nmr-processing 9.7.8 → 9.8.0

package/lib-esm/xyz/xyzJResAnalyzer.js

@@ -5,10 +5,10 @@ import jAnalyzer from '../signals/utils/jAnalyzer';
 import { formatZones } from './util/formatZone';
 const { parse, stringify } = JSON;
 export function xyzJResAnalyzer(signals, options = {}) {
-    let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
+    const { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
         jAxisKey: { jAxis: 'y', intensity: 'z' },
     }, } = options;
-    let temporalSignals = compilePattern(signals, {
+    const temporalSignals = compilePattern(signals, {
         observedFrequencies,
         tolerances,
         nuclei,
@@ -17,7 +17,7 @@ export function xyzJResAnalyzer(signals, options = {}) {
     //check if the signal are symmetric around the reference
     let signals2D = [];
     for (const tempSignal of temporalSignals) {
-        let delta = tempSignal.y.delta;
+        const delta = tempSignal.y.delta;
         if (Math.abs(delta - reference) > referenceMaxShiftError)
             continue;
         signals2D.push(tempSignal);
@@ -26,8 +26,8 @@ export function xyzJResAnalyzer(signals, options = {}) {
     return getZones ? formatZones(signals2D) : signals2D;
 }
 function compilePattern(signals, options) {
-    let { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
-    let signalOptions = {
+    const { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
+    const signalOptions = {
         observedFrequencies,
         tolerances,
         nuclei,
@@ -38,7 +38,7 @@ function compilePattern(signals, options) {
     const newSignals = [];
     //adapt to 1D jAnalyzer
     for (const signal of signals) {
-        let peaks = [];
+        const peaks = [];
         for (const peak of signal.peaks || []) {
             peaks.push({
                 ...peak,
@@ -68,10 +68,10 @@ function compilePattern(signals, options) {
             signal.multiplicity !== 'm' &&
             signal.multiplicity !== '') {
             // Create a new signal with the removed peaks
-            let peaksO = [];
+            const peaksO = [];
             for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
                 if (!signal.maskPattern[j]) {
-                    let peakR = signal.peaks.splice(j, 1)[0];
+                    const peakR = signal.peaks.splice(j, 1)[0];
                     peaksO.push(peakR);
                     signal.mask.splice(j, 1);
                     signal.mask2?.splice(j, 1);
@@ -81,7 +81,7 @@ function compilePattern(signals, options) {
             }
             if (peaksO.length > 0) {
                 peaksO.reverse();
-                let signals2D = createSignals2D(peaksO, signalOptions);
+                const signals2D = createSignals2D(peaksO, signalOptions);
                 for (const signal of signals2D) {
                     newSignals.push(signal);
                 }
@@ -94,14 +94,14 @@ function compilePattern(signals, options) {
     return signals;
 }
 function createSignals2D(peaksInput, options) {
-    let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
+    const { observedFrequencies, tolerances, nuclei, dx, dy } = options;
     const peaks = parse(stringify(peaksInput));
-    let [nucleusX, nucleusY] = nuclei;
-    let [toleranceX, toleranceY] = tolerances;
-    let [observeFrequencyX, observeFrequencyY] = observedFrequencies;
+    const [nucleusX, nucleusY] = nuclei;
+    const [toleranceX, toleranceY] = tolerances;
+    const [observeFrequencyX, observeFrequencyY] = observedFrequencies;
     // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
     // array like form
-    let connectivity = [];
+    const connectivity = [];
     for (let i = 0; i < peaks.length; i++) {
         for (let j = i; j < peaks.length; j++) {
             if (Math.abs(peaks[i].x - peaks[j].x) * observeFrequencyX < toleranceX &&
@@ -114,11 +114,11 @@ function createSignals2D(peaksInput, options) {
             }
         }
     }
-    let clusters = simpleClustering(connectivity);
-    let signals = [];
+    const clusters = simpleClustering(connectivity);
+    const signals = [];
     if (clusters) {
-        for (let cluster of clusters) {
-            let signal = {
+        for (const cluster of clusters) {
+            const signal = {
                 id: generateID(),
                 nucleusX,
                 nucleusY,
@@ -135,9 +135,9 @@ function createSignals2D(peaksInput, options) {
                 shiftX: 0,
                 shiftY: 0,
             };
-            let peaks2D = [];
-            let minMax1 = [Number.MAX_VALUE, 0];
-            let minMax2 = [Number.MAX_VALUE, 0];
+            const peaks2D = [];
+            const minMax1 = [Number.MAX_VALUE, 0];
+            const minMax2 = [Number.MAX_VALUE, 0];
             let sumZ = 0;
             for (let jPeak = cluster.length - 1; jPeak >= 0; jPeak--) {
                 if (cluster[jPeak] === 1) {

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

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package/lib-esm/xyz/xyzPhaseCorrectionDirectDimension.js

@@ -0,0 +1,26 @@
+import { degreeToRadians } from '../constants/degreeToRadians';
+import { reimPhaseCorrection } from 'ml-spectra-processing';
+import { applyOverImag } from './util/phaseCorrection/applyOverImag';
+import { applyOverReal } from './util/phaseCorrection/applyOverReal';
+export function xyzPhaseCorrectionDirectDimension(data, options) {
+    applyOverReal(data, { ...options, applyPhaseCorrection });
+    if ('ri' in data && 'ii' in data) {
+        applyOverImag(data, { ...options, applyPhaseCorrection });
+    }
+    return data;
+}
+function applyPhaseCorrection(data, options) {
+    const ph0 = options.ph0 * degreeToRadians;
+    const ph1 = options.ph1 * degreeToRadians;
+    const nbRows = data.re.rows;
+    for (let i = 0; i < nbRows; i++) {
+        const { re, im } = reimPhaseCorrection({
+            re: data.re.getRow(i),
+            im: data.im.getRow(i),
+        }, ph0, ph1);
+        data.re.setRow(i, re);
+        data.im.setRow(i, im);
+    }
+    return data;
+}
+//# sourceMappingURL=xyzPhaseCorrectionDirectDimension.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"xyzPhaseCorrectionDirectDimension.js","sourceRoot":"","sources":["../../src/xyz/xyzPhaseCorrectionDirectDimension.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAE/D,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EAAE,aAAa,EAAE,MAAM,sCAAsC,CAAC;AACrE,OAAO,EAAE,aAAa,EAAE,MAAM,sCAAsC,CAAC;AAerE,MAAM,UAAU,iCAAiC,CAC/C,IAAiB,EACjB,OAA+B;IAE/B,aAAa,CAAC,IAAI,EAAE,EAAE,GAAG,OAAO,EAAE,oBAAoB,EAAE,CAAC,CAAC;IAC1D,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,EAAE;QAChC,aAAa,CAAC,IAAI,EAAE,EAAE,GAAG,OAAO,EAAE,oBAAoB,EAAE,CAAC,CAAC;KAC3D;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,SAAS,oBAAoB,CAC3B,IAAgC,EAChC,OAAqC;IAErC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,eAAe,CAAC;IAC1C,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,eAAe,CAAC;IAC1C,MAAM,MAAM,GAAG,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC;IAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,MAAM,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,mBAAmB,CACpC;YACE,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC;YACrB,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC;SACtB,EACD,GAAG,EACH,GAAG,CACJ,CAAC;QACF,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACtB,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;KACvB;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/xyz/xyzPhaseCorrectionIndirectDimension.js

@@ -0,0 +1,28 @@
+import { degreeToRadians } from '../constants/degreeToRadians';
+import { reimPhaseCorrection } from 'ml-spectra-processing';
+import { applyOverImag } from './util/phaseCorrection/applyOverImag';
+import { applyOverReal } from './util/phaseCorrection/applyOverReal';
+export function xyzPhaseCorrectionIndirectDimension(data, options) {
+    const { quad } = options;
+    if (quad === 'real') {
+        return applyOverReal(data, { ...options, applyPhaseCorrection });
+    }
+    else if (quad === 'imag') {
+        return applyOverImag(data, { ...options, applyPhaseCorrection });
+    }
+}
+function applyPhaseCorrection(data, options) {
+    const ph0 = options.ph0 * degreeToRadians;
+    const ph1 = options.ph1 * degreeToRadians;
+    const nbColumns = data.re.columns;
+    for (let i = 0; i < nbColumns; i++) {
+        const { re, im } = reimPhaseCorrection({
+            re: data.re.getColumn(i),
+            im: data.im.getColumn(i),
+        }, ph0, ph1);
+        data.re.setColumn(i, re);
+        data.im.setColumn(i, im);
+    }
+    return data;
+}
+//# sourceMappingURL=xyzPhaseCorrectionIndirectDimension.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"xyzPhaseCorrectionIndirectDimension.js","sourceRoot":"","sources":["../../src/xyz/xyzPhaseCorrectionIndirectDimension.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,eAAe,EAAE,MAAM,8BAA8B,CAAC;AAE/D,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EAAE,aAAa,EAAE,MAAM,sCAAsC,CAAC;AAErE,OAAO,EAAE,aAAa,EAAE,MAAM,sCAAsC,CAAC;AAMrE,MAAM,UAAU,mCAAmC,CACjD,IAAiB,EACjB,OAAgD;IAEhD,MAAM,EAAE,IAAI,EAAE,GAAG,OAAO,CAAC;IACzB,IAAI,IAAI,KAAK,MAAM,EAAE;QACnB,OAAO,aAAa,CAAC,IAAI,EAAE,EAAE,GAAG,OAAO,EAAE,oBAAoB,EAAE,CAAC,CAAC;KAClE;SAAM,IAAI,IAAI,KAAK,MAAM,EAAE;QAC1B,OAAO,aAAa,CAAC,IAAI,EAAE,EAAE,GAAG,OAAO,EAAE,oBAAoB,EAAE,CAAC,CAAC;KAClE;AACH,CAAC;AAED,SAAS,oBAAoB,CAC3B,IAAgC,EAChC,OAAqC;IAErC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,eAAe,CAAC;IAC1C,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,eAAe,CAAC;IAC1C,MAAM,SAAS,GAAG,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC;IAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE;QAClC,MAAM,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,mBAAmB,CACpC;YACE,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC;YACxB,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC;SACzB,EACD,GAAG,EACH,GAAG,CACJ,CAAC;QACF,IAAI,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACzB,IAAI,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;KAC1B;IACD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.7.8",
+  "version": "9.8.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -41,8 +41,8 @@
     "@types/jest": "^29.5.0",
     "cheminfo-build": "^1.2.0",
     "cheminfo-types": "^1.7.2",
-    "eslint": "^8.36.0",
-    "eslint-config-cheminfo-typescript": "^11.3.1",
+    "eslint": "^8.45.0",
+    "eslint-config-cheminfo-typescript": "^12.0.3",
     "fifo-logger": "^0.6.1",
     "jest": "^29.5.0",
     "jest-matcher-deep-close-to": "^3.0.2",
@@ -82,7 +82,7 @@
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.3.3",
     "nmredata": "^0.9.2",
-    "openchemlib-utils": "^2.4.0",
+    "openchemlib-utils": "^2.7.1",
     "spectrum-generator": "^8.0.8"
   }
 }

package/src/apodization/compose.ts

@@ -28,7 +28,7 @@ export interface ShapeOptions {
 
 export function compose(shapeOptions: ShapeOptions) {
   const { length: dataLength, shapes = [] } = shapeOptions;
-  let data = new Float64Array(dataLength).fill(1);
+  const data = new Float64Array(dataLength).fill(1);
   shapes.forEach((options) => {
     const { shape, start = 0 } = options;
     const { options: shapeOptions } = shape;

package/src/assignment/get13CAssignments.ts

@@ -13,7 +13,10 @@ import type {
   NMRSignal1DWithAtomsAndDiaIDs,
   Targets,
 } from './get1HAssignments';
-import { RestrictionByCS1D, buildAssignments } from './utils/buildAssignments';
+import {
+  RestrictionByCS1D,
+  buildAssignments,
+} from './utils/oneDimensionalAssignment/buildAssignments';
 
 function checkAtomsAndDiaIDs(
   signals: NMRSignal1D[],
@@ -26,7 +29,7 @@ function checkAtomsAndDiaIDs(
 }
 
 function checkIntegration(ranges: NMRRange[]) {
-  for (let range of ranges) {
+  for (const range of ranges) {
     if (range.integration === undefined) range.integration = 0;
   }
   return ranges as NMRRangeWithIntegration[];
@@ -65,7 +68,7 @@ export async function get13CAssignments(
   molecule: Molecule,
   options: Get13CAssignmentsOptions = {},
 ) {
-  let {
+  const {
     restrictionByCS = {},
     minScore = 1,
     maxSolutions = 10,

package/src/assignment/get1HAssignments.ts

@@ -10,7 +10,10 @@ import {
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { MakeMandatory } from '../utilities/MakeMandatory';
 
-import { buildAssignments, RestrictionByCS1D } from './utils/buildAssignments';
+import {
+  buildAssignments,
+  RestrictionByCS1D,
+} from './utils/oneDimensionalAssignment/buildAssignments';
 
 export type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<
   NMRSignal1D,
@@ -32,7 +35,7 @@ export type NMRRangeWithIntegration = MakeMandatory<NMRRange, 'integration'>;
 function checkForIntegration(
   ranges: NMRRange[],
 ): asserts ranges is NMRRangeWithIntegration[] {
-  for (let range of ranges) {
+  for (const range of ranges) {
     if (range.integration === undefined) {
       throw new Error('ranges has not integration property');
     }
@@ -67,16 +70,14 @@ export interface Get1HAssignmentsOptions {
   predictionOptions?: PredictProtonOptions;
 }
 
-export interface Targets {
-  [key: string]: NMRRangeWithIntegration;
-}
+export type Targets = Record<string, NMRRangeWithIntegration>;
 
 export async function get1HAssignments(
   ranges: NMRRange[],
   molecule: Molecule,
   options: Get1HAssignmentsOptions = {},
 ) {
-  let {
+  const {
     restrictionByCS,
     minScore = 1,
     maxSolutions = 10,

package/src/assignment/getAssignments.ts

@@ -11,10 +11,10 @@ import {
   AtomTypes,
   buildAssignments,
   RestrictionByCS,
-} from './utils/getAssignment/buildAssignments';
-import { checkIDs } from './utils/getAssignment/checkIDs';
-import { getTargetsAndCorrelations } from './utils/getAssignment/getTargetsAndCorrelations';
-import getWorkFlow from './utils/getAssignment/getWorkFlow';
+} from './utils/generalAssignment/buildAssignments';
+import { checkIDs } from './utils/generalAssignment/checkIDs';
+import { getTargetsAndCorrelations } from './utils/generalAssignment/getTargetsAndCorrelations';
+import getWorkFlow from './utils/generalAssignment/getWorkFlow';
 
 export interface SpectraData1D {
   id?: string;
@@ -43,7 +43,7 @@ export interface GetAutoAssignmentInput {
 }
 
 export interface GetAssignmentsOptions {
-  justAssign?: Array<AtomTypes[]>;
+  justAssign?: AtomTypes[][];
 
   restrictionByCS?: Partial<RestrictionByCS>;
   /**
@@ -60,7 +60,7 @@ export interface GetAssignmentsOptions {
    * number of allowed unassignment signals
    * @default 0
    */
-  nbAllowedUnAssigned?: { [key: string]: number };
+  nbAllowedUnAssigned?: Record<string, number>;
   /**
    * time limit in miliseconds to finish the assignment procedure.
    * @default 6000
@@ -92,7 +92,7 @@ export async function getAssignments(
   input: GetAutoAssignmentInput,
   options: GetAssignmentsOptions = {},
 ) {
-  let {
+  const {
     restrictionByCS = {},
     justAssign,
     minScore = 0.01,

package/src/assignment/nmrAssigment.ts

@@ -8,12 +8,12 @@ export type NMRSignal2DWithId = MakeMandatory<NMRSignal2D, 'id'>;
 
 export interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
   id: string;
-  signals: Array<NMRSignal2DWithId>;
+  signals: NMRSignal2DWithId[];
 }
 
 export interface NMRRangeWithIds extends Omit<NMRRange, 'id' | 'signals'> {
   id: string;
-  signals: Array<NMRSignal1DWithId>;
+  signals: NMRSignal1DWithId[];
 }
 
 export interface SpectraData1DWithIds extends Omit<SpectraData1D, 'ranges'> {

package/src/assignment/utils/addSolution.ts

@@ -0,0 +1,45 @@
+import {
+  Predictions1Dassignments,
+  StoreAssignments,
+} from './oneDimensionalAssignment/buildAssignments';
+
+export interface SolutionAssignment {
+  assignment: string[];
+  score: number;
+}
+
+interface AddSolutionProps {
+  score: number;
+  maxSolutions: number;
+  partial: Array<string | null>;
+  predictions: Predictions1Dassignments;
+}
+
+export function addSolution(store: StoreAssignments, props: AddSolutionProps) {
+  const { score, maxSolutions, partial, predictions } = props;
+  store.nSolutions++;
+  const solution: SolutionAssignment = {
+    assignment: JSON.parse(JSON.stringify(partial)),
+    score: score / doubleAssignmentPenalty(partial, predictions),
+  };
+
+  if (store.nSolutions >= maxSolutions) {
+    if (solution.score > store.solutions.last().score) {
+      store.solutions.pollLast();
+      store.solutions.add(solution);
+    }
+  } else {
+    store.solutions.add(solution);
+    store.nSolutions++;
+  }
+}
+
+function doubleAssignmentPenalty(
+  partial: Array<string | null>,
+  predictions: Predictions1Dassignments,
+) {
+  const nbSources = Object.keys(predictions).length;
+  const assignments = new Set(partial);
+  const nbDoubleAssignment = nbSources - assignments.size;
+  return nbDoubleAssignment > 0 ? 2 * nbDoubleAssignment : 1;
+}

package/src/assignment/utils/{getAssignment → generalAssignment}/buildAssignments.ts

@@ -12,7 +12,7 @@ import { predictCarbon } from '../../../prediction/predictCarbon';
 import { predictProton } from '../../../prediction/predictProton';
 import { MakeMandatory } from '../../../utilities/MakeMandatory';
 import { SpectraDataWithIds } from '../../nmrAssigment';
-import { StoreAssignments } from '../buildAssignments';
+import { StoreAssignments } from '../oneDimensionalAssignment/buildAssignments';
 
 import {
   createMapPossibleAssignment,
@@ -30,18 +30,14 @@ const comparator = (a: AssignmentSolution, b: AssignmentSolution) => {
 const predictor = { H: predictProton, C: predictCarbon };
 
 export type AtomTypes = 'H' | 'C';
-export type CurrentAtoms = Array<AtomTypes>;
-export interface Partial {
-  [key: string]: Array<string | null>;
-}
+export type CurrentAtoms = AtomTypes[];
+export type Partial = Record<string, Array<string | null>>;
 
-export interface DiaIDPeerPossibleAssignment {
-  [key: string]: string[];
-}
+export type DiaIDPeerPossibleAssignment = Record<string, string[]>;
 
 export interface RestrictionByCS {
   chemicalShiftRestriction: boolean;
-  tolerance: { [key: string]: number };
+  tolerance: Record<string, number>;
   useChemicalShiftScore: boolean;
 }
 
@@ -51,10 +47,10 @@ export interface BuildAssignmentInput {
   restrictionByCS: RestrictionByCS;
   timeout: number;
   minScore: number;
-  nbAllowedUnAssigned?: { [key: string]: number };
+  nbAllowedUnAssigned?: Record<string, number>;
   maxSolutions: number;
   correlations: Values;
-  assignmentOrder: Array<Array<AtomTypes>>;
+  assignmentOrder: AtomTypes[][];
   predictions: {
     H?: NMRSignal1D[];
     C?: NMRSignal1D[];
@@ -80,7 +76,7 @@ function checkNMRSignal1D(
     'atoms',
   ];
   for (const signal of signals) {
-    for (let key of keys) {
+    for (const key of keys) {
       if (!signal[key]) throw new Error(`property ${key} does not exist`);
     }
   }
@@ -93,21 +89,18 @@ export interface Prediction extends NMRSignal1DFromPrediction {
   pathLength: number[];
 }
 
-export interface Predictions {
-  [key: string]: Prediction;
-}
+export type Predictions = Record<string, Prediction>;
 
-export interface PredictionsByAtomType {
-  [key: string]: Predictions;
-}
+export type PredictionsByAtomType = Record<string, Predictions>;
 
-export interface InfoByAtomType {
-  [key: string]: {
+export type InfoByAtomType = Record<
+  string,
+  {
     nSources: number;
     currentIndex: number;
     nbAllowedUnAssigned: number;
-  };
-}
+  }
+>;
 
 export const getAllHydrogens = {
   C: (m: Molecule, i: number) => m.getAllHydrogens(i),
@@ -130,7 +123,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
     targets,
   } = props;
 
-  let lowerBoundScore = minScore;
+  const lowerBoundScore = minScore;
 
   let store: StoreAssignments = {
     solutions: new TreeSet(comparator),
@@ -141,7 +134,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
     pathLength: true,
   });
 
-  let infoByAtomType: InfoByAtomType = {};
+  const infoByAtomType: InfoByAtomType = {};
   const predictions: PredictionsByAtomType = {};
   let possibleAssignmentMap: MapPossibleAssignments = {};
   let diaIDPeerPossibleAssignment: DiaIDPeerPossibleAssignment = {};
@@ -150,7 +143,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
     for (const atomType of atomTypesToPredict) {
       const options = predictionOptions[atomType];
       const predictedSignals = inputPrediction[atomType];
-      let { joinedSignals } = predictedSignals
+      const { joinedSignals } = predictedSignals
         ? { joinedSignals: predictedSignals }
         : await predictor[atomType](molecule, options);
 
@@ -159,7 +152,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
       if (!predictions[atomType]) predictions[atomType] = {};
 
       let totalHydrogens = 0;
-      for (let prediction of joinedSignals) {
+      for (const prediction of joinedSignals) {
         const diaID = prediction.diaIDs[0];
         const index = prediction.atoms[0];
         const allHydrogens = getAllHydrogens[atomType](molecule, index);
@@ -172,7 +165,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
           pathLength: pathLengthMatrix[index] as number[],
         };
       }
-      for (let diaID in predictions[atomType]) {
+      for (const diaID in predictions[atomType]) {
         predictions[atomType][diaID].allHydrogens *= 100 / totalHydrogens;
       }
       infoByAtomType[atomType] = {
@@ -195,7 +188,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
       );
     }
 
-    let sourceOfPartials = getSourceOfPartials(
+    const sourceOfPartials = getSourceOfPartials(
       store,
       infoByAtomType,
       atomTypesToPredict,
@@ -208,7 +201,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
 
     const timeStart = Date.now();
 
-    for (let partial of sourceOfPartials) {
+    for (const partial of sourceOfPartials) {
       exploreTree(
         {
           currentAtomTypes: atomTypesToPredict,
@@ -252,7 +245,7 @@ function annotateSpectraData(input: AnnotateSpectraDataInput) {
   for (const atomType of atomTypes) {
     const targetByAtomType = targets[atomType];
     for (const targetId in targetByAtomType) {
-      let target = targetByAtomType[targetId];
+      const target = targetByAtomType[targetId];
       for (const link of target.link) {
         const signalId = link.signal.id;
         if (mapSignalId[signalId]) continue;
@@ -262,7 +255,7 @@ function annotateSpectraData(input: AnnotateSpectraDataInput) {
   }
 
   const result = [];
-  for (let solution of solutions.elements) {
+  for (const solution of solutions.elements) {
     const spectraResult = JSON.parse(
       JSON.stringify(spectra),
     ) as SpectraDataWithIds[];
@@ -279,15 +272,15 @@ function annotateSpectraData(input: AnnotateSpectraDataInput) {
         const target = targetByAtomType[targetID];
         const diaId = diaIDPeerPossibleAssignment[atomType][index];
 
-        for (let link of target.link) {
+        for (const link of target.link) {
           const { spectrumIndex, elementIndex, signalIndex } =
             mapSignalId[link.signal.id];
           const spectrum = spectraResult[spectrumIndex];
 
           if (isSpectraData1D(spectrum)) {
-            let { ranges } = spectrum;
-            let range = ranges[elementIndex];
-            let signal = range.signals[signalIndex];
+            const { ranges } = spectrum;
+            const range = ranges[elementIndex];
+            const signal = range.signals[signalIndex];
             if (!signal.diaIDs) signal.diaIDs = [];
             if (signal.diaIDs.includes(diaId)) continue;
             signal.diaIDs.push(diaId);
@@ -316,7 +309,7 @@ function getSourceOfPartials(
 ) {
   return store.nSolutions > 0
     ? store.solutions.elements.map((e) => {
-        let currentAssignment = e.assignment;
+        const currentAssignment = e.assignment;
         for (const atom of currentAtoms) {
           currentAssignment[atom] = fillPartial(infoByAtomType[atom].nSources);
         }

package/src/assignment/utils/{getAssignment → generalAssignment}/checkIDs.ts

@@ -11,8 +11,8 @@ import type {
 import { isSpectraData1D } from './isSpectraData1D';
 
 export function checkIDs(input: SpectraData[] = []): SpectraDataWithIds[] {
-  let inputClone = JSON.parse(JSON.stringify(input)) as SpectraData[];
-  let spectra: SpectraDataWithIds[] = [];
+  const inputClone = JSON.parse(JSON.stringify(input)) as SpectraData[];
+  const spectra: SpectraDataWithIds[] = [];
   for (const spectraData of inputClone) {
     if (!('info' in spectraData)) {
       throw new Error(
@@ -22,10 +22,10 @@ export function checkIDs(input: SpectraData[] = []): SpectraDataWithIds[] {
 
     const { info, id } = spectraData;
     if (isSpectraData1D(spectraData)) {
-      let ranges = addIDs(spectraData.ranges) as NMRRangeWithIds[];
+      const ranges = addIDs(spectraData.ranges) as NMRRangeWithIds[];
       spectra.push({ id, info, ranges });
     } else {
-      let data = addIDs(spectraData.zones) as NMRZoneWithIds[];
+      const data = addIDs(spectraData.zones) as NMRZoneWithIds[];
       spectra.push({ id, info, zones: data });
     }
   }
@@ -37,7 +37,7 @@ export function hasIDs(
 ): asserts data is NMRRangeWithIds[] | NMRZoneWithIds[] {
   for (const element of data) {
     if (!element.id) throw new Error('A range/zone has not an ID');
-    for (let signal of element.signals || []) {
+    for (const signal of element.signals || []) {
       if (!signal.id) throw new Error('A signal has not an ID');
     }
   }
@@ -46,7 +46,7 @@ export function hasIDs(
 export function addIDs<T extends NMRRange[] | NMRZone[]>(data: T) {
   for (const element of data) {
     if (!element.id) element.id = generateID();
-    for (let signal of element.signals || []) {
+    for (const signal of element.signals || []) {
       if (!signal.id) signal.id = generateID();
     }
   }