nmr-processing 9.3.0 → 9.3.1
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/get1HAssignments.d.ts +3 -3
- package/lib/assignment/getAssignments.d.ts +2 -2
- 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/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/predictAllSpectra.d.ts +1 -1
- package/lib/prediction/predictCOSY.d.ts +1 -1
- package/lib/prediction/predictCarbon.d.ts +2 -2
- package/lib/prediction/predictHMBC.d.ts +1 -1
- package/lib/prediction/predictHSQC.d.ts +1 -1
- package/lib/prediction/predictProton.d.ts +2 -2
- package/lib/prediction/utils/fetchPrediction.d.ts +1 -1
- package/lib/prediction/utils/getFilteredIDiaIDs.d.ts +2 -2
- package/lib/prediction/utils/getPredictions.d.ts +1 -1
- package/lib/prediction/utils/predict2D.d.ts +2 -2
- 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/peaks/peaksToRanges.js +20 -19
- package/lib-esm/peaks/peaksToRanges.js.map +1 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js +4 -1
- package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
- package/package.json +7 -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 +1 -1
- package/src/peaks/peaksToRanges.ts +23 -19
- package/src/prediction/Prediction1D.ts +1 -1
- package/src/prediction/predictAll.ts +1 -1
- package/src/prediction/predictAllSpectra.ts +1 -1
- package/src/prediction/predictCOSY.ts +1 -1
- package/src/prediction/predictCarbon.ts +1 -1
- package/src/prediction/predictHMBC.ts +1 -1
- package/src/prediction/predictHSQC.ts +1 -1
- package/src/prediction/predictProton.ts +1 -1
- package/src/prediction/utils/fetchPrediction.ts +1 -1
- package/src/prediction/utils/getFilteredIDiaIDs.ts +1 -1
- package/src/prediction/utils/getPredictions.ts +1 -1
- package/src/prediction/utils/predict2D.ts +1 -1
- package/src/utilities/hasProperty.ts +1 -1
- package/src/xy/xyAutoPeaksPicking.ts +5 -1
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@@ -1,11 +1,11 @@
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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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@@ -1,4 +1,4 @@
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import { Molecule } from 'openchemlib';
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import { Molecule } from 'openchemlib/full';
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import { NMRSignal1D } from '..';
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import type { PredictCarbonOptions } from '../prediction/predictCarbon';
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import type { PredictProtonOptions } from '../prediction/predictProton';
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@@ -19,7 +19,7 @@ export interface SpectraData2D {
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*/
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info: any;
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}
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export
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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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import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '..';
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import { MakeMandatory } from '../utilities/MakeMandatory';
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import type { SpectraData1D, SpectraData2D } from './getAssignments';
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export
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export
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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 interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
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id: string;
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signals: Array<NMRSignal2DWithId>;
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@@ -17,4 +17,4 @@ export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
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export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
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zones: NMRZoneWithIds[];
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}
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export
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export type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
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import { MakeMandatory } from '../../utilities/MakeMandatory';
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import type { Targets } from '../get1HAssignments';
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import type { RestrictionByCS1D, Predictions1Dassignments } from './buildAssignments';
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type RestrictionByCSMandatory = MakeMandatory<RestrictionByCS1D, 'chemicalShiftRestriction' | 'tolerance' | 'useChemicalShiftScore'>;
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interface CreateMapPossibleAssignments {
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predictions: Predictions1Dassignments;
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restrictionByCS: RestrictionByCSMandatory;
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import { Values } from 'nmr-correlation';
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import { Molecule } from 'openchemlib';
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import { Molecule } from 'openchemlib/full';
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import { NMRSignal1D, PredictCarbonOptions, PredictProtonOptions } from '../../..';
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import { MakeMandatory } from '../../../utilities/MakeMandatory';
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import { SpectraDataWithIds } from '../../nmrAssigment';
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import { TargetsByAtomType } from './getTargetsAndCorrelations';
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export
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export
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export type AtomTypes = 'H' | 'C';
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export type CurrentAtoms = Array<AtomTypes>;
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export interface Partial {
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[key: string]: Array<string | null>;
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}
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};
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targets: TargetsByAtomType;
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}
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type NMRSignal1DFromPrediction = MakeMandatory<NMRSignal1D, 'nbAtoms' | 'diaIDs' | 'atoms'>;
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export interface Prediction extends NMRSignal1DFromPrediction {
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diaIDIndex: number;
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allHydrogens: number;
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@@ -9,6 +9,6 @@ interface SpectraData2DFormatted extends Omit<SpectraData2DWithIds, 'zones'> {
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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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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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let sumObserved = 0;
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for (const signal of signals) {
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sumObserved += Math.abs(Math.round(signal.integralData.value));
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}
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if (sumObserved !== integrationSum) {
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sumIntegral = integrationSum / sumObserved;
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for (const signal of signals) {
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signal.integralData.value *= sumIntegral;
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}
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}
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updateIntegration(signals, integrationSum);
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}
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signals.sort((a, b) => {
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return b.delta - a.delta;
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delta: signal.delta,
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kind: signal.kind || 'signal',
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multiplicity: signal.multiplicity,
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integration: signal.integralData.value,
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};
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if (keepPeaks) {
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signalResult.peaks = signal.peaks.map((peak) => {
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let peaks;
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let signals = [];
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let prevPeak = { x: Number.MIN_SAFE_INTEGER };
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let spectrumIntegral = 0;
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frequencyCluster /= frequency;
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for (const peak of peakList) {
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if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
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else {
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integration.value = integralPeaks;
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}
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spectrumIntegral += integration.value;
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}
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if (integrationSum > 0) {
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for (let signal of signals) {
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let integration = signal.integralData;
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integration.value *= integralFactor;
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}
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updateIntegration(signals, integrationSum);
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}
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return signals;
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}
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function computeArea(peak, frequency) {
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return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
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}
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/**
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* update the integration Values
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* @param signals
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* @param integrationSum
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*/
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function updateIntegration(signals, integrationSum) {
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let sumIntegral = 0;
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let sumObserved = 0;
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for (const signal of signals) {
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sumObserved += Math.abs(Math.round(signal.integralData.value));
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}
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if (sumObserved !== integrationSum) {
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sumIntegral = integrationSum / sumObserved;
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for (const signal of signals) {
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signal.integralData.value *= sumIntegral;
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}
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}
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}
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//# sourceMappingURL=peaksToRanges.js.map
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@@ -1,6 +1,6 @@
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1
1
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import { MakeMandatory } from '../../utilities/MakeMandatory';
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2
2
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import { NMRPeak1D } from '../NMRPeak1D';
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3
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-
export
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3
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+
export type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
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4
4
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export interface ConvertWidthOptions<T> {
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5
5
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convertTo: string & {
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6
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_kind?: 'hz' | 'ppm';
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@@ -1,4 +1,4 @@
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1
1
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import { NMRPeak1D } from '../NMRPeak1D';
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2
2
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import { ConvertWidthOptions } from './convertWidth';
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3
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-
export
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3
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+
export type ConvertWidthTo<T> = Omit<ConvertWidthOptions<T>, 'convertTo'>;
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4
4
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export declare function convertWidthToHz<T extends NMRPeak1D>(peaks: T[], options: ConvertWidthTo<T>): T[];
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@@ -1,5 +1,5 @@
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1
1
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import { FromTo, PointXY } from 'cheminfo-types';
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2
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-
import type { Molecule } from 'openchemlib';
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2
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+
import type { Molecule } from 'openchemlib/full';
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3
3
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import { PredictAllOptions } from './predictAll';
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4
4
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/**
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5
5
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* This function will generate an object compatible with NMR-ium
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@@ -1,5 +1,5 @@
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1
1
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/// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
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2
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-
import { Molecule } from 'openchemlib';
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2
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+
import { Molecule } from 'openchemlib/full';
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3
3
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import type { Prediction1D } from './Prediction1D';
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4
4
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import { PredictProtonOptions } from './predictProton';
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5
5
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import { Predictor } from './utils/predict2D';
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@@ -1,4 +1,4 @@
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1
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-
import type { Molecule } from 'openchemlib';
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1
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+
import type { Molecule } from 'openchemlib/full';
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2
2
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import type { Prediction1D } from './Prediction1D';
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3
3
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import type { DataBaseStructure } from './dataStructure';
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4
4
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export interface PredictCarbonOptions {
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@@ -22,7 +22,7 @@ export interface PredictCarbonOptions {
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22
22
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*/
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23
23
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maxSphereSize?: number;
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24
24
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}
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25
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-
export
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25
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+
export type PredictCarbon = typeof predictCarbon;
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26
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/**
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27
27
|
* Make a query to a hose code based database to predict carbon chemical shift
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28
28
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* @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
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@@ -1,5 +1,5 @@
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1
1
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/// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
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2
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-
import { Molecule } from 'openchemlib';
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2
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+
import { Molecule } from 'openchemlib/full';
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3
3
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import type { Prediction1D } from './Prediction1D';
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4
4
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import type { PredictCarbonOptions } from './predictCarbon';
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5
5
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import type { PredictProtonOptions } from './predictProton';
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@@ -1,5 +1,5 @@
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1
1
|
/// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
|
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2
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-
import { Molecule } from 'openchemlib';
|
|
2
|
+
import { Molecule } from 'openchemlib/full';
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|
3
3
|
import type { Prediction1D } from './Prediction1D';
|
|
4
4
|
import { PredictCarbonOptions } from './predictCarbon';
|
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5
5
|
import { PredictProtonOptions } from './predictProton';
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import type { Molecule } from 'openchemlib';
|
|
1
|
+
import type { Molecule } from 'openchemlib/full';
|
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2
2
|
import type { Prediction1D } from './Prediction1D';
|
|
3
3
|
/**
|
|
4
4
|
* Makes a prediction using proton.
|
|
@@ -10,5 +10,5 @@ export interface PredictProtonOptions {
|
|
|
10
10
|
*/
|
|
11
11
|
cache?: (molfile: string, result?: string) => void | string | undefined;
|
|
12
12
|
}
|
|
13
|
-
export
|
|
13
|
+
export type PredictProton = typeof predictProton;
|
|
14
14
|
export declare function predictProton(molecule: Molecule, options?: PredictProtonOptions): Promise<Prediction1D>;
|
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@@ -1,10 +1,10 @@
|
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|
1
1
|
/// <reference path="../../../src/openchemlib-utils.d.ts" />
|
|
2
|
-
import type { Molecule } from 'openchemlib';
|
|
2
|
+
import type { Molecule } from 'openchemlib/full';
|
|
3
3
|
import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
|
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4
4
|
export interface GroupDiaIDsWithHose extends GroupDiastereotopicAtomIDs {
|
|
5
5
|
hose: string[];
|
|
6
6
|
}
|
|
7
|
-
export
|
|
7
|
+
export type GroupedDiaIDsWithHose = GroupDiaIDsWithHose[];
|
|
8
8
|
export declare function getFilteredIDiaIDs(molecule: Molecule, options: {
|
|
9
9
|
maxSphereSize: number;
|
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10
10
|
}): {
|
|
@@ -1,4 +1,4 @@
|
|
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1
|
-
import type { Molecule } from 'openchemlib';
|
|
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 { Predictions, PredictOptions, Predictors } from './predict2D';
|
|
4
4
|
export declare function getPredictions(key: string, molecule: Molecule, predictOptions: PredictOptions, predictor?: Predictors, predictions?: Predictions): Promise<Prediction1D | undefined>;
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
/// <reference path="../../../src/ml-matrix-peaks-finder.d.ts" />
|
|
2
|
-
import { Molecule } from 'openchemlib';
|
|
2
|
+
import { Molecule } from 'openchemlib/full';
|
|
3
3
|
import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
|
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4
4
|
import type { Prediction1D } from '../Prediction1D';
|
|
5
5
|
import type { PredictCarbon, PredictCarbonOptions } from '../predictCarbon';
|
|
@@ -8,7 +8,7 @@ import type { PredictProton, PredictProtonOptions } from '../predictProton';
|
|
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8
8
|
* Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
|
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9
9
|
* @returns {object} - object with molfile, diaIDs, 2D signals and zones.
|
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10
10
|
*/
|
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-
export
|
|
11
|
+
export type Predictor = PredictCarbon | PredictProton;
|
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12
|
export interface Predictors {
|
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13
13
|
[key: string]: Predictor | undefined;
|
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14
14
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H?: Predictor;
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@@ -14,8 +14,8 @@ export interface InternalSignal {
|
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14
14
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fromIndexCoupling: number;
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15
15
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toIndexCoupling: number;
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}
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-
export
|
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export
|
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+
export type Parameter = 'delta' | 'intensity' | 'fwhm' | 'mu' | 'coupling';
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+
export type ParametersFromOptions = Record<Parameter, Record<string, number | ((options?: {
|
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19
19
|
signal?: Signal;
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20
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shape?: Shape1D;
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21
21
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index?: number;
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@@ -35,7 +35,7 @@ export interface GetInternalSignalsOptions {
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35
35
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shape?: Shape1D;
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36
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parameters?: ParametersFromOptions;
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}
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-
export
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+
export type Shape1DWithFWHM = Omit<Shape1D, 'fwhm'> & {
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fwhm: number;
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};
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|
export declare function getInternalSignals(data: DataXY, signals: Signal[], minMaxY: Record<string, number>, options: GetInternalSignalsOptions): {
|
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@@ -1,4 +1,4 @@
|
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1
1
|
import { InternalSignal } from './getInternalSignals';
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2
2
|
import { SignalsToPointXYOptions } from './signalsToPointXY';
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3
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-
export
|
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3
|
+
export type SumOfShapes = (parameters: number[]) => (x: number) => number;
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4
|
export declare function getSumOfShapes(internalSignals: InternalSignal[], options: SignalsToPointXYOptions): (parameters: number[]) => (currentX: number) => number;
|
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@@ -4,7 +4,7 @@ import { NMRPeak1D } from '../peaks/NMRPeak1D';
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4
4
|
import { NMRSignal1D } from './NMRSignal1D';
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5
5
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import { ParametersFromOptions, Shape1DWithFWHM } from './optimization/getInternalSignals';
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6
|
import { SignalsToPointXYOptions } from './optimization/signalsToPointXY';
|
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7
|
-
|
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7
|
+
type ParametersFromSignal = Record<string, Record<string, number>>;
|
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8
|
export interface Signal extends NMRSignal1D {
|
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9
9
|
intensity?: number;
|
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10
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shape?: Shape1D;
|
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@@ -9,9 +9,9 @@ export interface SignalsJoinOptions {
|
|
|
9
9
|
*/
|
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10
10
|
joinCouplings?: SignalJoinCouplingsOptions;
|
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11
|
}
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
12
|
+
type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'multiplicity' | 'diaIDs' | 'pathLength'>;
|
|
13
|
+
type Signal1DWidthDiaID = MakeMandatory<NMRSignal1D, 'diaIDs'>;
|
|
14
|
+
type Signal1DWidthJsAndDiaID = Omit<Signal1DWidthDiaID, 'js'> & {
|
|
15
15
|
js: JcouplingFromPrediction[];
|
|
16
16
|
};
|
|
17
17
|
/**
|
|
@@ -13,6 +13,6 @@ interface SignalsToRangesOptions {
|
|
|
13
13
|
*/
|
|
14
14
|
frequency?: number;
|
|
15
15
|
}
|
|
16
|
-
|
|
16
|
+
type RangeFullfiled = MakeMandatory<NMRRange, 'integration' | 'signals' | 'id'>;
|
|
17
17
|
export declare function signalsToRanges(signals: NMRSignal1D[], options?: SignalsToRangesOptions): RangeFullfiled[];
|
|
18
18
|
export {};
|
|
@@ -10,7 +10,7 @@ interface IntergralData {
|
|
|
10
10
|
from: number;
|
|
11
11
|
to: number;
|
|
12
12
|
}
|
|
13
|
-
export
|
|
13
|
+
export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
|
|
14
14
|
intensity: number;
|
|
15
15
|
};
|
|
16
16
|
export interface SignalIntern {
|
|
@@ -37,7 +37,7 @@ export interface SignalIntern {
|
|
|
37
37
|
peaks: Peak1DIntern[];
|
|
38
38
|
peaksComp?: Peak1DIntern[];
|
|
39
39
|
}
|
|
40
|
-
|
|
40
|
+
type SignalInternMandatory = MakeMandatory<SignalIntern, 'symRank' | 'mask' | 'peaksComp'>;
|
|
41
41
|
export interface OpitonsCompilePatter {
|
|
42
42
|
jAxisKey?: JAxisKeys;
|
|
43
43
|
}
|
|
@@ -9,7 +9,7 @@ export interface ObjervedNucleusData {
|
|
|
9
9
|
*/
|
|
10
10
|
frequency: number;
|
|
11
11
|
}
|
|
12
|
-
|
|
12
|
+
type Nucleus = Nuclei | (string & Record<never, never>);
|
|
13
13
|
/**
|
|
14
14
|
* calculate the frequency of a nucleus with respect to a reference nucleus
|
|
15
15
|
*/
|
|
@@ -42,5 +42,5 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
|
|
|
42
42
|
*/
|
|
43
43
|
frequency: number;
|
|
44
44
|
}
|
|
45
|
-
export
|
|
45
|
+
export type NMRPeak1DWithShapeID = MakeMandatory<NMRPeak1D, 'id' | 'shape'>;
|
|
46
46
|
export declare function xyAutoPeaksPicking(data: DataXY, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithShapeID[];
|
|
@@ -6,7 +6,10 @@ const ml_spectra_processing_1 = require("ml-spectra-processing");
|
|
|
6
6
|
const convertWidthToHz_1 = require("../peaks/util/convertWidthToHz");
|
|
7
7
|
function xyAutoPeaksPicking(data, options) {
|
|
8
8
|
const { from, to, frequency, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, direction = 'positive', } = options;
|
|
9
|
-
|
|
9
|
+
let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
|
|
10
|
+
// we can consider a peak with of 0.5 Hz for the windowSize
|
|
11
|
+
let ws = Math.max(Math.round(pointsPerHz / 2), 5);
|
|
12
|
+
const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
|
|
10
13
|
if (data.x.length < windowSize)
|
|
11
14
|
return [];
|
|
12
15
|
if (from !== undefined && to !== undefined) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAUgB;AAEhB,iEAI+B;AAG/B,qEAAkE;AAgElE,SAAgB,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;
|
|
1
|
+
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAUgB;AAEhB,iEAI+B;AAG/B,qEAAkE;AAgElE,SAAgB,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,IAAI,WAAW,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC1D,2DAA2D;IAC3D,IAAI,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IAElD,MAAM,EAAE,UAAU,GAAG,EAAE,GAAG,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;IAErE,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU;QAAE,OAAO,EAAE,CAAC;IAE1C,IAAI,IAAI,KAAK,SAAS,IAAI,EAAE,KAAK,SAAS,EAAE;QAC1C,IAAI,GAAG,IAAA,iCAAS,EAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,CAAC;KACnD;IAED,MAAM,MAAM,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,CAAC,CAAC;IAE9E,IAAI,cAAc,GAAuB;QACvC,KAAK;QACL,SAAS;QACT,UAAU;QACV,QAAQ;QACR,YAAY;QACZ,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE;QACrC,WAAW;QACX,UAAU;QACV,UAAU,EAAE,MAAM,CAAC,QAAQ;QAC3B,OAAO;QACP,YAAY;QACZ,gBAAgB;KACjB,CAAC;IAEF,QAAQ,SAAS,EAAE;QACjB,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;SAC1C;QACD,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC,CAAC;SACvD;QACD,KAAK,MAAM,CAAC,CAAC;YACX,OAAO;gBACL,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC;gBACpC,GAAG,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC;aAClD,CAAC;SACH;QACD,OAAO,CAAC,CAAC;YACP,MAAM,SAAS,GAAU,SAAS,CAAC;YACnC,4EAA4E;YAC5E,MAAM,KAAK,CAAC,wBAAwB,SAAS,EAAE,CAAC,CAAC;SAClD;KACF;AACH,CAAC;AAzED,gDAyEC;AAED,SAAS,gBAAgB,CACvB,IAAY,EACZ,MAA4B,EAC5B,cAAkC;IAElC,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;IAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;IACnC,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;AAC3C,CAAC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAA2B;IAC5D,MAAM,EACJ,KAAK,EACL,SAAS,EACT,UAAU,EACV,QAAQ,EACR,WAAW,EACX,YAAY,EACZ,SAAS,EACT,WAAW,EACX,UAAU,EACV,UAAU,EACV,OAAO,EACP,YAAY,EACZ,gBAAgB,GACjB,GAAG,OAAO,CAAC;IAEZ,MAAM,KAAK,GAAG,IAAA,YAAG,EAAC,IAAI,EAAE;QACtB,SAAS;QACT,WAAW;QACX,WAAW;QACX,UAAU;QACV,OAAO;QACP,gBAAgB;KACjB,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG,IAAA,iBAAQ,EAAC,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;IAE3D,MAAM,QAAQ,GAAG,UAAU;QACzB,CAAC,CAAC,IAAA,uBAAc,EAAC,QAAQ,EAAE;YACvB,UAAU;YACV,UAAU;YACV,KAAK;YACL,YAAY;SACb,CAAC,CAAC,GAAG,CAAC,oBAAoB,CAAC;QAC9B,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,oBAAoB,CAAC,CAAC;IAEvC,OAAO,IAAA,mCAAgB,EACrB,QAAQ;QACN,CAAC,CAAC,IAAA,sBAAa,EAAC,IAAI,EAAE,QAAQ,EAAE;YAC5B,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC,CAAC,GAAG,CAAC,oBAAoB,CAAC;QAC9B,CAAC,CAAC,QAAQ,EACZ,EAAE,SAAS,EAAE,CACd,CAAC;AACJ,CAAC;AAED,SAAS,SAAS,CAAC,IAA6B,EAAE,OAAyB;IACzE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,OAAO,CAAC;IAE5D,MAAM,YAAY,GAAG,CAAC,UAAkB,EAAE,EAAE,CAC1C,OAAO,UAAU,KAAK,QAAQ;QAC5B,CAAC,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,CAAC,UAAU,EAAE;QACjD,CAAC,CAAC,UAAU,CAAC;IAEjB,IAAI,UAAU,EAAE;QACd,OAAO,YAAY,CAAC,UAAU,CAAC,CAAC;KACjC;SAAM;QACL,OAAO,UAAU;YACf,CAAC,CAAC,IAAA,qCAAa,EAAC,IAAI,EAAE,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC;YACrD,CAAC,CAAC,YAAY,CAAC,IAAA,uCAAe,EAAC,IAAI,CAAC,GAAG,eAAe,CAAC,CAAC;KAC3D;AACH,CAAC;AAED,SAAS,oBAAoB,CAC3B,IAAyC;IAEzC,MAAM,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,GAAG,IAAI,CAAC;IACxC,OAAO;QACL,EAAE;QACF,CAAC;QACD,CAAC;QACD,KAAK;QACL,KAAK;KACN,CAAC;AACJ,CAAC"}
|
|
@@ -65,8 +65,8 @@ export interface XYZAutoZonesPickingOptions {
|
|
|
65
65
|
*/
|
|
66
66
|
kernel?: GetKernelOptions;
|
|
67
67
|
}
|
|
68
|
-
export
|
|
69
|
-
export
|
|
68
|
+
export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<NMRSignal2D<T>, 'id'>;
|
|
69
|
+
export type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
|
|
70
70
|
export declare function xyzAutoZonesPicking(spectraData: Data2D, options: XYZAutoZonesPickingOptions): NMRZoneWithID[];
|
|
71
71
|
/**
|
|
72
72
|
* This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed
|
|
@@ -108,17 +108,7 @@ export function peaksToRanges(data, peakList, options = {}) {
|
|
|
108
108
|
}
|
|
109
109
|
}
|
|
110
110
|
// it was a updateIntegrals function.
|
|
111
|
-
|
|
112
|
-
let sumObserved = 0;
|
|
113
|
-
for (const signal of signals) {
|
|
114
|
-
sumObserved += Math.abs(Math.round(signal.integralData.value));
|
|
115
|
-
}
|
|
116
|
-
if (sumObserved !== integrationSum) {
|
|
117
|
-
sumIntegral = integrationSum / sumObserved;
|
|
118
|
-
for (const signal of signals) {
|
|
119
|
-
signal.integralData.value *= sumIntegral;
|
|
120
|
-
}
|
|
121
|
-
}
|
|
111
|
+
updateIntegration(signals, integrationSum);
|
|
122
112
|
}
|
|
123
113
|
signals.sort((a, b) => {
|
|
124
114
|
return b.delta - a.delta;
|
|
@@ -143,7 +133,6 @@ export function peaksToRanges(data, peakList, options = {}) {
|
|
|
143
133
|
delta: signal.delta,
|
|
144
134
|
kind: signal.kind || 'signal',
|
|
145
135
|
multiplicity: signal.multiplicity,
|
|
146
|
-
integration: signal.integralData.value,
|
|
147
136
|
};
|
|
148
137
|
if (keepPeaks) {
|
|
149
138
|
signalResult.peaks = signal.peaks.map((peak) => {
|
|
@@ -185,7 +174,6 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
185
174
|
let peaks;
|
|
186
175
|
let signals = [];
|
|
187
176
|
let prevPeak = { x: Number.MIN_SAFE_INTEGER };
|
|
188
|
-
let spectrumIntegral = 0;
|
|
189
177
|
frequencyCluster /= frequency;
|
|
190
178
|
for (const peak of peakList) {
|
|
191
179
|
if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
|
|
@@ -231,14 +219,9 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
231
219
|
else {
|
|
232
220
|
integration.value = integralPeaks;
|
|
233
221
|
}
|
|
234
|
-
spectrumIntegral += integration.value;
|
|
235
222
|
}
|
|
236
223
|
if (integrationSum > 0) {
|
|
237
|
-
|
|
238
|
-
for (let signal of signals) {
|
|
239
|
-
let integration = signal.integralData;
|
|
240
|
-
integration.value *= integralFactor;
|
|
241
|
-
}
|
|
224
|
+
updateIntegration(signals, integrationSum);
|
|
242
225
|
}
|
|
243
226
|
return signals;
|
|
244
227
|
}
|
|
@@ -249,4 +232,22 @@ export function detectSignals(data, peakList, options = {}) {
|
|
|
249
232
|
function computeArea(peak, frequency) {
|
|
250
233
|
return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
|
|
251
234
|
}
|
|
235
|
+
/**
|
|
236
|
+
* update the integration Values
|
|
237
|
+
* @param signals
|
|
238
|
+
* @param integrationSum
|
|
239
|
+
*/
|
|
240
|
+
function updateIntegration(signals, integrationSum) {
|
|
241
|
+
let sumIntegral = 0;
|
|
242
|
+
let sumObserved = 0;
|
|
243
|
+
for (const signal of signals) {
|
|
244
|
+
sumObserved += Math.abs(Math.round(signal.integralData.value));
|
|
245
|
+
}
|
|
246
|
+
if (sumObserved !== integrationSum) {
|
|
247
|
+
sumIntegral = integrationSum / sumObserved;
|
|
248
|
+
for (const signal of signals) {
|
|
249
|
+
signal.integralData.value *= sumIntegral;
|
|
250
|
+
}
|
|
251
|
+
}
|
|
252
|
+
}
|
|
252
253
|
//# sourceMappingURL=peaksToRanges.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
@@ -3,7 +3,10 @@ import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processin
|
|
|
3
3
|
import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
|
|
4
4
|
export function xyAutoPeaksPicking(data, options) {
|
|
5
5
|
const { from, to, frequency, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, direction = 'positive', } = options;
|
|
6
|
-
|
|
6
|
+
let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
|
|
7
|
+
// we can consider a peak with of 0.5 Hz for the windowSize
|
|
8
|
+
let ws = Math.max(Math.round(pointsPerHz / 2), 5);
|
|
9
|
+
const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
|
|
7
10
|
if (data.x.length < windowSize)
|
|
8
11
|
return [];
|
|
9
12
|
if (from !== undefined && to !== undefined) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":"AACA,OAAO,EACL,GAAG,EACH,aAAa,EACb,cAAc,EAMd,QAAQ,GACT,MAAM,QAAQ,CAAC;AAEhB,OAAO,EACL,SAAS,EACT,aAAa,EACb,eAAe,GAChB,MAAM,uBAAuB,CAAC;AAG/B,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAgElE,MAAM,UAAU,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;
|
|
1
|
+
{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":"AACA,OAAO,EACL,GAAG,EACH,aAAa,EACb,cAAc,EAMd,QAAQ,GACT,MAAM,QAAQ,CAAC;AAEhB,OAAO,EACL,SAAS,EACT,aAAa,EACb,eAAe,GAChB,MAAM,uBAAuB,CAAC;AAG/B,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAgElE,MAAM,UAAU,kBAAkB,CAChC,IAAY,EACZ,OAAkC;IAElC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,SAAS,EACT,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,SAAS,GAAG,UAAU,GACvB,GAAG,OAAO,CAAC;IAEZ,IAAI,WAAW,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC1D,2DAA2D;IAC3D,IAAI,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IAElD,MAAM,EAAE,UAAU,GAAG,EAAE,GAAG,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;IAErE,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU;QAAE,OAAO,EAAE,CAAC;IAE1C,IAAI,IAAI,KAAK,SAAS,IAAI,EAAE,KAAK,SAAS,EAAE;QAC1C,IAAI,GAAG,SAAS,CAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,CAAC;KACnD;IAED,MAAM,MAAM,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,CAAC,CAAC;IAE9E,IAAI,cAAc,GAAuB;QACvC,KAAK;QACL,SAAS;QACT,UAAU;QACV,QAAQ;QACR,YAAY;QACZ,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE;QACrC,WAAW;QACX,UAAU;QACV,UAAU,EAAE,MAAM,CAAC,QAAQ;QAC3B,OAAO;QACP,YAAY;QACZ,gBAAgB;KACjB,CAAC;IAEF,QAAQ,SAAS,EAAE;QACjB,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;SAC1C;QACD,KAAK,UAAU,CAAC,CAAC;YACf,OAAO,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC,CAAC;SACvD;QACD,KAAK,MAAM,CAAC,CAAC;YACX,OAAO;gBACL,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC;gBACpC,GAAG,gBAAgB,CAAC,IAAI,EAAE,MAAM,EAAE,cAAc,CAAC;aAClD,CAAC;SACH;QACD,OAAO,CAAC,CAAC;YACP,MAAM,SAAS,GAAU,SAAS,CAAC;YACnC,4EAA4E;YAC5E,MAAM,KAAK,CAAC,wBAAwB,SAAS,EAAE,CAAC,CAAC;SAClD;KACF;AACH,CAAC;AAED,SAAS,gBAAgB,CACvB,IAAY,EACZ,MAA4B,EAC5B,cAAkC;IAElC,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;IAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;IACnC,OAAO,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC;AAC3C,CAAC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAA2B;IAC5D,MAAM,EACJ,KAAK,EACL,SAAS,EACT,UAAU,EACV,QAAQ,EACR,WAAW,EACX,YAAY,EACZ,SAAS,EACT,WAAW,EACX,UAAU,EACV,UAAU,EACV,OAAO,EACP,YAAY,EACZ,gBAAgB,GACjB,GAAG,OAAO,CAAC;IAEZ,MAAM,KAAK,GAAG,GAAG,CAAC,IAAI,EAAE;QACtB,SAAS;QACT,WAAW;QACX,WAAW;QACX,UAAU;QACV,OAAO;QACP,gBAAgB;KACjB,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;IAE3D,MAAM,QAAQ,GAAG,UAAU;QACzB,CAAC,CAAC,cAAc,CAAC,QAAQ,EAAE;YACvB,UAAU;YACV,UAAU;YACV,KAAK;YACL,YAAY;SACb,CAAC,CAAC,GAAG,CAAC,oBAAoB,CAAC;QAC9B,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,oBAAoB,CAAC,CAAC;IAEvC,OAAO,gBAAgB,CACrB,QAAQ;QACN,CAAC,CAAC,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE;YAC5B,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC,CAAC,GAAG,CAAC,oBAAoB,CAAC;QAC9B,CAAC,CAAC,QAAQ,EACZ,EAAE,SAAS,EAAE,CACd,CAAC;AACJ,CAAC;AAED,SAAS,SAAS,CAAC,IAA6B,EAAE,OAAyB;IACzE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,OAAO,CAAC;IAE5D,MAAM,YAAY,GAAG,CAAC,UAAkB,EAAE,EAAE,CAC1C,OAAO,UAAU,KAAK,QAAQ;QAC5B,CAAC,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,CAAC,UAAU,EAAE;QACjD,CAAC,CAAC,UAAU,CAAC;IAEjB,IAAI,UAAU,EAAE;QACd,OAAO,YAAY,CAAC,UAAU,CAAC,CAAC;KACjC;SAAM;QACL,OAAO,UAAU;YACf,CAAC,CAAC,aAAa,CAAC,IAAI,EAAE,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC;YACrD,CAAC,CAAC,YAAY,CAAC,eAAe,CAAC,IAAI,CAAC,GAAG,eAAe,CAAC,CAAC;KAC3D;AACH,CAAC;AAED,SAAS,oBAAoB,CAC3B,IAAyC;IAEzC,MAAM,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,GAAG,IAAI,CAAC;IACxC,OAAO;QACL,EAAE;QACF,CAAC;QACD,CAAC;QACD,KAAK;QACL,KAAK;KACN,CAAC;AACJ,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "nmr-processing",
|
|
3
|
-
"version": "9.3.
|
|
3
|
+
"version": "9.3.1",
|
|
4
4
|
"description": "Pure functions allowing to process NMR spectra.",
|
|
5
5
|
"main": "./lib/index.js",
|
|
6
6
|
"module": "./lib-esm/index.js",
|
|
@@ -38,20 +38,20 @@
|
|
|
38
38
|
},
|
|
39
39
|
"homepage": "https://github.com/cheminfo/nmr-processing#readme",
|
|
40
40
|
"devDependencies": {
|
|
41
|
-
"@types/jest": "^29.2.
|
|
41
|
+
"@types/jest": "^29.2.3",
|
|
42
42
|
"cheminfo-build": "^1.1.11",
|
|
43
43
|
"cheminfo-types": "^1.4.0",
|
|
44
|
-
"eslint": "^8.
|
|
44
|
+
"eslint": "^8.28.0",
|
|
45
45
|
"eslint-config-cheminfo-typescript": "^11.2.2",
|
|
46
46
|
"jest": "^29.3.1",
|
|
47
47
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
48
48
|
"md5": "^2.3.0",
|
|
49
49
|
"nmr-xy-testdata": "^0.5.1",
|
|
50
50
|
"openchemlib": "^8.0.1",
|
|
51
|
-
"prettier": "^2.
|
|
51
|
+
"prettier": "^2.8.0",
|
|
52
52
|
"rimraf": "^3.0.2",
|
|
53
53
|
"ts-jest": "^29.0.3",
|
|
54
|
-
"typescript": "^4.
|
|
54
|
+
"typescript": "^4.9.3"
|
|
55
55
|
},
|
|
56
56
|
"dependencies": {
|
|
57
57
|
"@lukeed/uuid": "^2.0.0",
|
|
@@ -77,7 +77,7 @@
|
|
|
77
77
|
"ml-spectra-processing": "^11.14.0",
|
|
78
78
|
"ml-tree-set": "^0.1.1",
|
|
79
79
|
"nmr-correlation": "^2.3.3",
|
|
80
|
-
"openchemlib-utils": "^2.
|
|
81
|
-
"spectrum-generator": "^8.0.
|
|
80
|
+
"openchemlib-utils": "^2.1.1",
|
|
81
|
+
"spectrum-generator": "^8.0.6"
|
|
82
82
|
}
|
|
83
83
|
}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
|
-
import { Molecule } from 'openchemlib';
|
|
2
|
+
import { Molecule } from 'openchemlib/full';
|
|
3
3
|
import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
|
|
4
4
|
|
|
5
5
|
import { NMRRange, NMRRangeWithIntegration } from '..';
|
|
@@ -206,17 +206,7 @@ export function peaksToRanges(
|
|
|
206
206
|
}
|
|
207
207
|
}
|
|
208
208
|
// it was a updateIntegrals function.
|
|
209
|
-
|
|
210
|
-
let sumObserved = 0;
|
|
211
|
-
for (const signal of signals) {
|
|
212
|
-
sumObserved += Math.abs(Math.round(signal.integralData.value));
|
|
213
|
-
}
|
|
214
|
-
if (sumObserved !== integrationSum) {
|
|
215
|
-
sumIntegral = integrationSum / sumObserved;
|
|
216
|
-
for (const signal of signals) {
|
|
217
|
-
signal.integralData.value *= sumIntegral;
|
|
218
|
-
}
|
|
219
|
-
}
|
|
209
|
+
updateIntegration(signals, integrationSum);
|
|
220
210
|
}
|
|
221
211
|
|
|
222
212
|
signals.sort((a, b) => {
|
|
@@ -230,6 +220,7 @@ export function peaksToRanges(
|
|
|
230
220
|
}
|
|
231
221
|
}
|
|
232
222
|
}
|
|
223
|
+
|
|
233
224
|
let ranges: NMRRange[] = [];
|
|
234
225
|
for (let i = 0; i < signals.length; i++) {
|
|
235
226
|
let signal = signals[i];
|
|
@@ -243,7 +234,6 @@ export function peaksToRanges(
|
|
|
243
234
|
delta: signal.delta,
|
|
244
235
|
kind: signal.kind || 'signal',
|
|
245
236
|
multiplicity: signal.multiplicity,
|
|
246
|
-
integration: signal.integralData.value,
|
|
247
237
|
};
|
|
248
238
|
if (keepPeaks) {
|
|
249
239
|
signalResult.peaks = signal.peaks.map((peak) => {
|
|
@@ -299,7 +289,7 @@ export function detectSignals(
|
|
|
299
289
|
let peaks;
|
|
300
290
|
let signals = [];
|
|
301
291
|
let prevPeak = { x: Number.MIN_SAFE_INTEGER };
|
|
302
|
-
|
|
292
|
+
|
|
303
293
|
frequencyCluster /= frequency;
|
|
304
294
|
for (const peak of peakList) {
|
|
305
295
|
if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
|
|
@@ -349,15 +339,10 @@ export function detectSignals(
|
|
|
349
339
|
} else {
|
|
350
340
|
integration.value = integralPeaks;
|
|
351
341
|
}
|
|
352
|
-
spectrumIntegral += integration.value;
|
|
353
342
|
}
|
|
354
343
|
|
|
355
344
|
if (integrationSum > 0) {
|
|
356
|
-
|
|
357
|
-
for (let signal of signals) {
|
|
358
|
-
let integration = signal.integralData;
|
|
359
|
-
integration.value *= integralFactor;
|
|
360
|
-
}
|
|
345
|
+
updateIntegration(signals, integrationSum);
|
|
361
346
|
}
|
|
362
347
|
|
|
363
348
|
return signals;
|
|
@@ -370,3 +355,22 @@ export function detectSignals(
|
|
|
370
355
|
function computeArea(peak: Peak1DIntern, frequency: number) {
|
|
371
356
|
return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
|
|
372
357
|
}
|
|
358
|
+
|
|
359
|
+
/**
|
|
360
|
+
* update the integration Values
|
|
361
|
+
* @param signals
|
|
362
|
+
* @param integrationSum
|
|
363
|
+
*/
|
|
364
|
+
function updateIntegration(signals: SignalIntern[], integrationSum: number) {
|
|
365
|
+
let sumIntegral = 0;
|
|
366
|
+
let sumObserved = 0;
|
|
367
|
+
for (const signal of signals) {
|
|
368
|
+
sumObserved += Math.abs(Math.round(signal.integralData.value));
|
|
369
|
+
}
|
|
370
|
+
if (sumObserved !== integrationSum) {
|
|
371
|
+
sumIntegral = integrationSum / sumObserved;
|
|
372
|
+
for (const signal of signals) {
|
|
373
|
+
signal.integralData.value *= sumIntegral;
|
|
374
|
+
}
|
|
375
|
+
}
|
|
376
|
+
}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { FromTo, PointXY } from 'cheminfo-types';
|
|
2
|
-
import type { Molecule } from 'openchemlib';
|
|
2
|
+
import type { Molecule } from 'openchemlib/full';
|
|
3
3
|
|
|
4
4
|
import { signals2DToZ } from '../signals/signals2DToZ';
|
|
5
5
|
import { OptionsSignalsToXY, signalsToXY } from '../signals/signalsToXY';
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
2
|
import fetch from 'cross-fetch';
|
|
3
|
-
import type { Molecule } from 'openchemlib';
|
|
3
|
+
import type { Molecule } from 'openchemlib/full';
|
|
4
4
|
|
|
5
5
|
import { setIDs } from '../peaks/util/setIDs';
|
|
6
6
|
import type { NMRSignal1D } from '../signals/NMRSignal1D';
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
2
|
import fetch from 'cross-fetch';
|
|
3
3
|
import FormData from 'form-data';
|
|
4
|
-
import type { Molecule } from 'openchemlib';
|
|
4
|
+
import type { Molecule } from 'openchemlib/full';
|
|
5
5
|
import {
|
|
6
6
|
addDiastereotopicMissingChirality,
|
|
7
7
|
getConnectivityMatrix,
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { v4 as generateID } from '@lukeed/uuid';
|
|
2
2
|
import { agnes, Cluster } from 'ml-hclust';
|
|
3
3
|
import { Matrix } from 'ml-matrix';
|
|
4
|
-
import { Molecule } from 'openchemlib';
|
|
4
|
+
import { Molecule } from 'openchemlib/full';
|
|
5
5
|
import {
|
|
6
6
|
getGroupedDiastereotopicAtomIDs,
|
|
7
7
|
getPathsInfo,
|
|
@@ -106,7 +106,11 @@ export function xyAutoPeaksPicking(
|
|
|
106
106
|
direction = 'positive',
|
|
107
107
|
} = options;
|
|
108
108
|
|
|
109
|
-
|
|
109
|
+
let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
|
|
110
|
+
// we can consider a peak with of 0.5 Hz for the windowSize
|
|
111
|
+
let ws = Math.max(Math.round(pointsPerHz / 2), 5);
|
|
112
|
+
|
|
113
|
+
const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
|
|
110
114
|
|
|
111
115
|
if (data.x.length < windowSize) return [];
|
|
112
116
|
|