nmr-processing 9.0.3 → 9.1.0

package/lib-esm/xyz/xyzJResAnalyzer.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.0.3",
+  "version": "9.1.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -54,6 +54,7 @@
     "typescript": "^4.7.4"
   },
   "dependencies": {
+    "@lukeed/uuid": "^2.0.0",
     "binary-search": "^1.3.6",
     "cross-fetch": "^3.1.5",
     "form-data": "^4.0.0",
@@ -63,7 +64,7 @@
     "ml-array-mean": "^1.1.6",
     "ml-array-rescale": "^1.3.7",
     "ml-array-sum": "^1.1.6",
-    "ml-gsd": "^12.0.0",
+    "ml-gsd": "^12.1.0",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.1.0",
     "ml-matrix": "^6.10.2",
@@ -78,4 +79,4 @@
     "openchemlib-utils": "^2.0.0",
     "spectrum-generator": "^8.0.4"
   }
-}
+}

package/src/assignment/get13CAssignments.ts

@@ -1,3 +1,4 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import { Molecule } from 'openchemlib';
 import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
 
@@ -13,7 +14,6 @@ import type {
   Targets,
 } from './get1HAssignments';
 import { RestrictionByCS1D, buildAssignments } from './utils/buildAssignments';
-import generateID from './utils/generateID';
 
 function checkAtomsAndDiaIDs(
   signals: NMRSignal1D[],

package/src/assignment/get1HAssignments.ts

@@ -1,3 +1,4 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import { Molecule } from 'openchemlib';
 import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
 
@@ -10,7 +11,6 @@ import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { MakeMandatory } from '../utilities/MakeMandatory';
 
 import { buildAssignments, RestrictionByCS1D } from './utils/buildAssignments';
-import generateID from './utils/generateID';
 
 export type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<
   NMRSignal1D,

package/src/assignment/utils/getAssignment/checkIDs.ts

@@ -1,3 +1,5 @@
+import { v4 as generateID } from '@lukeed/uuid';
+
 import type { NMRRange, NMRZone } from '../../..';
 import type { SpectraData } from '../../getAssignments';
 import type {
@@ -5,7 +7,6 @@ import type {
   NMRRangeWithIds,
   NMRZoneWithIds,
 } from '../../nmrAssigment';
-import generateID from '../generateID';
 
 import { isSpectraData1D } from './isSpectraData1D';
 

package/src/ml-matrix-peaks-finder.d.ts

@@ -9,6 +9,7 @@ declare module 'ml-matrix-peaks-finder' {
     labelling?: 'drain' | 'floodfill';
   }
   interface Peak2D {
+    id?: string;
     x: number;
     y: number;
     z: number;

package/src/peaks/NMRPeak1D.ts

@@ -2,6 +2,7 @@ import type { PeakXYWidth } from 'cheminfo-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
 
 export interface NMRPeak1D extends PeakXYWidth {
+  id?: string;
   kind?: string;
   shape?: Shape1D;
 }

package/src/peaks/peakToXY.ts

@@ -1,6 +1,17 @@
+import { addMissingShape } from 'ml-gsd';
+import { getShape1D } from 'ml-peak-shape-generator';
+
 import { NMRPeak1D } from './NMRPeak1D';
 import { peaksToXY, PeaksToXYOptions } from './peaksToXY';
 
 export function peakToXY(peak: NMRPeak1D, options: PeaksToXYOptions) {
-  return peaksToXY([peak], options);
+  const newPeak = addMissingShape([peak])[0];
+  const factor = getShape1D(newPeak.shape).getFactor();
+
+  const {
+    from = newPeak.x - (peak.width * factor) / options.frequency,
+    to = newPeak.x + (peak.width * factor) / options.frequency,
+  } = options;
+
+  return peaksToXY([peak], { ...options, from, to });
 }

package/src/peaks/peaksFilterImpurities.ts

@@ -34,8 +34,8 @@ interface OptionsCheckImpurity {
  * Try to remove peaks of impurities.
  */
 
-export function peaksFilterImpurities(
-  peakList: NMRPeak1D[],
+export function peaksFilterImpurities<T extends NMRPeak1D>(
+  peakList: T[],
   options: OptionsPeaksFilterImpurities = {},
 ) {
   let { solvent, error = 0.025, remove = false } = options;
@@ -56,8 +56,8 @@ export function peaksFilterImpurities(
   return peakList;
 }
 
-function checkImpurity(
-  peakList: NMRPeak1D[],
+function checkImpurity<T extends NMRPeak1D>(
+  peakList: T[],
   impurity: ImpuritySignal[],
   options: OptionsCheckImpurity,
 ) {

package/src/peaks/peaksToRanges.ts

@@ -1,3 +1,4 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import type { DataXY } from 'cheminfo-types';
 import { xyIntegration } from 'ml-spectra-processing';
 
@@ -90,6 +91,7 @@ const assignSignal = (
   nucleus: string,
 ): SignalIntern => {
   return {
+    id: generateID(),
     delta: NaN,
     nbPeaks: 1,
     kind: 'signal',
@@ -232,6 +234,7 @@ export function peaksToRanges(
   for (let i = 0; i < signals.length; i++) {
     let signal = signals[i];
     const range: NMRRange = {
+      id: generateID(),
       from: signal.integralData.from,
       to: signal.integralData.to,
       integration: signal.integralData.value,

package/src/peaks/peaksToXY.ts

@@ -26,8 +26,11 @@ export interface PeaksToXYOptions extends OptionsSG1D {
 
 export function peaksToXY(peaks: NMRPeak1D[], options: PeaksToXYOptions) {
   const { frequency, nbPoints = 1024, shape } = options;
-  const newPeaks = convertWidthToPPM(peaks, { frequency });
 
+  if (!frequency) {
+    throw new Error('frequency is mandatory');
+  }
+  const newPeaks = convertWidthToPPM(peaks, { frequency });
   return generateSpectrum(newPeaks, {
     generator: {
       ...getFromTo(newPeaks, options),
@@ -50,8 +53,8 @@ function getFromTo(newPeaks: NMRPeak1D[], options: PeaksToXYOptions) {
   const lastPeak = newPeaks[newPeaks.length - 1];
 
   const {
-    from = firstPeak.x - firstPeak.width * 2,
-    to = lastPeak.x + lastPeak.width * 2,
+    from = firstPeak.x - (firstPeak.width * 2) / options.frequency,
+    to = lastPeak.x + (lastPeak.width * 2) / options.frequency,
   } = options;
 
   return {

package/src/peaks/solventSuppression.ts

@@ -9,6 +9,7 @@ import { addDummySignals } from '../signals/addDummySignals';
 import { signalsToSpinSystem } from '../signals/simulation/signalsToSpinSystem';
 import { simulateXYPeaks } from '../signals/simulation/simulateXYPeaks';
 import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
+import { cloneArray } from '../utilities/clone';
 
 import { NMRPeak1D } from './NMRPeak1D';
 
@@ -17,7 +18,7 @@ export function solventSuppression<T extends NMRPeak1D>(
   solvent: NMRSignal1D[],
   options: { markSolventPeaks?: boolean; solventZoneExtension?: number } = {},
 ) {
-  const peaks = [...peakList].sort((a, b) => a.x - b.x);
+  const peaks = cloneArray(peakList).sort((a, b) => a.x - b.x);
 
   const xValues = peaks.map((peak) => peak.x);
 

package/src/peaks/util/addMissingIDs.ts

@@ -0,0 +1,17 @@
+import { v4 as generateID } from '@lukeed/uuid';
+
+const { parse, stringify } = JSON;
+
+export function addMissingIDs<T extends { id?: string }>(
+  peaks: T[],
+  options: { output?: T[] } = {},
+) {
+  const { output = parse(stringify(peaks)) as T[] } = options;
+  for (const peak of output) {
+    if (!('id' in peak)) {
+      peak.id = generateID();
+    }
+  }
+
+  return output as (T & { id: string })[];
+}

package/src/peaks/util/convertWidth.ts

@@ -1,40 +1,45 @@
+import { Shape1D } from 'ml-peak-shape-generator';
+
 import { MakeMandatory } from '../../utilities/MakeMandatory';
+import { hasProperty } from '../../utilities/hasProperty';
 import { NMRPeak1D } from '../NMRPeak1D';
 
+const { parse, stringify } = JSON;
+
 export type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
 
-export interface ConvertWidthOptions {
+export interface ConvertWidthOptions<T> {
   convertTo: string & { _kind?: 'hz' | 'ppm' };
   frequency: number;
-  output?: NMRPeak1D[];
+  output?: T[];
 }
 /**
  * convert width and fwhm to ppm
  */
-export function convertWidth(peaks: NMRPeak1D[], options: ConvertWidthOptions) {
+export function convertWidth<T extends NMRPeak1D>(
+  peaks: T[],
+  options: ConvertWidthOptions<T>,
+): T[] {
   const {
     frequency,
     convertTo,
-    output = JSON.parse(JSON.stringify(peaks)),
+    output = parse(stringify(peaks)) as T[],
   } = options;
 
   const convert = getConverter(convertTo, frequency);
 
   for (const peak of output) {
     peak.width = convert(peak.width);
-    if (hasShape(peak)) {
-      if (peak.shape.fwhm) {
-        peak.shape.fwhm = convert(peak.shape.fwhm);
+    if (hasProperty(peak, 'shape')) {
+      const shape = peak.shape as Shape1D;
+      if (shape.fwhm) {
+        shape.fwhm = convert(shape.fwhm);
       }
     }
   }
   return output;
 }
 
-function hasShape(peak: NMRPeak1D): peak is NMRPeak1DWithShape {
-  return 'shape' in peak;
-}
-
 function getConverter(convertTo: string, frequency: number) {
   switch (convertTo) {
     case 'ppm':

package/src/peaks/util/convertWidthToHz.ts

@@ -2,8 +2,11 @@ import { NMRPeak1D } from '../NMRPeak1D';
 
 import { convertWidth, ConvertWidthOptions } from './convertWidth';
 
-export type ConvertWidthTo = Omit<ConvertWidthOptions, 'convertTo'>;
+export type ConvertWidthTo<T> = Omit<ConvertWidthOptions<T>, 'convertTo'>;
 
-export function convertWidthToHz(peaks: NMRPeak1D[], options: ConvertWidthTo) {
+export function convertWidthToHz<T extends NMRPeak1D>(
+  peaks: T[],
+  options: ConvertWidthTo<T>,
+): T[] {
   return convertWidth(peaks, { ...options, convertTo: 'hz' });
 }

package/src/peaks/util/convertWidthToPPM.ts

@@ -3,6 +3,9 @@ import { NMRPeak1D } from '../NMRPeak1D';
 import { convertWidth } from './convertWidth';
 import { ConvertWidthTo } from './convertWidthToHz';
 
-export function convertWidthToPPM(peaks: NMRPeak1D[], options: ConvertWidthTo) {
+export function convertWidthToPPM<T extends NMRPeak1D>(
+  peaks: T[],
+  options: ConvertWidthTo<T>,
+) {
   return convertWidth(peaks, { ...options, convertTo: 'ppm' });
 }

package/src/peaks/util/determineRealTop.ts

@@ -9,7 +9,7 @@ const direction16Y = [-2, -1, 0, 1, 2, -2, 2, -2, 2, -2, 2, -2, -1, 0, 1, 2];
 
 type Data = number[] | Float64Array;
 
-export function determineRealTop(peaks: Peak2D[], options: any) {
+export function determineRealTop<T extends Peak2D>(peaks: T[], options: any) {
   let { nCols, absoluteData, originalData, minX, maxX, minY, maxY } = options;
   for (let i = 0; i < peaks.length; i++) {
     let xIndex = Math.round(peaks[i].x);

package/src/peaks/util/setIDs.ts

@@ -0,0 +1,14 @@
+import { v4 as generateID } from '@lukeed/uuid';
+
+const { parse, stringify } = JSON;
+
+export function setIDs<T>(peaks: T[], options: { output?: T[] } = {}) {
+  const output = (options.output || parse(stringify(peaks))) as (T & {
+    id?: string;
+  })[];
+  for (const peak of output) {
+    peak.id = generateID();
+  }
+
+  return output as (T & { id: string })[];
+}

package/src/prediction/predictCarbon.ts

@@ -1,6 +1,8 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import fetch from 'cross-fetch';
 import type { Molecule } from 'openchemlib';
 
+import { setIDs } from '../peaks/util/setIDs';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { signalsToRanges } from '../signals/signalsToRanges';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
@@ -117,6 +119,7 @@ function formatSignals(predictions: Prediction[]) {
   for (const prediction of predictions) {
     const { atoms, nbAtoms, delta, diaIDs, statistic } = prediction;
     const signal = {
+      id: generateID(),
       delta: delta || NaN,
       atoms,
       diaIDs,
@@ -144,5 +147,5 @@ function joinSignalByDiaID(signals: NMRSignal1D[]) {
       joinedSignals[diaID].atoms.push(...signal.atoms);
     }
   }
-  return Object.values(joinedSignals);
+  return setIDs(Object.values(joinedSignals));
 }

package/src/prediction/predictProton.ts

@@ -1,3 +1,4 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import fetch from 'cross-fetch';
 import FormData from 'form-data';
 import type { Molecule } from 'openchemlib';
@@ -86,6 +87,7 @@ function protonParser(
     let couplings = fields.slice(4);
     let atom = Number(fields[0]) - 1;
     let signal: NMRSignal1D = {
+      id: generateID(),
       atoms: [atom],
       diaIDs: [diaIDs[atom]],
       nbAtoms: 1,

package/src/prediction/utils/predict2D.ts

@@ -1,3 +1,4 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import { agnes, Cluster } from 'ml-hclust';
 import { Matrix } from 'ml-matrix';
 import { Molecule } from 'openchemlib';
@@ -20,6 +21,7 @@ import type { Prediction1D } from '../prediction1D';
 
 import { getNuclei } from './getNuclei';
 import { getPredictions } from './getPredictions';
+import { setIDs } from '../../peaks/util/setIDs';
 
 /**
  * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
@@ -216,8 +218,8 @@ export async function predict2D(
         continue;
       }
 
-      let peak: any = { z: 100 };
-      let signal: any = { x: {}, y: {} };
+      let peak: any = { id: generateID(), z: 100 };
+      let signal: any = { id: generateID(), x: {}, y: {} };
       for (let axis in fromToDiaID) {
         let diaID = fromToDiaID[axis].oclID;
         peak[axis] = signalsByDiaID[axis][diaID].delta;
@@ -262,7 +264,7 @@ function splitSignals(joinedSignals: NMRSignal2D[]) {
       }
     }
   }
-  return signals;
+  return setIDs(signals);
 }
 
 interface AddSelftCorrelationOptions {
@@ -333,6 +335,7 @@ function createZones(signals: NMRSignal2D[], options: CreateZonesOptions) {
     }
 
     zones.push({
+      id: generateID(),
       ...fromTo(signal, { joinDistance, from, to }),
       signals: signal,
     });

package/src/ranges/markSolventSignal.ts

@@ -1,11 +1,13 @@
+import { v4 as generateID } from '@lukeed/uuid';
+
 import { NMRRangeWithIds, NMRSignal1DWithId } from '../assignment/nmrAssigment';
-import generateID from '../assignment/utils/generateID';
 import { addIDs } from '../assignment/utils/getAssignment/checkIDs';
 import { NMRPeak1D } from '../peaks/NMRPeak1D';
 import { detectSignals } from '../peaks/peaksToRanges';
 import { solventSuppression } from '../peaks/solventSuppression';
 import { NMRSignal1D } from '../signals/NMRSignal1D';
 import { SignalIntern } from '../signals/utils/jAnalyzer';
+import { cloneArray } from '../utilities/clone';
 import { NMRRange } from '../xy/NMRRange';
 
 interface NMRPeak1DWithSignalID extends NMRPeak1D {
@@ -19,7 +21,7 @@ export function markSolventPeaks<T extends NMRRange>(
   options: any = {},
 ) {
   const { frequency = 400 } = options;
-  const ranges = addIDs([...input]) as NMRRangeWithIds[];
+  const ranges = addIDs(cloneArray(input)) as NMRRangeWithIds[];
 
   let peakList: NMRPeak1DWithSignalID[] = [];
   for (const range of ranges) {

package/src/ranges/utils/joinRanges.ts

@@ -1,3 +1,5 @@
+import { v4 as generateID } from '@lukeed/uuid';
+
 import type { NMRRange } from '../../xy/NMRRange';
 
 export function joinRanges(ranges: NMRRange[]) {
@@ -8,6 +10,7 @@ export function joinRanges(ranges: NMRRange[]) {
     const nextRange = ranges[i + 1];
 
     if (currentRange.to > nextRange.from) {
+      currentRange.id = generateID();
       currentRange.to = Math.max(nextRange.to, currentRange.to);
       if (currentRange.signals && nextRange.signals) {
         currentRange.signals = currentRange.signals.concat(nextRange.signals);

package/src/signals/signalsJoin.ts

@@ -1,3 +1,4 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import mean from 'ml-array-mean';
 import sum from 'ml-array-sum';
 
@@ -93,6 +94,7 @@ export function signalsJoin(
       });
     }
     let signal: Signal1DWidthJsAndDiaID = {
+      id: generateID(),
       nbAtoms: sum(group.map((item) => item.nbAtoms || 0)),
       delta: mean(group.map((item) => item.delta)),
       diaIDs: group[0].diaIDs,

package/src/signals/signalsToRanges.ts

@@ -1,3 +1,5 @@
+import { v4 as generateID } from '@lukeed/uuid';
+
 import type { MakeMandatory } from '../utilities/MakeMandatory';
 import { rangeFromSignal } from '../utilities/rangeFromSignal';
 import type { NMRRange } from '../xy/NMRRange';
@@ -18,7 +20,7 @@ interface SignalsToRangesOptions {
 }
 
 type Signals1DWithNbAtoms = MakeMandatory<NMRSignal1D, 'nbAtoms'>;
-type RangeFullfiled = MakeMandatory<NMRRange, 'integration' | 'signals'>;
+type RangeFullfiled = MakeMandatory<NMRRange, 'integration' | 'signals' | 'id'>;
 
 interface WrappedSignal {
   from: number;
@@ -37,7 +39,7 @@ function checkNbAtoms(
 export function signalsToRanges(
   signals: NMRSignal1D[],
   options: SignalsToRangesOptions = {},
-): NMRRange[] {
+): RangeFullfiled[] {
   checkNbAtoms(signals);
 
   const { tolerance = 0.05, frequency = 400 } = options;
@@ -59,6 +61,7 @@ export function signalsToRanges(
   for (let signal of wrapped) {
     if (range.from === undefined || signal.from > range.to) {
       range = {
+        id: generateID(),
         from: signal.from,
         to: signal.to,
         integration: signal.original.nbAtoms,

package/src/signals/utils/jAnalyzer.ts

@@ -34,6 +34,7 @@ export type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
 };
 
 export interface SignalIntern {
+  id: string;
   delta: number;
   nbPeaks: number;
   startX: number;

package/src/utilities/clone.ts

@@ -0,0 +1,5 @@
+const { stringify, parse } = JSON;
+
+export function cloneArray<T>(data: T[]) {
+  return parse(stringify(data)) as T[];
+}

package/src/utilities/hasProperty.ts

@@ -0,0 +1,6 @@
+export function hasProperty<T, K extends keyof T>(
+  data: T,
+  key: K,
+): data is T & { [P in K]-?: T[P] } {
+  return key in data;
+}

package/src/xy/xyAutoPeaksPicking.ts

@@ -1,9 +1,13 @@
 import { DataXY } from 'cheminfo-types';
-import { gsd, optimizePeaks, joinBroadPeaks } from 'ml-gsd';
-import type {
+import {
+  gsd,
+  optimizePeaks,
+  joinBroadPeaks,
+  GSDPeakID,
   GSDOptions,
   OptimizePeaksOptions,
   JoinBroadPeaksOptions,
+  GSDPeakOptimizedID,
 } from 'ml-gsd';
 import {
   xyExtract,
@@ -13,6 +17,7 @@ import {
 
 import { NMRPeak1D } from '..';
 import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
+import { MakeMandatory } from '../utilities/MakeMandatory';
 
 /**
  * Implementation of the peak picking method described by Cobas in:
@@ -72,10 +77,12 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
   frequency: number;
 }
 
+export type NMRPeak1DWithID = MakeMandatory<NMRPeak1D, 'id'>;
+
 export function xyAutoPeaksPicking(
   data: DataXY,
   options: OptionsXYAutoPeaksPicking,
-): NMRPeak1D[] {
+): NMRPeak1DWithID[] {
   const {
     from,
     to,
@@ -180,23 +187,23 @@ function getPeakList(data: DataXY, options: GetPeakListOptions) {
     realTopDetection,
   });
 
-  if (broadWidth) {
-    peakList = joinBroadPeaks(peakList, {
-      broadRatio,
-      broadWidth,
-      shape,
-      optimization,
-    });
-  }
+  const newPeaks = broadWidth
+    ? joinBroadPeaks(peakList, {
+        broadRatio,
+        broadWidth,
+        shape,
+        optimization,
+      }).map(toNMRPeak1DStructure)
+    : peakList.map(toNMRPeak1DStructure);
 
   return convertWidthToHz(
     optimize
-      ? optimizePeaks(data, peakList, {
+      ? optimizePeaks(data, newPeaks, {
           shape,
           factorLimits,
           optimization,
-        })
-      : peakList,
+        }).map(toNMRPeak1DStructure)
+      : newPeaks,
     { frequency },
   );
 }
@@ -217,3 +224,16 @@ function getCutOff(data: number[] | Float64Array, options: OptionsGetCutOff) {
       : formatResult(xAbsoluteMedian(data) * thresholdFactor);
   }
 }
+
+function toNMRPeak1DStructure(
+  peak: GSDPeakID | GSDPeakOptimizedID,
+): NMRPeak1DWithID {
+  const { id, shape, x, y, width } = peak;
+  return {
+    id,
+    x,
+    y,
+    width,
+    shape,
+  };
+}

package/src/xy/xyPeaksOptimization.ts

@@ -10,9 +10,9 @@ export interface XYPeaksOptimizationOptions extends OptimizePeaksOptions {
    */
   frequency: number;
 }
-export function xyPeaksOptimization(
+export function xyPeaksOptimization<T extends PeakXYWidth>(
   data: DataXY,
-  peaks: PeakXYWidth[],
+  peaks: T[],
   options: XYPeaksOptimizationOptions,
 ) {
   const { frequency } = options;