nmr-processing 10.0.4 → 10.0.6
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/datum/FiltersManager.js +1 -0
- package/lib/datum/FiltersManager.js.map +1 -1
- package/lib/datum/data1d/filter1d/baselineCorrection.js +1 -1
- package/lib/datum/data1d/filter1d/baselineCorrection.js.map +1 -1
- package/lib/prediction/predict.js +14 -25
- package/lib/prediction/predict.js.map +1 -1
- package/lib/prediction/predictCOSY.d.ts +2 -20
- package/lib/prediction/predictCOSY.js +2 -2
- package/lib/prediction/predictCOSY.js.map +1 -1
- package/lib/prediction/predictCarbon.d.ts +2 -15
- package/lib/prediction/predictCarbon.js +14 -16
- package/lib/prediction/predictCarbon.js.map +1 -1
- package/lib/prediction/predictHMBC.d.ts +2 -12
- package/lib/prediction/predictHMBC.js +2 -2
- package/lib/prediction/predictHMBC.js.map +1 -1
- package/lib/prediction/predictHSQC.d.ts +2 -12
- package/lib/prediction/predictHSQC.js +2 -2
- package/lib/prediction/predictHSQC.js.map +1 -1
- package/lib/prediction/predictProton.d.ts +2 -9
- package/lib/prediction/predictProton.js +9 -10
- package/lib/prediction/predictProton.js.map +1 -1
- package/lib/prediction/predictSpectra.d.ts +3 -2
- package/lib/prediction/predictSpectra.js +12 -7
- package/lib/prediction/predictSpectra.js.map +1 -1
- package/lib/prediction/utils/predict2D.d.ts +2 -12
- package/lib/prediction/utils/predict2D.js +9 -9
- package/lib/prediction/utils/predict2D.js.map +1 -1
- package/lib/prediction/utils/queryByHOSE.d.ts +2 -1
- package/lib/prediction/utils/queryByHOSE.js +29 -27
- package/lib/prediction/utils/queryByHOSE.js.map +1 -1
- package/lib/ranges/rangesToACS.js.map +1 -1
- package/lib/xyz/xyzAutoSignalsPicking.js +2 -2
- package/lib/xyz/xyzAutoSignalsPicking.js.map +1 -1
- package/lib-esm/datum/FiltersManager.js +1 -0
- package/lib-esm/datum/FiltersManager.js.map +1 -1
- package/lib-esm/datum/data1d/filter1d/baselineCorrection.js +1 -1
- package/lib-esm/datum/data1d/filter1d/baselineCorrection.js.map +1 -1
- package/lib-esm/prediction/predict.js +15 -26
- package/lib-esm/prediction/predict.js.map +1 -1
- package/lib-esm/prediction/predictCOSY.js +2 -2
- package/lib-esm/prediction/predictCOSY.js.map +1 -1
- package/lib-esm/prediction/predictCarbon.js +16 -18
- package/lib-esm/prediction/predictCarbon.js.map +1 -1
- package/lib-esm/prediction/predictHMBC.js +2 -2
- package/lib-esm/prediction/predictHMBC.js.map +1 -1
- package/lib-esm/prediction/predictHSQC.js +2 -2
- package/lib-esm/prediction/predictHSQC.js.map +1 -1
- package/lib-esm/prediction/predictProton.js +9 -10
- package/lib-esm/prediction/predictProton.js.map +1 -1
- package/lib-esm/prediction/predictSpectra.js +10 -5
- package/lib-esm/prediction/predictSpectra.js.map +1 -1
- package/lib-esm/prediction/utils/predict2D.js +9 -9
- package/lib-esm/prediction/utils/predict2D.js.map +1 -1
- package/lib-esm/prediction/utils/queryByHOSE.js +29 -27
- package/lib-esm/prediction/utils/queryByHOSE.js.map +1 -1
- package/lib-esm/ranges/rangesToACS.js.map +1 -1
- package/lib-esm/xyz/xyzAutoSignalsPicking.js +2 -2
- package/lib-esm/xyz/xyzAutoSignalsPicking.js.map +1 -1
- package/package.json +2 -2
- package/src/datum/FiltersManager.ts +1 -0
- package/src/datum/data1d/filter1d/baselineCorrection.ts +1 -1
- package/src/prediction/predict.ts +15 -40
- package/src/prediction/predictCOSY.ts +3 -19
- package/src/prediction/predictCarbon.ts +19 -33
- package/src/prediction/predictHMBC.ts +3 -13
- package/src/prediction/predictHSQC.ts +3 -13
- package/src/prediction/predictProton.ts +11 -19
- package/src/prediction/predictSpectra.ts +14 -6
- package/src/prediction/utils/predict2D.ts +13 -29
- package/src/prediction/utils/queryByHOSE.ts +31 -30
- package/src/ranges/rangesToACS.ts +1 -0
- package/src/xyz/xyzAutoSignalsPicking.ts +2 -2
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@@ -3,9 +3,8 @@ import fetch from 'cross-fetch';
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import FormData from 'form-data';
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import { signalsJoin } from '../signals/signalsJoin';
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import { signalsToRanges } from '../signals/signalsToRanges';
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-
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-
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if (!isMolfileNotEmpty(molfile)) {
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export async function predictProton(topicMolecule, options = {}) {
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if (topicMolecule.molecule.getAllAtoms() === 0) {
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return {
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nucleus: '1H',
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joinedSignals: [],
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@@ -16,11 +15,11 @@ export async function predictProton(molfile, options) {
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const { cache } = options;
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let result;
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if (cache) {
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result = cache(
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result = cache(topicMolecule.idCode);
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}
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if (result === undefined) {
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const formData = new FormData();
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formData.append('molfile',
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formData.append('molfile', topicMolecule.toMolfile());
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const response = await fetch('https://www.nmrdb.org/service/predictor', {
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method: 'POST',
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// @ts-expect-error RequestInit type does not include FormData.
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@@ -28,11 +27,10 @@ export async function predictProton(molfile, options) {
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});
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result = await response.text();
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if (cache) {
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cache(
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cache(topicMolecule.idCode, result);
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}
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}
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const
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const signals = protonParser(result, { diaIDs, distanceMatrix });
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const signals = protonParser(result, topicMolecule);
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const joinedSignals = signalsJoin(signals);
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return {
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nucleus: '1H',
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@@ -41,11 +39,12 @@ export async function predictProton(molfile, options) {
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ranges: signalsToRanges(joinedSignals),
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};
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}
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function protonParser(result,
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function protonParser(result, topicMolecule) {
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if (result.includes('ERR')) {
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throw Error(`Spinus optimization: ${result}`);
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}
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const
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const diaIDs = topicMolecule.diaIDs;
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const distanceMatrix = topicMolecule.distanceMatrix;
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const lines = result.split('\n').filter((line) => line);
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const signals = [];
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for (const line of lines) {
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@@ -1 +1 @@
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-
{"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;
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{"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;AAIjC,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAkB7D,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,aAA4B,EAC5B,UAAgC,EAAE;IAElC,IAAI,aAAa,CAAC,QAAQ,CAAC,WAAW,EAAE,KAAK,CAAC,EAAE;QAC9C,OAAO;YACL,OAAO,EAAE,IAAI;YACb,aAAa,EAAE,EAAE;YACjB,OAAO,EAAE,EAAE;YACX,MAAM,EAAE,EAAE;SACX,CAAC;KACH;IACD,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC;IAE1B,IAAI,MAAM,CAAC;IACX,IAAI,KAAK,EAAE;QACT,MAAM,GAAG,KAAK,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;KACtC;IACD,IAAI,MAAM,KAAK,SAAS,EAAE;QACxB,MAAM,QAAQ,GAAG,IAAI,QAAQ,EAAE,CAAC;QAChC,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,CAAC,CAAC;QACtD,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,aAAa,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;SACrC;KACF;IAED,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,EAAE,aAAa,CAAC,CAAC;IACpD,MAAM,aAAa,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC;IAC3C,OAAO;QACL,OAAO,EAAE,IAAI;QACb,aAAa;QACb,OAAO;QACP,MAAM,EAAE,eAAe,CAAC,aAAa,CAAC;KACvC,CAAC;AACJ,CAAC;AAED,SAAS,YAAY,CACnB,MAAc,EACd,aAA4B;IAE5B,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE;QAC1B,MAAM,KAAK,CAAC,wBAAwB,MAAM,EAAE,CAAC,CAAC;KAC/C;IACD,MAAM,MAAM,GAAG,aAAa,CAAC,MAAM,CAAC;IACpC,MAAM,cAAc,GAAG,aAAa,CAAC,cAAc,CAAC;IACpD,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC;IACxD,MAAM,OAAO,GAAG,EAAE,CAAC;IACnB,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,MAAM,MAAM,GAAa,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QAC1C,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QACnC,MAAM,MAAM,GAAgB;YAC1B,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,MAAM,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACxC,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"}
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@@ -2,14 +2,15 @@ import { signals2DToZ } from '../signals/signals2DToZ';
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import { signalsToXY } from '../signals/signalsToXY';
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import { getFrequency } from '../utilities/getFrequency';
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import { predict } from './predict';
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export async function
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const { simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction:
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const { spectra } = await predict(molecule,
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export async function predictSpectra(molecule, options = {}) {
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const { logger, simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction: predictOptions = {}, } = options;
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const { spectra } = await predict(molecule, { logger, ...predictOptions });
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const oneDOptions = {
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...{
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proton: { from: 0, to: 14 },
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carbon: { from: 0, to: 200 },
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nbPoints: 65536,
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frequency: 400,
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lineWidth: 1,
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},
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...(simulationOptions.oneD || {}),
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},
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...(simulationOptions.twoD || {}),
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};
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if (!('frequency' in simulationOptions) && logger) {
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logger.warn(`Frequency is settled to 400 MHz`);
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}
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const { frequency = 400 } = simulationOptions;
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const newSpectra = [];
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for (const experiment in spectra) {
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switch (experiment) {
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lineWidth: oneDOptions.lineWidth,
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...oneDOptions[experiment],
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experiment,
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frequency
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frequency,
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}));
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break;
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}
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newSpectra.push(get2DSpectrum(spectra[experiment], {
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...twoDOptions,
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frequency
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}));
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break;
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}
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{"version":3,"file":"predictSpectra.js","sourceRoot":"","sources":["../../src/prediction/predictSpectra.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AACvD,OAAO,EAAsB,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACzE,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAEzD,OAAO,EAAqB,OAAO,EAAE,MAAM,WAAW,CAAC;
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+
{"version":3,"file":"predictSpectra.js","sourceRoot":"","sources":["../../src/prediction/predictSpectra.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,YAAY,EAAE,MAAM,yBAAyB,CAAC;AACvD,OAAO,EAAsB,WAAW,EAAE,MAAM,wBAAwB,CAAC;AACzE,OAAO,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAEzD,OAAO,EAAqB,OAAO,EAAE,MAAM,WAAW,CAAC;AA+BvD,MAAM,CAAC,KAAK,UAAU,cAAc,CAClC,QAAkB,EAClB,UAAoC,EAAE;IAEtC,MAAM,EACJ,MAAM,EACN,UAAU,EAAE,iBAAiB,GAAG,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAuB,EAC3E,UAAU,EAAE,cAAc,GAAG,EAAE,GAChC,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,OAAO,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,GAAG,cAAc,EAAE,CAAC,CAAC;IAE3E,MAAM,WAAW,GAAgB;QAC/B,GAAG;YACD,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;YAC3B,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE;YAC5B,QAAQ,EAAE,KAAK;YACf,SAAS,EAAE,GAAG;YACd,SAAS,EAAE,CAAC;SACb;QACD,GAAG,CAAC,iBAAiB,CAAC,IAAI,IAAI,EAAE,CAAC;KAClC,CAAC;IAEF,MAAM,WAAW,GAAgB;QAC/B,GAAG;YACD,IAAI,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE;YAChE,EAAE,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,EAAE,EAAE;YAC1D,QAAQ,EAAE,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,IAAI,EAAE;SAC/B;QACD,GAAG,CAAC,iBAAiB,CAAC,IAAI,IAAI,EAAE,CAAC;KAClC,CAAC;IAEF,IAAI,CAAC,CAAC,WAAW,IAAI,iBAAiB,CAAC,IAAI,MAAM,EAAE;QACjD,MAAM,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAC;KAChD;IACD,MAAM,EAAE,SAAS,GAAG,GAAG,EAAE,GAAG,iBAAiB,CAAC;IAE9C,MAAM,UAAU,GAAU,EAAE,CAAC;IAC7B,KAAK,MAAM,UAAU,IAAI,OAAO,EAAE;QAChC,QAAQ,UAAU,EAAE;YAClB,KAAK,QAAQ,CAAC;YACd,KAAK,QAAQ,CAAC,CAAC;gBACb,UAAU,CAAC,IAAI,CACb,aAAa,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE;oBACjC,QAAQ,EAAE,WAAW,CAAC,QAAQ;oBAC9B,SAAS,EAAE,WAAW,CAAC,SAAS;oBAChC,GAAG,WAAW,CAAC,UAAU,CAAC;oBAC1B,UAAU;oBACV,SAAS;iBACV,CAAC,CACH,CAAC;gBACF,MAAM;aACP;YACD,KAAK,MAAM,CAAC;YACZ,KAAK,MAAM,CAAC;YACZ,KAAK,MAAM,CAAC,CAAC;gBACX,UAAU,CAAC,IAAI,CACb,aAAa,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE;oBACjC,GAAG,WAAW;oBACd,UAAU;oBACV,SAAS;iBACV,CAAC,CACH,CAAC;gBACF,MAAM;aACP;YACD;gBACE,MAAM;SACT;KACF;IAED,OAAO;QACL,OAAO,EAAE,UAAU;QACnB,SAAS,EAAE,CAAC,EAAE,OAAO,EAAE,QAAQ,CAAC,SAAS,EAAE,EAAE,CAAC;KAC/C,CAAC;AACJ,CAAC;AAOD,SAAS,aAAa,CAAC,UAAe,EAAE,OAA6B;IACnE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,UAAU,CAAC;IAC9C,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC;IAEzD,MAAM,KAAK,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC;IACjC,MAAM,SAAS,GAAG,kBAAkB,CAAC,MAAM,EAAE,aAAa,CAAC,CAAC;IAE5D,MAAM,aAAa,GAAG,YAAY,CAAC,OAAO,EAAE;QAC1C,GAAG,OAAO;QACV,KAAK;QACL,MAAM,EAAE,CAAC;KACV,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG;QACf,IAAI,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,aAAa,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE;QAC/C,IAAI,EAAE;YACJ,OAAO,EAAE,MAAM;YACf,eAAe,EAAE,SAAS;YAC1B,aAAa,EAAE,SAAS;YACxB,aAAa,EAAE,UAAU;YACzB,UAAU,EAAE,IAAI;SACjB;QACD,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE;KACzB,CAAC;IACF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,UAAU,CAAC,OAAiB;IACnC,OAAO,OAAO,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC;AACnE,CAAC;AAID,SAAS,aAAa,CAAC,UAAe,EAAE,OAA6B;IACnE,MAAM,EAAE,SAAS,GAAG,GAAG,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC;IAChD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC;IACxC,MAAM,aAAa,GAAG,kBAAkB,CAAC,OAAO,EAAE,SAAS,CAAW,CAAC;IACvE,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,WAAW,CAAC,OAAO,EAAE;QACpC,GAAG,OAAO;QACV,SAAS,EAAE,aAAa;KACzB,CAAC,CAAC;IACH,MAAM,QAAQ,GAAG;QACf,oDAAoD;QACpD,IAAI,EAAE,EAAE,CAAC,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE;QACvD,IAAI,EAAE;YACJ,OAAO,EAAE,UAAU,CAAC,OAAO;YAC3B,SAAS,EAAE,CAAC;YACZ,SAAS,EAAE,KAAK;YAChB,eAAe,EAAE,aAAa;YAC9B,aAAa,EAAE,aAAa;YAC5B,aAAa,EAAE,YAAY;YAC3B,UAAU;YACV,IAAI,EAAE,IAAI;SACX;QACD,MAAM,EAAE,EAAE,MAAM,EAAE,UAAU,CAAC,MAAM,EAAE;KACtC,CAAC;IAEF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,kBAAkB,CACzB,OAA0B,EAC1B,SAAiB;IAEjB,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE;QAC/B,OAAO,YAAY,CAAC,OAAO,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,CAAC,CAAC;KAC5D;SAAM,IAAI,OAAO,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,EAAE;QACpC,OAAO,GAAG,SAAS,IAAI,SAAS,EAAE,CAAC;KACpC;SAAM;QACL,OAAO,GAAG,SAAS,IAAI,YAAY,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAC9C,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC;YACnB,SAAS;SACV,CAAC,EAAE,CAAC;KACN;AACH,CAAC"}
|
|
@@ -9,19 +9,16 @@ function checkFromTo(options) {
|
|
|
9
9
|
throw new Error('options from and to are mandatory');
|
|
10
10
|
}
|
|
11
11
|
}
|
|
12
|
-
export async function predict2D(
|
|
12
|
+
export async function predict2D(topicMolecule, options) {
|
|
13
13
|
checkFromTo(options);
|
|
14
|
-
|
|
15
|
-
const
|
|
16
|
-
const pathsInfo = getPossibleCorrelations({
|
|
17
|
-
molecule,
|
|
14
|
+
const { from, to, minLength = 0, maxLength, predictions, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
|
|
15
|
+
const pathsInfo = getPossibleCorrelations(topicMolecule, {
|
|
18
16
|
fromLabel: from,
|
|
19
17
|
toLabel: to,
|
|
20
|
-
diaIDs,
|
|
21
|
-
distanceMatrix,
|
|
22
18
|
minLength,
|
|
23
19
|
maxLength,
|
|
24
20
|
});
|
|
21
|
+
const groupedDiaIDs = topicMolecule.getGroupedDiastereotopicAtomIDs();
|
|
25
22
|
const diaIDswithAtomInfo = [];
|
|
26
23
|
for (const diaID of groupedDiaIDs) {
|
|
27
24
|
diaIDswithAtomInfo.push({
|
|
@@ -94,8 +91,11 @@ export async function predict2D(molecule, options) {
|
|
|
94
91
|
zones,
|
|
95
92
|
};
|
|
96
93
|
}
|
|
97
|
-
function getPossibleCorrelations(options) {
|
|
98
|
-
const { fromLabel, toLabel,
|
|
94
|
+
function getPossibleCorrelations(topicMolecule, options) {
|
|
95
|
+
const { fromLabel, toLabel, minLength, maxLength } = options;
|
|
96
|
+
const diaIDs = topicMolecule.diaIDs;
|
|
97
|
+
const molecule = topicMolecule.moleculeWithH;
|
|
98
|
+
const distanceMatrix = topicMolecule.distanceMatrix;
|
|
99
99
|
const fromAtomicNumber = Molecule.getAtomicNoFromLabel(fromLabel);
|
|
100
100
|
const toAtomicNumber = Molecule.getAtomicNoFromLabel(toLabel);
|
|
101
101
|
const atomPathInfo = [];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
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@@ -1,35 +1,37 @@
|
|
|
1
|
-
export function queryByHose(
|
|
2
|
-
const { maxSphereSize } = options;
|
|
3
|
-
const
|
|
4
|
-
for (
|
|
1
|
+
export function queryByHose(diaIDsWithInfo, db, options) {
|
|
2
|
+
const { maxSphereSize, atomLabel } = options;
|
|
3
|
+
const results = [];
|
|
4
|
+
for (let i = 0; i < diaIDsWithInfo.length; i++) {
|
|
5
|
+
const entry = diaIDsWithInfo[i];
|
|
6
|
+
if (atomLabel && entry.atomLabel !== atomLabel)
|
|
7
|
+
continue;
|
|
5
8
|
let res;
|
|
6
9
|
let level = null;
|
|
7
|
-
for (let k = maxSphereSize;
|
|
8
|
-
if (db[k]) {
|
|
9
|
-
res = db[k][
|
|
10
|
+
for (let k = maxSphereSize; k >= 0; k--) {
|
|
11
|
+
if (db[k]?.[entry.hoses[k]]) {
|
|
12
|
+
res = db[k][entry.hoses[k]];
|
|
10
13
|
level = k;
|
|
14
|
+
break;
|
|
11
15
|
}
|
|
12
16
|
}
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
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16
|
-
|
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17
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-
|
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18
|
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|
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19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
toReturn.push(atom);
|
|
31
|
-
}
|
|
17
|
+
const result = {
|
|
18
|
+
diaIDs: [entry.idCode],
|
|
19
|
+
delta: res ? res[0] : null,
|
|
20
|
+
atoms: [i],
|
|
21
|
+
nbAtoms: 1,
|
|
22
|
+
level,
|
|
23
|
+
statistic: res && res.length > 1 // only if DB contains statistics
|
|
24
|
+
? {
|
|
25
|
+
mean: res[1],
|
|
26
|
+
sd: res[2],
|
|
27
|
+
min: res[3],
|
|
28
|
+
max: res[4],
|
|
29
|
+
nb: res[5],
|
|
30
|
+
}
|
|
31
|
+
: undefined,
|
|
32
|
+
};
|
|
33
|
+
results.push(result);
|
|
32
34
|
}
|
|
33
|
-
return
|
|
35
|
+
return results;
|
|
34
36
|
}
|
|
35
37
|
//# sourceMappingURL=queryByHOSE.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"queryByHOSE.js","sourceRoot":"","sources":["../../../src/prediction/utils/queryByHOSE.ts"],"names":[],"mappings":"AAkBA,MAAM,UAAU,WAAW,CACzB,
|
|
1
|
+
{"version":3,"file":"queryByHOSE.js","sourceRoot":"","sources":["../../../src/prediction/utils/queryByHOSE.ts"],"names":[],"mappings":"AAkBA,MAAM,UAAU,WAAW,CACzB,cAAmB,EACnB,EAAqB,EACrB,OAAqD;IAErD,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC;IAE7C,MAAM,OAAO,GAAG,EAAE,CAAC;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC9C,MAAM,KAAK,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC;QAChC,IAAI,SAAS,IAAI,KAAK,CAAC,SAAS,KAAK,SAAS;YAAE,SAAS;QAEzD,IAAI,GAAG,CAAC;QACR,IAAI,KAAK,GAAG,IAAI,CAAC;QACjB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;YACvC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE;gBAC3B,GAAG,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;gBAC5B,KAAK,GAAG,CAAC,CAAC;gBACV,MAAM;aACP;SACF;QACD,MAAM,MAAM,GAAG;YACb,MAAM,EAAE,CAAC,KAAK,CAAC,MAAM,CAAC;YACtB,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI;YAC1B,KAAK,EAAE,CAAC,CAAC,CAAC;YACV,OAAO,EAAE,CAAC;YACV,KAAK;YACL,SAAS,EACP,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,iCAAiC;gBACrD,CAAC,CAAC;oBACE,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC;oBACZ,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;oBACV,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;oBACX,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;oBACX,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;iBACX;gBACH,CAAC,CAAC,SAAS;SAChB,CAAC;QACF,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KACtB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"rangesToACS.js","sourceRoot":"","sources":["../../src/ranges/rangesToACS.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;
|
|
1
|
+
{"version":3,"file":"rangesToACS.js","sourceRoot":"","sources":["../../src/ranges/rangesToACS.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAE1C,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,yBAAyB,EAAE,MAAM,qCAAqC,CAAC;AAIhF,MAAM,aAAa,GAQf;IACF,CAAC,EAAE;QACD,OAAO,EAAE,IAAI;QACb,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;IACD,CAAC,EAAE;QACD,OAAO,EAAE,KAAK;QACd,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;IACD,CAAC,EAAE;QACD,OAAO,EAAE,KAAK;QACd,cAAc,EAAE,CAAC;QACjB,UAAU,EAAE,CAAC;QACb,iBAAiB,EAAE,GAAG;KACvB;CACF,CAAC;AAmCF,MAAM,UAAU,WAAW,CACzB,MAAkB,EAClB,UAA8B,EAAE;IAEhC,IAAI,CAAC,OAAO,CAAC,OAAO;QAAE,OAAO,CAAC,OAAO,GAAG,IAAI,CAAC;IAC7C,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;IACpE,MAAM,cAAc,GAAG,aAAa,CAAC,OAAO,CAAC,CAAC;IAC9C,OAAO,GAAG;QACR,GAAG,cAAc;QACjB,SAAS,EAAE,KAAK;QAChB,MAAM,EAAE,MAAM;QACd,GAAG,OAAO;KACX,CAAC;IAEF,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;IAC5C,IAAI,OAAO,CAAC,SAAS,KAAK,IAAI,EAAE;QAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACnB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;YACrC,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC;YACrC,OAAO,KAAK,GAAG,KAAK,CAAC;QACvB,CAAC,CAAC,CAAC;KACJ;IAED,IAAI,SAAS,GAAG,SAAS,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC3C,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC;QAAE,SAAS,IAAI,GAAG,CAAC;IAE3C,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,SAAS,CAAC,MAAkB,EAAE,OAAY;IACjD,IAAI,GAAG,GAAG,kBAAkB,CAAC,OAAO,CAAC,CAAC;IACtC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC;QAAE,GAAG,GAAG,IAAI,CAAC;IACjC,MAAM,SAAS,GAAa,EAAE,CAAC;IAC/B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,IAAI,WAAW,CAAC,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC;YAAE,SAAS;QACtD,SAAS,CAAC,KAAK,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;KACtC;IACD,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE;QACxB,OAAO,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;KACnC;SAAM;QACL,OAAO,EAAE,CAAC;KACX;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,OAAY;IACtC,MAAM,WAAW,GAAG,EAAE,CAAC;IACvB,IAAI,OAAO,GAAG,GAAG,aAAa,CAAC,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC;IACtD,IAAI,OAAO,CAAC,OAAO,EAAE;QACnB,WAAW,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC;KAC7C;IACD,IAAI,OAAO,CAAC,iBAAiB,EAAE;QAC7B,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,iBAAiB,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;KACvE;IACD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE;QAC1B,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;KAC/C;SAAM;QACL,OAAO,IAAI,MAAM,CAAC;KACnB;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,SAAS,SAAS,CAAC,KAAe,EAAE,SAAmB,EAAE,OAAY;IACnE,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,IAAI,WAAW,GAAQ,EAAE,CAAC;IAC1B,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,CAAC,CAAC;IAEtC,IAAI,KAAK,CAAC,OAAO,EAAE;QACjB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAClC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC,CACtD,CAAC;KACH;IAED,IAAI,KAAK,CAAC,OAAO,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;QAC7C,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC;QAC9B,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE;YACtB,IAAI,OAAO,CAAC,SAAS,KAAK,IAAI,EAAE;gBAC9B,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;oBACpB,OAAO,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;gBAC3B,CAAC,CAAC,CAAC;aACJ;YACD,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;YAC3D,OAAO,IAAI,KAAK,WAAW,CAAC,KAAK,EAAE,OAAO,CAAC,EAAE,CAAC;YAE9C,IACE,OAAO,CAAC,IAAI,CACV,CAAC,MAAM,EAAE,EAAE,CACT,MAAM,CAAC,YAAY,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,MAAM,CAAC,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAC7D,EACD;gBACA,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;oBAC5B,WAAW,GAAG,EAAE,CAAC;oBACjB,IAAI,MAAM,CAAC,KAAK,KAAK,SAAS,EAAE;wBAC9B,OAAO,GAAG,eAAe,CAAC,OAAO,CAAC,CAAC;wBACnC,OAAO,IAAI,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC;qBACzD;oBACD,MAAM,KAAK,GAAa;wBACtB,IAAI,EAAE,MAAM,CAAC,gBAAgB;wBAC7B,EAAE,EAAE,MAAM,CAAC,gBAAgB;qBAC5B,CAAC;oBACF,YAAY,CAAC,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;oBAClD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;wBAAE,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;iBACvE;aACF;YACD,OAAO,IAAI,GAAG,CAAC;SAChB;aAAM;YACL,WAAW,GAAG,EAAE,CAAC;YACjB,IAAI,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,EAAE;gBAClC,OAAO,IAAI,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC;gBAC5D,YAAY,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;gBACtD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;oBAAE,OAAO,IAAI,KAAK,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;aACvE;iBAAM;gBACL,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;gBAC3D,YAAY,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,OAAO,CAAC,CAAC;gBACtD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;oBAAE,OAAO,IAAI,KAAK,WAAW,GAAG,CAAC;aAC5D;SACF;KACF;SAAM;QACL,OAAO,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CACvC,OAAO,CAAC,cAAc,CACvB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC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@@ -1,4 +1,5 @@
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1
1
|
import { v4 as generateID } from '@lukeed/uuid';
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2
|
+
import { isAnyArray } from 'is-any-array';
|
|
2
3
|
import * as convolution from 'ml-matrix-convolution';
|
|
3
4
|
import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
|
|
4
5
|
import simpleClustering from 'ml-simple-clustering';
|
|
@@ -7,7 +8,6 @@ import { determineRealTop } from '../peaks/util/determineRealTop';
|
|
|
7
8
|
import { getKernel } from '../peaks/util/getKernel';
|
|
8
9
|
import * as PeakOptimizer from '../peaks/util/peakOptimizer';
|
|
9
10
|
import { padData } from './util/padData';
|
|
10
|
-
import { isAnyArray } from 'is-any-array';
|
|
11
11
|
const smallFilter = [
|
|
12
12
|
[0, 0, 1, 2, 2, 2, 1, 0, 0],
|
|
13
13
|
[0, 1, 4, 7, 7, 7, 4, 1, 0],
|
|
@@ -22,7 +22,7 @@ const smallFilter = [
|
|
|
22
22
|
export function xyzAutoSignalsPicking(spectraData, options) {
|
|
23
23
|
const { sizeToPad = 14, realTopDetection = true, nuclei = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
|
|
24
24
|
let { thresholdFactor = 0.5 } = options;
|
|
25
|
-
if (isAnyArray(observedFrequencies)) {
|
|
25
|
+
if (!isAnyArray(observedFrequencies)) {
|
|
26
26
|
throw new Error('observedFrequencies is mandatory');
|
|
27
27
|
}
|
|
28
28
|
thresholdFactor = thresholdFactor === 0 ? 1 : Math.abs(thresholdFactor);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyzAutoSignalsPicking.js","sourceRoot":"","sources":["../../src/xyz/xyzAutoSignalsPicking.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAEhD,OAAO,KAAK,WAAW,MAAM,uBAAuB,CAAC;AACrD,OAAO,KAAK,iBAAiB,MAAM,wBAAwB,CAAC;AAE5D,OAAO,gBAAgB,MAAM,sBAAsB,CAAC;AAEpD,OAAO,EAAE,aAAa,EAAE,MAAM,6BAA6B,CAAC;AAC5D,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAClE,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,OAAO,KAAK,aAAa,MAAM,6BAA6B,CAAC;AAI7D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAC;
|
|
1
|
+
{"version":3,"file":"xyzAutoSignalsPicking.js","sourceRoot":"","sources":["../../src/xyz/xyzAutoSignalsPicking.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,EAAE,IAAI,UAAU,EAAE,MAAM,cAAc,CAAC;AAEhD,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAC;AAC1C,OAAO,KAAK,WAAW,MAAM,uBAAuB,CAAC;AACrD,OAAO,KAAK,iBAAiB,MAAM,wBAAwB,CAAC;AAE5D,OAAO,gBAAgB,MAAM,sBAAsB,CAAC;AAEpD,OAAO,EAAE,aAAa,EAAE,MAAM,6BAA6B,CAAC;AAC5D,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAClE,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,OAAO,KAAK,aAAa,MAAM,6BAA6B,CAAC;AAI7D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAC;AAEzC,MAAM,WAAW,GAAG;IAClB,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IACjC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IACjC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IACjC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IAC3B,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;CAC5B,CAAC;AA+DF,MAAM,UAAU,qBAAqB,CACnC,WAA6B,EAC7B,OAAqC;IAErC,MAAM,EACJ,SAAS,GAAG,EAAE,EACd,gBAAgB,GAAG,IAAI,EACvB,MAAM,GAAG,CAAC,IAAI,EAAE,IAAI,CAAC,EACrB,mBAAmB,EACnB,eAAe,GAAG,KAAK,EACvB,KAAK,GAAG,IAAI,EACZ,gBAAgB,GAAG,IAAI,EACvB,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,EACrB,gBAAgB,GAAG,IAAI,EACvB,MAAM,EAAE,aAAa,GACtB,GAAG,OAAO,CAAC;IAEZ,IAAI,EAAE,eAAe,GAAG,GAAG,EAAE,GAAG,OAAO,CAAC;IAExC,IAAI,CAAC,UAAU,CAAC,mBAAmB,CAAC,EAAE;QACpC,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAC;KACrD;IAED,eAAe,GAAG,eAAe,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC;IAExE,IAAI,QAAQ,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;IACvC,IAAI,YAAY,GAAG,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC;IAExC,IAAI,YAAY,GAAG,SAAS,EAAE;QAC5B,WAAW,GAAG,OAAO,CAAC,WAAW,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC,CAAC;QACzD,QAAQ,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;QACnC,YAAY,GAAG,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC;KACrC;IAED,MAAM,YAAY,GAAG,IAAI,YAAY,CAAC,QAAQ,GAAG,YAAY,CAAC,CAAC;IAC/D,MAAM,YAAY,GAAG,IAAI,YAAY,CAAC,QAAQ,GAAG,YAAY,CAAC,CAAC;IAE/D,KAAK,IAAI,WAAW,GAAG,CAAC,EAAE,WAAW,GAAG,YAAY,EAAE,WAAW,EAAE,EAAE;QACnE,MAAM,QAAQ,GAAG,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;QAC5C,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,QAAQ,EAAE,IAAI,EAAE,EAAE;YAC1C,MAAM,KAAK,GAAG,WAAW,GAAG,QAAQ,GAAG,IAAI,CAAC;YAC5C,YAAY,CAAC,KAAK,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;YAC/C,YAAY,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,8CAA8C;SACrF;KACF;IAED,MAAM,MAAM,GAAG,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC;IAEtE,MAAM,kBAAkB,GAAG,gBAAgB;QACzC,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,YAAY,EAAE,MAAM,EAAE;YACpC,IAAI,EAAE,YAAY;YAClB,IAAI,EAAE,QAAQ;SACf,CAAC;QACJ,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,YAAY,EAAE,MAAM,EAAE;YACvC,IAAI,EAAE,YAAY;YAClB,IAAI,EAAE,QAAQ;SACf,CAAC,CAAC;IAEP,IAAI,QAAQ,GAAG,iBAAiB,CAAC,iBAAiB,CAAC,YAAY,EAAE;QAC/D,YAAY;QACZ,YAAY,EAAE,kBAAkB;QAChC,IAAI,EAAE,YAAY;QAClB,IAAI,EAAE,QAAQ;QACd,OAAO,EAAE,eAAe;KACzB,CAAC,CAAC;IAEH,IAAI,KAAK,EAAE;QACT,sEAAsE;QACtE,QAAQ,GAAG,aAAa,CAAC,KAAK,CAAC,QAAQ,EAAE,gBAAgB,CAAC,CAAC;KAC5D;IAED,IAAI,OAAO,GAAG,eAAe,CAAC,aAAa,CAAC,QAAQ,CAAC,EAAE;QACrD,KAAK,EAAE,YAAY;QACnB,KAAK,EAAE,QAAQ;QACf,IAAI,EAAE,WAAW,CAAC,IAAI;QACtB,IAAI,EAAE,WAAW,CAAC,IAAI;QACtB,IAAI,EAAE,WAAW,CAAC,IAAI;QACtB,IAAI,EAAE,WAAW,CAAC,IAAI;QACtB,YAAY;QACZ,YAAY;QACZ,UAAU;QACV,MAAM;QACN,mBAAmB;QACnB,gBAAgB;KACjB,CAAC,CAAC;IAEH,IAAI,eAAe,EAAE;QACnB,OAAO,GAAG,aAAa,CAAC,eAAe,CAAC,OAAO,CAAC,CAAC;KAClD;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AAuBD,SAAS,eAAe,CACtB,KAAU,EACV,OAA+B;IAE/B,MAAM,EACJ,KAAK,EACL,KAAK,EACL,YAAY,EACZ,YAAY,EACZ,mBAAmB,EACnB,UAAU,EACV,MAAM,EACN,gBAAgB,EAChB,IAAI,EACJ,IAAI,EACJ,IAAI,EACJ,IAAI,GACL,GAAG,OAAO,CAAC;IAEZ,MAAM,CAAC,QAAQ,EAAE,QAAQ,CAAC,GAAG,MAAM,CAAC;IACpC,MAAM,CAAC,UAAU,EAAE,UAAU,CAAC,GAAG,UAAU,CAAC;IAC5C,MAAM,CAAC,iBAAiB,EAAE,iBAAiB,CAAC,GAAG,mBAAmB,CAAC;IAEnE,MAAM,EAAE,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IACvC,MAAM,EAAE,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IAEvC,IAAI,gBAAgB,EAAE;QACpB,KAAK,GAAG,gBAAgB,CAAC,KAAK,EAAE;YAC9B,KAAK;YACL,YAAY;YACZ,YAAY;YACZ,IAAI;YACJ,IAAI;YACJ,IAAI;YACJ,IAAI;SACL,CAAC,CAAC;KACJ;IAED,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE;QAC1C,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;QAC1B,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,GAAG,CAAC,CAAC;QAC3B,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,GAAG,CAAC,CAAC;QAC3B,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,IAAI,GAAG,EAAE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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "10.0.
|
|
3
|
+
"version": "10.0.6",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -48,7 +48,7 @@
|
|
|
48
48
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
49
49
|
"md5": "^2.3.0",
|
|
50
50
|
"nmr-xy-testdata": "^0.5.1",
|
|
51
|
-
"openchemlib": "^8.
|
|
51
|
+
"openchemlib": "^8.5.0",
|
|
52
52
|
"prettier": "^3.0.1",
|
|
53
53
|
"rimraf": "^5.0.1",
|
|
54
54
|
"ts-jest": "^29.1.1",
|
|
@@ -9,7 +9,7 @@ export const id = 'baselineCorrection';
|
|
|
9
9
|
export const name = 'Baseline correction';
|
|
10
10
|
export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
|
|
11
11
|
updateXDomain: false,
|
|
12
|
-
updateYDomain:
|
|
12
|
+
updateYDomain: false,
|
|
13
13
|
};
|
|
14
14
|
|
|
15
15
|
export type BaselineAlgorithms = 'airpls' | 'polynomial';
|
|
@@ -1,9 +1,6 @@
|
|
|
1
1
|
import type { Logger } from 'cheminfo-types';
|
|
2
2
|
import type { Molecule } from 'openchemlib/full';
|
|
3
|
-
import {
|
|
4
|
-
getHoseCodesAndInfo,
|
|
5
|
-
groupDiastereotopicAtomIDs,
|
|
6
|
-
} from 'openchemlib-utils';
|
|
3
|
+
import { TopicMolecule } from 'openchemlib-utils';
|
|
7
4
|
|
|
8
5
|
import { PredictionBase1D } from './PredictionBase1D';
|
|
9
6
|
import { PredictionBase2D } from './PredictionBase2D';
|
|
@@ -114,40 +111,20 @@ export async function predict(
|
|
|
114
111
|
} as PredictionOptionsByExperiment,
|
|
115
112
|
} = options;
|
|
116
113
|
|
|
117
|
-
const
|
|
118
|
-
maxSphereSize: predictOptions?.C?.maxSphereSize,
|
|
119
|
-
});
|
|
120
|
-
const {
|
|
121
|
-
diaIDs = [],
|
|
122
|
-
moleculeWithHydrogens,
|
|
123
|
-
hoses,
|
|
124
|
-
molfileWithH,
|
|
125
|
-
distanceMatrix,
|
|
126
|
-
} = hoseCodesAndInfo;
|
|
127
|
-
|
|
128
|
-
const groupedDiaIDs = groupDiastereotopicAtomIDs(
|
|
129
|
-
diaIDs,
|
|
130
|
-
moleculeWithHydrogens,
|
|
131
|
-
);
|
|
114
|
+
const topicMolecule = new TopicMolecule(molecule);
|
|
132
115
|
|
|
133
116
|
const protonPrediction = shouldPredict('H', predictOptions)
|
|
134
|
-
? await predictProton(
|
|
117
|
+
? await predictProton(topicMolecule, {
|
|
135
118
|
...predictOptions?.H,
|
|
136
|
-
diaIDs,
|
|
137
|
-
distanceMatrix,
|
|
138
119
|
})
|
|
139
120
|
: undefined;
|
|
140
121
|
|
|
141
122
|
const carbonPrediction = shouldPredict('C', predictOptions)
|
|
142
|
-
? await predictCarbon(
|
|
143
|
-
...predictOptions?.C,
|
|
144
|
-
molfile: molfileWithH,
|
|
145
|
-
groupedDiaIDs,
|
|
146
|
-
hoses,
|
|
147
|
-
})
|
|
123
|
+
? await predictCarbon(topicMolecule, predictOptions?.C)
|
|
148
124
|
: undefined;
|
|
149
125
|
|
|
150
126
|
const spectra: any = {};
|
|
127
|
+
const diaIDs = topicMolecule.diaIDs;
|
|
151
128
|
const predictions: Record<string, PredictionBase1D> = {};
|
|
152
129
|
if (check1DPrediction(protonPrediction, diaIDs)) {
|
|
153
130
|
predictions.H = protonPrediction;
|
|
@@ -158,20 +135,13 @@ export async function predict(
|
|
|
158
135
|
if ('C' in predictOptions) spectra.carbon = carbonPrediction;
|
|
159
136
|
}
|
|
160
137
|
|
|
161
|
-
const optionsTwoD = {
|
|
162
|
-
predictions,
|
|
163
|
-
joinDistance,
|
|
164
|
-
distanceMatrix,
|
|
165
|
-
groupedDiaIDs,
|
|
166
|
-
diaIDs,
|
|
167
|
-
};
|
|
168
|
-
|
|
169
138
|
for (const key in predictOptions) {
|
|
170
139
|
if (key === 'H' || key === 'C') continue;
|
|
171
140
|
const { predictor, required, message } = toPredict[key as keyof ToPredict];
|
|
172
141
|
if (required.every((key) => key in predictions)) {
|
|
173
|
-
spectra[key] = await predictor(
|
|
174
|
-
|
|
142
|
+
spectra[key] = await predictor(topicMolecule, {
|
|
143
|
+
predictions,
|
|
144
|
+
joinDistance,
|
|
175
145
|
...predictOptions[key as keyof PredictionOptionsByExperiment],
|
|
176
146
|
});
|
|
177
147
|
} else if (logger) {
|
|
@@ -180,8 +150,13 @@ export async function predict(
|
|
|
180
150
|
}
|
|
181
151
|
|
|
182
152
|
return {
|
|
183
|
-
|
|
184
|
-
|
|
153
|
+
diaIDs: topicMolecule.diaIDs,
|
|
154
|
+
hoses: topicMolecule.hoseCodes,
|
|
155
|
+
distanceMatrix: topicMolecule.distanceMatrix,
|
|
156
|
+
moleculeWithHydrogens: topicMolecule.moleculeWithH,
|
|
157
|
+
groupedDiaIDs: topicMolecule.getGroupedDiastereotopicAtomIDs(),
|
|
158
|
+
molfile: topicMolecule.toMolfile(),
|
|
159
|
+
molfileWithH: topicMolecule.toMolfileWithH(),
|
|
185
160
|
spectra,
|
|
186
161
|
};
|
|
187
162
|
}
|
|
@@ -1,8 +1,6 @@
|
|
|
1
|
-
import
|
|
1
|
+
import { TopicMolecule } from 'openchemlib-utils';
|
|
2
2
|
|
|
3
|
-
import { GroupDiastereotopicAtomIDs } from './GroupDiastereotopicAtomIDs';
|
|
4
3
|
import type { PredictionBase1D } from './PredictionBase1D';
|
|
5
|
-
import { PredictProtonOptions } from './predictProton';
|
|
6
4
|
import { predict2D } from './utils/predict2D';
|
|
7
5
|
|
|
8
6
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export interface PredictCOSYOptions {
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@@ -16,11 +14,6 @@ export interface PredictCOSYOptions {
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* @default 2
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*/
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minLength?: number;
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19
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-
/**
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20
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-
* mono dimensional signal to generate the bidimenionals cross peaks.
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21
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* The object should has properties with name equal to "H" and "C".
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-
*/
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23
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-
predictOptions?: { H?: PredictProtonOptions };
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17
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/**
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* signals with euclidean distance in ppm less than this it will
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* joined into a zone.
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@@ -41,15 +34,6 @@ export interface PredictCOSYOptions {
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41
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* @default true
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42
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*/
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includeDiagonal?: boolean;
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44
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-
/**
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45
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* diastereotopic atom ids of the molecule.
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46
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-
*/
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47
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-
diaIDs: string[];
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48
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/**
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49
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* grouped diastereotopic atom ids of the molecule.
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50
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-
*/
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51
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-
groupedDiaIDs: GroupDiastereotopicAtomIDs[];
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52
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-
distanceMatrix: number[][];
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53
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}
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54
38
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/**
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55
39
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* Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
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@@ -57,7 +41,7 @@ export interface PredictCOSYOptions {
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57
41
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*/
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58
42
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59
43
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export async function predictCOSY(
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60
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-
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44
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+
topicMolecule: TopicMolecule,
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61
45
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options: PredictCOSYOptions,
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62
46
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) {
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63
47
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const {
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@@ -67,7 +51,7 @@ export async function predictCOSY(
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67
51
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includeDiagonal = true,
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68
52
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} = options;
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69
53
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70
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-
return predict2D(
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54
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+
return predict2D(topicMolecule, {
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71
55
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...options,
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72
56
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from: 'H',
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73
57
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to: 'H',
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