string]: DataBaseStructure } = {};
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@@ -48,6 +49,10 @@ export interface PredictCarbonOptions {
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* @default 'maximum level in the database'
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*/
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maxSphereSize?: number;
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/**
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* diastereotopic atom ids.
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+
*/
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+
diaIDs?: string[];
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}
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export type PredictCarbon = typeof predictCarbon;
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@@ -72,7 +77,12 @@ export async function predictCarbon(
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molecule: Molecule,
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options: PredictCarbonOptions = {},
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): Promise<Prediction1D> {
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-
let {
|
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+
let {
|
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81
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+
url,
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82
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database,
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83
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webserviceURL,
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84
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+
diaIDs = getDiastereotopicAtomIDs(molecule),
|
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85
|
+
} = options;
|
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76
86
|
|
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77
87
|
if (webserviceURL) {
|
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78
88
|
return fetchPrediction(molecule, { webserviceURL });
|
|
@@ -90,12 +100,10 @@ export async function predictCarbon(
|
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90
100
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91
101
|
if (maxSphereSize > maxLevel) maxSphereSize = maxLevel;
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102
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-
const {
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94
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-
|
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95
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-
|
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96
|
-
|
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|
-
},
|
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|
-
);
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103
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+
const { carbonDiaIDs, molfile } = getFilteredIDiaIDs(molecule, {
|
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+
maxSphereSize,
|
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105
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+
diaIDs,
|
|
106
|
+
});
|
|
99
107
|
|
|
100
108
|
let predictions = queryByHose(carbonDiaIDs, database, {
|
|
101
109
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maxSphereSize,
|
|
@@ -106,7 +114,7 @@ export async function predictCarbon(
|
|
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106
114
|
return {
|
|
107
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|
molfile,
|
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108
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|
nucleus: '13C',
|
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109
|
-
diaIDs
|
|
117
|
+
diaIDs,
|
|
110
118
|
joinedSignals,
|
|
111
119
|
signals,
|
|
112
120
|
ranges: signalsToRanges(joinedSignals),
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
2
|
import fetch from 'cross-fetch';
|
|
3
3
|
import FormData from 'form-data';
|
|
4
|
-
import type { Molecule } from 'openchemlib';
|
|
4
|
+
import type { Molecule } from 'openchemlib/full';
|
|
5
5
|
import {
|
|
6
6
|
addDiastereotopicMissingChirality,
|
|
7
7
|
getConnectivityMatrix,
|
|
@@ -24,6 +24,10 @@ export interface PredictProtonOptions {
|
|
|
24
24
|
* A callback receiving a molfile and the result
|
|
25
25
|
*/
|
|
26
26
|
cache?: (molfile: string, result?: string) => void | string | undefined;
|
|
27
|
+
/**
|
|
28
|
+
* diastereotopic atom ids.
|
|
29
|
+
*/
|
|
30
|
+
diaIDs?: string[];
|
|
27
31
|
}
|
|
28
32
|
|
|
29
33
|
export type PredictProton = typeof predictProton;
|
|
@@ -56,7 +60,7 @@ export async function predictProton(
|
|
|
56
60
|
}
|
|
57
61
|
}
|
|
58
62
|
|
|
59
|
-
const diaIDs = getDiastereotopicAtomIDs(molecule);
|
|
63
|
+
const { diaIDs = getDiastereotopicAtomIDs(molecule) } = options;
|
|
60
64
|
const signals = protonParser(result, molecule, diaIDs);
|
|
61
65
|
const joinedSignals = signalsJoin(signals);
|
|
62
66
|
return {
|
|
@@ -1,8 +1,9 @@
|
|
|
1
|
-
import type { Molecule } from 'openchemlib';
|
|
1
|
+
import type { Molecule } from 'openchemlib/full';
|
|
2
2
|
import {
|
|
3
3
|
getGroupedDiastereotopicAtomIDs,
|
|
4
4
|
getHoseCodesFromDiastereotopicID,
|
|
5
5
|
addDiastereotopicMissingChirality,
|
|
6
|
+
groupDiasterotopicAtomIDs,
|
|
6
7
|
} from 'openchemlib-utils';
|
|
7
8
|
import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
8
9
|
|
|
@@ -14,9 +15,9 @@ export type GroupedDiaIDsWithHose = GroupDiaIDsWithHose[];
|
|
|
14
15
|
|
|
15
16
|
export function getFilteredIDiaIDs(
|
|
16
17
|
molecule: Molecule,
|
|
17
|
-
options: { maxSphereSize: number },
|
|
18
|
+
options: { maxSphereSize: number; diaIDs: string[] },
|
|
18
19
|
) {
|
|
19
|
-
const { maxSphereSize } = options;
|
|
20
|
+
const { maxSphereSize, diaIDs } = options;
|
|
20
21
|
|
|
21
22
|
molecule.addImplicitHydrogens();
|
|
22
23
|
molecule.addMissingChirality();
|
|
@@ -24,16 +25,16 @@ export function getFilteredIDiaIDs(
|
|
|
24
25
|
|
|
25
26
|
const molfile = molecule.toMolfile();
|
|
26
27
|
|
|
27
|
-
let groupedDiaIDs =
|
|
28
|
+
let groupedDiaIDs = groupDiasterotopicAtomIDs(diaIDs, molecule, {
|
|
29
|
+
atomLabel: 'C',
|
|
30
|
+
});
|
|
28
31
|
|
|
29
|
-
let carbonDiaIDs = groupedDiaIDs
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
return a.atomLabel < b.atomLabel ? 1 : -1;
|
|
36
|
-
}) as any;
|
|
32
|
+
let carbonDiaIDs = groupedDiaIDs.sort((a, b) => {
|
|
33
|
+
if (a.atomLabel === b.atomLabel) {
|
|
34
|
+
return b.counter - a.counter;
|
|
35
|
+
}
|
|
36
|
+
return a.atomLabel < b.atomLabel ? 1 : -1;
|
|
37
|
+
}) as any;
|
|
37
38
|
|
|
38
39
|
const OCL = molecule.getOCL();
|
|
39
40
|
for (const diaId of carbonDiaIDs) {
|
|
@@ -48,7 +49,6 @@ export function getFilteredIDiaIDs(
|
|
|
48
49
|
let toReturn = {
|
|
49
50
|
molfile,
|
|
50
51
|
carbonDiaIDs: carbonDiaIDs as GroupedDiaIDsWithHose,
|
|
51
|
-
groupedDiaIDs,
|
|
52
52
|
};
|
|
53
53
|
|
|
54
54
|
return toReturn;
|
|
@@ -1,10 +1,11 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
2
|
import { agnes, Cluster } from 'ml-hclust';
|
|
3
3
|
import { Matrix } from 'ml-matrix';
|
|
4
|
-
import { Molecule } from 'openchemlib';
|
|
4
|
+
import { Molecule } from 'openchemlib/full';
|
|
5
5
|
import {
|
|
6
6
|
getGroupedDiastereotopicAtomIDs,
|
|
7
7
|
getPathsInfo,
|
|
8
|
+
groupDiasterotopicAtomIDs,
|
|
8
9
|
} from 'openchemlib-utils';
|
|
9
10
|
import type {
|
|
10
11
|
AtomInfo,
|
|
@@ -86,6 +87,10 @@ export interface Predict2DOptions {
|
|
|
86
87
|
* @default false
|
|
87
88
|
*/
|
|
88
89
|
includeDiagonal?: boolean;
|
|
90
|
+
/**
|
|
91
|
+
* diastereotopic atom ids of the molecule.
|
|
92
|
+
*/
|
|
93
|
+
diaIDs?: string[];
|
|
89
94
|
}
|
|
90
95
|
|
|
91
96
|
export interface PredictOptions {
|
|
@@ -125,9 +130,12 @@ export async function predict2D(
|
|
|
125
130
|
) {
|
|
126
131
|
checkFromTo(options);
|
|
127
132
|
|
|
133
|
+
molecule.addImplicitHydrogens();
|
|
134
|
+
|
|
128
135
|
let {
|
|
129
136
|
from,
|
|
130
137
|
to,
|
|
138
|
+
diaIDs,
|
|
131
139
|
minLength = 0,
|
|
132
140
|
maxLength,
|
|
133
141
|
predictOptions = {},
|
|
@@ -137,10 +145,6 @@ export async function predict2D(
|
|
|
137
145
|
includeDiagonal = false,
|
|
138
146
|
} = options;
|
|
139
147
|
|
|
140
|
-
molecule.addImplicitHydrogens();
|
|
141
|
-
|
|
142
|
-
let diaIDs = getGroupedDiastereotopicAtomIDs(molecule);
|
|
143
|
-
|
|
144
148
|
const pathsInfo = getPathsInfo(molecule, {
|
|
145
149
|
fromLabel: from,
|
|
146
150
|
toLabel: to,
|
|
@@ -148,8 +152,10 @@ export async function predict2D(
|
|
|
148
152
|
maxLength,
|
|
149
153
|
});
|
|
150
154
|
|
|
155
|
+
const groupedDiaIDS = diaIDs ? groupDiasterotopicAtomIDs(diaIDs, molecule) : getGroupedDiastereotopicAtomIDs(molecule)
|
|
156
|
+
|
|
151
157
|
let diaIDswithAtomInfo: GroupDiastereotopicAtomIDsWithAtomInfo[] = [];
|
|
152
|
-
for (let diaID of
|
|
158
|
+
for (let diaID of groupedDiaIDS) {
|
|
153
159
|
diaIDswithAtomInfo.push({
|
|
154
160
|
...diaID,
|
|
155
161
|
pathInfo: JSON.parse(
|