nmr-processing 5.0.0 → 6.0.0

package/lib-esm/signal/signalJoinCouplings.js

@@ -11,7 +11,7 @@ const takeCareDiaIDs = (a, b, tolerance) => localeCompareJcouplingKeys(a, b) ===
 /**
  * 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, options = {}) {
     const { tolerance = 0.05, ignoreDiaIDs = false } = options;
@@ -55,7 +55,7 @@ function groupJCouplings(signal, comparator, tolerance) {
             .filter((group) => group.diaIDs)
             .map((group) => group.diaIDs)
             .flat());
-        let distances = distinctValues(group.map((group) => group.distance));
+        let distances = distinctValues(group.map((group) => group.pathLength));
         let multiplicity = joinPatterns(group
             .filter((group) => group.multiplicity)
             .map((group) => group.multiplicity));
@@ -66,7 +66,7 @@ function groupJCouplings(signal, comparator, tolerance) {
         if (diaIDs.length === 1)
             newJ.diaIDs = diaIDs;
         if (distances.length === 1 && distances[0])
-            newJ.distance = distances[0];
+            newJ.pathLength = distances[0];
         if (assignment.length > 0)
             newJ.assignment = assignment;
         if (atoms.length > 0)

package/lib-esm/signal/signalJoinCouplings.js.map

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

@@ -3,8 +3,8 @@ import sum from 'ml-array-sum';
 import { signalJoinCouplings } from '../signal/signalJoinCouplings';
 const localeCompare = (a, b) => a.localeCompare(b);
 const localeCompareJcouplingKeys = (a, b) => {
-    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(signals) {
@@ -16,8 +16,8 @@ function checkForMandatory(signals) {
         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');
         }
     }
 }
@@ -35,7 +35,7 @@ export function signalsJoin(signals, options = {}) {
         signal.js = signal.js.sort(localeCompareJcouplingKeys);
         const keyDiaIDs = signal.diaIDs.join(' ');
         let id = `${keyDiaIDs} ${signal.js
-            .map((j) => `${j.diaIDs.join(' ')} ${j.distance}`)
+            .map((j) => `${j.diaIDs.join(' ')} ${j.pathLength}`)
             .sort(localeCompare)
             .join(' ')}`;
         if (!groupedSignals[id]) {
@@ -46,13 +46,13 @@ export function signalsJoin(signals, options = {}) {
     // for each group we need to combine assignments and average couplings
     let newSignals = [];
     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 = [];
         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/lib-esm/signals/signalsJoin.js.map

@@ -1 +1 @@
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package/lib-esm/signals/simulation/splitSpinSystem.js.map

@@ -1 +1 @@
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package/lib-esm/types/modules/nmr-parser.js

@@ -0,0 +1,2 @@
+"use strict";
+//# sourceMappingURL=nmr-parser.js.map

package/lib-esm/types/modules/nmr-parser.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"nmr-parser.js","sourceRoot":"","sources":["../../../src/types/modules/nmr-parser.ts"],"names":[],"mappings":""}

package/lib-esm/utilities/joinPatterns.js.map

@@ -1 +1 @@
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+{"version":3,"file":"joinPatterns.js","sourceRoot":"","sources":["../../src/utilities/joinPatterns.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAE7D,MAAM,UAAU,YAAY,CAAC,QAAkB;IAC7C,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE;QAC3C,IAAI,KAAK,CAAC,cAAc,CAAC,OAAO,CAAC,CAAC,EAAE;YAClC,MAAM,IAAI,KAAK,CACb,WAAW,OAAO,cAAc,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CACxE,CAAC;SACH;QACD,OAAO,GAAG,GAAG,cAAc,CAAC,OAAO,CAAC,CAAC;IACvC,CAAC,EAAE,CAAC,CAAC,CAAC;IAEN,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,EAAE;QAC1B,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAC;KACrD;IAED,OAAO,gBAAgB,CAAC,GAAG,CAAC,CAAC;AAC/B,CAAC"}

package/lib-esm/xyz/{xyzAutoPeaksPicking.js → xyzAutoZonesPicking.js}

@@ -16,7 +16,7 @@ const smallFilter = [
     [0, 1, 3, 7, 7, 7, 3, 1, 0],
     [0, 0, 1, 2, 2, 2, 1, 0, 0],
 ];
-export function xyzAutoPeaksPicking(spectraData, options) {
+export function xyzAutoZonesPicking(spectraData, 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) &&
         !ArrayBuffer.isView(observedFrequencies)) {
@@ -78,7 +78,40 @@ export function xyzAutoPeaksPicking(spectraData, options) {
     if (enhanceSymmetry) {
         signals = PeakOptimizer.enhanceSymmetry(signals);
     }
-    return signals;
+    return formatZones(signals);
+}
+function formatZones(signals) {
+    let zones = [];
+    for (const signal of signals) {
+        let minMax1 = [Number.MAX_VALUE, 0];
+        let minMax2 = [Number.MAX_VALUE, 0];
+        for (const peak of signal.peaks || []) {
+            if (peak.minX < minMax1[0]) {
+                minMax1[0] = peak.minX;
+            }
+            if (peak.maxX > minMax1[1]) {
+                minMax1[1] = peak.maxX;
+            }
+            if (peak.minY < minMax2[0]) {
+                minMax2[0] = peak.minY;
+            }
+            if (peak.maxY > minMax2[1]) {
+                minMax2[1] = peak.maxY;
+            }
+        }
+        zones.push({
+            x: {
+                from: minMax1[0],
+                to: minMax1[1],
+            },
+            y: {
+                from: minMax2[0],
+                to: minMax2[1],
+            },
+            signals: [signal],
+        });
+    }
+    return zones;
 }
 const createSignals2D = (peaks, options) => {
     let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
@@ -107,9 +140,6 @@ const createSignals2D = (peaks, options) => {
         peaks[i].maxX = minX + dx * peaks[i].maxX;
         peaks[i].maxY = minY + dy * peaks[i].maxY;
         // Still having problems to correctly detect peaks on those areas. So I'm removing everything there.
-        if (peaks[i].y < -1 || peaks[i].y >= 210) {
-            peaks.splice(i, 1);
-        }
     }
     // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
     // array like form
@@ -143,8 +173,6 @@ const createSignals2D = (peaks, options) => {
                 },
             };
             let peaks2D = [];
-            let minMax1 = [Number.MAX_VALUE, 0];
-            let minMax2 = [Number.MAX_VALUE, 0];
             let sumZ = 0;
             for (let jPeak = 0; jPeak < cluster.length; jPeak++) {
                 if (cluster[jPeak] === 1) {
@@ -152,24 +180,8 @@ const createSignals2D = (peaks, options) => {
                     signal.x.delta += peaks[jPeak].x * peaks[jPeak].z;
                     signal.y.delta += peaks[jPeak].y * peaks[jPeak].z;
                     sumZ += peaks[jPeak].z;
-                    if (peaks[jPeak].minX < minMax1[0]) {
-                        minMax1[0] = peaks[jPeak].minX;
-                    }
-                    if (peaks[jPeak].maxX > minMax1[1]) {
-                        minMax1[1] = peaks[jPeak].maxX;
-                    }
-                    if (peaks[jPeak].minY < minMax2[0]) {
-                        minMax2[0] = peaks[jPeak].minY;
-                    }
-                    if (peaks[jPeak].maxY > minMax2[1]) {
-                        minMax2[1] = peaks[jPeak].maxY;
-                    }
                 }
             }
-            signal.x.from = minMax1[0];
-            signal.y.from = minMax2[0];
-            signal.x.to = minMax1[1];
-            signal.y.to = minMax2[1];
             signal.x.delta /= sumZ;
             signal.y.delta /= sumZ;
             signal.peaks = peaks2D;
@@ -207,4 +219,4 @@ const padData = (spectraData, options) => {
         maxY: maxY + yOffset * yInterval,
     };
 };
-//# sourceMappingURL=xyzAutoPeaksPicking.js.map
+//# sourceMappingURL=xyzAutoZonesPicking.js.map

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

@@ -0,0 +1 @@
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package/lib-esm/xyz/xyzJResAnalyzer.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "5.0.0",
+  "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": "^9.0.1",
+    "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": "^3.0.3",
+    "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": "^6.0.1"
+    "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';

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,

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/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

@@ -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/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;
-}
+}