nmr-processing 9.3.0 → 9.3.1-pre.1669891843
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/apodization/shapes/WindowFunctions.d.ts +1 -1
- package/lib/assignment/get13CAssignments.d.ts +1 -1
- package/lib/assignment/get13CAssignments.js.map +1 -1
- package/lib/assignment/get1HAssignments.d.ts +3 -3
- package/lib/assignment/get1HAssignments.js.map +1 -1
- package/lib/assignment/getAssignments.d.ts +2 -2
- package/lib/assignment/getAssignments.js.map +1 -1
- package/lib/assignment/nmrAssigment.d.ts +3 -3
- package/lib/assignment/utils/createMapPossibleAssignments.d.ts +1 -1
- package/lib/assignment/utils/getAssignment/buildAssignments.d.ts +4 -4
- package/lib/assignment/utils/getAssignment/buildAssignments.js.map +1 -1
- package/lib/assignment/utils/getAssignment/formatData.d.ts +1 -1
- package/lib/peaks/peaksFilterImpurities.d.ts +1 -1
- package/lib/peaks/peaksToRanges.d.ts +1 -1
- package/lib/peaks/peaksToRanges.js +20 -19
- package/lib/peaks/peaksToRanges.js.map +1 -1
- package/lib/peaks/util/convertWidth.d.ts +1 -1
- package/lib/peaks/util/convertWidthToHz.d.ts +1 -1
- package/lib/prediction/Prediction1D.d.ts +1 -1
- package/lib/prediction/dataStructure.d.ts +1 -1
- package/lib/prediction/predictAll.d.ts +1 -1
- package/lib/prediction/predictAll.js +3 -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 +6 -2
- 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 +6 -2
- 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 +3 -4
- 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 +6 -2
- package/lib/prediction/utils/predict2D.js +5 -3
- package/lib/prediction/utils/predict2D.js.map +1 -1
- package/lib/signals/optimization/getInternalSignals.d.ts +3 -3
- package/lib/signals/optimization/getSumOfShapes.d.ts +1 -1
- package/lib/signals/optimizeSignals.d.ts +1 -1
- package/lib/signals/signalsJoin.d.ts +3 -3
- package/lib/signals/signalsToRanges.d.ts +1 -1
- package/lib/signals/utils/jAnalyzer.d.ts +2 -2
- package/lib/utilities/MakeMandatory.d.ts +1 -1
- package/lib/utilities/getFrequency.d.ts +1 -1
- package/lib/utilities/hasProperty.d.ts +1 -1
- package/lib/xy/xyAutoPeaksPicking.d.ts +1 -1
- package/lib/xy/xyAutoPeaksPicking.js +4 -1
- package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
- package/lib/xyz/xyzAutoZonesPicking.d.ts +2 -2
- 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/peaks/peaksToRanges.js +20 -19
- package/lib-esm/peaks/peaksToRanges.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/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/xy/xyAutoPeaksPicking.js +4 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/package.json +8 -7
- 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 +10 -1
- package/src/peaks/peaksToRanges.ts +23 -19
- package/src/prediction/Prediction1D.ts +1 -1
- package/src/prediction/predictAll.ts +5 -2
- package/src/prediction/predictAllSpectra.ts +1 -1
- package/src/prediction/predictCOSY.ts +1 -1
- package/src/prediction/predictCarbon.ts +17 -10
- 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 -14
- package/src/prediction/utils/getPredictions.ts +1 -1
- package/src/prediction/utils/predict2D.ts +14 -6
- package/src/utilities/hasProperty.ts +1 -1
- package/src/xy/xyAutoPeaksPicking.ts +5 -1
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{"version":3,"file":"get13CAssignments.js","sourceRoot":"","sources":["../../src/assignment/get13CAssignments.ts"],"names":[],"mappings":";;;AAAA,uCAAgD;AAChD,yDAAsE;AAItE,+DAGqC;AAOrC,+DAA+E;AAE/E,SAAS,mBAAmB,CAC1B,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAC;QACpE,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;QACtE,IAAI,CAAC,MAAM,CAAC,OAAO;YAAE,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACzE;AACH,CAAC;AAED,SAAS,gBAAgB,CAAC,MAAkB;IAC1C,KAAK,IAAI,KAAK,IAAI,MAAM,EAAE;QACxB,IAAI,KAAK,CAAC,WAAW,KAAK,SAAS;YAAE,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC;KAC5D;IACD,OAAO,MAAmC,CAAC;AAC7C,CAAC;AA8BM,KAAK,UAAU,iBAAiB,CACrC,MAAkB,EAClB,QAAkB,EAClB,UAAoC,EAAE;IAEtC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,QAAQ,GAAG,CAAC,EACZ,YAAY,GAAG,EAAE,EACjB,mBAAmB,GAAG,CAAC,EACvB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,GACvB,GAAG,OAAO,CAAC;IAEZ,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,gDAAgD,CAAC,CAAC;KACnE;IAED,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,IAAA,6BAAa,EAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC;IAE3E,mBAAmB,CAAC,aAAa,CAAC,CAAC;IACnC,MAAM,UAAU,GAAG,gBAAgB,CAAC,MAAM,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAY,EAAE,CAAC;IAC5B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE;QAC9B,MAAM,EAAE,EAAE,GAAG,IAAA,SAAU,GAAE,EAAE,GAAG,KAAK,CAAC;QACpC,OAAO,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC;KACjD;IAED,OAAO,IAAA,mCAAgB,EAAC;QACtB,eAAe;QACf,OAAO;QACP,QAAQ;QACR,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,aAAa;QACb,yBAAyB,EAAE,KAAK;KACjC,CAAC,CAAC;AACL,CAAC;AAxCD,8CAwCC"}
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import { Molecule } from 'openchemlib';
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import { Molecule } from 'openchemlib/full';
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import { NMRRange } from '..';
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import { PredictProtonOptions } from '../prediction/predictProton';
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import type { NMRSignal1D } from '../signals/NMRSignal1D';
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import { MakeMandatory } from '../utilities/MakeMandatory';
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import { RestrictionByCS1D } from './utils/buildAssignments';
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export
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export
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export type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<NMRSignal1D, 'atoms' | 'diaIDs' | 'nbAtoms'>;
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export type NMRRangeWithIntegration = MakeMandatory<NMRRange, 'integration'>;
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export interface Get1HAssignmentsOptions {
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restrictionByCS?: Partial<RestrictionByCS1D>;
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/**
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{"version":3,"file":"get1HAssignments.js","sourceRoot":"","sources":["../../src/assignment/get1HAssignments.ts"],"names":[],"mappings":";;;AAAA,uCAAgD;
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{"version":3,"file":"get1HAssignments.js","sourceRoot":"","sources":["../../src/assignment/get1HAssignments.ts"],"names":[],"mappings":";;;AAAA,uCAAgD;AAChD,yDAAsE;AAItE,+DAGqC;AAIrC,+DAA+E;AAO/E,SAAS,mBAAmB,CAC1B,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAC;QACpE,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;QACtE,IAAI,CAAC,MAAM,CAAC,OAAO;YAAE,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACzE;AACH,CAAC;AAID,SAAS,mBAAmB,CAC1B,MAAkB;IAElB,KAAK,IAAI,KAAK,IAAI,MAAM,EAAE;QACxB,IAAI,KAAK,CAAC,WAAW,KAAK,SAAS,EAAE;YACnC,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAC;SACxD;KACF;AACH,CAAC;AAkCM,KAAK,UAAU,gBAAgB,CACpC,MAAkB,EAClB,QAAkB,EAClB,UAAmC,EAAE;IAErC,IAAI,EACF,eAAe,EACf,QAAQ,GAAG,CAAC,EACZ,YAAY,GAAG,EAAE,EACjB,mBAAmB,GAAG,CAAC,EACvB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,GACvB,GAAG,OAAO,CAAC;IAEZ,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,gDAAgD,CAAC,CAAC;KACnE;IAED,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,IAAA,6BAAa,EAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC;IAE3E,mBAAmB,CAAC,MAAM,CAAC,CAAC;IAC5B,mBAAmB,CAAC,aAAa,CAAC,CAAC;IAEnC,MAAM,OAAO,GAAY,EAAE,CAAC;IAC5B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,MAAM,EAAE,EAAE,GAAG,IAAA,SAAU,GAAE,EAAE,GAAG,KAAK,CAAC;QACpC,OAAO,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC;KACjD;IAED,OAAO,IAAA,mCAAgB,EAAC;QACtB,eAAe;QACf,OAAO;QACP,QAAQ;QACR,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,aAAa;QACb,yBAAyB,EAAE,IAAI;KAChC,CAAC,CAAC;AACL,CAAC;AA1CD,4CA0CC"}
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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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*/
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info: any;
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}
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export type SpectraData = SpectraData1D | SpectraData2D;
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export interface GetAutoAssignmentInput {
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spectra: SpectraData[];
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/**
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{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":";;;;;;
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{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":";;;;;;AAAA,yDAAsE;AAStE,6EAIgD;AAChD,6DAA0D;AAC1D,+FAA4F;AAC5F,oFAA4D;AA0ErD,KAAK,UAAU,cAAc,CAClC,KAA6B,EAC7B,UAAiC,EAAE;IAEnC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,UAAU,EACV,QAAQ,GAAG,IAAI,EACf,YAAY,GAAG,EAAE,EACjB,mBAAmB,EACnB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,EACtB,WAAW,GAAG,EAAE,EAChB,WAAW,EAAE,kBAAkB,GAAG,EAAE,GACrC,GAAG,OAAO,CAAC;IAEZ,MAAM,EACJ,SAAS,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,EAC5B,qBAAqB,GAAG,KAAK,EAC7B,wBAAwB,GAAG,IAAI,GAChC,GAAG,eAAe,CAAC;IAEpB,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAEhC,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IAEpE,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,IAAA,mBAAQ,EAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAA,qDAAyB,EACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,qBAAW,EAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,IAAA,mCAAgB,EAAC;QACvC,eAAe,EAAE;YACf,SAAS;YACT,qBAAqB;YACrB,wBAAwB;SACzB;QACD,OAAO;QACP,QAAQ;QACR,OAAO;QACP,QAAQ;QACR,YAAY;QACZ,eAAe;QACf,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,iBAAiB;QACjB,WAAW;KACZ,CAAC,CAAC;IAEH,OAAO,SAAS,CAAC;AACnB,CAAC;AAzDD,wCAyDC"}
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import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '..';
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export type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
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export type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
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export type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
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type RestrictionByCSMandatory = MakeMandatory<RestrictionByCS1D, 'chemicalShiftRestriction' | 'tolerance' | 'useChemicalShiftScore'>;
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type NMRSignal1DFromPrediction = MakeMandatory<NMRSignal1D, 'nbAtoms' | 'diaIDs' | 'atoms'>;
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{"version":3,"file":"buildAssignments.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/buildAssignments.ts"],"names":[],"mappings":";;;;;;AAAA,8DAAkC;
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{"version":3,"file":"buildAssignments.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/buildAssignments.ts"],"names":[],"mappings":";;;;;;AAAA,8DAAkC;AAElC,yDAA0D;AAQ1D,qEAAkE;AAClE,qEAAkE;AAKlE,+EAGuC;AACvC,+CAAgE;AAEhE,uDAAoD;AACpD,mDAAgD;AAEhD,MAAM,UAAU,GAAG,CAAC,CAAqB,EAAE,CAAqB,EAAE,EAAE;IAClE,OAAO,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;AAC3B,CAAC,CAAC;AAEF,MAAM,SAAS,GAAG,EAAE,CAAC,EAAE,6BAAa,EAAE,CAAC,EAAE,6BAAa,EAAE,CAAC;AA4CzD,SAAS,gBAAgB,CACvB,OAAsB;IAEtB,MAAM,IAAI,GAA0C;QAClD,SAAS;QACT,QAAQ;QACR,OAAO;KACR,CAAC;IACF,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,KAAK,IAAI,GAAG,IAAI,IAAI,EAAE;YACpB,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC;gBAAE,MAAM,IAAI,KAAK,CAAC,YAAY,GAAG,iBAAiB,CAAC,CAAC;SACrE;KACF;AACH,CAAC;AAyBY,QAAA,eAAe,GAAG;IAC7B,CAAC,EAAE,CAAC,CAAW,EAAE,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC;IACnD,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC;CACX,CAAC;AAEK,KAAK,UAAU,gBAAgB,CAAC,KAA2B;IAChE,MAAM,EACJ,OAAO,EACP,QAAQ,EACR,eAAe,EACf,OAAO,EACP,QAAQ,EACR,mBAAmB,GAAG,EAAE,EACxB,YAAY,EACZ,YAAY,EACZ,eAAe,EACf,iBAAiB,EACjB,WAAW,EAAE,eAAe,GAAG,EAAE,EACjC,OAAO,GACR,GAAG,KAAK,CAAC;IAEV,IAAI,IAAI,GAAG,IAAI,IAAI,EAAE,CAAC;IACtB,IAAI,SAAS,GAAG,IAAI,CAAC,OAAO,EAAE,CAAC;IAC/B,IAAI,eAAe,GAAG,QAAQ,CAAC;IAE/B,IAAI,KAAK,GAAqB;QAC5B,SAAS,EAAE,IAAI,qBAAO,CAAC,UAAU,CAAC;QAClC,UAAU,EAAE,CAAC;KACd,CAAC;IAEF,MAAM,gBAAgB,GAAG,IAAA,yCAAqB,EAAC,QAAQ,EAAE;QACvD,UAAU,EAAE,IAAI;KACjB,CAAC,CAAC;IAEH,IAAI,cAAc,GAAmB,EAAE,CAAC;IACxC,MAAM,WAAW,GAA0B,EAAE,CAAC;IAC9C,IAAI,qBAAqB,GAA2B,EAAE,CAAC;IACvD,IAAI,2BAA2B,GAAgC,EAAE,CAAC;IAElE,KAAK,MAAM,kBAAkB,IAAI,eAAe,EAAE;QAChD,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE;YACzC,MAAM,OAAO,GAAG,iBAAiB,CAAC,QAAQ,CAAC,CAAC;YAC5C,MAAM,gBAAgB,GAAG,eAAe,CAAC,QAAQ,CAAC,CAAC;YACnD,IAAI,EAAE,aAAa,EAAE,GAAG,gBAAgB;gBACtC,CAAC,CAAC,EAAE,aAAa,EAAE,gBAAgB,EAAE;gBACrC,CAAC,CAAC,MAAM,SAAS,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;YAEjD,gBAAgB,CAAC,aAAa,CAAC,CAAC;YAEhC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC;gBAAE,WAAW,CAAC,QAAQ,CAAC,GAAG,EAAE,CAAC;YAEvD,IAAI,cAAc,GAAG,CAAC,CAAC;YACvB,KAAK,IAAI,UAAU,IAAI,aAAa,EAAE;gBACpC,MAAM,KAAK,GAAG,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;gBACnC,MAAM,KAAK,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;gBAClC,MAAM,YAAY,GAAG,uBAAe,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;gBAChE,cAAc,IAAI,UAAU,CAAC,OAAO,GAAG,YAAY,CAAC;gBACpD,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,GAAG;oBAC7B,GAAG,UAAU;oBACb,UAAU,EAAE,KAAK;oBACjB,YAAY,EAAE,UAAU,CAAC,OAAO,GAAG,YAAY;oBAC/C,YAAY,EAAE,YAAY;oBAC1B,UAAU,EAAE,gBAAgB,CAAC,KAAK,CAAa;iBAChD,CAAC;aACH;YACD,KAAK,IAAI,KAAK,IAAI,WAAW,CAAC,QAAQ,CAAC,EAAE;gBACvC,WAAW,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,CAAC,YAAY,IAAI,GAAG,GAAG,cAAc,CAAC;aACnE;YACD,cAAc,CAAC,QAAQ,CAAC,GAAG;gBACzB,QAAQ,EAAE,aAAa,CAAC,MAAM;gBAC9B,YAAY,EAAE,CAAC;gBACf,mBAAmB,EAAE,mBAAmB,CAAC,QAAQ,CAAC,IAAI,CAAC;aACxD,CAAC;SACH;QAED,qBAAqB,GAAG,IAAA,yDAA2B,EAAC,qBAAqB,EAAE;YACzE,eAAe;YACf,WAAW;YACX,OAAO;SACR,CAAC,CAAC;QAEH,2BAA2B,GAAG,EAAE,CAAC;QACjC,KAAK,MAAM,QAAQ,IAAI,qBAAqB,EAAE;YAC5C,2BAA2B,CAAC,QAAQ,CAAC,GAAG,MAAM,CAAC,IAAI,CACjD,qBAAqB,CAAC,QAAQ,CAAC,CAChC,CAAC;SACH;QAED,IAAI,gBAAgB,GAAG,mBAAmB,CACxC,KAAK,EACL,cAAc,EACd,kBAAkB,CACnB,CAAC;QAEF,KAAK,GAAG;YACN,SAAS,EAAE,IAAI,qBAAO,CAAC,UAAU,CAAC;YAClC,UAAU,EAAE,CAAC;SACd,CAAC;QAEF,KAAK,IAAI,OAAO,IAAI,gBAAgB,EAAE;YACpC,IAAA,yBAAW,EACT;gBACE,gBAAgB,EAAE,kBAAkB;gBACpC,eAAe;gBACf,OAAO;gBACP,SAAS;gBACT,OAAO;gBACP,WAAW;gBACX,YAAY;gBACZ,YAAY;gBACZ,eAAe;gBACf,qBAAqB;gBACrB,2BAA2B;aAC5B,EACD,cAAc,EACd,OAAO,EACP,KAAK,CACN,CAAC;SACH;KACF;IACD,OAAO,mBAAmB,CAAC;QACzB,KAAK;QACL,OAAO;QACP,2BAA2B;QAC3B,OAAO;KACR,CAAC,CAAC;AACL,CAAC;AAzHD,4CAyHC;AASD,SAAS,mBAAmB,CAAC,KAA+B;;IAC1D,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,2BAA2B,EAAE,OAAO,EAAE,GAAG,KAAK,CAAC;IACvE,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAC;IAC5B,MAAM,WAAW,GAAQ,EAAE,CAAC;IAC5B,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAgB,CAAC;IACtD,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;QAChC,MAAM,gBAAgB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;QAC3C,KAAK,MAAM,QAAQ,IAAI,gBAAgB,EAAE;YACvC,IAAI,MAAM,GAAG,gBAAgB,CAAC,QAAQ,CAAC,CAAC;YACxC,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;gBAC9B,MAAM,QAAQ,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;gBAChC,IAAI,WAAW,CAAC,QAAQ,CAAC;oBAAE,SAAS;gBACpC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,GAAG,IAAA,6BAAa,EAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;aAChE;SACF;KACF;IAED,MAAM,MAAM,GAAG,EAAE,CAAC;IAClB,KAAK,IAAI,QAAQ,IAAI,SAAS,CAAC,QAAQ,EAAE;QACvC,MAAM,aAAa,GAAG,IAAI,CAAC,KAAK,CAC9B,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CACA,CAAC;QAC1B,MAAM,EAAE,UAAU,EAAE,KAAK,EAAE,GAAG,QAAQ,CAAC;QACvC,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,UAAU,CAAgB,CAAC;QACzD,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;YAChC,MAAM,gBAAgB,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;YAC3C,MAAM,sBAAsB,GAAG,UAAU,CAAC,QAAQ,CAAC,CAAC;YACpD,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,sBAAsB,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBAClE,MAAM,QAAQ,GAAG,sBAAsB,CAAC,KAAK,CAAC,CAAC;gBAE/C,IAAI,QAAQ,KAAK,GAAG,IAAI,CAAC,QAAQ;oBAAE,SAAS;gBAE5C,MAAM,MAAM,GAAG,gBAAgB,CAAC,QAAQ,CAAC,CAAC;gBAC1C,MAAM,KAAK,GAAG,2BAA2B,CAAC,QAAQ,CAAC,CAAC,KAAK,CAAC,CAAC;gBAE3D,KAAK,IAAI,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE;oBAC5B,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,WAAW,EAAE,GAChD,WAAW,CAAC,IAAI,CAAC,MAA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@@ -9,6 +9,6 @@ interface SpectraData2DFormatted extends Omit<SpectraData2DWithIds, 'zones'> {
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9
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values: NMRZoneWithIds[];
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};
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}
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-
export
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+
export type SpectraDataFormatted = SpectraData1DFormatted | SpectraData2DFormatted;
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export declare function formatData(input?: SpectraDataWithIds[]): SpectraDataFormatted[];
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export {};
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@@ -55,7 +55,7 @@ export interface OptionsDetectSignals {
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frequency?: number;
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nucleus?: string;
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}
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-
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+
type NMRPeak1DIntern = Omit<NMRPeak1D, 'fwhm' | 'shape'>;
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/**
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* This function clustering peaks and calculate the integration value for each range from the peak list returned from extractPeaks function.
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*/
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@@ -114,17 +114,7 @@ function peaksToRanges(data, peakList, options = {}) {
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}
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}
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// it was a updateIntegrals function.
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-
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118
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-
let sumObserved = 0;
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119
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-
for (const signal of signals) {
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120
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-
sumObserved += Math.abs(Math.round(signal.integralData.value));
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-
}
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122
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-
if (sumObserved !== integrationSum) {
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123
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-
sumIntegral = integrationSum / sumObserved;
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124
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-
for (const signal of signals) {
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125
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-
signal.integralData.value *= sumIntegral;
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126
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-
}
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127
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-
}
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117
|
+
updateIntegration(signals, integrationSum);
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128
118
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}
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129
119
|
signals.sort((a, b) => {
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130
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return b.delta - a.delta;
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@@ -149,7 +139,6 @@ function peaksToRanges(data, peakList, options = {}) {
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149
139
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delta: signal.delta,
|
|
150
140
|
kind: signal.kind || 'signal',
|
|
151
141
|
multiplicity: signal.multiplicity,
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|
152
|
-
integration: signal.integralData.value,
|
|
153
142
|
};
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|
154
143
|
if (keepPeaks) {
|
|
155
144
|
signalResult.peaks = signal.peaks.map((peak) => {
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@@ -192,7 +181,6 @@ function detectSignals(data, peakList, options = {}) {
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|
192
181
|
let peaks;
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|
193
182
|
let signals = [];
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|
194
183
|
let prevPeak = { x: Number.MIN_SAFE_INTEGER };
|
|
195
|
-
let spectrumIntegral = 0;
|
|
196
184
|
frequencyCluster /= frequency;
|
|
197
185
|
for (const peak of peakList) {
|
|
198
186
|
if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
|
|
@@ -238,14 +226,9 @@ function detectSignals(data, peakList, options = {}) {
|
|
|
238
226
|
else {
|
|
239
227
|
integration.value = integralPeaks;
|
|
240
228
|
}
|
|
241
|
-
spectrumIntegral += integration.value;
|
|
242
229
|
}
|
|
243
230
|
if (integrationSum > 0) {
|
|
244
|
-
|
|
245
|
-
for (let signal of signals) {
|
|
246
|
-
let integration = signal.integralData;
|
|
247
|
-
integration.value *= integralFactor;
|
|
248
|
-
}
|
|
231
|
+
updateIntegration(signals, integrationSum);
|
|
249
232
|
}
|
|
250
233
|
return signals;
|
|
251
234
|
}
|
|
@@ -257,4 +240,22 @@ exports.detectSignals = detectSignals;
|
|
|
257
240
|
function computeArea(peak, frequency) {
|
|
258
241
|
return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
|
|
259
242
|
}
|
|
243
|
+
/**
|
|
244
|
+
* update the integration Values
|
|
245
|
+
* @param signals
|
|
246
|
+
* @param integrationSum
|
|
247
|
+
*/
|
|
248
|
+
function updateIntegration(signals, integrationSum) {
|
|
249
|
+
let sumIntegral = 0;
|
|
250
|
+
let sumObserved = 0;
|
|
251
|
+
for (const signal of signals) {
|
|
252
|
+
sumObserved += Math.abs(Math.round(signal.integralData.value));
|
|
253
|
+
}
|
|
254
|
+
if (sumObserved !== integrationSum) {
|
|
255
|
+
sumIntegral = integrationSum / sumObserved;
|
|
256
|
+
for (const signal of signals) {
|
|
257
|
+
signal.integralData.value *= sumIntegral;
|
|
258
|
+
}
|
|
259
|
+
}
|
|
260
|
+
}
|
|
260
261
|
//# sourceMappingURL=peaksToRanges.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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@@ -1,6 +1,6 @@
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1
1
|
import { MakeMandatory } from '../../utilities/MakeMandatory';
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|
2
2
|
import { NMRPeak1D } from '../NMRPeak1D';
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|
3
|
-
export
|
|
3
|
+
export type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
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|
4
4
|
export interface ConvertWidthOptions<T> {
|
|
5
5
|
convertTo: string & {
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|
6
6
|
_kind?: 'hz' | 'ppm';
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@@ -1,4 +1,4 @@
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|
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1
1
|
import { NMRPeak1D } from '../NMRPeak1D';
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|
2
2
|
import { ConvertWidthOptions } from './convertWidth';
|
|
3
|
-
export
|
|
3
|
+
export type ConvertWidthTo<T> = Omit<ConvertWidthOptions<T>, 'convertTo'>;
|
|
4
4
|
export declare function convertWidthToHz<T extends NMRPeak1D>(peaks: T[], options: ConvertWidthTo<T>): T[];
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@@ -1,6 +1,7 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.predictAll = void 0;
|
|
4
|
+
const openchemlib_utils_1 = require("openchemlib-utils");
|
|
4
5
|
const predictCOSY_1 = require("./predictCOSY");
|
|
5
6
|
const predictCarbon_1 = require("./predictCarbon");
|
|
6
7
|
const predictHMBC_1 = require("./predictHMBC");
|
|
@@ -13,6 +14,7 @@ const getPredictions_1 = require("./utils/getPredictions");
|
|
|
13
14
|
*/
|
|
14
15
|
async function predictAll(molecule, options = {}) {
|
|
15
16
|
let { from = 'H', to = 'C', predictor = { H: predictProton_1.predictProton, C: predictCarbon_1.predictCarbon }, predictions, joinDistance = { H: 0.05, C: 0.5 }, predictOptions = {}, } = options;
|
|
17
|
+
const diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule);
|
|
16
18
|
const xPrediction = await (0, getPredictions_1.getPredictions)(from, molecule, predictOptions, predictor, predictions);
|
|
17
19
|
const yPrediction = await (0, getPredictions_1.getPredictions)(to, molecule, predictOptions, predictor, predictions);
|
|
18
20
|
if (!xPrediction || !yPrediction) {
|
|
@@ -22,7 +24,7 @@ async function predictAll(molecule, options = {}) {
|
|
|
22
24
|
H: xPrediction,
|
|
23
25
|
C: yPrediction,
|
|
24
26
|
};
|
|
25
|
-
const { molfile
|
|
27
|
+
const { molfile } = xPrediction;
|
|
26
28
|
const spectra = {
|
|
27
29
|
proton: predictions.H,
|
|
28
30
|
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":";;;AAAA,yDAA6D;AAI7D,+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;IAElD,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"}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { FromTo, PointXY } from 'cheminfo-types';
|
|
2
|
-
import type { Molecule } from 'openchemlib';
|
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2
|
+
import type { Molecule } from 'openchemlib/full';
|
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3
3
|
import { PredictAllOptions } from './predictAll';
|
|
4
4
|
/**
|
|
5
5
|
* This function will generate an object compatible with NMR-ium
|
|
@@ -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';
|
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3
3
|
import type { Prediction1D } from './Prediction1D';
|
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4
4
|
import { PredictProtonOptions } from './predictProton';
|
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5
5
|
import { Predictor } from './utils/predict2D';
|
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@@ -1,4 +1,4 @@
|
|
|
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
|
import type { DataBaseStructure } from './dataStructure';
|
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4
4
|
export interface PredictCarbonOptions {
|
|
@@ -21,8 +21,12 @@ 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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24
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+
/**
|
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|
+
* diastereotopic atom ids.
|
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|
+
*/
|
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27
|
+
diaIDs?: string[];
|
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}
|
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|
-
export
|
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29
|
+
export type PredictCarbon = typeof predictCarbon;
|
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|
/**
|
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27
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|
* Make a query to a hose code based database to predict carbon chemical shift
|
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28
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|
* @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
|
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@@ -6,10 +6,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
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6
6
|
exports.predictCarbon = void 0;
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7
7
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const uuid_1 = require("@lukeed/uuid");
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8
8
|
const cross_fetch_1 = __importDefault(require("cross-fetch"));
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9
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+
const openchemlib_utils_1 = require("openchemlib-utils");
|
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9
10
|
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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12
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-
const flatGroupedDiaIDs_1 = require("./utils/flatGroupedDiaIDs");
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13
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const getFilteredIDiaIDs_1 = require("./utils/getFilteredIDiaIDs");
|
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14
14
|
const queryByHOSE_1 = require("./utils/queryByHOSE");
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|
const cache = {};
|
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@@ -35,7 +35,7 @@ function checkFromPrediction(signal) {
|
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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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38
|
-
let { url, database, webserviceURL } = options;
|
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38
|
+
let { url, database, webserviceURL, diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule), } = options;
|
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39
|
if (webserviceURL) {
|
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|
return (0, fetchPrediction_1.fetchPrediction)(molecule, { webserviceURL });
|
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}
|
|
@@ -48,8 +48,9 @@ async function predictCarbon(molecule, options = {}) {
|
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48
48
|
let { maxSphereSize = maxLevel } = options;
|
|
49
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|
if (maxSphereSize > maxLevel)
|
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|
maxSphereSize = maxLevel;
|
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-
const {
|
|
51
|
+
const { carbonDiaIDs, molfile } = (0, getFilteredIDiaIDs_1.getFilteredIDiaIDs)(molecule, {
|
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|
maxSphereSize,
|
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+
diaIDs,
|
|
53
54
|
});
|
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54
55
|
let predictions = (0, queryByHOSE_1.queryByHose)(carbonDiaIDs, database, {
|
|
55
56
|
maxSphereSize,
|
|
@@ -59,7 +60,7 @@ async function predictCarbon(molecule, options = {}) {
|
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|
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60
|
return {
|
|
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|
molfile,
|
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62
|
nucleus: '13C',
|
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62
|
-
diaIDs
|
|
63
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+
diaIDs,
|
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64
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joinedSignals,
|
|
64
65
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signals,
|
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65
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ranges: (0, signalsToRanges_1.signalsToRanges)(joinedSignals),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictCarbon.js","sourceRoot":"","sources":["../../src/prediction/predictCarbon.ts"],"names":[],"mappings":";;;;;;AAAA,uCAAgD;AAChD,8DAAgC;
|
|
1
|
+
{"version":3,"file":"predictCarbon.js","sourceRoot":"","sources":["../../src/prediction/predictCarbon.ts"],"names":[],"mappings":";;;;;;AAAA,uCAAgD;AAChD,8DAAgC;AAChC,yDAA6D;AAG7D,iDAA8C;AAE9C,gEAA6D;AAK7D,6DAA0D;AAC1D,mEAAgE;AAChE,qDAA8D;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,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"}
|
|
@@ -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 { Prediction1D } from './Prediction1D';
|
|
4
4
|
import type { PredictCarbonOptions } from './predictCarbon';
|
|
5
5
|
import type { PredictProtonOptions } from './predictProton';
|
|
@@ -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 { Prediction1D } from './Prediction1D';
|
|
4
4
|
import { PredictCarbonOptions } from './predictCarbon';
|
|
5
5
|
import { PredictProtonOptions } from './predictProton';
|
|
@@ -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
|
/**
|
|
4
4
|
* Makes a prediction using proton.
|
|
@@ -9,6 +9,10 @@ export interface PredictProtonOptions {
|
|
|
9
9
|
* A callback receiving a molfile and the result
|
|
10
10
|
*/
|
|
11
11
|
cache?: (molfile: string, result?: string) => void | string | undefined;
|
|
12
|
+
/**
|
|
13
|
+
* diastereotopic atom ids.
|
|
14
|
+
*/
|
|
15
|
+
diaIDs?: string[];
|
|
12
16
|
}
|
|
13
|
-
export
|
|
17
|
+
export type PredictProton = typeof predictProton;
|
|
14
18
|
export declare function predictProton(molecule: Molecule, options?: PredictProtonOptions): Promise<Prediction1D>;
|
|
@@ -33,7 +33,7 @@ async function predictProton(molecule, options = {}) {
|
|
|
33
33
|
cache(molfile, result);
|
|
34
34
|
}
|
|
35
35
|
}
|
|
36
|
-
const diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule);
|
|
36
|
+
const { diaIDs = (0, openchemlib_utils_1.getDiastereotopicAtomIDs)(molecule) } = options;
|
|
37
37
|
const signals = protonParser(result, molecule, diaIDs);
|
|
38
38
|
const joinedSignals = (0, signalsJoin_1.signalsJoin)(signals);
|
|
39
39
|
return {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":";;;;;;AAAA,uCAAgD;AAChD,8DAAgC;AAChC,0DAAiC;
|
|
1
|
+
{"version":3,"file":"predictProton.js","sourceRoot":"","sources":["../../src/prediction/predictProton.ts"],"names":[],"mappings":";;;;;;AAAA,uCAAgD;AAChD,8DAAgC;AAChC,0DAAiC;AACjC,yDAI2B;AAI3B,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"}
|
|
@@ -1,14 +1,13 @@
|
|
|
1
|
-
/// <reference path="../../../src/openchemlib-utils.d.ts" />
|
|
2
|
-
import type { Molecule } from 'openchemlib';
|
|
3
1
|
import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
|
|
2
|
+
import type { Molecule } from 'openchemlib/full';
|
|
4
3
|
export interface GroupDiaIDsWithHose extends GroupDiastereotopicAtomIDs {
|
|
5
4
|
hose: string[];
|
|
6
5
|
}
|
|
7
|
-
export
|
|
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.groupDiastereotopicAtomIDs)(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":";;;
|
|
1
|
+
{"version":3,"file":"getFilteredIDiaIDs.js","sourceRoot":"","sources":["../../../src/prediction/utils/getFilteredIDiaIDs.ts"],"names":[],"mappings":";;;AAAA,yDAI2B;AAU3B,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,8CAA0B,EAAC,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,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"}
|