nmr-processing - npm Package Compare versions

Comparing version 3.2.0 to 3.3.0

CHANGELOG.md

 # Changelog
 
+## [3.3.0](https://www.github.com/cheminfo/nmr-processing/compare/v3.2.0...v3.3.0) (2021-10-12)
+
+
+### Features
+
+* add integration in impurities ([26d97ea](https://www.github.com/cheminfo/nmr-processing/commit/26d97ea839505b53ed138631c6f4c567703c4263))
+* add smiles in solvent impurities ([e2c3d6f](https://www.github.com/cheminfo/nmr-processing/commit/e2c3d6f9a44a901445e81e2f74361f2b8264070f))
+* add some smiles in database ([bff15d7](https://www.github.com/cheminfo/nmr-processing/commit/bff15d7a4ff2b68b4138bb85c23d00aa79d6ad95))
+* update n adapt to new version of ml-gsd ([#108](https://www.github.com/cheminfo/nmr-processing/issues/108)) ([d008691](https://www.github.com/cheminfo/nmr-processing/commit/d008691cf3d9c9e2dd908d7bb5639ee4dc41a2e3))
+
+
+### Bug Fixes
+
+* add multiplicity in range ([1d4eaf5](https://www.github.com/cheminfo/nmr-processing/commit/1d4eaf56f9ae039dc9ee48b1a2ee1d54259e4ead))
+* check default values at interfaces close [#105](https://www.github.com/cheminfo/nmr-processing/issues/105) ([ba6c82c](https://www.github.com/cheminfo/nmr-processing/commit/ba6c82ce7cafdc851d1c61ecb98f26006f064e59))
+* correct integration and range in impurities ([96c687c](https://www.github.com/cheminfo/nmr-processing/commit/96c687cdf025423ef6a233082b1521de6d4e9072))
+* remove useless ranges ([2b6119d](https://www.github.com/cheminfo/nmr-processing/commit/2b6119d47d6d05943266db5c871c5b7f3e45742f))
+* rename nucleus to nuclei when it is array ([d815868](https://www.github.com/cheminfo/nmr-processing/commit/d8158687a94d8f62768830983384edfad93f6696))
+* **resurrect:** regular expression for frequency ([fad1ed3](https://www.github.com/cheminfo/nmr-processing/commit/fad1ed3965ffcd1796a4b3defdc54333a49097ee))
+* wrong info for water in impurities ([290eb9e](https://www.github.com/cheminfo/nmr-processing/commit/290eb9ef297e972bf103209ee05380bef797cbb7))
+
 ## [3.2.0](https://www.github.com/cheminfo/nmr-processing/compare/v3.1.0...v3.2.0) (2021-10-05)
@@ -4,0 +25,0 @@

lib-esm/index.js

@@ -22,2 +22,3 @@ /**
 export * from './utilities/resurrect';
+export * from './utilities/rangeFromSignal';
 export * from './xy/xyAutoPeaksPicking';
@@ -24,0 +25,0 @@ export * from './xy/xyAutoRangesPicking';

lib-esm/peaks/peaksFilterImpurities.js

@@ -32,3 +32,3 @@ import { impurities } from '../constants/impurities';
         while (j--) {
-            tolerance = error + peakList[j].width;
+            tolerance = error + peakList[j].shape.width;
             difference = Math.abs(impurity[i].shift - peakList[j].x);
@@ -35,0 +35,0 @@ if (difference < tolerance) {

lib-esm/peaks/peaksToRanges.js

@@ -20,9 +20,9 @@ import { xyIntegration } from 'ml-spectra-processing';
         kind: 'signal',
-        startX: peak.x - peak.width,
-        stopX: peak.x + peak.width,
+        startX: peak.x - peak.shape.width,
+        stopX: peak.x + peak.shape.width,
         observe: frequency,
         nucleus,
         integralData: {
-            from: peak.x - peak.width * 3,
-            to: peak.x + peak.width * 3,
+            from: peak.x - peak.shape.width * 3,
+            to: peak.x + peak.shape.width * 3,
             value: 0,
@@ -34,3 +34,5 @@ },
                 intensity: peak.y,
-                width: peak.width,
+                shape: {
+                    width: peak.shape.width,
+                },
             },
@@ -81,3 +83,9 @@ ],
                         let peakR = signal.peaks.splice(j, 1)[0];
-                        peaksO.push({ x: peakR.x, y: peakR.intensity, width: peakR.width });
+                        peaksO.push({
+                            x: peakR.x,
+                            y: peakR.intensity,
+                            shape: {
+                                width: peakR.shape.width,
+                            },
+                        });
                         signal.mask.splice(j, 1);
@@ -192,3 +200,3 @@ signal.mask2.splice(j, 1);
         else {
-            let tmp = peak.x + peak.width;
+            let tmp = peak.x + peak.shape.width;
             signal1D.stopX = Math.max(signal1D.stopX, tmp);
@@ -200,6 +208,8 @@ signal1D.startX = Math.min(signal1D.startX, tmp);
                 intensity: peak.y,
-                width: peak.width,
+                shape: {
+                    width: peak.shape.width,
+                },
             });
-            signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
-            signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
+            signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.shape.width * 3);
+            signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.shape.width * 3);
             if (peak.kind)
@@ -248,4 +258,4 @@ signal1D.kind = peak.kind;
 function computeArea(peak) {
-    return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
+    return Math.abs(peak.intensity * peak.shape.width * 1.57); // todo add an option with this value: 1.772453851
 }
 //# sourceMappingURL=peaksToRanges.js.map

lib-esm/peaks/util/jAnalyzer.js

@@ -153,8 +153,9 @@ /*
     let nbPeaks = peaks.length;
-    signal.startX = peaks[0].x / signal.observe - peaks[0].width;
+    signal.startX = peaks[0].x / signal.observe - peaks[0].shape.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;
+        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width;
+    signal.integralData.from =
+        peaks[0].x / signal.observe - peaks[0].shape.width * 3;
     signal.integralData.to =
-        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
+        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width * 3;
     // Compile the pattern and format the constant couplings
@@ -378,3 +379,5 @@ signal.maskPattern = signal.mask2;
             intensity: peak[intensity],
-            width: peak.width,
+            shape: {
+                width: peak.shape.width,
+            },
         };
@@ -391,3 +394,3 @@ }
             peaks[i].intensity /= 2;
-            peaks[i].width += peaks[i + 1].width;
+            peaks[i].shape.width += peaks[i + 1].shape.width;
             peaks.splice(i + 1, 1);
@@ -440,5 +443,5 @@ }
                     avg = Math.min(peaks[left].intensity, peaks[right].intensity);
-                    avgWidth = Math.min(peaks[left].width, peaks[right].width);
+                    avgWidth = Math.min(peaks[left].shape.width, peaks[right].shape.width);
                     peaks[left].intensity = peaks[right].intensity = avg;
-                    peaks[left].width = peaks[right].width = avgWidth;
+                    peaks[left].shape.width = peaks[right].shape.width = avgWidth;
                     middle = [
@@ -620,4 +623,4 @@ middle[0] + (peaks[right].x + peaks[left].x) / 2,
 function getArea(peak) {
-    return Math.abs(peak.intensity * peak.width * 1.57); // 1.772453851);
+    return Math.abs(peak.intensity * peak.shape.width * 1.57); // 1.772453851);
 }
 //# sourceMappingURL=jAnalyzer.js.map

lib-esm/prediction/utils/predict2D.js

 import { agnes } from 'ml-hclust';
 import { Matrix } from 'ml-matrix';
 import { getGroupedDiastereotopicAtomIDs, getPathsInfo, } from 'openchemlib-utils';
-import { getNucleus } from './getNucleus';
+import { getNuclei } from './getNuclei';
 import { getPredictions } from './getPredictions';
@@ -91,3 +91,3 @@ function checkFromTo(options) {
         diaIDs: spectra.x.diaIDs,
-        nucleus: getNucleus({ from, to }),
+        nuclei: getNuclei({ from, to }),
         joinedSignals,
@@ -94,0 +94,0 @@ signals: splitSignals(joinedSignals),

lib-esm/ranges/rangesToXY.js

@@ -0,4 +1,4 @@
+import arraySequentialFill from 'ml-array-sequential-fill';
 import { SpectrumGenerator } from 'spectrum-generator';
 import { hackSignalsToXY } from '../signals/hackSignalsToXY';
-import { fromToArray } from '../utilities/fromToArray';
 function checkForSignals(ranges) {
@@ -44,3 +44,3 @@ for (let range of ranges) {
     return {
-        x: fromToArray(from, to, nbPoints),
+        x: arraySequentialFill({ from, to, size: nbPoints }),
         y: spectrum,
@@ -47,0 +47,0 @@ };

lib-esm/signals/signalsToRanges.js

@@ -0,1 +1,2 @@
+import { rangeFromSignal } from '../utilities/rangeFromSignal';
 function checkNbAtoms(signals) {
@@ -14,7 +15,5 @@ for (let signal of signals) {
     wrapped.forEach((signal) => {
-        let halfWidth = (signal.original.js || []).reduce((total, j) => (total += j.coupling / frequency), 0) /
-            2 +
-            tolerance;
-        signal.from = signal.original.delta - halfWidth;
-        signal.to = signal.original.delta + halfWidth;
+        const fromTo = rangeFromSignal(signal.original, { frequency, tolerance });
+        signal.from = fromTo.from;
+        signal.to = fromTo.to;
     });
@@ -21,0 +20,0 @@ wrapped = wrapped.sort((signal1, signal2) => signal1.from - signal2.from);

lib-esm/signals/signalsToXY.js

 import rescale from 'ml-array-rescale';
-import { fromToArray } from '../utilities/fromToArray';
+import arraySequentialFill from 'ml-array-sequential-fill';
 import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
@@ -30,3 +30,3 @@ import simulate1D from './simulation/simulate1D';
         return {
-            x: fromToArray(from, to, nbPoints),
+            x: arraySequentialFill({ from, to, size: nbPoints }),
             y: Array.from(new Float64Array(nbPoints)),
@@ -33,0 +33,0 @@ };

lib-esm/utilities/resurrect.js

@@ -25,3 +25,4 @@ import { resurrectRange } from './resurrectRange';
         else {
-            const range = resurrectRange(part);
+            const { frequency, nucleus } = data.experiment;
+            const range = resurrectRange(part, { frequency, nucleus });
             if (range)
@@ -50,3 +51,3 @@ data.ranges.push(range);
         if (frequencyParts.length) {
-            const frequency = frequencyParts[0].replace(/[^[0-9.]]/g, '');
+            const frequency = frequencyParts[0].replace(/[^0-9]/g, '');
             if (frequency.length > 1)
@@ -53,0 +54,0 @@ data.experiment.frequency = Number(frequency);

lib-esm/utilities/resurrectRange.js

@@ -0,5 +1,6 @@
+import { rangeFromSignal } from './rangeFromSignal';
 import { splitParenthesis } from './splitParenthesis';
 import { splitPatterns } from './splitPatterns';
 export function resurrectRange(part, options = {}) {
-    const { tolerance = 0.05, frequency = 400 } = options;
+    const { nucleus = '1h', frequency = 400 } = options;
     const split = splitParenthesis(part);
@@ -65,7 +66,3 @@ if (!split.before)
     if (range.from === range.to) {
-        let halfWidth = (signal.js || []).reduce((total, j) => (total += j.coupling / frequency), 0) /
-            2 +
-            tolerance;
-        range.from = signal.delta - halfWidth;
-        range.to = signal.delta + halfWidth;
+        range = { ...range, ...rangeFromSignal(signal, { nucleus, frequency }) };
     }
@@ -72,0 +69,0 @@ return range;

lib-esm/xy/xyAutoPeaksPicking.js

@@ -32,2 +32,3 @@ import { gsd, joinBroadPeaks, optimizePeaks } from 'ml-gsd';
     let peakList = gsd(data, {
+        shape,
         sgOptions,
@@ -34,0 +35,0 @@ minMaxRatio,

lib-esm/xyz/xyzAutoPeaksPicking.js

@@ -20,3 +20,3 @@ import { Matrix } from 'ml-matrix';
 export function xyzAutoPeaksPicking(spectraData, options) {
-    let { sizeToPad = 14, realTopDetection = true, thresholdFactor = 0.5, nucleus = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
+    let { sizeToPad = 14, realTopDetection = true, thresholdFactor = 0.5, nuclei = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
     if (!Array.isArray(observedFrequencies) &&
@@ -75,3 +75,3 @@ !ArrayBuffer.isView(observedFrequencies)) {
         tolerances,
-        nucleus,
+        nuclei,
         observedFrequencies,
@@ -86,4 +86,4 @@ realTopDetection,
 const createSignals2D = (peaks, options) => {
-    let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nucleus, realTopDetection, minY, maxY, minX, maxX, } = options;
-    let [nucleusX, nucleusY] = nucleus;
+    let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
+    let [nucleusX, nucleusY] = nuclei;
     let [toleranceX, toleranceY] = tolerances;
@@ -90,0 +90,0 @@ let [observeFrequencyX, observeFrequencyY] = observedFrequencies;

lib-esm/xyz/xyzJResAnalyzer.js

 import simpleClustering from 'ml-simple-clustering';
 import jAnalyzer from '../peaks/util/jAnalyzer';
 export function xyzJResAnalyzer(signals, options = {}) {
-    let { reference = 0, referenceMaxShiftError = 0.08, tolerances = [10, 100], nucleus = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
+    let { reference = 0, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
         jAxisKey: { jAxis: 'y', intensity: 'z' },
@@ -10,3 +10,3 @@ }, } = options;
         tolerances,
-        nucleus,
+        nuclei,
         jAnalyzer,
@@ -25,7 +25,7 @@ });
 function compilePattern(signals, options) {
-    let { observedFrequencies, tolerances, nucleus, jAnalyzer: jAnalyzerOptions, } = options;
+    let { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
     let signalOptions = {
         observedFrequencies,
         tolerances,
-        nucleus,
+        nuclei,
         dx: signals[0].x.resolution,
@@ -85,5 +85,5 @@ dy: signals[0].y.resolution,
 function createSignals2D(peaksInput, options) {
-    let { observedFrequencies, tolerances, nucleus, dx, dy } = options;
+    let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
     const peaks = JSON.parse(JSON.stringify(peaksInput));
-    let [nucleusX, nucleusY] = nucleus;
+    let [nucleusX, nucleusY] = nuclei;
     let [toleranceX, toleranceY] = tolerances;
@@ -90,0 +90,0 @@ let [observeFrequencyX, observeFrequencyY] = observedFrequencies;

lib/databases/carbonImpurities.d.ts

@@ -1,2 +0,2 @@
-import { DatabaseNMREntry } from './DatabaseNMREntry';
+import type { DatabaseNMREntry } from './DatabaseNMREntry';
 export declare const carbonImpurities: DatabaseNMREntry[];

lib/databases/protonImpurities.d.ts

@@ -1,2 +0,2 @@
-import { DatabaseNMREntry } from './DatabaseNMREntry';
+import type { DatabaseNMREntry } from './DatabaseNMREntry';
 export declare const protonImpurities: DatabaseNMREntry[];

lib/index.d.ts

@@ -22,2 +22,3 @@ /**
 export * from './utilities/resurrect';
+export * from './utilities/rangeFromSignal';
 export * from './xy/xyAutoPeaksPicking';
@@ -24,0 +25,0 @@ export * from './xy/xyAutoRangesPicking';

lib/index.js

@@ -34,2 +34,3 @@ "use strict";
 __exportStar(require("./utilities/resurrect"), exports);
+__exportStar(require("./utilities/rangeFromSignal"), exports);
 __exportStar(require("./xy/xyAutoPeaksPicking"), exports);
@@ -36,0 +37,0 @@ __exportStar(require("./xy/xyAutoRangesPicking"), exports);

lib/peaks/peaksFilterImpurities.d.ts

 import { impurities } from '../constants/impurities';
-import { GSDPeak } from '../types/GSDPeak';
+import type { NMRPeak1D } from '../types/NMRPeak1D';
 declare type Solvent = keyof typeof impurities;
@@ -23,3 +23,3 @@ export interface OptionsPeaksFilterImpurities {
  */
-export declare function peaksFilterImpurities(peakList: GSDPeak[], options?: OptionsPeaksFilterImpurities): GSDPeak[];
+export declare function peaksFilterImpurities(peakList: NMRPeak1D[], options?: OptionsPeaksFilterImpurities): NMRPeak1D[];
 export {};

lib/peaks/peaksFilterImpurities.js

@@ -36,3 +36,3 @@ "use strict";
         while (j--) {
-            tolerance = error + peakList[j].width;
+            tolerance = error + peakList[j].shape.width;
             difference = Math.abs(impurity[i].shift - peakList[j].x);
@@ -39,0 +39,0 @@ if (difference < tolerance) {

lib/peaks/peaksToRanges.d.ts

 import type { DataXY } from 'cheminfo-types';
-import type { GSDPeak } from '../types/GSDPeak';
+import { NMRPeak1D } from '../types/NMRPeak1D';
 import type { NMRRange } from '../types/NMRRange';
@@ -60,2 +60,2 @@ export interface OptionsPeaksToRanges {
  */
-export declare function peaksToRanges(data: DataXY, peakList: GSDPeak[], options?: OptionsPeaksToRanges): NMRRange[];
+export declare function peaksToRanges(data: DataXY, peakList: NMRPeak1D[], options?: OptionsPeaksToRanges): NMRRange[];

lib/peaks/peaksToRanges.js

@@ -26,9 +26,9 @@ "use strict";
         kind: 'signal',
-        startX: peak.x - peak.width,
-        stopX: peak.x + peak.width,
+        startX: peak.x - peak.shape.width,
+        stopX: peak.x + peak.shape.width,
         observe: frequency,
         nucleus,
         integralData: {
-            from: peak.x - peak.width * 3,
-            to: peak.x + peak.width * 3,
+            from: peak.x - peak.shape.width * 3,
+            to: peak.x + peak.shape.width * 3,
             value: 0,
@@ -40,3 +40,5 @@ },
                 intensity: peak.y,
-                width: peak.width,
+                shape: {
+                    width: peak.shape.width,
+                },
             },
@@ -87,3 +89,9 @@ ],
                         let peakR = signal.peaks.splice(j, 1)[0];
-                        peaksO.push({ x: peakR.x, y: peakR.intensity, width: peakR.width });
+                        peaksO.push({
+                            x: peakR.x,
+                            y: peakR.intensity,
+                            shape: {
+                                width: peakR.shape.width,
+                            },
+                        });
                         signal.mask.splice(j, 1);
@@ -199,3 +207,3 @@ signal.mask2.splice(j, 1);
         else {
-            let tmp = peak.x + peak.width;
+            let tmp = peak.x + peak.shape.width;
             signal1D.stopX = Math.max(signal1D.stopX, tmp);
@@ -207,6 +215,8 @@ signal1D.startX = Math.min(signal1D.startX, tmp);
                 intensity: peak.y,
-                width: peak.width,
+                shape: {
+                    width: peak.shape.width,
+                },
             });
-            signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
-            signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
+            signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.shape.width * 3);
+            signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.shape.width * 3);
             if (peak.kind)
@@ -255,4 +265,4 @@ signal1D.kind = peak.kind;
 function computeArea(peak) {
-    return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
+    return Math.abs(peak.intensity * peak.shape.width * 1.57); // todo add an option with this value: 1.772453851
 }
 //# sourceMappingURL=peaksToRanges.js.map

lib/peaks/util/jAnalyzer.d.ts

@@ -1,3 +0,3 @@
-import type { GSDPeak } from '../../types/GSDPeak';
 import { MakeMandatory } from '../../types/MakeMandatory';
+import { NMRPeak1D } from '../../types/NMRPeak1D';
 export interface JAxisKeys {
@@ -13,3 +13,3 @@ [key: string]: string;
 }
-export declare type Peak1DIntern = Omit<GSDPeak, 'y'> & {
+export declare type Peak1DIntern = Omit<NMRPeak1D, 'y'> & {
     intensity: number;
@@ -16,0 +16,0 @@ };

lib/peaks/util/jAnalyzer.js

@@ -155,8 +155,9 @@ "use strict";
     let nbPeaks = peaks.length;
-    signal.startX = peaks[0].x / signal.observe - peaks[0].width;
+    signal.startX = peaks[0].x / signal.observe - peaks[0].shape.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;
+        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width;
+    signal.integralData.from =
+        peaks[0].x / signal.observe - peaks[0].shape.width * 3;
     signal.integralData.to =
-        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
+        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width * 3;
     // Compile the pattern and format the constant couplings
@@ -380,3 +381,5 @@ signal.maskPattern = signal.mask2;
             intensity: peak[intensity],
-            width: peak.width,
+            shape: {
+                width: peak.shape.width,
+            },
         };
@@ -393,3 +396,3 @@ }
             peaks[i].intensity /= 2;
-            peaks[i].width += peaks[i + 1].width;
+            peaks[i].shape.width += peaks[i + 1].shape.width;
             peaks.splice(i + 1, 1);
@@ -442,5 +445,5 @@ }
                     avg = Math.min(peaks[left].intensity, peaks[right].intensity);
-                    avgWidth = Math.min(peaks[left].width, peaks[right].width);
+                    avgWidth = Math.min(peaks[left].shape.width, peaks[right].shape.width);
                     peaks[left].intensity = peaks[right].intensity = avg;
-                    peaks[left].width = peaks[right].width = avgWidth;
+                    peaks[left].shape.width = peaks[right].shape.width = avgWidth;
                     middle = [
@@ -622,4 +625,4 @@ middle[0] + (peaks[right].x + peaks[left].x) / 2,
 function getArea(peak) {
-    return Math.abs(peak.intensity * peak.width * 1.57); // 1.772453851);
+    return Math.abs(peak.intensity * peak.shape.width * 1.57); // 1.772453851);
 }
 //# sourceMappingURL=jAnalyzer.js.map

lib/prediction/predictCOSY.d.ts

@@ -61,3 +61,3 @@ import { Molecule } from 'openchemlib';
     diaIDs: string[];
-    nucleus: string[];
+    nuclei: string[];
     joinedSignals: import("../types/NMRSignal2D").NMRSignal2D[];
@@ -64,0 +64,0 @@ signals: any[];

lib/prediction/predictHMBC.d.ts

@@ -60,3 +60,3 @@ import { Molecule } from 'openchemlib';
     diaIDs: string[];
-    nucleus: string[];
+    nuclei: string[];
     joinedSignals: import("../types/NMRSignal2D").NMRSignal2D[];
@@ -63,0 +63,0 @@ signals: any[];

lib/prediction/predictHSQC.d.ts

@@ -60,3 +60,3 @@ import { Molecule } from 'openchemlib';
     diaIDs: string[];
-    nucleus: string[];
+    nuclei: string[];
     joinedSignals: import("../types/NMRSignal2D").NMRSignal2D[];
@@ -63,0 +63,0 @@ signals: any[];

lib/prediction/predictProton.d.ts

@@ -5,5 +5,2 @@ import type { Molecule } from 'openchemlib';
  * Makes a prediction using proton.
- * @param {Molecule} molecule - OCL Molecule instance.
- * @param {object} [options={}]
- * @param {function} [options.cache] A callback receiving a molfile and the result
  * @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
@@ -10,0 +7,0 @@ */

lib/prediction/utils/predict2D.d.ts

@@ -79,3 +79,3 @@ import { Molecule } from 'openchemlib';
     diaIDs: string[];
-    nucleus: string[];
+    nuclei: string[];
     joinedSignals: NMRSignal2D[];
@@ -82,0 +82,0 @@ signals: any[];

lib/prediction/utils/predict2D.js

@@ -7,3 +7,3 @@ "use strict";
 const openchemlib_utils_1 = require("openchemlib-utils");
-const getNucleus_1 = require("./getNucleus");
+const getNuclei_1 = require("./getNuclei");
 const getPredictions_1 = require("./getPredictions");
@@ -95,3 +95,3 @@ function checkFromTo(options) {
         diaIDs: spectra.x.diaIDs,
-        nucleus: (0, getNucleus_1.getNucleus)({ from, to }),
+        nuclei: (0, getNuclei_1.getNuclei)({ from, to }),
         joinedSignals,
@@ -98,0 +98,0 @@ signals: splitSignals(joinedSignals),

lib/ranges/rangesToACS.d.ts

 import type { NMRRange } from '../types/NMRRange';
 export interface RangesToACSOptions {
+    /**
+     * nucleus
+     * @default '1H'
+     */
     nucleus?: string;
@@ -8,6 +12,8 @@ ascending?: boolean;
      * default value depends of nucleus
+     * @default 1|2
      */
     nbDecimalDelta?: number;
     /**
-     * default value depends of nucleus
+     * Number of decimals to round the scalar coupling value
+     * @default 1
      */
@@ -17,2 +23,3 @@ nbDecimalJ?: number;
      * default value depends of nucleus
+     * @default 400|100
      */
@@ -19,0 +26,0 @@ observedFrequency?: number;

lib/ranges/rangesToXY.d.ts

@@ -0,5 +1,38 @@
+import type { Shape1DOption } from 'spectrum-generator';
 import type { NMRRange } from '../types/NMRRange';
+export interface RangeToXYOptions {
+    /**
+     * frequency observed
+     * @default 400
+     */
+    frequency: number;
+    /**
+     * line width to draw the signals
+     * @default 1
+     */
+    lineWidth: number;
+    /**
+     * lower limit in the spectrum.
+     * @default 0
+     */
+    from: number;
+    /**
+     * upper limit in the spectrum.
+     * @default 10
+     */
+    to: number;
+    /**
+     * number of points of the spectrum.
+     * @default 16384
+     */
+    nbPoints: number;
+    /**
+     * options of signals.
+     * @default { kind: 'gaussian' }
+     */
+    shape: Shape1DOption;
+}
 export declare function rangesToXY(ranges: NMRRange[], options?: any): {
-    x: Float64Array;
+    x: number[];
     y: Float64Array;
 };

lib/ranges/rangesToXY.js

 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.rangesToXY = void 0;
+const ml_array_sequential_fill_1 = __importDefault(require("ml-array-sequential-fill"));
 const spectrum_generator_1 = require("spectrum-generator");
 const hackSignalsToXY_1 = require("../signals/hackSignalsToXY");
-const fromToArray_1 = require("../utilities/fromToArray");
 function checkForSignals(ranges) {
@@ -47,3 +50,3 @@ for (let range of ranges) {
     return {
-        x: (0, fromToArray_1.fromToArray)(from, to, nbPoints),
+        x: (0, ml_array_sequential_fill_1.default)({ from, to, size: nbPoints }),
         y: spectrum,
@@ -50,0 +53,0 @@ };

lib/signals/signals2DToZ.d.ts

 import type { XYNumber } from 'spectrum-generator';
 import type { NMRSignal2D } from '../types/NMRSignal2D';
 interface signals2DToZOptions {
+    /**
+     * lower limit in the spectrum, if it is a number the value will be defined for both axes
+     * @default -1
+     */
     from?: number | XYNumber;
+    /**
+     * upper limit in the spectrum, if it is a number the value will be defined for both axes
+     * @default 12
+     */
     to?: number | XYNumber;
+    /**
+     * Number of points of each dimension of the spectrum,
+     * if it is a number the value will be defined for both axes
+     * @default 512
+     */
     nbPoints?: number | XYNumber;
+    /**
+     * full width at half maximum of signals for each dimension,
+     * if it is a number the value will be defined for both axes.
+     * @default 0.02
+     */
     width?: number | XYNumber;
@@ -8,0 +26,0 @@ }

lib/signals/signalsToRanges.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.signalsToRanges = void 0;
+const rangeFromSignal_1 = require("../utilities/rangeFromSignal");
 function checkNbAtoms(signals) {
@@ -17,7 +18,5 @@ for (let signal of signals) {
     wrapped.forEach((signal) => {
-        let halfWidth = (signal.original.js || []).reduce((total, j) => (total += j.coupling / frequency), 0) /
-            2 +
-            tolerance;
-        signal.from = signal.original.delta - halfWidth;
-        signal.to = signal.original.delta + halfWidth;
+        const fromTo = (0, rangeFromSignal_1.rangeFromSignal)(signal.original, { frequency, tolerance });
+        signal.from = fromTo.from;
+        signal.to = fromTo.to;
     });
@@ -24,0 +23,0 @@ wrapped = wrapped.sort((signal1, signal2) => signal1.from - signal2.from);

lib/signals/signalsToXY.js

@@ -8,3 +8,3 @@ "use strict";
 const ml_array_rescale_1 = __importDefault(require("ml-array-rescale"));
-const fromToArray_1 = require("../utilities/fromToArray");
+const ml_array_sequential_fill_1 = __importDefault(require("ml-array-sequential-fill"));
 const signalsToSpinSystem_1 = require("./simulation/signalsToSpinSystem");
@@ -37,3 +37,3 @@ const simulate1D_1 = __importDefault(require("./simulation/simulate1D"));
         return {
-            x: (0, fromToArray_1.fromToArray)(from, to, nbPoints),
+            x: (0, ml_array_sequential_fill_1.default)({ from, to, size: nbPoints }),
             y: Array.from(new Float64Array(nbPoints)),
@@ -40,0 +40,0 @@ };

lib/utilities/resurrect.js

@@ -29,3 +29,4 @@ "use strict";
         else {
-            const range = (0, resurrectRange_1.resurrectRange)(part);
+            const { frequency, nucleus } = data.experiment;
+            const range = (0, resurrectRange_1.resurrectRange)(part, { frequency, nucleus });
             if (range)
@@ -54,3 +55,3 @@ data.ranges.push(range);
         if (frequencyParts.length) {
-            const frequency = frequencyParts[0].replace(/[^[0-9.]]/g, '');
+            const frequency = frequencyParts[0].replace(/[^0-9]/g, '');
             if (frequency.length > 1)
@@ -57,0 +58,0 @@ data.experiment.frequency = Number(frequency);

lib/utilities/resurrectRange.d.ts

@@ -1,2 +0,2 @@
-import { NMRRange } from '../types/NMRRange';
+import type { NMRRange } from '../types/NMRRange';
 export declare function resurrectRange(part: string, options?: any): NMRRange | undefined;

lib/utilities/resurrectRange.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.resurrectRange = void 0;
+const rangeFromSignal_1 = require("./rangeFromSignal");
 const splitParenthesis_1 = require("./splitParenthesis");
 const splitPatterns_1 = require("./splitPatterns");
 function resurrectRange(part, options = {}) {
-    const { tolerance = 0.05, frequency = 400 } = options;
+    const { nucleus = '1h', frequency = 400 } = options;
     const split = (0, splitParenthesis_1.splitParenthesis)(part);
@@ -68,7 +69,3 @@ if (!split.before)
     if (range.from === range.to) {
-        let halfWidth = (signal.js || []).reduce((total, j) => (total += j.coupling / frequency), 0) /
-            2 +
-            tolerance;
-        range.from = signal.delta - halfWidth;
-        range.to = signal.delta + halfWidth;
+        range = { ...range, ...(0, rangeFromSignal_1.rangeFromSignal)(signal, { nucleus, frequency }) };
     }
@@ -75,0 +72,0 @@ return range;

lib/xy/xyAutoPeaksPicking.d.ts

 import { DataXY } from 'cheminfo-types';
-import { GSDPeak } from '../types/GSDPeak';
+import type { NMRPeak1D } from '../types/NMRPeak1D';
 interface OptionsGetPeakList {
@@ -90,3 +90,3 @@ /**
 }
-export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): GSDPeak[];
+export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): NMRPeak1D[];
 export {};

lib/xy/xyAutoPeaksPicking.js

@@ -36,2 +36,3 @@ "use strict";
     let peakList = (0, ml_gsd_1.gsd)(data, {
+        shape,
         sgOptions,
@@ -38,0 +39,0 @@ minMaxRatio,

lib/xyz/xyzAutoPeaksPicking.d.ts

@@ -27,6 +27,6 @@ import type { GetKernelOptions } from '../peaks/util/getKernel';
     /**
-     * specify the nucleus of each dimension
+     * specify the nuclei of each dimension
      * @default ['1H','1H']
      */
-    nucleus?: string[];
+    nuclei?: string[];
     /**
@@ -79,3 +79,3 @@ * specify the frequency for each dimension.
     tolerances: number[];
-    nucleus: string[];
+    nuclei: string[];
     realTopDetection: boolean;
@@ -82,0 +82,0 @@ minY: number;

lib/xyz/xyzAutoPeaksPicking.js

@@ -45,3 +45,3 @@ "use strict";
 function xyzAutoPeaksPicking(spectraData, options) {
-    let { sizeToPad = 14, realTopDetection = true, thresholdFactor = 0.5, nucleus = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
+    let { sizeToPad = 14, realTopDetection = true, thresholdFactor = 0.5, nuclei = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
     if (!Array.isArray(observedFrequencies) &&
@@ -100,3 +100,3 @@ !ArrayBuffer.isView(observedFrequencies)) {
         tolerances,
-        nucleus,
+        nuclei,
         observedFrequencies,
@@ -112,4 +112,4 @@ realTopDetection,
 const createSignals2D = (peaks, options) => {
-    let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nucleus, realTopDetection, minY, maxY, minX, maxX, } = options;
-    let [nucleusX, nucleusY] = nucleus;
+    let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
+    let [nucleusX, nucleusY] = nuclei;
     let [toleranceX, toleranceY] = tolerances;
@@ -116,0 +116,0 @@ let [observeFrequencyX, observeFrequencyY] = observedFrequencies;

lib/xyz/xyzJResAnalyzer.d.ts

@@ -6,3 +6,3 @@ import type { JAxisKeys } from '../peaks/util/jAnalyzer';
     tolerances?: number[] | Float64Array;
-    nucleus?: string[];
+    nuclei?: string[];
     jAnalyzer?: {
@@ -13,3 +13,11 @@ jAxisKey: JAxisKeys;
 interface XYZJResAnalyzerOptions extends CompilePatternOptions {
+    /**
+     * maximum difference in Hz to discard if the signal is symmetric.
+     * @default 0.08
+     */
     referenceMaxShiftError?: number;
+    /**
+     * reference value in Hz
+     * @default 0
+     */
     reference?: number;
@@ -16,0 +24,0 @@ }

lib/xyz/xyzJResAnalyzer.js

@@ -10,3 +10,3 @@ "use strict";
 function xyzJResAnalyzer(signals, options = {}) {
-    let { reference = 0, referenceMaxShiftError = 0.08, tolerances = [10, 100], nucleus = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
+    let { reference = 0, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
         jAxisKey: { jAxis: 'y', intensity: 'z' },
@@ -17,3 +17,3 @@ }, } = options;
         tolerances,
-        nucleus,
+        nuclei,
         jAnalyzer,
@@ -33,7 +33,7 @@ });
 function compilePattern(signals, options) {
-    let { observedFrequencies, tolerances, nucleus, jAnalyzer: jAnalyzerOptions, } = options;
+    let { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
     let signalOptions = {
         observedFrequencies,
         tolerances,
-        nucleus,
+        nuclei,
         dx: signals[0].x.resolution,
@@ -93,5 +93,5 @@ dy: signals[0].y.resolution,
 function createSignals2D(peaksInput, options) {
-    let { observedFrequencies, tolerances, nucleus, dx, dy } = options;
+    let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
     const peaks = JSON.parse(JSON.stringify(peaksInput));
-    let [nucleusX, nucleusY] = nucleus;
+    let [nucleusX, nucleusY] = nuclei;
     let [toleranceX, toleranceY] = tolerances;
@@ -98,0 +98,0 @@ let [observeFrequencyX, observeFrequencyY] = observedFrequencies;

package.json

 {
   "name": "nmr-processing",
-  "version": "3.2.0",
+  "version": "3.3.0",
   "description": "Pure functions allowing to process NMR spectra.",
@@ -50,18 +50,18 @@ "main": "./lib/index.js",
   "devDependencies": {
-    "@types/jest": "^27.0.1",
+    "@types/jest": "^27.0.2",
     "cheminfo-build": "^1.1.11",
-    "cheminfo-types": "^0.3.1",
+    "cheminfo-types": "^0.6.0",
     "eslint": "^7.32.0",
     "eslint-config-cheminfo-typescript": "^8.0.9",
     "esm": "^3.2.25",
-    "jest": "^27.0.6",
-    "jest-matcher-deep-close-to": "^2.0.1",
+    "jest": "^27.2.4",
+    "jest-matcher-deep-close-to": "^3.0.0",
     "md5": "^2.3.0",
     "ml-array-median": "^1.1.5",
     "nmr-xy-testdata": "^0.2.1",
-    "openchemlib": "^7.4.2",
-    "prettier": "^2.3.2",
+    "openchemlib": "^7.4.3",
+    "prettier": "^2.4.1",
     "rimraf": "^3.0.2",
     "ts-jest": "^27.0.5",
-    "typescript": "^4.4.2"
+    "typescript": "^4.4.3"
   },
@@ -73,8 +73,9 @@ "dependencies": {
     "form-data": "^4.0.0",
-    "is-any-array": "^1.0.0",
+    "is-any-array": "^1.0.1",
     "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": "^6.8.2",
-    "ml-hclust": "^3.0.0",
+    "ml-gsd": "^7.0.1",
+    "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^3.1.1",
@@ -89,5 +90,5 @@ "ml-matrix": "^6.8.0",
     "ml-tree-set": "^0.1.1",
-    "openchemlib-utils": "^1.5.0",
+    "openchemlib-utils": "^1.5.1",
     "spectrum-generator": "^5.4.0"
   }
 }

src/index.ts

@@ -28,2 +28,3 @@ /**
 export * from './utilities/resurrect';
+export * from './utilities/rangeFromSignal';
 
@@ -30,0 +31,0 @@ export * from './xy/xyAutoPeaksPicking';

src/peaks/peaksFilterImpurities.ts

 import { impurities } from '../constants/impurities';
 import type { ImpuritySignal } from '../constants/impurities';
-import { GSDPeak } from '../types/GSDPeak';
+import type { NMRPeak1D } from '../types/NMRPeak1D';
 
@@ -37,3 +37,3 @@ const toCheck = ['solvent', 'h2o', 'tms'];
 export function peaksFilterImpurities(
-  peakList: GSDPeak[],
+  peakList: NMRPeak1D[],
   options: OptionsPeaksFilterImpurities = {},
@@ -60,3 +60,3 @@ ) {
 function checkImpurity(
-  peakList: GSDPeak[],
+  peakList: NMRPeak1D[],
   impurity: ImpuritySignal[],
@@ -71,3 +71,3 @@ options: OptionsCheckImpurity,
     while (j--) {
-      tolerance = error + peakList[j].width;
+      tolerance = error + peakList[j].shape.width;
       difference = Math.abs(impurity[i].shift - peakList[j].x);
@@ -74,0 +74,0 @@ if (difference < tolerance) {

src/peaks/peaksToRanges.ts

 import type { DataXY } from 'cheminfo-types';
+import type { GSDPeak } from 'ml-gsd';
 import { xyIntegration } from 'ml-spectra-processing';
 
-import type { GSDPeak } from '../types/GSDPeak';
 import { MakeMandatory } from '../types/MakeMandatory';
+import { NMRPeak1D } from '../types/NMRPeak1D';
 import type { NMRRange } from '../types/NMRRange';
@@ -86,3 +87,3 @@ import type { NMRSignal1D } from '../types/NMRSignal1D';
 const assignSignal = (
-  peak: GSDPeak,
+  peak: NMRPeak1D,
   frequency: number,
@@ -95,9 +96,9 @@ nucleus: string,
     kind: 'signal',
-    startX: peak.x - peak.width,
-    stopX: peak.x + peak.width,
+    startX: peak.x - peak.shape.width,
+    stopX: peak.x + peak.shape.width,
     observe: frequency,
     nucleus,
     integralData: {
-      from: peak.x - peak.width * 3,
-      to: peak.x + peak.width * 3,
+      from: peak.x - peak.shape.width * 3,
+      to: peak.x + peak.shape.width * 3,
       value: 0,
@@ -109,3 +110,5 @@ },
         intensity: peak.y,
-        width: peak.width,
+        shape: {
+          width: peak.shape.width,
+        },
       },
@@ -121,3 +124,3 @@ ],
   data: DataXY,
-  peakList: GSDPeak[],
+  peakList: NMRPeak1D[],
   options: OptionsPeaksToRanges = {},
@@ -179,3 +182,9 @@ ): NMRRange[] {
             let peakR = signal.peaks.splice(j, 1)[0];
-            peaksO.push({ x: peakR.x, y: peakR.intensity, width: peakR.width });
+            peaksO.push({
+              x: peakR.x,
+              y: peakR.intensity,
+              shape: {
+                width: peakR.shape.width,
+              },
+            });
             signal.mask.splice(j, 1);
@@ -283,3 +292,3 @@ signal.mask2.splice(j, 1);
   data: DataXY,
-  peakList: GSDPeak[],
+  peakList: NMRPeak1D[],
   options: OptionsDetectSignals = {},
@@ -307,3 +316,3 @@ ): SignalIntern[] {
     } else {
-      let tmp = peak.x + peak.width;
+      let tmp = peak.x + peak.shape.width;
       signal1D.stopX = Math.max(signal1D.stopX, tmp);
@@ -315,11 +324,13 @@ signal1D.startX = Math.min(signal1D.startX, tmp);
         intensity: peak.y,
-        width: peak.width,
+        shape: {
+          width: peak.shape.width,
+        },
       });
       signal1D.integralData.from = Math.min(
         signal1D.integralData.from,
-        peak.x - peak.width * 3,
+        peak.x - peak.shape.width * 3,
       );
       signal1D.integralData.to = Math.max(
         signal1D.integralData.to,
-        peak.x + peak.width * 3,
+        peak.x + peak.shape.width * 3,
       );
@@ -372,3 +383,3 @@ if (peak.kind) signal1D.kind = peak.kind;
 function computeArea(peak: Peak1DIntern) {
-  return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
+  return Math.abs(peak.intensity * peak.shape.width * 1.57); // todo add an option with this value: 1.772453851
 }

src/peaks/util/jAnalyzer.ts

@@ -1,3 +0,3 @@
-import type { GSDPeak } from '../../types/GSDPeak';
 import { MakeMandatory } from '../../types/MakeMandatory';
+import { NMRPeak1D } from '../../types/NMRPeak1D';
 
@@ -32,3 +32,3 @@ /*
 
-export type Peak1DIntern = Omit<GSDPeak, 'y'> & { intensity: number };
+export type Peak1DIntern = Omit<NMRPeak1D, 'y'> & { intensity: number };
 
@@ -223,8 +223,9 @@ export interface SignalIntern {
   let nbPeaks = peaks.length;
-  signal.startX = peaks[0].x / signal.observe - peaks[0].width;
+  signal.startX = peaks[0].x / signal.observe - peaks[0].shape.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;
+    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width;
+  signal.integralData.from =
+    peaks[0].x / signal.observe - peaks[0].shape.width * 3;
   signal.integralData.to =
-    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
+    peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width * 3;
   // Compile the pattern and format the constant couplings
@@ -470,3 +471,5 @@ signal.maskPattern = signal.mask2;
       intensity: peak[intensity],
-      width: peak.width,
+      shape: {
+        width: peak.shape.width,
+      },
     };
@@ -483,3 +486,3 @@ }
       peaks[i].intensity /= 2;
-      peaks[i].width += peaks[i + 1].width;
+      peaks[i].shape.width += peaks[i + 1].shape.width;
       peaks.splice(i + 1, 1);
@@ -531,5 +534,8 @@ }
           avg = Math.min(peaks[left].intensity, peaks[right].intensity);
-          avgWidth = Math.min(peaks[left].width, peaks[right].width);
+          avgWidth = Math.min(
+            peaks[left].shape.width,
+            peaks[right].shape.width,
+          );
           peaks[left].intensity = peaks[right].intensity = avg;
-          peaks[left].width = peaks[right].width = avgWidth;
+          peaks[left].shape.width = peaks[right].shape.width = avgWidth;
           middle = [
@@ -714,3 +720,3 @@ middle[0] + (peaks[right].x + peaks[left].x) / 2,
 function getArea(peak: Peak1DIntern) {
-  return Math.abs(peak.intensity * peak.width * 1.57); // 1.772453851);
+  return Math.abs(peak.intensity * peak.shape.width * 1.57); // 1.772453851);
 }

src/prediction/predictProton.ts

@@ -17,5 +17,2 @@ import fetch from 'cross-fetch';
  * Makes a prediction using proton.
- * @param {Molecule} molecule - OCL Molecule instance.
- * @param {object} [options={}]
- * @param {function} [options.cache] A callback receiving a molfile and the result
  * @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.
@@ -22,0 +19,0 @@ */

src/prediction/utils/predict2D.ts

@@ -21,3 +21,3 @@ import { agnes, Cluster } from 'ml-hclust';
 
-import { getNucleus } from './getNucleus';
+import { getNuclei } from './getNuclei';
 import { getPredictions } from './getPredictions';
@@ -244,3 +244,3 @@
     diaIDs: spectra.x.diaIDs,
-    nucleus: getNucleus({ from, to }),
+    nuclei: getNuclei({ from, to }),
     joinedSignals,
@@ -247,0 +247,0 @@ signals: splitSignals(joinedSignals),

src/ranges/rangesToACS.ts

@@ -28,2 +28,6 @@ import { signalJoinCouplings } from '../signal/signalJoinCouplings';
 export interface RangesToACSOptions {
+  /**
+   * nucleus
+   * @default '1H'
+   */
   nucleus?: string;
@@ -34,6 +38,8 @@ ascending?: boolean;
    * default value depends of nucleus
+   * @default 1|2
    */
   nbDecimalDelta?: number;
   /**
-   * default value depends of nucleus
+   * Number of decimals to round the scalar coupling value
+   * @default 1
    */
@@ -43,2 +49,3 @@ nbDecimalJ?: number;
    * default value depends of nucleus
+   * @default 400|100
    */
@@ -45,0 +52,0 @@ observedFrequency?: number;

src/ranges/rangesToXY.ts

 import { DoubleArray } from 'cheminfo-types';
+import arraySequentialFill from 'ml-array-sequential-fill';
 import { SpectrumGenerator } from 'spectrum-generator';
+import type { Shape1DOption } from 'spectrum-generator';
 
 import { hackSignalsToXY } from '../signals/hackSignalsToXY';
-import { MakeMandatory } from '../types/MakeMandatory';
+import type { MakeMandatory } from '../types/MakeMandatory';
 import type { NMRRange } from '../types/NMRRange';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
-import { fromToArray } from '../utilities/fromToArray';
 
+
 type rangeWithSignal = MakeMandatory<NMRRange, 'signals'>;
 
+export interface RangeToXYOptions {
+  /**
+   * frequency observed
+   * @default 400
+   */
+  frequency: number;
+  /**
+   * line width to draw the signals
+   * @default 1
+   */
+  lineWidth: number;
+  /**
+   * lower limit in the spectrum.
+   * @default 0
+   */
+  from: number;
+  /**
+   * upper limit in the spectrum.
+   * @default 10
+   */
+  to: number;
+  /**
+   * number of points of the spectrum.
+   * @default 16384
+   */
+  nbPoints: number;
+  /**
+   * options of signals.
+   * @default { kind: 'gaussian' }
+   */
+  shape: Shape1DOption;
+}
 function checkForSignals(
@@ -65,3 +99,3 @@ ranges: NMRRange[],
   return {
-    x: fromToArray(from, to, nbPoints),
+    x: arraySequentialFill({ from, to, size: nbPoints }),
     y: spectrum,
@@ -68,0 +102,0 @@ };

src/signals/signals2DToZ.ts

@@ -7,5 +7,23 @@ import { generateSpectrum2D } from 'spectrum-generator';
 interface signals2DToZOptions {
+  /**
+   * lower limit in the spectrum, if it is a number the value will be defined for both axes
+   * @default -1
+   */
   from?: number | XYNumber;
+  /**
+   * upper limit in the spectrum, if it is a number the value will be defined for both axes
+   * @default 12
+   */
   to?: number | XYNumber;
+  /**
+   * Number of points of each dimension of the spectrum,
+   * if it is a number the value will be defined for both axes
+   * @default 512
+   */
   nbPoints?: number | XYNumber;
+  /**
+   * full width at half maximum of signals for each dimension,
+   * if it is a number the value will be defined for both axes.
+   * @default 0.02
+   */
   width?: number | XYNumber;
@@ -12,0 +30,0 @@ }

src/signals/signalsToRanges.ts

 import { MakeMandatory } from '../types/MakeMandatory';
 import type { NMRRange } from '../types/NMRRange';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
+import { rangeFromSignal } from '../utilities/rangeFromSignal';
 
@@ -27,3 +28,5 @@ interface SignalsToRangesOptions {
 
-function checkNbAtoms(signals: NMRSignal1D[]): asserts signals is Signals1DWithNbAtoms[] {
+function checkNbAtoms(
+  signals: NMRSignal1D[],
+): asserts signals is Signals1DWithNbAtoms[] {
   for (let signal of signals) {
@@ -47,11 +50,5 @@ if (!signal.nbAtoms) throw new Error('nbAtoms is mandatory');
   wrapped.forEach((signal) => {
-    let halfWidth =
-      (signal.original.js || []).reduce(
-        (total, j) => (total += j.coupling / frequency),
-        0,
-      ) /
-        2 +
-      tolerance;
-    signal.from = signal.original.delta - halfWidth;
-    signal.to = signal.original.delta + halfWidth;
+    const fromTo = rangeFromSignal(signal.original, { frequency, tolerance });
+    signal.from = fromTo.from;
+    signal.to = fromTo.to;
   });
@@ -64,3 +61,2 @@
   for (let signal of wrapped) {
-
     if (range.from === undefined || signal.from > range.to) {
@@ -67,0 +63,0 @@ range = {

src/signals/signalsToXY.ts

 import rescale from 'ml-array-rescale';
+import arraySequentialFill from 'ml-array-sequential-fill';
 import type { Shape1DOption } from 'spectrum-generator';
@@ -7,3 +8,2 @@
 import { Jcoupling } from '../types/jcoupling';
-import { fromToArray } from '../utilities/fromToArray';
 
@@ -95,3 +95,3 @@ import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
     return {
-      x: fromToArray(from, to, nbPoints),
+      x: arraySequentialFill({ from, to, size: nbPoints }),
       y: Array.from(new Float64Array(nbPoints)),
@@ -98,0 +98,0 @@ };

src/types/NMRRange.d.ts

@@ -10,3 +10,4 @@ import type { NMRSignal1D } from './NMRSignal1D';
   integration?: number;
+  multiplicity?: string;
   signals?: NMRSignal1D[];
 }

src/types/NMRSignal1D.d.ts

@@ -1,3 +0,3 @@
-import { GSDPeak } from './GSDPeak';
 import type { Jcoupling } from './jcoupling';
+import { GSDPeak } from './ml-gsd/index.d';
 
@@ -4,0 +4,0 @@ interface NMRSignal1D {

src/utilities/resurrect.ts

@@ -40,3 +40,4 @@ import type { NMRRange } from '../types/NMRRange';
     } else {
-      const range = resurrectRange(part);
+      const { frequency, nucleus } = data.experiment;
+      const range = resurrectRange(part, { frequency, nucleus });
       if (range) data.ranges.push(range);
@@ -67,3 +68,4 @@ }
     if (frequencyParts.length) {
-      const frequency = frequencyParts[0].replace(/[^[0-9.]]/g, '');
+      const frequency = frequencyParts[0].replace(/[^0-9]/g, '');
+
       if (frequency.length > 1) data.experiment.frequency = Number(frequency);
@@ -70,0 +72,0 @@ }

src/utilities/resurrectRange.ts

@@ -1,4 +0,5 @@
-import { NMRRange } from '../types/NMRRange';
-import { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRRange } from '../types/NMRRange';
+import type { NMRSignal1D } from '../types/NMRSignal1D';
 
+import { rangeFromSignal } from './rangeFromSignal';
 import { splitParenthesis } from './splitParenthesis';
@@ -8,3 +9,3 @@ import { splitPatterns } from './splitPatterns';
 export function resurrectRange(part: string, options: any = {}) {
-  const { tolerance = 0.05, frequency = 400 } = options;
+  const { nucleus = '1h', frequency = 400 } = options;
   const split = splitParenthesis(part);
@@ -77,11 +78,3 @@ if (!split.before) return;
   if (range.from === range.to) {
-    let halfWidth =
-      (signal.js || []).reduce(
-        (total, j) => (total += j.coupling / frequency),
-        0,
-      ) /
-        2 +
-      tolerance;
-    range.from = signal.delta - halfWidth;
-    range.to = signal.delta + halfWidth;
+    range = { ...range, ...rangeFromSignal(signal, { nucleus, frequency }) };
   }
@@ -88,0 +81,0 @@

src/xy/xyAutoPeaksPicking.ts

@@ -9,3 +9,3 @@ import { DataXY } from 'cheminfo-types';
 
-import { GSDPeak } from '../types/GSDPeak';
+import type { NMRPeak1D } from '../types/NMRPeak1D';
 /**
@@ -109,3 +109,3 @@ * Implementation of the peak picking method described by Cobas in:
   options: OptionsXYAutoPeaksPicking = {},
-): GSDPeak[] {
+): NMRPeak1D[] {
   const {
@@ -156,3 +156,2 @@ from,
   }
-
   return peaks;
@@ -177,2 +176,3 @@ }
   let peakList = gsd(data, {
+    shape,
     sgOptions,
@@ -179,0 +179,0 @@ minMaxRatio,

src/xyz/xyzAutoPeaksPicking.ts

@@ -50,6 +50,6 @@ import { Matrix } from 'ml-matrix';
   /**
-   * specify the nucleus of each dimension
+   * specify the nuclei of each dimension
    * @default ['1H','1H']
    */
-  nucleus?: string[];
+  nuclei?: string[];
   /**
@@ -98,3 +98,3 @@ * specify the frequency for each dimension.
     thresholdFactor = 0.5,
-    nucleus = ['1H', '1H'],
+    nuclei = ['1H', '1H'],
     observedFrequencies,
@@ -174,3 +174,3 @@ enhanceSymmetry = false,
     tolerances,
-    nucleus,
+    nuclei,
     observedFrequencies,
@@ -200,3 +200,3 @@ realTopDetection,
   tolerances: number[];
-  nucleus: string[];
+  nuclei: string[];
   realTopDetection: boolean;
@@ -216,3 +216,3 @@ minY: number;
     tolerances,
-    nucleus,
+    nuclei,
     realTopDetection,
@@ -225,3 +225,3 @@ minY,
 
-  let [nucleusX, nucleusY] = nucleus;
+  let [nucleusX, nucleusY] = nuclei;
   let [toleranceX, toleranceY] = tolerances;
@@ -228,0 +228,0 @@ let [observeFrequencyX, observeFrequencyY] = observedFrequencies;

src/xyz/xyzJResAnalyzer.ts

@@ -12,3 +12,3 @@ import simpleClustering from 'ml-simple-clustering';
   tolerances?: number[] | Float64Array;
-  nucleus?: string[];
+  nuclei?: string[];
   jAnalyzer?: { jAxisKey: JAxisKeys };
@@ -18,3 +18,11 @@ }
 interface XYZJResAnalyzerOptions extends CompilePatternOptions {
+  /**
+   * maximum difference in Hz to discard if the signal is symmetric.
+   * @default 0.08
+   */
   referenceMaxShiftError?: number;
+  /**
+   * reference value in Hz
+   * @default 0
+   */
   reference?: number;
@@ -25,3 +33,3 @@ }
   CompilePatternOptions,
-  'observedFrequencies' | 'tolerances' | 'nucleus' | 'jAnalyzer'
+  'observedFrequencies' | 'tolerances' | 'nuclei' | 'jAnalyzer'
 >;
@@ -37,3 +45,3 @@
     tolerances = [10, 100],
-    nucleus = ['1H', '1H'],
+    nuclei = ['1H', '1H'],
     observedFrequencies = [400, 400],
@@ -47,3 +55,3 @@ jAnalyzer = {
     tolerances,
-    nucleus,
+    nuclei,
     jAnalyzer,
@@ -68,3 +76,3 @@ });
     tolerances,
-    nucleus,
+    nuclei,
     jAnalyzer: jAnalyzerOptions,
@@ -76,3 +84,3 @@ } = options;
     tolerances,
-    nucleus,
+    nuclei,
     dx: signals[0].x.resolution,
@@ -152,7 +160,7 @@ dy: signals[0].y.resolution,
 function createSignals2D(peaksInput: MPFPeak[], options: any) {
-  let { observedFrequencies, tolerances, nucleus, dx, dy } = options;
+  let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
 
   const peaks: Peak2DHack[] = JSON.parse(JSON.stringify(peaksInput));
 
-  let [nucleusX, nucleusY] = nucleus;
+  let [nucleusX, nucleusY] = nuclei;
   let [toleranceX, toleranceY] = tolerances;
@@ -159,0 +167,0 @@ let [observeFrequencyX, observeFrequencyY] = observedFrequencies;

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increased by8.64%

Number of package files

339

increased by0.3%

Lines of code

109846

increased by5.94%

Number of medium supply chain risk alerts

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decreased by-20%

Worsened metrics

Dependency count

22

increased by4.76%

Dependency changes

• + Addedml-array-sequential-fill@^1.1.7

• + Addedml-gsd@7.0.1(transitive)

• + Addedml-spectra-fitting@2.0.0(transitive)

• Updatedis-any-array@^1.0.1

• Updatedml-gsd@^7.0.1

• Updatedml-hclust@^3.1.0

• Updatedopenchemlib-utils@^1.5.1