nmr-processing 3.4.0 → 6.0.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "3.4.0",
+  "version": "6.0.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -16,9 +16,12 @@
   "scripts": {
     "clean": "rimraf lib lib-esm",
     "build": "npm run tsc && cheminfo-build",
-    "eslint": "eslint src --ext ts --cache",
+    "check-types": "tsc --noEmit",
+    "eslint": "eslint src --cache",
     "eslint-fix": "npm run eslint -- --fix",
     "prepack": "npm run tsc",
+    "prettier": "prettier --check src",
+    "prettier-write": "prettier --write src",
     "test": "npm run test-coverage && npm run eslint",
     "test-coverage": "npm run test-only -- --coverage",
     "test-only": "jest",
@@ -46,45 +49,45 @@
     "trailingComma": "all"
   },
   "devDependencies": {
-    "@types/jest": "^27.0.2",
+    "@types/jest": "^27.0.3",
     "cheminfo-build": "^1.1.11",
-    "cheminfo-types": "^0.6.0",
-    "eslint": "^8.0.1",
-    "eslint-config-cheminfo-typescript": "^10.1.1",
+    "cheminfo-types": "^0.8.0",
+    "eslint": "^8.3.0",
+    "eslint-config-cheminfo-typescript": "^10.2.4",
     "esm": "^3.2.25",
-    "jest": "^27.2.4",
+    "jest": "^27.4.2",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "ml-array-median": "^1.1.5",
     "nmr-xy-testdata": "^0.2.1",
     "openchemlib": "^7.4.3",
-    "prettier": "^2.4.1",
+    "prettier": "^2.5.0",
     "rimraf": "^3.0.2",
-    "ts-jest": "^27.0.5",
-    "typescript": "^4.4.3"
+    "ts-jest": "^27.0.7",
+    "typescript": "^4.5.2"
   },
   "dependencies": {
     "assign-deep": "^1.0.1",
     "binary-search": "^1.3.6",
     "cross-fetch": "^3.1.4",
     "form-data": "^4.0.0",
-    "is-any-array": "^1.0.1",
+    "is-any-array": "^2.0.0",
     "ml-array-mean": "^1.1.5",
     "ml-array-rescale": "^1.3.6",
     "ml-array-sequential-fill": "^1.1.7",
     "ml-array-sum": "^1.1.5",
-    "ml-gsd": "^7.0.1",
+    "ml-gsd": "^9.0.3",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^3.1.1",
-    "ml-matrix": "^6.8.0",
+    "ml-matrix": "^6.8.2",
     "ml-matrix-convolution": "^1.0.0",
     "ml-matrix-peaks-finder": "^1.0.0",
-    "ml-peak-shape-generator": "^2.0.2",
+    "ml-peak-shape-generator": "^4.0.1",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
     "ml-spectra-processing": "^6.8.0",
     "ml-tree-set": "^0.1.1",
-    "openchemlib-utils": "^1.5.1",
-    "spectrum-generator": "^5.4.1"
+    "openchemlib-utils": "^1.6.0",
+    "spectrum-generator": "^6.0.2"
   }
 }

package/src/assignment/get13CAssignments.ts

@@ -8,7 +8,10 @@ import {
 } from '../prediction/predictCarbon';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
 
-import type { NMRSignal1DWithAtomsAndDiaIDs, Targets } from './get1HAssignments';
+import type {
+  NMRSignal1DWithAtomsAndDiaIDs,
+  Targets,
+} from './get1HAssignments';
 import { RestrictionByCS, buildAssignments } from './utils/buildAssignments';
 import generateID from './utils/generateID';
 

package/src/assignment/utils/buildAssignments.ts

@@ -1,9 +1,6 @@
 import treeSet from 'ml-tree-set';
 
-import {
-  Targets,
-  NMRSignal1DWithAtomsAndDiaIDs,
-} from '../get1HAssignments';
+import { Targets, NMRSignal1DWithAtomsAndDiaIDs } from '../get1HAssignments';
 
 import { createMapPossibleAssignments } from './createMapPossibleAssignments';
 import { exploreTreeRec } from './exploreTreeRec';
@@ -94,7 +91,7 @@ export async function buildAssignments(props: BuildAssignmentsProps) {
     predictions,
     targets,
   });
-  console.log('possibles', possibleAssignmentMap)
+
   const diaIDPeerPossibleAssignment = Object.keys(possibleAssignmentMap);
 
   let partial = fillPartial(nSources);

package/src/assignment/utils/createMapPossibleAssignments.ts

@@ -1,7 +1,10 @@
 import { MakeMandatory } from '../../types/MakeMandatory';
 import type { Targets } from '../get1HAssignments';
 
-import type { RestrictionByCS, Predictions1Dassignments } from './buildAssignments';
+import type {
+  RestrictionByCS,
+  Predictions1Dassignments,
+} from './buildAssignments';
 
 type RestrictionByCSMandatory = MakeMandatory<
   RestrictionByCS,
@@ -27,7 +30,6 @@ export function createMapPossibleAssignments(
   const { tolerance: toleranceCS, chemicalShiftRestriction } = restrictionByCS;
 
   let errorAbs = Math.abs(toleranceCS);
-  console.log('use INT', useIntegrationRestriction)
   const expandMap: PossibleAssignmentMap = {};
   for (const diaID in predictions) {
     let prediction = predictions[diaID];

package/src/constants/couplingValues.ts

@@ -1,4 +1,4 @@
-export const couplingValues: {[key: string]: number} = {
+export const couplingValues: { [key: string]: number } = {
   s: 0,
   d: 1,
   t: 2,

package/src/index.ts

@@ -27,7 +27,7 @@ export * from './utilities/rangeFromSignal';
 export * from './xy/xyAutoPeaksPicking';
 export * from './xy/xyAutoRangesPicking';
 
-export * from './xyz/xyzAutoPeaksPicking';
+export * from './xyz/xyzAutoZonesPicking';
 export * from './xyz/xyzJResAnalyzer';
 
 export * from './databases/getDatabase';

package/src/peaks/peaksFilterImpurities.ts

@@ -66,7 +66,7 @@ function checkImpurity(
   while (i--) {
     j = peakList.length;
     while (j--) {
-      tolerance = error + peakList[j].shape.width;
+      tolerance = error + peakList[j].width;
       difference = Math.abs(impurity[i].shift - peakList[j].x);
       if (difference < tolerance) {
         // && (impurity[i].multiplicity === '' || (impurity[i].multiplicity.indexOf(peakList[j].multiplicity)) { // some impurities has multiplicities like 'bs' but at presents it is unsupported

package/src/peaks/peaksToRanges.ts

@@ -91,22 +91,20 @@ const assignSignal = (
     delta: NaN,
     nbPeaks: 1,
     kind: 'signal',
-    startX: peak.x - peak.shape.width,
-    stopX: peak.x + peak.shape.width,
+    startX: peak.x - peak.width,
+    stopX: peak.x + peak.width,
     observe: frequency,
     nucleus,
     integralData: {
-      from: peak.x - peak.shape.width * 3,
-      to: peak.x + peak.shape.width * 3,
+      from: peak.x - peak.width * 3,
+      to: peak.x + peak.width * 3,
       value: 0,
     },
     peaks: [
       {
         x: peak.x,
         intensity: peak.y,
-        shape: {
-          width: peak.shape.width,
-        },
+        width: peak.width,
       },
     ],
   };
@@ -177,9 +175,7 @@ export function peaksToRanges(
             peaksO.push({
               x: peakR.x,
               y: peakR.intensity,
-              shape: {
-                width: peakR.shape.width,
-              },
+              width: peakR.width,
             });
             signal.mask.splice(j, 1);
             signal.mask2.splice(j, 1);
@@ -306,24 +302,22 @@ function detectSignals(
       if (peak.kind) signal1D.kind = peak.kind;
       signals.push(signal1D);
     } else {
-      let tmp = peak.x + peak.shape.width;
+      let tmp = peak.x + peak.width;
       signal1D.stopX = Math.max(signal1D.stopX, tmp);
       signal1D.startX = Math.min(signal1D.startX, tmp);
       signal1D.nbPeaks++;
       signal1D.peaks.push({
         x: peak.x,
         intensity: peak.y,
-        shape: {
-          width: peak.shape.width,
-        },
+        width: peak.width,
       });
       signal1D.integralData.from = Math.min(
         signal1D.integralData.from,
-        peak.x - peak.shape.width * 3,
+        peak.x - peak.width * 3,
       );
       signal1D.integralData.to = Math.max(
         signal1D.integralData.to,
-        peak.x + peak.shape.width * 3,
+        peak.x + peak.width * 3,
       );
       if (peak.kind) signal1D.kind = peak.kind;
     }
@@ -371,5 +365,5 @@ function detectSignals(
  * @private
  */
 function computeArea(peak: Peak1DIntern) {
-  return Math.abs(peak.intensity * peak.shape.width * 1.57); // todo add an option with this value: 1.772453851
+  return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
 }

package/src/peaks/util/determineRealTop.ts

@@ -1,9 +1,6 @@
 import LM from 'ml-levenberg-marquardt';
-import { gaussian2D } from 'ml-peak-shape-generator';
-
-import type { MPFPeak } from '../../types/MPFPeak';
-
-const { fct: gaussian2DFct } = gaussian2D;
+import type { Peak2D } from 'ml-matrix-peaks-finder';
+import { Gaussian2D } from 'ml-peak-shape-generator';
 
 const direction8X = [-1, -1, -1, 0, 0, 1, 1, 1];
 const direction8Y = [-1, 0, 1, -1, 1, -1, 0, 1];
@@ -12,7 +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: MPFPeak[], options: any) {
+export function determineRealTop(peaks: Peak2D[], 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);
@@ -142,6 +139,7 @@ function fitGaussian(
 }
 
 function paramGaussian2D(intervalX: number, intervalY: number, nCols: number) {
+  const gaussian2D = new Gaussian2D();
   return (p: number[]) => {
     return (t: number) => {
       let nL = p.length / 5;
@@ -149,13 +147,12 @@ function paramGaussian2D(intervalX: number, intervalY: number, nCols: number) {
       let xIndex = t % nCols;
       let yIndex = (t - xIndex) / nCols;
       for (let i = 0; i < nL; i++) {
+        gaussian2D.fwhm = { x: p[i + 3 * nL], y: p[i + 4 * nL] };
         result +=
           p[i + 2 * nL] *
-          gaussian2DFct(
+          gaussian2D.fct(
             (xIndex - p[i]) * intervalX,
             (yIndex - p[i + nL]) * intervalY,
-            p[i + 3 * nL],
-            p[i + 4 * nL],
           );
       }
       return result;

package/src/peaks/util/jAnalyzer.ts

@@ -154,7 +154,11 @@ export default {
           k = 1;
           let nFlagged = 2;
           maxFlagged = Math.pow(2, n) - 1;
-          while (jCouplings.length < n && nFlagged < maxFlagged && k < peaks.length) {
+          while (
+            jCouplings.length < n &&
+            nFlagged < maxFlagged &&
+            k < peaks.length
+          ) {
             counter += 1;
             // 4.1. Increment j. Set k to the number of the first unflagged component.
             j++;
@@ -219,13 +223,12 @@ function updateSignal(signal: SignalInternMandatory, jCouplings: number[]) {
   // Update the limits of the signal
   let peaks = signal.peaksComp; // Always in Hz
   let nbPeaks = peaks.length;
-  signal.startX = peaks[0].x / signal.observe - peaks[0].shape.width;
+  signal.startX = peaks[0].x / signal.observe - peaks[0].width;
   signal.stopX =
-    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width;
-  signal.integralData.from =
-    peaks[0].x / signal.observe - peaks[0].shape.width * 3;
+    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width;
+  signal.integralData.from = peaks[0].x / signal.observe - peaks[0].width * 3;
   signal.integralData.to =
-    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width * 3;
+    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
   // Compile the pattern and format the constant couplings
   signal.maskPattern = signal.mask2;
   signal.multiplicity = abstractPattern(signal, jCouplings);
@@ -466,9 +469,7 @@ function symmetrize(
     peaks[i] = {
       x: peak[jAxis] * newSignal.observe,
       intensity: peak[intensity],
-      shape: {
-        width: peak.shape.width,
-      },
+      width: peak.width,
     };
   }
   // Join the peaks that are closer than 0.25 Hz
@@ -480,7 +481,7 @@ function symmetrize(
       peaks[i].intensity = peaks[i].intensity + peaks[i + 1].intensity;
       peaks[i].x /= peaks[i].intensity;
       peaks[i].intensity /= 2;
-      peaks[i].shape.width += peaks[i + 1].shape.width;
+      peaks[i].width += peaks[i + 1].width;
       peaks.splice(i + 1, 1);
     }
   }
@@ -527,12 +528,9 @@ function symmetrize(
 
         if (Math.abs(diffL - diffR) < maxError) {
           avg = Math.min(peaks[left].intensity, peaks[right].intensity);
-          avgWidth = Math.min(
-            peaks[left].shape.width,
-            peaks[right].shape.width,
-          );
+          avgWidth = Math.min(peaks[left].width, peaks[right].width);
           peaks[left].intensity = peaks[right].intensity = avg;
-          peaks[left].shape.width = peaks[right].shape.width = avgWidth;
+          peaks[left].width = peaks[right].width = avgWidth;
           middle = [
             middle[0] + (peaks[right].x + peaks[left].x) / 2,
             middle[1] + 1,
@@ -712,5 +710,5 @@ function chemicalShift(peaks: Peak1DIntern[], mask: boolean[] = []) {
  * @private
  */
 function getArea(peak: Peak1DIntern) {
-  return Math.abs(peak.intensity * peak.shape.width * 1.57); // 1.772453851);
+  return Math.abs(peak.intensity * peak.width * 1.57); // 1.772453851);
 }

package/src/peaks/util/peakOptimizer.ts

@@ -1,10 +1,11 @@
-import type { MPFPeak } from '../../types/MPFPeak';
+import type { Peak2D } from 'ml-matrix-peaks-finder';
+
 import type { NMRSignal2D } from '../../types/NMRSignal2D';
 
 let diagonalError = 0.05;
 let tolerance = 0.05;
 
-export function clean(peaks: MPFPeak[], threshold: number) {
+export function clean(peaks: Peak2D[], threshold: number) {
   let max = Number.NEGATIVE_INFINITY;
   // double min = Double.MAX_VALUE;
   for (let i = peaks.length - 1; i >= 0; i--) {
@@ -151,7 +152,7 @@ function completeMissingIfNeeded(
       },
       peaks: [{ x: thisSignal.x.delta, y: thisSignal.x.delta, z: 1 }],
     };
-    newSignal.peaks = [{ x: thisSignal.x.delta, y: thisSignal.x.delta, z: 1 }]
+    newSignal.peaks = [{ x: thisSignal.x.delta, y: thisSignal.x.delta, z: 1 }];
     output.push(newSignal);
     tmpProp = [0, thisProp[1]];
     properties.push(tmpProp);

package/src/prediction/predictAll.ts

@@ -10,7 +10,6 @@ import { predictProton, PredictProtonOptions } from './predictProton';
 import { getPredictions } from './utils/getPredictions';
 import type { Predictor } from './utils/predict2D';
 
-
 export interface PredictAllOptions {
   /**
    * nucleus label to use in the X axis
@@ -93,13 +92,14 @@ export async function predictAll(
     predictions,
   );
 
-  if (!xPrediction || !yPrediction)
-    {throw new Error('predictions are not availaible');}
+  if (!xPrediction || !yPrediction) {
+    throw new Error('predictions are not availaible');
+  }
 
   predictions = {
     H: xPrediction,
-    C: yPrediction
-  }
+    C: yPrediction,
+  };
 
   const { molfile, diaIDs } = xPrediction;
 

package/src/prediction/predictHSQC.ts

@@ -49,7 +49,10 @@ export interface PredictHSQCOptions {
  * @returns {Promise<object>} - object with molfile, diaIDs, 2D signals joined signals and zones.
  */
 
-export async function predictHSQC(molecule: Molecule, options: PredictHSQCOptions = {}) {
+export async function predictHSQC(
+  molecule: Molecule,
+  options: PredictHSQCOptions = {},
+) {
   let {
     minLength = 1,
     maxLength = 1,

package/src/prediction/predictProton.ts

@@ -102,7 +102,7 @@ function protonParser(
         atoms: [linked],
         diaIDs: [diaIDs[linked]],
         multiplicity: 'd',
-        distance: distanceMatrix[atom][linked],
+        pathLength: distanceMatrix[atom][linked],
       });
       signal.js.sort((a, b) => b.coupling - a.coupling);
     }

package/src/prediction/utils/getFilteredIDiaIDs.ts

@@ -24,8 +24,7 @@ export function getFilteredIDiaIDs(
 
   const molfile = molecule.toMolfile();
 
-  let groupedDiaIDs =
-    getGroupedDiastereotopicAtomIDs(molecule);
+  let groupedDiaIDs = getGroupedDiastereotopicAtomIDs(molecule);
 
   let carbonDiaIDs = groupedDiaIDs
     .filter((e) => e.atomLabel === 'C')

package/src/prediction/utils/getNuclei.ts

@@ -1,8 +1,8 @@
-const nucleusMap: {[key: string]: string;} = {
+const nucleusMap: { [key: string]: string } = {
   h: '1H',
   c: '13C',
 };
 
-export function getNuclei(input: {[key: string]: string}) {
-  return Object.values(input).map((e) => (nucleusMap[e.toLowerCase()]));
+export function getNuclei(input: { [key: string]: string }) {
+  return Object.values(input).map((e) => nucleusMap[e.toLowerCase()]);
 }

package/src/prediction/utils/getPredictions.ts

@@ -1,6 +1,6 @@
-import type { Molecule } from "openchemlib";
+import type { Molecule } from 'openchemlib';
 
-import type { Prediction1D } from "../../types/prediction1D";
+import type { Prediction1D } from '../../types/prediction1D';
 
 import type { Predictions, PredictOptions, Predictors } from './predict2D';
 
@@ -21,4 +21,4 @@ export async function getPredictions(
       : undefined;
   }
   return prediction;
-}
+}

package/src/prediction/utils/queryByHOSE.ts

@@ -37,7 +37,7 @@ export function queryByHose(
     for (const atomNumber of element.atoms) {
       let atom = {
         diaIDs: [element.oclID],
-        delta: res ? res[0]: null,
+        delta: res ? res[0] : null,
         atoms: [atomNumber],
         nbAtoms: 1,
         level: level,

package/src/ranges/rangesToXY.ts

@@ -1,14 +1,13 @@
 import { DoubleArray } from 'cheminfo-types';
 import arraySequentialFill from 'ml-array-sequential-fill';
+import type { Shape1D } from 'ml-peak-shape-generator';
 import { SpectrumGenerator } from 'spectrum-generator';
-import type { Shape1DOptions } from 'spectrum-generator';
 
 import { hackSignalsToXY } from '../signals/hackSignalsToXY';
 import type { MakeMandatory } from '../types/MakeMandatory';
 import type { NMRRange } from '../types/NMRRange';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
 
-
 type RangeWithSignal = MakeMandatory<NMRRange, 'signals'>;
 
 export interface RangeToXYOptions {
@@ -41,7 +40,7 @@ export interface RangeToXYOptions {
    * options of signals.
    * @default { kind: 'gaussian' }
    */
-  shape: Shape1DOptions;
+  shape: Shape1D;
 }
 function checkForSignals(
   ranges: NMRRange[],
@@ -78,7 +77,15 @@ export function rangesToXY(ranges: NMRRange[], options: any = {}) {
 
   let spectrum: DoubleArray = new Float64Array(nbPoints);
   for (const range of ranges) {
-    const { integration, signals } = range;
+    const { integration, signals = [] } = range;
+    const { multiplicity: rangeMulplicity = '' } = range;
+    if (rangeMulplicity === 'm' && signals.length < 1) {
+      const { from, to } = range;
+      signals.push({
+        delta: (from + to) / 2,
+        multiplicity: 'm',
+      });
+    }
     let rangeSpectrum: DoubleArray = new Float64Array(nbPoints);
     for (const signal of signals) {
       const { multiplicity } = signal;
@@ -168,8 +175,8 @@ function normalizeSpectrum(
     0,
   );
 
-  const norma = (integration / sum) * 1e6;
   if (sum !== 0) {
+    const norma = (integration / sum) * 1e6;
     for (let i = 0; i < spectrum.length; i++) {
       spectrum[i] *= norma;
     }

package/src/signal/signalJoinCouplings.ts

@@ -46,7 +46,7 @@ const takeCareDiaIDs = (
 /**
  * Join couplings smaller than a define tolerance.
  * The resulting coupling should be an average of the existing one.
- * If distance is specified and is not always the same this property will be removed.
+ * If pathLength is specified and is not always the same this property will be removed.
  */
 export function signalJoinCouplings(
   signal: NMRSignal1D,
@@ -111,7 +111,7 @@ function groupJCouplings(
     ) as string[];
 
     let distances = distinctValues(
-      group.map((group) => group.distance) as number[],
+      group.map((group) => group.pathLength) as number[],
     ) as number[];
 
     let multiplicity = joinPatterns(
@@ -126,7 +126,7 @@ function groupJCouplings(
     };
 
     if (diaIDs.length === 1) newJ.diaIDs = diaIDs;
-    if (distances.length === 1 && distances[0]) newJ.distance = distances[0];
+    if (distances.length === 1 && distances[0]) newJ.pathLength = distances[0];
     if (assignment.length > 0) newJ.assignment = assignment;
     if (atoms.length > 0) newJ.atoms = atoms;
     signal.js.push(newJ);

package/src/signals/signalsJoin.ts

@@ -17,7 +17,7 @@ export interface SignalsJoinOptions {
 
 type JcouplingFromPrediction = MakeMandatory<
   Jcoupling,
-  'multiplicity' | 'diaIDs' | 'distance'
+  'multiplicity' | 'diaIDs' | 'pathLength'
 >;
 type Signal1DWidthDiaID = MakeMandatory<NMRSignal1D, 'diaIDs'>;
 type Signal1DWidthJsAndDiaID = Omit<Signal1DWidthDiaID, 'js'> & {
@@ -29,8 +29,8 @@ const localeCompareJcouplingKeys = (
   a: JcouplingFromPrediction,
   b: JcouplingFromPrediction,
 ) => {
-  const aa = `${a.diaIDs.join(' ')}${a.distance}`;
-  const bb = `${b.diaIDs.join(' ')}${b.distance}`;
+  const aa = `${a.diaIDs.join(' ')}${a.pathLength}`;
+  const bb = `${b.diaIDs.join(' ')}${b.pathLength}`;
   return localeCompare(aa, bb);
 };
 function checkForMandatory(
@@ -41,7 +41,7 @@ function checkForMandatory(
     if (!signal.diaIDs) throw new Error('there is not diaIDs');
     for (const jcoupling of signal.js) {
       if (!jcoupling.diaIDs) throw new Error('there is not diaIDs');
-      if (!jcoupling.distance) throw new Error('there is not distance');
+      if (!jcoupling.pathLength) throw new Error('there is not pathLength');
     }
   }
 }
@@ -68,7 +68,7 @@ export function signalsJoin(
     const keyDiaIDs = signal.diaIDs.join(' ');
     let id = `${keyDiaIDs} ${signal.js
       .map(
-        (j: JcouplingFromPrediction) => `${j.diaIDs.join(' ')} ${j.distance}`,
+        (j: JcouplingFromPrediction) => `${j.diaIDs.join(' ')} ${j.pathLength}`,
       )
       .sort(localeCompare)
       .join(' ')}`;
@@ -80,13 +80,13 @@ export function signalsJoin(
   // for each group we need to combine assignments and average couplings
   let newSignals: Signal1DWidthJsAndDiaID[] = [];
   Object.values(groupedSignals).forEach((group) => {
-    // joining couplings only if diaID and distance are equal
+    // joining couplings only if diaID and pathLength are equal
     let js: JcouplingFromPrediction[] = [];
     for (let i = 0; i < group[0].js.length; i++) {
       const coupling = group[0].js[i];
       js.push({
         diaIDs: coupling.diaIDs,
-        distance: coupling.distance,
+        pathLength: coupling.pathLength,
         multiplicity: coupling.multiplicity,
         coupling: mean(group.map((item) => item.js[i].coupling)),
       });

package/src/signals/signalsToXY.ts

@@ -1,6 +1,6 @@
 import rescale from 'ml-array-rescale';
 import arraySequentialFill from 'ml-array-sequential-fill';
-import type { Shape1DOptions } from 'spectrum-generator';
+import type { Shape1D } from 'ml-peak-shape-generator';
 
 import type { MakeMandatory } from '../types/MakeMandatory';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
@@ -25,7 +25,7 @@ export interface OptionsSignalsToXY {
   /**
    * Shape options for ml-spectrum-generator
    */
-  shape?: Shape1DOptions;
+  shape?: Shape1D;
   /**
    * The linewidth of the output spectrum, expresed in Hz.
    * @default 1
@@ -48,7 +48,7 @@ export interface OptionsSignalsToXY {
   maxClusterSize?: number;
 }
 
-type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'distance'>;
+type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'pathLength'>;
 type Signal1DWidthAtomsIDsAndDiaID = MakeMandatory<NMRSignal1D, 'atoms'>;
 type Signal1DWidthJsAndDiaID = Omit<Signal1DWidthAtomsIDsAndDiaID, 'js'> & {
   js: JcouplingFromPrediction[];