nmr-processing 9.2.0 → 9.3.0-pre.1669145798

package/README.md

@@ -4,6 +4,7 @@
 [![build status][ci-image]][ci-url]
 [![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5153274.svg)](https://doi.org/10.5281/zenodo.5153274)
 
 ## Introduction
 

package/lib/apodization/shapes/WindowFunctions.d.ts

@@ -8,5 +8,5 @@ interface LorentToGauss {
     kind: 'lorentzToGauss';
     options: LorentzToGaussOptions;
 }
-export declare type WindowFunctions = Exponential | LorentToGauss;
+export type WindowFunctions = Exponential | LorentToGauss;
 export {};

package/lib/assignment/get1HAssignments.d.ts

@@ -4,8 +4,8 @@ import { PredictProtonOptions } from '../prediction/predictProton';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { MakeMandatory } from '../utilities/MakeMandatory';
 import { RestrictionByCS1D } from './utils/buildAssignments';
-export declare type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<NMRSignal1D, 'atoms' | 'diaIDs' | 'nbAtoms'>;
-export declare type NMRRangeWithIntegration = MakeMandatory<NMRRange, 'integration'>;
+export type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<NMRSignal1D, 'atoms' | 'diaIDs' | 'nbAtoms'>;
+export type NMRRangeWithIntegration = MakeMandatory<NMRRange, 'integration'>;
 export interface Get1HAssignmentsOptions {
     restrictionByCS?: Partial<RestrictionByCS1D>;
     /**

package/lib/assignment/getAssignments.d.ts

@@ -19,7 +19,7 @@ export interface SpectraData2D {
      */
     info: any;
 }
-export declare type SpectraData = SpectraData1D | SpectraData2D;
+export type SpectraData = SpectraData1D | SpectraData2D;
 export interface GetAutoAssignmentInput {
     spectra: SpectraData[];
     /**

package/lib/assignment/nmrAssigment.d.ts

@@ -1,8 +1,8 @@
 import type { NMRRange, NMRSignal1D, NMRSignal2D, NMRZone } from '..';
 import { MakeMandatory } from '../utilities/MakeMandatory';
 import type { SpectraData1D, SpectraData2D } from './getAssignments';
-export declare type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
-export declare type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
+export type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
+export type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
 export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
     id: string;
     signals: Array<NMRSignal2DWithId>;
@@ -17,4 +17,4 @@ export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {
 export interface SpectraData2DWithIds extends Omit<SpectraData2D, 'zones'> {
     zones: NMRZoneWithIds[];
 }
-export declare type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;
+export type SpectraDataWithIds = SpectraData1DWithIds | SpectraData2DWithIds;

package/lib/assignment/utils/createMapPossibleAssignments.d.ts

@@ -1,7 +1,7 @@
 import { MakeMandatory } from '../../utilities/MakeMandatory';
 import type { Targets } from '../get1HAssignments';
 import type { RestrictionByCS1D, Predictions1Dassignments } from './buildAssignments';
-declare type RestrictionByCSMandatory = MakeMandatory<RestrictionByCS1D, 'chemicalShiftRestriction' | 'tolerance' | 'useChemicalShiftScore'>;
+type RestrictionByCSMandatory = MakeMandatory<RestrictionByCS1D, 'chemicalShiftRestriction' | 'tolerance' | 'useChemicalShiftScore'>;
 interface CreateMapPossibleAssignments {
     predictions: Predictions1Dassignments;
     restrictionByCS: RestrictionByCSMandatory;

package/lib/assignment/utils/getAssignment/buildAssignments.d.ts

@@ -4,8 +4,8 @@ import { NMRSignal1D, PredictCarbonOptions, PredictProtonOptions } from '../../.
 import { MakeMandatory } from '../../../utilities/MakeMandatory';
 import { SpectraDataWithIds } from '../../nmrAssigment';
 import { TargetsByAtomType } from './getTargetsAndCorrelations';
-export declare type AtomTypes = 'H' | 'C';
-export declare type CurrentAtoms = Array<AtomTypes>;
+export type AtomTypes = 'H' | 'C';
+export type CurrentAtoms = Array<AtomTypes>;
 export interface Partial {
     [key: string]: Array<string | null>;
 }
@@ -41,7 +41,7 @@ export interface BuildAssignmentInput {
     };
     targets: TargetsByAtomType;
 }
-declare type NMRSignal1DFromPrediction = MakeMandatory<NMRSignal1D, 'nbAtoms' | 'diaIDs' | 'atoms'>;
+type NMRSignal1DFromPrediction = MakeMandatory<NMRSignal1D, 'nbAtoms' | 'diaIDs' | 'atoms'>;
 export interface Prediction extends NMRSignal1DFromPrediction {
     diaIDIndex: number;
     allHydrogens: number;

package/lib/assignment/utils/getAssignment/formatData.d.ts

@@ -9,6 +9,6 @@ interface SpectraData2DFormatted extends Omit<SpectraData2DWithIds, 'zones'> {
         values: NMRZoneWithIds[];
     };
 }
-export declare type SpectraDataFormatted = SpectraData1DFormatted | SpectraData2DFormatted;
+export type SpectraDataFormatted = SpectraData1DFormatted | SpectraData2DFormatted;
 export declare function formatData(input?: SpectraDataWithIds[]): SpectraDataFormatted[];
 export {};

package/lib/index.d.ts

@@ -20,6 +20,7 @@ export * from './signals/signalsToRanges';
 export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './signals/optimizeSignals';
+export * from './signals/signalsToFID';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
 export * from './utilities/getFrequency';

package/lib/index.js

@@ -36,6 +36,7 @@ __exportStar(require("./signals/signalsToRanges"), exports);
 __exportStar(require("./signals/signalsToXY"), exports);
 __exportStar(require("./signals/signals2DToZ"), exports);
 __exportStar(require("./signals/optimizeSignals"), exports);
+__exportStar(require("./signals/signalsToFID"), exports);
 __exportStar(require("./utilities/resurrect"), exports);
 __exportStar(require("./utilities/rangeFromSignal"), exports);
 __exportStar(require("./utilities/getFrequency"), exports);

package/lib/index.js.map

@@ -1 +1 @@
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package/lib/peaks/peaksFilterImpurities.d.ts

@@ -1,6 +1,6 @@
 import { impurities } from '../constants/impurities';
 import type { NMRPeak1D } from './NMRPeak1D';
-declare type Solvent = keyof typeof impurities;
+type Solvent = keyof typeof impurities;
 export interface OptionsPeaksFilterImpurities {
     /**
      * Solvent name.

package/lib/peaks/peaksToRanges.d.ts

@@ -55,7 +55,7 @@ export interface OptionsDetectSignals {
     frequency?: number;
     nucleus?: string;
 }
-declare type NMRPeak1DIntern = Omit<NMRPeak1D, 'fwhm' | 'shape'>;
+type NMRPeak1DIntern = Omit<NMRPeak1D, 'fwhm' | 'shape'>;
 /**
  * This function clustering peaks and calculate the integration value for each range from the peak list returned from extractPeaks function.
  */

package/lib/peaks/peaksToRanges.js

@@ -114,17 +114,7 @@ function peaksToRanges(data, peakList, options = {}) {
             }
         }
         // it was a updateIntegrals function.
-        let sumIntegral = 0;
-        let sumObserved = 0;
-        for (const signal of signals) {
-            sumObserved += Math.abs(Math.round(signal.integralData.value));
-        }
-        if (sumObserved !== integrationSum) {
-            sumIntegral = integrationSum / sumObserved;
-            for (const signal of signals) {
-                signal.integralData.value *= sumIntegral;
-            }
-        }
+        updateIntegration(signals, integrationSum);
     }
     signals.sort((a, b) => {
         return b.delta - a.delta;
@@ -149,7 +139,6 @@ function peaksToRanges(data, peakList, options = {}) {
             delta: signal.delta,
             kind: signal.kind || 'signal',
             multiplicity: signal.multiplicity,
-            integration: signal.integralData.value,
         };
         if (keepPeaks) {
             signalResult.peaks = signal.peaks.map((peak) => {
@@ -192,7 +181,6 @@ function detectSignals(data, peakList, options = {}) {
     let peaks;
     let signals = [];
     let prevPeak = { x: Number.MIN_SAFE_INTEGER };
-    let spectrumIntegral = 0;
     frequencyCluster /= frequency;
     for (const peak of peakList) {
         if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
@@ -238,14 +226,9 @@ function detectSignals(data, peakList, options = {}) {
         else {
             integration.value = integralPeaks;
         }
-        spectrumIntegral += integration.value;
     }
     if (integrationSum > 0) {
-        let integralFactor = integrationSum / spectrumIntegral;
-        for (let signal of signals) {
-            let integration = signal.integralData;
-            integration.value *= integralFactor;
-        }
+        updateIntegration(signals, integrationSum);
     }
     return signals;
 }
@@ -257,4 +240,22 @@ exports.detectSignals = detectSignals;
 function computeArea(peak, frequency) {
     return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
 }
+/**
+ * update the integration Values
+ * @param signals
+ * @param integrationSum
+ */
+function updateIntegration(signals, integrationSum) {
+    let sumIntegral = 0;
+    let sumObserved = 0;
+    for (const signal of signals) {
+        sumObserved += Math.abs(Math.round(signal.integralData.value));
+    }
+    if (sumObserved !== integrationSum) {
+        sumIntegral = integrationSum / sumObserved;
+        for (const signal of signals) {
+            signal.integralData.value *= sumIntegral;
+        }
+    }
+}
 //# sourceMappingURL=peaksToRanges.js.map

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package/lib/peaks/util/convertWidth.d.ts

@@ -1,6 +1,6 @@
 import { MakeMandatory } from '../../utilities/MakeMandatory';
 import { NMRPeak1D } from '../NMRPeak1D';
-export declare type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
+export type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
 export interface ConvertWidthOptions<T> {
     convertTo: string & {
         _kind?: 'hz' | 'ppm';

package/lib/peaks/util/convertWidthToHz.d.ts

@@ -1,4 +1,4 @@
 import { NMRPeak1D } from '../NMRPeak1D';
 import { ConvertWidthOptions } from './convertWidth';
-export declare type ConvertWidthTo<T> = Omit<ConvertWidthOptions<T>, 'convertTo'>;
+export type ConvertWidthTo<T> = Omit<ConvertWidthOptions<T>, 'convertTo'>;
 export declare function convertWidthToHz<T extends NMRPeak1D>(peaks: T[], options: ConvertWidthTo<T>): T[];

package/lib/prediction/dataStructure.d.ts

@@ -1,4 +1,4 @@
 export interface DataBaseLevelStructure {
     [key: string]: number[] | undefined;
 }
-export declare type DataBaseStructure = DataBaseLevelStructure[];
+export type DataBaseStructure = DataBaseLevelStructure[];

package/lib/prediction/predictCarbon.d.ts

@@ -22,7 +22,7 @@ export interface PredictCarbonOptions {
      */
     maxSphereSize?: number;
 }
-export declare type PredictCarbon = typeof predictCarbon;
+export type PredictCarbon = typeof predictCarbon;
 /**
  * Make a query to a hose code based database to predict carbon chemical shift
  * @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.

package/lib/prediction/predictProton.d.ts

@@ -10,5 +10,5 @@ export interface PredictProtonOptions {
      */
     cache?: (molfile: string, result?: string) => void | string | undefined;
 }
-export declare type PredictProton = typeof predictProton;
+export type PredictProton = typeof predictProton;
 export declare function predictProton(molecule: Molecule, options?: PredictProtonOptions): Promise<Prediction1D>;

package/lib/prediction/utils/getFilteredIDiaIDs.d.ts

@@ -4,7 +4,7 @@ import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
 export interface GroupDiaIDsWithHose extends GroupDiastereotopicAtomIDs {
     hose: string[];
 }
-export declare type GroupedDiaIDsWithHose = GroupDiaIDsWithHose[];
+export type GroupedDiaIDsWithHose = GroupDiaIDsWithHose[];
 export declare function getFilteredIDiaIDs(molecule: Molecule, options: {
     maxSphereSize: number;
 }): {

package/lib/prediction/utils/predict2D.d.ts

@@ -8,7 +8,7 @@ import type { PredictProton, PredictProtonOptions } from '../predictProton';
  * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
  * @returns {object} - object with molfile, diaIDs, 2D signals and zones.
  */
-export declare type Predictor = PredictCarbon | PredictProton;
+export type Predictor = PredictCarbon | PredictProton;
 export interface Predictors {
     [key: string]: Predictor | undefined;
     H?: Predictor;

package/lib/signals/optimization/getInternalSignals.d.ts

@@ -14,8 +14,8 @@ export interface InternalSignal {
     fromIndexCoupling: number;
     toIndexCoupling: number;
 }
-export declare type Parameter = 'delta' | 'intensity' | 'fwhm' | 'mu' | 'coupling';
-export declare type ParametersFromOptions = Record<Parameter, Record<string, number | ((options?: {
+export type Parameter = 'delta' | 'intensity' | 'fwhm' | 'mu' | 'coupling';
+export type ParametersFromOptions = Record<Parameter, Record<string, number | ((options?: {
     signal?: Signal;
     shape?: Shape1D;
     index?: number;
@@ -35,7 +35,7 @@ export interface GetInternalSignalsOptions {
     shape?: Shape1D;
     parameters?: ParametersFromOptions;
 }
-export declare type Shape1DWithFWHM = Omit<Shape1D, 'fwhm'> & {
+export type Shape1DWithFWHM = Omit<Shape1D, 'fwhm'> & {
     fwhm: number;
 };
 export declare function getInternalSignals(data: DataXY, signals: Signal[], minMaxY: Record<string, number>, options: GetInternalSignalsOptions): {

package/lib/signals/optimization/getSumOfShapes.d.ts

@@ -1,4 +1,4 @@
 import { InternalSignal } from './getInternalSignals';
 import { SignalsToPointXYOptions } from './signalsToPointXY';
-export declare type SumOfShapes = (parameters: number[]) => (x: number) => number;
+export type SumOfShapes = (parameters: number[]) => (x: number) => number;
 export declare function getSumOfShapes(internalSignals: InternalSignal[], options: SignalsToPointXYOptions): (parameters: number[]) => (currentX: number) => number;

package/lib/signals/optimizeSignals.d.ts

@@ -4,7 +4,7 @@ import { NMRPeak1D } from '../peaks/NMRPeak1D';
 import { NMRSignal1D } from './NMRSignal1D';
 import { ParametersFromOptions, Shape1DWithFWHM } from './optimization/getInternalSignals';
 import { SignalsToPointXYOptions } from './optimization/signalsToPointXY';
-declare type ParametersFromSignal = Record<string, Record<string, number>>;
+type ParametersFromSignal = Record<string, Record<string, number>>;
 export interface Signal extends NMRSignal1D {
     intensity?: number;
     shape?: Shape1D;

package/lib/signals/signalsJoin.d.ts

@@ -9,9 +9,9 @@ export interface SignalsJoinOptions {
      */
     joinCouplings?: SignalJoinCouplingsOptions;
 }
-declare type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'multiplicity' | 'diaIDs' | 'pathLength'>;
-declare type Signal1DWidthDiaID = MakeMandatory<NMRSignal1D, 'diaIDs'>;
-declare type Signal1DWidthJsAndDiaID = Omit<Signal1DWidthDiaID, 'js'> & {
+type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'multiplicity' | 'diaIDs' | 'pathLength'>;
+type Signal1DWidthDiaID = MakeMandatory<NMRSignal1D, 'diaIDs'>;
+type Signal1DWidthJsAndDiaID = Omit<Signal1DWidthDiaID, 'js'> & {
     js: JcouplingFromPrediction[];
 };
 /**

package/lib/signals/signalsToFID.d.ts

@@ -0,0 +1,42 @@
+import { NMRSignal1D } from './NMRSignal1D';
+export interface SignalsToFIDOptions {
+    /**
+     * at the end of the superposition of all component, an exponential apodization will be applied
+     * in order to have FID like shape.
+     * @default 1
+     */
+    lb?: number;
+    /**
+     * lower limit of the spectrum
+     * @default 0
+     */
+    from?: number;
+    /**
+     * upper limit of the spectrum
+     * @default 10
+     */
+    to?: number;
+    /**
+     * number of points of the resulting FID
+     */
+    nbPoints?: number;
+    /**
+     * It is the frequency of the carrier (e.g. SFO1 for bruker spectrometers)
+     */
+    frequency?: number;
+    /**
+     * Maximum number of atoms on each cluster that can be considered to be simulated together.
+     * It affects the the quality and speed of the simulation.
+     */
+    maxClusterSize?: number;
+}
+/**
+ * it use the chemical shifts and the coupling between them in order to generate a FID.
+ * It does not propagate the hamiltonian of the spin system, instead it simulate all the
+ * frequencies in the spectrum (including second order) and add all the waves in a real and
+ * imaginary parts, that is why the couplings should be assigned in order to generate the spin system.
+ */
+export declare function signalsToFID(signals: NMRSignal1D[], options: SignalsToFIDOptions): {
+    re: import("cheminfo-types").DoubleArray;
+    im: import("cheminfo-types").DoubleArray;
+};

package/lib/signals/signalsToFID.js

@@ -0,0 +1,62 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.signalsToFID = void 0;
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const apodization_1 = require("../apodization/apodization");
+const signalsToSpinSystem_1 = require("./simulation/signalsToSpinSystem");
+const simulateXYPeaks_1 = require("./simulation/simulateXYPeaks");
+const splitSpinSystem_1 = require("./simulation/splitSpinSystem");
+const twoPi = Math.PI * 2;
+/**
+ * it use the chemical shifts and the coupling between them in order to generate a FID.
+ * It does not propagate the hamiltonian of the spin system, instead it simulate all the
+ * frequencies in the spectrum (including second order) and add all the waves in a real and
+ * imaginary parts, that is why the couplings should be assigned in order to generate the spin system.
+ */
+function signalsToFID(signals, options) {
+    const { lb = 1, from = 0, to = 10, nbPoints = 1024, frequency = 400, maxClusterSize = 8, } = options;
+    let spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(signals);
+    spinSystem.clusters = (0, splitSpinSystem_1.splitSpinSystem)(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = (0, simulateXYPeaks_1.simulateXYPeaks)(spinSystem, { frequency });
+    const re = new Float64Array(nbPoints);
+    const im = new Float64Array(nbPoints);
+    const sw = Math.abs(to - from);
+    const adquisitionTime = nbPoints / (sw * frequency);
+    const time = (0, ml_spectra_processing_1.xSequentialFill)({
+        size: nbPoints,
+        from: 0,
+        to: adquisitionTime,
+    });
+    for (const peak of peaks) {
+        const { x, y } = peak;
+        const cs = x * frequency * twoPi;
+        for (let i = 0; i < nbPoints; i++) {
+            re[i] += y * Math.cos(cs * time[i]);
+            im[i] += y * Math.sin(cs * time[i]);
+        }
+    }
+    const { windowData, ...result } = (0, apodization_1.apodization)({ re, im }, {
+        pointsToShift: 0,
+        compose: {
+            length: nbPoints,
+            shapes: [
+                {
+                    start: 0,
+                    shape: {
+                        kind: 'exponential',
+                        options: {
+                            dw: adquisitionTime / (nbPoints - 1),
+                            lb,
+                        },
+                    },
+                },
+            ],
+        },
+    });
+    return result;
+}
+exports.signalsToFID = signalsToFID;
+//# sourceMappingURL=signalsToFID.js.map

package/lib/signals/signalsToFID.js.map

@@ -0,0 +1 @@
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package/lib/signals/signalsToRanges.d.ts

@@ -13,6 +13,6 @@ interface SignalsToRangesOptions {
      */
     frequency?: number;
 }
-declare type RangeFullfiled = MakeMandatory<NMRRange, 'integration' | 'signals' | 'id'>;
+type RangeFullfiled = MakeMandatory<NMRRange, 'integration' | 'signals' | 'id'>;
 export declare function signalsToRanges(signals: NMRSignal1D[], options?: SignalsToRangesOptions): RangeFullfiled[];
 export {};

package/lib/signals/utils/jAnalyzer.d.ts

@@ -10,7 +10,7 @@ interface IntergralData {
     from: number;
     to: number;
 }
-export declare type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
+export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
     intensity: number;
 };
 export interface SignalIntern {
@@ -37,7 +37,7 @@ export interface SignalIntern {
     peaks: Peak1DIntern[];
     peaksComp?: Peak1DIntern[];
 }
-declare type SignalInternMandatory = MakeMandatory<SignalIntern, 'symRank' | 'mask' | 'peaksComp'>;
+type SignalInternMandatory = MakeMandatory<SignalIntern, 'symRank' | 'mask' | 'peaksComp'>;
 export interface OpitonsCompilePatter {
     jAxisKey?: JAxisKeys;
 }

package/lib/utilities/MakeMandatory.d.ts

@@ -1,3 +1,3 @@
-export declare type MakeMandatory<T, K extends keyof T> = T & {
+export type MakeMandatory<T, K extends keyof T> = T & {
     [P in K]-?: T[P];
 };

package/lib/utilities/getFrequency.d.ts

@@ -9,7 +9,7 @@ export interface ObjervedNucleusData {
      */
     frequency: number;
 }
-declare type Nucleus = Nuclei | (string & Record<never, never>);
+type Nucleus = Nuclei | (string & Record<never, never>);
 /**
  * calculate the frequency of a nucleus with respect to a reference nucleus
  */

package/lib/utilities/hasProperty.d.ts

@@ -1,3 +1,3 @@
-export declare function hasProperty<T, K extends keyof T>(data: T, key: K): data is T & {
+export declare function hasProperty<T extends object, K extends keyof T>(data: T, key: K): data is T & {
     [P in K]-?: T[P];
 };

package/lib/xy/xyAutoPeaksPicking.d.ts

@@ -42,5 +42,5 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
      */
     frequency: number;
 }
-export declare type NMRPeak1DWithShapeID = MakeMandatory<NMRPeak1D, 'id' | 'shape'>;
+export type NMRPeak1DWithShapeID = MakeMandatory<NMRPeak1D, 'id' | 'shape'>;
 export declare function xyAutoPeaksPicking(data: DataXY, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithShapeID[];

package/lib/xy/xyAutoPeaksPicking.js

@@ -6,7 +6,10 @@ const ml_spectra_processing_1 = require("ml-spectra-processing");
 const convertWidthToHz_1 = require("../peaks/util/convertWidthToHz");
 function xyAutoPeaksPicking(data, options) {
     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;
-    const { windowSize = 9, polynomial = 3 } = sgOptions;
+    let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
+    // we can consider a peak with of 0.5 Hz for the windowSize
+    let ws = Math.max(Math.round(pointsPerHz / 2), 5);
+    const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
     if (data.x.length < windowSize)
         return [];
     if (from !== undefined && to !== undefined) {

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package/lib/xyz/xyzAutoZonesPicking.d.ts

@@ -65,8 +65,8 @@ export interface XYZAutoZonesPickingOptions {
      */
     kernel?: GetKernelOptions;
 }
-export declare type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<NMRSignal2D<T>, 'id'>;
-export declare type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
+export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<NMRSignal2D<T>, 'id'>;
+export type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
 export declare function xyzAutoZonesPicking(spectraData: Data2D, options: XYZAutoZonesPickingOptions): NMRZoneWithID[];
 /**
  * This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed

package/lib-esm/index.js

@@ -20,6 +20,7 @@ export * from './signals/signalsToRanges';
 export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './signals/optimizeSignals';
+export * from './signals/signalsToFID';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
 export * from './utilities/getFrequency';

package/lib-esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAE7C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,mBAAmB,CAAC;AAClC,cAAc,kBAAkB,CAAC;AAEjC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAE/C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,6BAA6B,CAAC;AAE5C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AACvC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,wBAAwB,CAAC;AAEvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,0BAA0B,CAAC;AAEzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AAEzC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AAEtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,8BAA8B,CAAC;AAE7C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAE3C,cAAc,2BAA2B,CAAC"}

package/lib-esm/peaks/peaksToRanges.js

@@ -108,17 +108,7 @@ export function peaksToRanges(data, peakList, options = {}) {
             }
         }
         // it was a updateIntegrals function.
-        let sumIntegral = 0;
-        let sumObserved = 0;
-        for (const signal of signals) {
-            sumObserved += Math.abs(Math.round(signal.integralData.value));
-        }
-        if (sumObserved !== integrationSum) {
-            sumIntegral = integrationSum / sumObserved;
-            for (const signal of signals) {
-                signal.integralData.value *= sumIntegral;
-            }
-        }
+        updateIntegration(signals, integrationSum);
     }
     signals.sort((a, b) => {
         return b.delta - a.delta;
@@ -143,7 +133,6 @@ export function peaksToRanges(data, peakList, options = {}) {
             delta: signal.delta,
             kind: signal.kind || 'signal',
             multiplicity: signal.multiplicity,
-            integration: signal.integralData.value,
         };
         if (keepPeaks) {
             signalResult.peaks = signal.peaks.map((peak) => {
@@ -185,7 +174,6 @@ export function detectSignals(data, peakList, options = {}) {
     let peaks;
     let signals = [];
     let prevPeak = { x: Number.MIN_SAFE_INTEGER };
-    let spectrumIntegral = 0;
     frequencyCluster /= frequency;
     for (const peak of peakList) {
         if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
@@ -231,14 +219,9 @@ export function detectSignals(data, peakList, options = {}) {
         else {
             integration.value = integralPeaks;
         }
-        spectrumIntegral += integration.value;
     }
     if (integrationSum > 0) {
-        let integralFactor = integrationSum / spectrumIntegral;
-        for (let signal of signals) {
-            let integration = signal.integralData;
-            integration.value *= integralFactor;
-        }
+        updateIntegration(signals, integrationSum);
     }
     return signals;
 }
@@ -249,4 +232,22 @@ export function detectSignals(data, peakList, options = {}) {
 function computeArea(peak, frequency) {
     return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
 }
+/**
+ * update the integration Values
+ * @param signals
+ * @param integrationSum
+ */
+function updateIntegration(signals, integrationSum) {
+    let sumIntegral = 0;
+    let sumObserved = 0;
+    for (const signal of signals) {
+        sumObserved += Math.abs(Math.round(signal.integralData.value));
+    }
+    if (sumObserved !== integrationSum) {
+        sumIntegral = integrationSum / sumObserved;
+        for (const signal of signals) {
+            signal.integralData.value *= sumIntegral;
+        }
+    }
+}
 //# sourceMappingURL=peaksToRanges.js.map

package/lib-esm/peaks/peaksToRanges.js.map

@@ -1 +1 @@
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package/lib-esm/signals/signalsToFID.js

@@ -0,0 +1,58 @@
+import { xSequentialFill } from 'ml-spectra-processing';
+import { apodization } from '../apodization/apodization';
+import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from './simulation/simulateXYPeaks';
+import { splitSpinSystem } from './simulation/splitSpinSystem';
+const twoPi = Math.PI * 2;
+/**
+ * it use the chemical shifts and the coupling between them in order to generate a FID.
+ * It does not propagate the hamiltonian of the spin system, instead it simulate all the
+ * frequencies in the spectrum (including second order) and add all the waves in a real and
+ * imaginary parts, that is why the couplings should be assigned in order to generate the spin system.
+ */
+export function signalsToFID(signals, options) {
+    const { lb = 1, from = 0, to = 10, nbPoints = 1024, frequency = 400, maxClusterSize = 8, } = options;
+    let spinSystem = signalsToSpinSystem(signals);
+    spinSystem.clusters = splitSpinSystem(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = simulateXYPeaks(spinSystem, { frequency });
+    const re = new Float64Array(nbPoints);
+    const im = new Float64Array(nbPoints);
+    const sw = Math.abs(to - from);
+    const adquisitionTime = nbPoints / (sw * frequency);
+    const time = xSequentialFill({
+        size: nbPoints,
+        from: 0,
+        to: adquisitionTime,
+    });
+    for (const peak of peaks) {
+        const { x, y } = peak;
+        const cs = x * frequency * twoPi;
+        for (let i = 0; i < nbPoints; i++) {
+            re[i] += y * Math.cos(cs * time[i]);
+            im[i] += y * Math.sin(cs * time[i]);
+        }
+    }
+    const { windowData, ...result } = apodization({ re, im }, {
+        pointsToShift: 0,
+        compose: {
+            length: nbPoints,
+            shapes: [
+                {
+                    start: 0,
+                    shape: {
+                        kind: 'exponential',
+                        options: {
+                            dw: adquisitionTime / (nbPoints - 1),
+                            lb,
+                        },
+                    },
+                },
+            ],
+        },
+    });
+    return result;
+}
+//# sourceMappingURL=signalsToFID.js.map

package/lib-esm/signals/signalsToFID.js.map

@@ -0,0 +1 @@
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package/lib-esm/xy/xyAutoPeaksPicking.js

@@ -3,7 +3,10 @@ import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processin
 import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
 export function xyAutoPeaksPicking(data, options) {
     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;
-    const { windowSize = 9, polynomial = 3 } = sgOptions;
+    let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
+    // we can consider a peak with of 0.5 Hz for the windowSize
+    let ws = Math.max(Math.round(pointsPerHz / 2), 5);
+    const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
     if (data.x.length < windowSize)
         return [];
     if (from !== undefined && to !== undefined) {

package/lib-esm/xy/xyAutoPeaksPicking.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.2.0",
+  "version": "9.3.0-pre.1669145798",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -38,20 +38,20 @@
   },
   "homepage": "https://github.com/cheminfo/nmr-processing#readme",
   "devDependencies": {
-    "@types/jest": "^28.1.6",
+    "@types/jest": "^29.2.2",
     "cheminfo-build": "^1.1.11",
     "cheminfo-types": "^1.4.0",
-    "eslint": "^8.22.0",
-    "eslint-config-cheminfo-typescript": "^11.0.1",
-    "jest": "^28.1.3",
+    "eslint": "^8.27.0",
+    "eslint-config-cheminfo-typescript": "^11.2.2",
+    "jest": "^29.3.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "nmr-xy-testdata": "^0.5.1",
-    "openchemlib": "^8.0.0",
+    "openchemlib": "^8.0.1",
     "prettier": "^2.7.1",
     "rimraf": "^3.0.2",
-    "ts-jest": "^28.0.8",
-    "typescript": "^4.7.4"
+    "ts-jest": "^29.0.3",
+    "typescript": "^4.8.4"
   },
   "dependencies": {
     "@lukeed/uuid": "^2.0.0",
@@ -68,16 +68,16 @@
     "ml-gsd": "^12.1.2",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.1.0",
-    "ml-matrix": "^6.10.2",
+    "ml-matrix": "^6.10.4",
     "ml-matrix-convolution": "^1.0.0",
     "ml-matrix-peaks-finder": "^1.0.0",
     "ml-peak-shape-generator": "^4.1.2",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^11.12.0",
+    "ml-spectra-processing": "^11.14.0",
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.3.3",
-    "openchemlib-utils": "^2.0.0",
+    "openchemlib-utils": "^2.1.0",
     "spectrum-generator": "^8.0.4"
   }
 }

package/src/index.ts

@@ -25,6 +25,7 @@ export * from './signals/signalsToRanges';
 export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './signals/optimizeSignals';
+export * from './signals/signalsToFID';
 
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';

package/src/peaks/peaksToRanges.ts

@@ -206,17 +206,7 @@ export function peaksToRanges(
       }
     }
     // it was a updateIntegrals function.
-    let sumIntegral = 0;
-    let sumObserved = 0;
-    for (const signal of signals) {
-      sumObserved += Math.abs(Math.round(signal.integralData.value));
-    }
-    if (sumObserved !== integrationSum) {
-      sumIntegral = integrationSum / sumObserved;
-      for (const signal of signals) {
-        signal.integralData.value *= sumIntegral;
-      }
-    }
+    updateIntegration(signals, integrationSum);
   }
 
   signals.sort((a, b) => {
@@ -230,6 +220,7 @@ export function peaksToRanges(
       }
     }
   }
+
   let ranges: NMRRange[] = [];
   for (let i = 0; i < signals.length; i++) {
     let signal = signals[i];
@@ -243,7 +234,6 @@ export function peaksToRanges(
       delta: signal.delta,
       kind: signal.kind || 'signal',
       multiplicity: signal.multiplicity,
-      integration: signal.integralData.value,
     };
     if (keepPeaks) {
       signalResult.peaks = signal.peaks.map((peak) => {
@@ -299,7 +289,7 @@ export function detectSignals(
   let peaks;
   let signals = [];
   let prevPeak = { x: Number.MIN_SAFE_INTEGER };
-  let spectrumIntegral = 0;
+
   frequencyCluster /= frequency;
   for (const peak of peakList) {
     if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
@@ -349,15 +339,10 @@ export function detectSignals(
     } else {
       integration.value = integralPeaks;
     }
-    spectrumIntegral += integration.value;
   }
 
   if (integrationSum > 0) {
-    let integralFactor = integrationSum / spectrumIntegral;
-    for (let signal of signals) {
-      let integration = signal.integralData;
-      integration.value *= integralFactor;
-    }
+    updateIntegration(signals, integrationSum);
   }
 
   return signals;
@@ -370,3 +355,22 @@ export function detectSignals(
 function computeArea(peak: Peak1DIntern, frequency: number) {
   return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
 }
+
+/**
+ * update the integration Values
+ * @param signals
+ * @param integrationSum
+ */
+function updateIntegration(signals: SignalIntern[], integrationSum: number) {
+  let sumIntegral = 0;
+  let sumObserved = 0;
+  for (const signal of signals) {
+    sumObserved += Math.abs(Math.round(signal.integralData.value));
+  }
+  if (sumObserved !== integrationSum) {
+    sumIntegral = integrationSum / sumObserved;
+    for (const signal of signals) {
+      signal.integralData.value *= sumIntegral;
+    }
+  }
+}

package/src/signals/signalsToFID.ts

@@ -0,0 +1,113 @@
+import { xSequentialFill } from 'ml-spectra-processing';
+
+import { apodization } from '../apodization/apodization';
+
+import { NMRSignal1D } from './NMRSignal1D';
+import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from './simulation/simulateXYPeaks';
+import { splitSpinSystem } from './simulation/splitSpinSystem';
+
+export interface SignalsToFIDOptions {
+  /**
+   * at the end of the superposition of all component, an exponential apodization will be applied
+   * in order to have FID like shape.
+   * @default 1
+   */
+  lb?: number;
+  /**
+   * lower limit of the spectrum
+   * @default 0
+   */
+  from?: number;
+  /**
+   * upper limit of the spectrum
+   * @default 10
+   */
+  to?: number;
+  /**
+   * number of points of the resulting FID
+   */
+  nbPoints?: number;
+  /**
+   * It is the frequency of the carrier (e.g. SFO1 for bruker spectrometers)
+   */
+  frequency?: number;
+  /**
+   * Maximum number of atoms on each cluster that can be considered to be simulated together.
+   * It affects the the quality and speed of the simulation.
+   */
+  maxClusterSize?: number;
+}
+
+const twoPi = Math.PI * 2;
+
+/**
+ * it use the chemical shifts and the coupling between them in order to generate a FID.
+ * It does not propagate the hamiltonian of the spin system, instead it simulate all the
+ * frequencies in the spectrum (including second order) and add all the waves in a real and
+ * imaginary parts, that is why the couplings should be assigned in order to generate the spin system.
+ */
+export function signalsToFID(
+  signals: NMRSignal1D[],
+  options: SignalsToFIDOptions,
+) {
+  const {
+    lb = 1,
+    from = 0,
+    to = 10,
+    nbPoints = 1024,
+    frequency = 400,
+    maxClusterSize = 8,
+  } = options;
+
+  let spinSystem = signalsToSpinSystem(signals);
+
+  spinSystem.clusters = splitSpinSystem(spinSystem, {
+    frequency,
+    maxClusterSize,
+  });
+
+  const peaks = simulateXYPeaks(spinSystem, { frequency });
+  const re = new Float64Array(nbPoints);
+  const im = new Float64Array(nbPoints);
+
+  const sw = Math.abs(to - from);
+  const adquisitionTime = nbPoints / (sw * frequency);
+  const time = xSequentialFill({
+    size: nbPoints,
+    from: 0,
+    to: adquisitionTime,
+  });
+
+  for (const peak of peaks) {
+    const { x, y } = peak;
+    const cs = x * frequency * twoPi;
+    for (let i = 0; i < nbPoints; i++) {
+      re[i] += y * Math.cos(cs * time[i]);
+      im[i] += y * Math.sin(cs * time[i]);
+    }
+  }
+
+  const { windowData, ...result } = apodization(
+    { re, im },
+    {
+      pointsToShift: 0,
+      compose: {
+        length: nbPoints,
+        shapes: [
+          {
+            start: 0,
+            shape: {
+              kind: 'exponential',
+              options: {
+                dw: adquisitionTime / (nbPoints - 1),
+                lb,
+              },
+            },
+          },
+        ],
+      },
+    },
+  );
+  return result;
+}

package/src/utilities/hasProperty.ts

@@ -1,4 +1,4 @@
-export function hasProperty<T, K extends keyof T>(
+export function hasProperty<T extends object, K extends keyof T>(
   data: T,
   key: K,
 ): data is T & { [P in K]-?: T[P] } {

package/src/xy/xyAutoPeaksPicking.ts

@@ -106,7 +106,11 @@ export function xyAutoPeaksPicking(
     direction = 'positive',
   } = options;
 
-  const { windowSize = 9, polynomial = 3 } = sgOptions;
+  let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
+  // we can consider a peak with of 0.5 Hz for the windowSize
+  let ws = Math.max(Math.round(pointsPerHz / 2), 5);
+
+  const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
 
   if (data.x.length < windowSize) return [];