nmr-processing 5.0.0 → 6.0.3

package/src/peaks/peaksFilterImpurities.ts

@@ -1,6 +1,7 @@
 import { impurities } from '../constants/impurities';
 import type { ImpuritySignal } from '../constants/impurities';
-import type { NMRPeak1D } from '../types/NMRPeak1D';
+
+import type { NMRPeak1D } from './NMRPeak1D';
 
 const toCheck = ['solvent', 'h2o', 'tms'];
 

package/src/peaks/peaksToRanges.ts

@@ -1,11 +1,11 @@
 import type { DataXY } from 'cheminfo-types';
 import { xyIntegration } from 'ml-spectra-processing';
 
-import type { MakeMandatory } from '../types/MakeMandatory';
-import type { NMRPeak1D } from '../types/NMRPeak1D';
-import type { NMRRange } from '../types/NMRRange';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import type { MakeMandatory } from '../utilities/MakeMandatory';
+import type { NMRRange } from '../xy/NMRRange';
 
+import type { NMRPeak1D } from './NMRPeak1D';
 import jAnalyzer from './util/jAnalyzer';
 import type { SignalIntern, Peak1DIntern } from './util/jAnalyzer';
 import { joinRanges } from './util/joinRanges';

package/src/peaks/util/determineRealTop.ts

@@ -1,8 +1,7 @@
 import LM from 'ml-levenberg-marquardt';
+import type { Peak2D } from 'ml-matrix-peaks-finder';
 import { Gaussian2D } from 'ml-peak-shape-generator';
 
-import type { MPFPeak } from '../../types/MPFPeak';
-
 const direction8X = [-1, -1, -1, 0, 0, 1, 1, 1];
 const direction8Y = [-1, 0, 1, -1, 1, -1, 0, 1];
 const direction16X = [-2, -2, -2, -2, -2, -1, -1, 0, 0, 1, 1, 2, 2, 2, 2, 2];
@@ -10,7 +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);
@@ -148,7 +147,7 @@ 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]};
+        gaussian2D.fwhm = { x: p[i + 3 * nL], y: p[i + 4 * nL] };
         result +=
           p[i + 2 * nL] *
           gaussian2D.fct(

package/src/peaks/util/jAnalyzer.ts

@@ -1,5 +1,5 @@
-import type { MakeMandatory } from '../../types/MakeMandatory';
-import type { NMRPeak1D } from '../../types/NMRPeak1D';
+import type { MakeMandatory } from '../../utilities/MakeMandatory';
+import type { NMRPeak1D } from '../NMRPeak1D';
 
 /*
  * This library implements the J analyser described by Cobas et al in the paper:
@@ -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++;
@@ -222,8 +226,7 @@ function updateSignal(signal: SignalInternMandatory, jCouplings: number[]) {
   signal.startX = peaks[0].x / signal.observe - peaks[0].width;
   signal.stopX =
     peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width;
-  signal.integralData.from =
-    peaks[0].x / signal.observe - peaks[0].width * 3;
+  signal.integralData.from = peaks[0].x / signal.observe - peaks[0].width * 3;
   signal.integralData.to =
     peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
   // Compile the pattern and format the constant couplings
@@ -525,10 +528,7 @@ function symmetrize(
 
         if (Math.abs(diffL - diffR) < maxError) {
           avg = Math.min(peaks[left].intensity, peaks[right].intensity);
-          avgWidth = Math.min(
-            peaks[left].width,
-            peaks[right].width,
-          );
+          avgWidth = Math.min(peaks[left].width, peaks[right].width);
           peaks[left].intensity = peaks[right].intensity = avg;
           peaks[left].width = peaks[right].width = avgWidth;
           middle = [

package/src/peaks/util/joinRanges.ts

@@ -1,4 +1,4 @@
-import type { NMRRange } from '../../types/NMRRange';
+import type { NMRRange } from '../../xy/NMRRange';
 
 export function joinRanges(ranges: NMRRange[]) {
   ranges.sort((a, b) => a.from - b.from);

package/src/peaks/util/peakOptimizer.ts

@@ -1,10 +1,11 @@
-import type { MPFPeak } from '../../types/MPFPeak';
-import type { NMRSignal2D } from '../../types/NMRSignal2D';
+import type { Peak2D } from 'ml-matrix-peaks-finder';
+
+import type { NMRSignal2D } from '../../xyz/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/{types → prediction}/dataStructure.ts

@@ -2,4 +2,4 @@ export interface DataBaseLevelStructure {
   [key: string]: number[] | undefined;
 }
 
-export type DataBaseStructure = DataBaseLevelStructure[];
+export type DataBaseStructure = DataBaseLevelStructure[];

package/src/prediction/predictAll.ts

@@ -1,16 +1,14 @@
 import type { Molecule } from 'openchemlib';
 
-import type { Prediction1D } from '../types/prediction1D';
-
 import { predictCOSY } from './predictCOSY';
 import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
 import { predictHMBC } from './predictHMBC';
 import { predictHSQC } from './predictHSQC';
 import { predictProton, PredictProtonOptions } from './predictProton';
+import type { Prediction1D } from './prediction1D';
 import { getPredictions } from './utils/getPredictions';
 import type { Predictor } from './utils/predict2D';
 
-
 export interface PredictAllOptions {
   /**
    * nucleus label to use in the X axis
@@ -93,13 +91,14 @@ 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/predictCOSY.ts

@@ -1,8 +1,7 @@
 import { Molecule } from 'openchemlib';
 
-import type { Prediction1D } from '../types/prediction1D';
-
 import { predictProton, PredictProtonOptions } from './predictProton';
+import type { Prediction1D } from './prediction1D';
 import { predict2D, Predictor } from './utils/predict2D';
 
 export interface PredictCOSYOptions {

package/src/prediction/predictCarbon.ts

@@ -1,12 +1,12 @@
 import fetch from 'cross-fetch';
 import type { Molecule } from 'openchemlib';
 
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { signalsToRanges } from '../signals/signalsToRanges';
-import type { MakeMandatory } from '../types/MakeMandatory';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
-import type { DataBaseStructure } from '../types/dataStructure';
-import type { Prediction1D } from '../types/prediction1D';
+import type { MakeMandatory } from '../utilities/MakeMandatory';
 
+import type { DataBaseStructure } from './dataStructure';
+import type { Prediction1D } from './prediction1D';
 import { fetchPrediction } from './utils/fetchPrediction';
 import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
 import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';

package/src/prediction/predictHMBC.ts

@@ -1,11 +1,10 @@
 import { Molecule } from 'openchemlib';
 
-import type { Prediction1D } from '../types/prediction1D';
-
 import { predictCarbon } from './predictCarbon';
 import type { PredictCarbonOptions } from './predictCarbon';
 import { predictProton } from './predictProton';
 import type { PredictProtonOptions } from './predictProton';
+import type { Prediction1D } from './prediction1D';
 import { predict2D } from './utils/predict2D';
 import type { Predictor } from './utils/predict2D';
 

package/src/prediction/predictHSQC.ts

@@ -1,9 +1,8 @@
 import { Molecule } from 'openchemlib';
 
-import type { Prediction1D } from '../types/prediction1D';
-
 import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
 import { predictProton, PredictProtonOptions } from './predictProton';
+import type { Prediction1D } from './prediction1D';
 import { predict2D, Predictor } from './utils/predict2D';
 
 export interface PredictHSQCOptions {
@@ -49,7 +48,10 @@ 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

@@ -7,10 +7,11 @@ import {
   getDiastereotopicAtomIDs,
 } from 'openchemlib-utils';
 
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { signalsJoin } from '../signals/signalsJoin';
 import { signalsToRanges } from '../signals/signalsToRanges';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
-import type { Prediction1D } from '../types/prediction1D';
+
+import type { Prediction1D } from './prediction1D';
 
 /**
  * Makes a prediction using proton.
@@ -45,7 +46,7 @@ export async function predictProton(
     formData.append('molfile', molfile);
     const response = await fetch('https://www.nmrdb.org/service/predictor', {
       method: 'POST',
-      //@ts-expect-error
+      // @ts-expect-error RequestInit type does not include FormData.
       body: formData,
     });
     result = await response.text();
@@ -102,7 +103,7 @@ 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/{types → prediction}/prediction1D.ts

@@ -1,7 +1,7 @@
 import type { Molecule } from 'openchemlib';
 
-import type { NMRRange } from "./NMRRange";
-import type { NMRSignal1D } from "./NMRSignal1D";
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import type { NMRRange } from '../xy/NMRRange';
 
 export interface Prediction1D {
   molfile: string;

package/src/prediction/utils/fetchPrediction.ts

@@ -1,7 +1,7 @@
 import { fetch } from 'cross-fetch';
 import { Molecule } from 'openchemlib';
 
-import type { Prediction1D } from '../../types/prediction1D';
+import type { Prediction1D } from '../prediction1D';
 
 interface FetchPredictionOptions {
   webserviceURL: string;

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 '../prediction1D';
 
 import type { Predictions, PredictOptions, Predictors } from './predict2D';
 
@@ -12,7 +12,7 @@ export async function getPredictions(
   predictions?: Predictions,
 ) {
   let prediction: Prediction1D | undefined;
-  if (predictions && predictions[key]) {
+  if (predictions?.[key]) {
     prediction = predictions[key];
   } else if (predictor) {
     const fromPredictor = predictor[key];
@@ -21,4 +21,4 @@ export async function getPredictions(
       : undefined;
   }
   return prediction;
-}
+}

package/src/prediction/utils/predict2D.ts

@@ -11,12 +11,12 @@ import type {
   PathInfo,
 } from 'openchemlib-utils';
 
-import type { MakeMandatory } from '../../types/MakeMandatory';
-import type { NMRSignal1D } from '../../types/NMRSignal1D';
-import type { NMRSignal2D } from '../../types/NMRSignal2D';
-import type { Prediction1D } from '../../types/prediction1D';
+import type { NMRSignal1D } from '../../signals/NMRSignal1D';
+import type { MakeMandatory } from '../../utilities/MakeMandatory';
+import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
 import type { PredictCarbon, PredictCarbonOptions } from '../predictCarbon';
 import type { PredictProton, PredictProtonOptions } from '../predictProton';
+import type { Prediction1D } from '../prediction1D';
 
 import { getNuclei } from './getNuclei';
 import { getPredictions } from './getPredictions';

package/src/prediction/utils/queryByHOSE.ts

@@ -1,4 +1,4 @@
-import type { DataBaseStructure } from '../../types/dataStructure';
+import type { DataBaseStructure } from '../dataStructure';
 
 import type { GroupedDiaIDsWithHose } from './getFilteredIDiaIDs';
 
@@ -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/rangesToACS.ts

@@ -1,9 +1,17 @@
 import { signalJoinCouplings } from '../signal/signalJoinCouplings';
 import { signalMultiplicityPattern } from '../signal/signalMultiplicityPattern';
-import type { NMRRange } from '../types/NMRRange';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import type { NMRRange } from '../xy/NMRRange';
 
-const globalOptions = {
+const globalOptions: Record<
+  string,
+  {
+    nucleus: string;
+    nbDecimalDelta: number;
+    nbDecimalJ: number;
+    observedFrequency: number;
+  }
+> = {
   h: {
     nucleus: '1H',
     nbDecimalDelta: 2,
@@ -62,9 +70,8 @@ export function rangesToACS(
   options: RangesToACSOptions = {},
 ) {
   if (!options.nucleus) options.nucleus = '1H';
-  let nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
-  //@ts-expect-error
-  let defaultOptions = globalOptions[nucleus];
+  const nucleus = options.nucleus.toLowerCase().replace(/[0-9]/g, '');
+  const defaultOptions = globalOptions[nucleus];
   options = Object.assign(
     {},
     defaultOptions,
@@ -75,13 +82,13 @@ export function rangesToACS(
   ranges = JSON.parse(JSON.stringify(ranges));
   if (options.ascending === true) {
     ranges.sort((a, b) => {
-      let fromA = Math.min(a.from, a.to);
-      let fromB = Math.min(b.from, b.to);
+      const fromA = Math.min(a.from, a.to);
+      const fromB = Math.min(b.from, b.to);
       return fromA - fromB;
     });
   }
-  let acsString = formatAcs(ranges, options);
 
+  let acsString = formatAcs(ranges, options);
   if (acsString.length > 0) acsString += '.';
 
   return acsString;
@@ -90,8 +97,8 @@ export function rangesToACS(
 function formatAcs(ranges: NMRRange[], options: any) {
   let acs = spectroInformation(options);
   if (acs.length === 0) acs = 'δ ';
-  let acsRanges: string[] = [];
-  for (let range of ranges) {
+  const acsRanges: string[] = [];
+  for (const range of ranges) {
     if (uselessKind(range.kind, options.filter)) continue;
     pushDelta(range, acsRanges, options);
   }
@@ -103,7 +110,7 @@ function formatAcs(ranges: NMRRange[], options: any) {
 }
 
 function spectroInformation(options: any) {
-  let parenthesis = [];
+  const parenthesis = [];
   let strings = `${formatNucleus(options.nucleus)} NMR`;
   if (options.solvent) {
     parenthesis.push(formatMF(options.solvent));
@@ -122,7 +129,7 @@ function spectroInformation(options: any) {
 function pushDelta(range: NMRRange, acsRanges: string[], options: any) {
   let strings = '';
   let parenthesis: any = [];
-  let fromTo = [range.from, range.to];
+  const fromTo = [range.from, range.to];
 
   if (range.signals) {
     range.signals = range.signals.filter(

package/src/ranges/rangesToXY.ts

@@ -3,10 +3,10 @@ import arraySequentialFill from 'ml-array-sequential-fill';
 import type { Shape1D } from 'ml-peak-shape-generator';
 import { SpectrumGenerator } from 'spectrum-generator';
 
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { hackSignalsToXY } from '../signals/hackSignalsToXY';
-import type { MakeMandatory } from '../types/MakeMandatory';
-import type { NMRRange } from '../types/NMRRange';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { MakeMandatory } from '../utilities/MakeMandatory';
+import type { NMRRange } from '../xy/NMRRange';
 
 type RangeWithSignal = MakeMandatory<NMRRange, 'signals'>;
 

package/src/signal/signalJoinCouplings.ts

@@ -1,8 +1,8 @@
 import sum from 'ml-array-sum';
 
-import type { MakeMandatory } from '../types/MakeMandatory';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
-import type { Jcoupling } from '../types/jcoupling';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import type { Jcoupling } from '../signals/jcoupling';
+import type { MakeMandatory } from '../utilities/MakeMandatory';
 import { joinPatterns } from '../utilities/joinPatterns';
 
 export interface SignalJoinCouplingsOptions {
@@ -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/signal/signalMultiplicityPattern.ts

@@ -1,4 +1,4 @@
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
 /**
  * Return
  * @param {*} signal

package/src/{types → signals}/NMRSignal1D.ts

@@ -1,4 +1,5 @@
-import type { NMRPeak1D } from './NMRPeak1D';
+import type { NMRPeak1D } from '../peaks/NMRPeak1D';
+
 import type { Jcoupling } from './jcoupling';
 
 export interface NMRSignal1D {

package/src/signals/hackSignalsToXY.ts

@@ -1,7 +1,7 @@
 import { couplingPatterns } from '../constants/couplingPatterns';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
-import type { Jcoupling } from '../types/jcoupling';
 
+import type { NMRSignal1D } from './NMRSignal1D';
+import type { Jcoupling } from './jcoupling';
 import { OptionsSignalsToXY, signalsToXY } from './signalsToXY';
 
 /**

package/src/{types → signals}/jcoupling.ts

@@ -4,5 +4,5 @@ export interface Jcoupling {
   assignment?: string | string[];
   diaIDs?: string[];
   multiplicity?: string;
-  distance?: number;
+  pathLength?: number;
 }

package/src/signals/signals2DToZ.ts

@@ -1,7 +1,7 @@
 import { generateSpectrum2D } from 'spectrum-generator';
 import type { XYNumber } from 'spectrum-generator';
 
-import type { NMRSignal2D } from '../types/NMRSignal2D';
+import type { NMRSignal2D } from '../xyz/NMRSignal2D';
 
 interface Signals2DToZOptions {
   /**

package/src/signals/signalsJoin.ts

@@ -3,9 +3,10 @@ import sum from 'ml-array-sum';
 
 import { signalJoinCouplings } from '../signal/signalJoinCouplings';
 import type { SignalJoinCouplingsOptions } from '../signal/signalJoinCouplings';
-import type { MakeMandatory } from '../types/MakeMandatory';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
-import type { Jcoupling } from '../types/jcoupling';
+import type { MakeMandatory } from '../utilities/MakeMandatory';
+
+import type { NMRSignal1D } from './NMRSignal1D';
+import type { Jcoupling } from './jcoupling';
 
 export interface SignalsJoinOptions {
   /**
@@ -17,7 +18,7 @@ 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 +30,8 @@ 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 +42,7 @@ 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 +69,7 @@ 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 +81,13 @@ 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/signalsToRanges.ts

@@ -1,7 +1,8 @@
-import type { MakeMandatory } from '../types/MakeMandatory';
-import type { NMRRange } from '../types/NMRRange';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { MakeMandatory } from '../utilities/MakeMandatory';
 import { rangeFromSignal } from '../utilities/rangeFromSignal';
+import type { NMRRange } from '../xy/NMRRange';
+
+import type { NMRSignal1D } from './NMRSignal1D';
 
 interface SignalsToRangesOptions {
   /**