nmr-processing 9.3.1 → 9.3.3
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.js.map +1 -1
- package/lib/assignment/get1HAssignments.js.map +1 -1
- package/lib/assignment/getAssignments.js.map +1 -1
- package/lib/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
- package/lib/prediction/predictAll.js +3 -1
- package/lib/prediction/predictAll.js.map +1 -1
- package/lib/prediction/predictAllSpectra.js +2 -2
- package/lib/prediction/predictAllSpectra.js.map +1 -1
- package/lib/prediction/predictCarbon.d.ts +4 -0
- package/lib/prediction/predictCarbon.js +5 -4
- package/lib/prediction/predictCarbon.js.map +1 -1
- package/lib/prediction/predictProton.d.ts +4 -0
- package/lib/prediction/predictProton.js +1 -1
- package/lib/prediction/predictProton.js.map +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/predict2D.d.ts +4 -0
- package/lib/prediction/utils/predict2D.js +5 -3
- package/lib/prediction/utils/predict2D.js.map +1 -1
- package/lib/ranges/rangesToACS.js +14 -12
- package/lib/ranges/rangesToACS.js.map +1 -1
- package/lib/signal/signalMultiplicityPattern.js +1 -1
- package/lib/signal/signalMultiplicityPattern.js.map +1 -1
- package/lib-esm/assignment/get13CAssignments.js.map +1 -1
- package/lib-esm/assignment/get1HAssignments.js.map +1 -1
- package/lib-esm/assignment/getAssignments.js.map +1 -1
- package/lib-esm/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
- package/lib-esm/prediction/predictAll.js +3 -1
- package/lib-esm/prediction/predictAll.js.map +1 -1
- package/lib-esm/prediction/predictAllSpectra.js +2 -2
- package/lib-esm/prediction/predictAllSpectra.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 +6 -4
- package/lib-esm/prediction/utils/predict2D.js.map +1 -1
- package/lib-esm/ranges/rangesToACS.js +14 -12
- package/lib-esm/ranges/rangesToACS.js.map +1 -1
- package/lib-esm/signal/signalMultiplicityPattern.js +1 -1
- package/lib-esm/signal/signalMultiplicityPattern.js.map +1 -1
- package/package.json +3 -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 +9 -0
- package/src/prediction/predictAll.ts +4 -1
- package/src/prediction/predictAllSpectra.ts +2 -2
- package/src/prediction/predictCarbon.ts +16 -9
- package/src/prediction/predictProton.ts +6 -2
- package/src/prediction/utils/getFilteredIDiaIDs.ts +13 -14
- package/src/prediction/utils/predict2D.ts +14 -6
- package/src/ranges/rangesToACS.ts +19 -11
- package/src/signal/signalMultiplicityPattern.ts +1 -1
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-
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{"version":3,"file":"predictAllSpectra.js","sourceRoot":"","sources":["../../src/prediction/predictAllSpectra.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,UAAU,EAAE,MAAM,cAAc,CAAC;AA8B7D,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,QAAkB,EAClB,UAAoC,EAAE;IAEtC,MAAM,EACJ,UAAU,EAAE,iBAAiB,GAAG,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAuB,EAC3E,UAAU,EAAE,iBAAiB,GAAG,EAAE,GACnC,GAAG,OAAO,CAAC;IAEZ,MAAM,WAAW,GAAG,MAAM,UAAU,CAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC;IAClE,MAAM,OAAO,GAAU,EAAE,CAAC;IAC1B,MAAM,MAAM,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,CAAC,EAAE,OAAO,EAAE,WAAW,CAAC,OAAO,EAAE,CAAC,EAAE,CAAC;IAE1E,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,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,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE;QACpC,QAAQ,UAAU,EAAE;YAClB,KAAK,QAAQ,CAAC;YACd,KAAK,QAAQ,CAAC,CAAC;gBACb,OAAO,CAAC,IAAI,CACV,aAAa,CAAC,WAAW,CAAC,UAAU,CAAC,EAAE;oBACrC,QAAQ,EAAE,WAAW,CAAC,QAAQ;oBAC9B,SAAS,EAAE,WAAW,CAAC,SAAS;oBAChC,GAAG,WAAW,CAAC,UAAU,CAAC;oBAC1B,UAAU;oBACV,SAAS,EAAE,iBAAiB,CAAC,SAAS;iBACvC,CAAC,CACH,CAAC;gBACF,MAAM;aACP;YACD,KAAK,MAAM,CAAC;YACZ,KAAK,MAAM,CAAC;YACZ,KAAK,MAAM,CAAC,CAAC;gBACX,OAAO,CAAC,IAAI,CACV,aAAa,CAAC,WAAW,CAAC,UAAU,CAAC,EAAE;oBACrC,GAAG,WAAW;oBACd,UAAU;oBACV,SAAS,EAAE,iBAAiB,CAAC,SAAS;iBACvC,CAAC,CACH,CAAC;gBACF,MAAM;aACP;YACD;gBACE,MAAM;SACT;KACF;IAED,OAAO,MAAM,CAAC;AAChB,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,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"}
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import { v4 as generateID } from '@lukeed/uuid';
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import fetch from 'cross-fetch';
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import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
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import { setIDs } from '../peaks/util/setIDs';
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import { signalsToRanges } from '../signals/signalsToRanges';
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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 { queryByHose } from './utils/queryByHOSE';
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const cache = {};
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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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export async function predictCarbon(molecule, options = {}) {
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let { url, database, webserviceURL } = options;
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let { url, database, webserviceURL, diaIDs = getDiastereotopicAtomIDs(molecule), } = options;
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if (webserviceURL) {
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return fetchPrediction(molecule, { webserviceURL });
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}
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let { maxSphereSize = maxLevel } = options;
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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 } = getFilteredIDiaIDs(molecule, {
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let predictions = queryByHose(carbonDiaIDs, database, {
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return {
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nucleus: '13C',
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diaIDs,
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{"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;AAChC,OAAO,EAAE,wBAAwB,EAAE,MAAM,mBAAmB,CAAC;AAG7D,OAAO,EAAE,MAAM,EAAE,MAAM,sBAAsB,CAAC;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,4BAA4B,CAAC;AAK7D,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAC1D,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAChE,OAAO,EAAc,WAAW,EAAE,MAAM,qBAAqB,CAAC;AAE9D,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;
|
|
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;AACjC,OAAO,EACL,iCAAiC,EACjC,qBAAqB,EACrB,wBAAwB,GACzB,MAAM,mBAAmB,CAAC;AAI3B,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, groupDiastereotopicAtomIDs, } 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 = groupDiastereotopicAtomIDs(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":"
|
|
1
|
+
{"version":3,"file":"getFilteredIDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/getFilteredIDiaIDs.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,gCAAgC,EAChC,iCAAiC,EACjC,0BAA0B,GAC3B,MAAM,mBAAmB,CAAC;AAU3B,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,0BAA0B,CAAC,MAAM,EAAE,QAAQ,EAAE;QAC/D,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, groupDiastereotopicAtomIDs, } 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 +12,19 @@ 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
|
|
24
|
+
? groupDiastereotopicAtomIDs(diaIDs, molecule)
|
|
25
|
+
: getGroupedDiastereotopicAtomIDs(molecule);
|
|
24
26
|
let diaIDswithAtomInfo = [];
|
|
25
|
-
for (let diaID of
|
|
27
|
+
for (let diaID of groupedDiaIDS) {
|
|
26
28
|
diaIDswithAtomInfo.push({
|
|
27
29
|
...diaID,
|
|
28
30
|
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;
|
|
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;AACnC,OAAO,EACL,+BAA+B,EAC/B,YAAY,EACZ,0BAA0B,GAC3B,MAAM,mBAAmB,CAAC;AAQ3B,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;QAC1B,CAAC,CAAC,0BAA0B,CAAC,MAAM,EAAE,QAAQ,CAAC;QAC9C,CAAC,CAAC,+BAA+B,CAAC,QAAQ,CAAC,CAAC;IAE9C,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,GA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|
|
@@ -95,19 +95,21 @@ function pushDelta(range, acsRanges, options) {
|
|
|
95
95
|
}
|
|
96
96
|
strings += `${Math.min(...fromTo).toFixed(options.nbDecimalDelta)}-${Math.max(...fromTo).toFixed(options.nbDecimalDelta)}`;
|
|
97
97
|
strings += ` (${getIntegral(range, options)}`;
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
|
|
102
|
-
|
|
98
|
+
if (signals.some((signal) => signal.multiplicity || (signal.js && signal.js.length > 0))) {
|
|
99
|
+
for (let signal of signals) {
|
|
100
|
+
parenthesis = [];
|
|
101
|
+
if (signal.delta !== undefined) {
|
|
102
|
+
strings = appendSeparator(strings);
|
|
103
|
+
strings += signal.delta.toFixed(options.nbDecimalDelta);
|
|
104
|
+
}
|
|
105
|
+
const range = {
|
|
106
|
+
from: Number.MIN_SAFE_INTEGER,
|
|
107
|
+
to: Number.MAX_SAFE_INTEGER,
|
|
108
|
+
};
|
|
109
|
+
switchFormat(range, signal, parenthesis, options);
|
|
110
|
+
if (parenthesis.length > 0)
|
|
111
|
+
strings += ` (${parenthesis.join(', ')})`;
|
|
103
112
|
}
|
|
104
|
-
const range = {
|
|
105
|
-
from: Number.MIN_SAFE_INTEGER,
|
|
106
|
-
to: Number.MAX_SAFE_INTEGER,
|
|
107
|
-
};
|
|
108
|
-
switchFormat(range, signal, parenthesis, options);
|
|
109
|
-
if (parenthesis.length > 0)
|
|
110
|
-
strings += ` (${parenthesis.join(', ')})`;
|
|
111
113
|
}
|
|
112
114
|
strings += ')';
|
|
113
115
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"signalMultiplicityPattern.js","sourceRoot":"","sources":["../../src/signal/signalMultiplicityPattern.ts"],"names":[],"mappings":"AACA;;;GAGG;AAEH,MAAM,UAAU,yBAAyB,CAAC,MAAmB;IAC3D,IAAI,EAAE,GAAG,MAAM,CAAC,EAAE,CAAC;IACnB,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,IAAI,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE;QACvB,KAAK,IAAI,QAAQ,IAAI,EAAE,EAAE;YACvB,OAAO,IAAI,QAAQ,CAAC,YAAY,CAAC;SAClC;KACF;SAAM,IAAI,MAAM,CAAC,KAAK,EAAE;QACvB,OAAO,GAAG,
|
|
1
|
+
{"version":3,"file":"signalMultiplicityPattern.js","sourceRoot":"","sources":["../../src/signal/signalMultiplicityPattern.ts"],"names":[],"mappings":"AACA;;;GAGG;AAEH,MAAM,UAAU,yBAAyB,CAAC,MAAmB;IAC3D,IAAI,EAAE,GAAG,MAAM,CAAC,EAAE,CAAC;IACnB,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,IAAI,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,EAAE;QACvB,KAAK,IAAI,QAAQ,IAAI,EAAE,EAAE;YACvB,OAAO,IAAI,QAAQ,CAAC,YAAY,CAAC;SAClC;KACF;SAAM,IAAI,MAAM,CAAC,KAAK,EAAE;QACvB,OAAO,GAAG,EAAE,CAAC;KACd;SAAM;QACL,OAAO,GAAG,GAAG,CAAC;KACf;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "9.3.
|
|
3
|
+
"version": "9.3.3",
|
|
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 +77,8 @@
|
|
|
77
77
|
"ml-spectra-processing": "^11.14.0",
|
|
78
78
|
"ml-tree-set": "^0.1.1",
|
|
79
79
|
"nmr-correlation": "^2.3.3",
|
|
80
|
-
"
|
|
80
|
+
"nmredata": "^0.9.2",
|
|
81
|
+
"openchemlib-utils": "^2.1.2",
|
|
81
82
|
"spectrum-generator": "^8.0.6"
|
|
82
83
|
}
|
|
83
84
|
}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
|
-
import { Molecule } from 'openchemlib/full';
|
|
3
2
|
import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
|
|
3
|
+
import { Molecule } from 'openchemlib/full';
|
|
4
4
|
|
|
5
5
|
import { NMRRange, NMRRangeWithIntegration } from '..';
|
|
6
6
|
import {
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { Molecule } from 'openchemlib/full';
|
|
2
1
|
import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
|
|
2
|
+
import { Molecule } from 'openchemlib/full';
|
|
3
3
|
|
|
4
4
|
import { NMRSignal1D } from '..';
|
|
5
5
|
import type { PredictCarbonOptions } from '../prediction/predictCarbon';
|
|
@@ -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 +158,10 @@ declare module 'openchemlib-utils' {
|
|
|
155
158
|
): number[][] | Float64Array[];
|
|
156
159
|
|
|
157
160
|
function getDiastereotopicAtomIDs(molecule: Molecule): string[];
|
|
161
|
+
|
|
162
|
+
function groupDiastereotopicAtomIDs(
|
|
163
|
+
diaIDs: string[],
|
|
164
|
+
molecule: Molecule,
|
|
165
|
+
options?: { atomLabel: string },
|
|
166
|
+
): GroupedDiastereotopicAtomIDs;
|
|
158
167
|
}
|
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
1
2
|
import type { Molecule } from 'openchemlib/full';
|
|
2
3
|
|
|
3
4
|
import type { Prediction1D } from './Prediction1D';
|
|
@@ -75,6 +76,8 @@ export async function predictAll(
|
|
|
75
76
|
predictOptions = {},
|
|
76
77
|
} = options;
|
|
77
78
|
|
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+
const diaIDs = getDiastereotopicAtomIDs(molecule);
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+
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const xPrediction = await getPredictions(
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from,
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molecule,
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@@ -100,7 +103,7 @@ export async function predictAll(
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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: any = {
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proton: predictions.H,
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@@ -114,14 +114,14 @@ function get2DSpectrum(prediction: any, options: Get2DSpectrumOptions) {
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const width = get2DWidth(nuclei);
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const frequency = calculateFrequency(nuclei, baseFrequency);
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const
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const minMaxContent = signals2DToZ(signals, {
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...options,
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width,
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factor: 3,
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});
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const spectrum = {
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data: { ...
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data: { rr: { ...minMaxContent, noise: 0.01 } },
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info: {
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nucleus: nuclei,
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originFrequency: frequency,
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@@ -1,5 +1,6 @@
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1
1
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import { v4 as generateID } from '@lukeed/uuid';
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2
2
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import fetch from 'cross-fetch';
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3
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+
import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
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3
4
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import type { Molecule } from 'openchemlib/full';
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4
5
|
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5
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import { setIDs } from '../peaks/util/setIDs';
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@@ -10,7 +11,6 @@ import type { MakeMandatory } from '../utilities/MakeMandatory';
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import type { Prediction1D } from './Prediction1D';
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import type { DataBaseStructure } from './dataStructure';
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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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16
|
|
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@@ -48,6 +48,10 @@ 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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|
+
*/
|
|
54
|
+
diaIDs?: string[];
|
|
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55
|
}
|
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52
56
|
|
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|
export type PredictCarbon = typeof predictCarbon;
|
|
@@ -72,7 +76,12 @@ export async function predictCarbon(
|
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molecule: Molecule,
|
|
73
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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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|
+
url,
|
|
81
|
+
database,
|
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82
|
+
webserviceURL,
|
|
83
|
+
diaIDs = getDiastereotopicAtomIDs(molecule),
|
|
84
|
+
} = options;
|
|
76
85
|
|
|
77
86
|
if (webserviceURL) {
|
|
78
87
|
return fetchPrediction(molecule, { webserviceURL });
|
|
@@ -90,12 +99,10 @@ export async function predictCarbon(
|
|
|
90
99
|
|
|
91
100
|
if (maxSphereSize > maxLevel) maxSphereSize = maxLevel;
|
|
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|
|
|
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|
-
const {
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
},
|
|
98
|
-
);
|
|
102
|
+
const { carbonDiaIDs, molfile } = getFilteredIDiaIDs(molecule, {
|
|
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|
+
maxSphereSize,
|
|
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|
+
diaIDs,
|
|
105
|
+
});
|
|
99
106
|
|
|
100
107
|
let predictions = queryByHose(carbonDiaIDs, database, {
|
|
101
108
|
maxSphereSize,
|
|
@@ -106,7 +113,7 @@ export async function predictCarbon(
|
|
|
106
113
|
return {
|
|
107
114
|
molfile,
|
|
108
115
|
nucleus: '13C',
|
|
109
|
-
diaIDs
|
|
116
|
+
diaIDs,
|
|
110
117
|
joinedSignals,
|
|
111
118
|
signals,
|
|
112
119
|
ranges: signalsToRanges(joinedSignals),
|
|
@@ -1,12 +1,12 @@
|
|
|
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/full';
|
|
5
4
|
import {
|
|
6
5
|
addDiastereotopicMissingChirality,
|
|
7
6
|
getConnectivityMatrix,
|
|
8
7
|
getDiastereotopicAtomIDs,
|
|
9
8
|
} from 'openchemlib-utils';
|
|
9
|
+
import type { Molecule } from 'openchemlib/full';
|
|
10
10
|
|
|
11
11
|
import type { NMRSignal1D } from '../signals/NMRSignal1D';
|
|
12
12
|
import { signalsJoin } from '../signals/signalsJoin';
|
|
@@ -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 {
|
|
@@ -1,10 +1,10 @@
|
|
|
1
|
-
import type { Molecule } from 'openchemlib/full';
|
|
2
1
|
import {
|
|
3
|
-
getGroupedDiastereotopicAtomIDs,
|
|
4
2
|
getHoseCodesFromDiastereotopicID,
|
|
5
3
|
addDiastereotopicMissingChirality,
|
|
4
|
+
groupDiastereotopicAtomIDs,
|
|
6
5
|
} from 'openchemlib-utils';
|
|
7
6
|
import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
7
|
+
import type { Molecule } from 'openchemlib/full';
|
|
8
8
|
|
|
9
9
|
export interface GroupDiaIDsWithHose extends GroupDiastereotopicAtomIDs {
|
|
10
10
|
hose: string[];
|
|
@@ -14,9 +14,9 @@ export type GroupedDiaIDsWithHose = GroupDiaIDsWithHose[];
|
|
|
14
14
|
|
|
15
15
|
export function getFilteredIDiaIDs(
|
|
16
16
|
molecule: Molecule,
|
|
17
|
-
options: { maxSphereSize: number },
|
|
17
|
+
options: { maxSphereSize: number; diaIDs: string[] },
|
|
18
18
|
) {
|
|
19
|
-
const { maxSphereSize } = options;
|
|
19
|
+
const { maxSphereSize, diaIDs } = options;
|
|
20
20
|
|
|
21
21
|
molecule.addImplicitHydrogens();
|
|
22
22
|
molecule.addMissingChirality();
|
|
@@ -24,16 +24,16 @@ export function getFilteredIDiaIDs(
|
|
|
24
24
|
|
|
25
25
|
const molfile = molecule.toMolfile();
|
|
26
26
|
|
|
27
|
-
let groupedDiaIDs =
|
|
27
|
+
let groupedDiaIDs = groupDiastereotopicAtomIDs(diaIDs, molecule, {
|
|
28
|
+
atomLabel: 'C',
|
|
29
|
+
});
|
|
28
30
|
|
|
29
|
-
let carbonDiaIDs = groupedDiaIDs
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
return a.atomLabel < b.atomLabel ? 1 : -1;
|
|
36
|
-
}) as any;
|
|
31
|
+
let carbonDiaIDs = groupedDiaIDs.sort((a, b) => {
|
|
32
|
+
if (a.atomLabel === b.atomLabel) {
|
|
33
|
+
return b.counter - a.counter;
|
|
34
|
+
}
|
|
35
|
+
return a.atomLabel < b.atomLabel ? 1 : -1;
|
|
36
|
+
}) as any;
|
|
37
37
|
|
|
38
38
|
const OCL = molecule.getOCL();
|
|
39
39
|
for (const diaId of carbonDiaIDs) {
|
|
@@ -48,7 +48,6 @@ export function getFilteredIDiaIDs(
|
|
|
48
48
|
let toReturn = {
|
|
49
49
|
molfile,
|
|
50
50
|
carbonDiaIDs: carbonDiaIDs as GroupedDiaIDsWithHose,
|
|
51
|
-
groupedDiaIDs,
|
|
52
51
|
};
|
|
53
52
|
|
|
54
53
|
return toReturn;
|