nmr-processing 9.7.8 → 9.8.0

package/lib/apodization/compose.js

@@ -6,7 +6,7 @@ const getFunction_1 = require("./getFunction");
 const getData_1 = require("./utils/getData");
 function compose(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/lib/apodization/compose.js.map

@@ -1 +1 @@
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+{"version":3,"file":"compose.js","sourceRoot":"","sources":["../../src/apodization/compose.ts"],"names":[],"mappings":";;;AAAA,+CAA4C;AAC5C,+CAA4C;AAE5C,6CAA0C;AAyB1C,SAAgB,OAAO,CAAC,YAA0B;IAChD,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,EAAE,EAAE,GAAG,YAAY,CAAC;IACzD,MAAM,IAAI,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClD,MAAM,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QACzB,MAAM,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;QACrC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,KAAK,CAAC;QACxC,MAAM,MAAM,GACV,QAAQ,IAAI,YAAY,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,GAAG,KAAK,CAAC;QAEtE,MAAM,UAAU,GAAG,IAAA,iBAAO,EAAC,IAAA,yBAAW,EAAC,KAAK,CAAC,EAAE,MAAM,CAAC,CAAC;QAEvD,IAAA,yBAAW,EAAC,IAAI,EAAE;YAChB,UAAU;YACV,MAAM;YACN,KAAK;YACL,MAAM,EAAE,IAAI;SACb,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IACH,OAAO,IAAI,CAAC;AACd,CAAC;AAnBD,0BAmBC"}

package/lib/assignment/get13CAssignments.d.ts

@@ -1,7 +1,7 @@
 import { Molecule } from 'openchemlib/full';
 import { NMRRange } from '..';
 import { PredictCarbonOptions } from '../prediction/predictCarbon';
-import { RestrictionByCS1D } from './utils/buildAssignments';
+import { RestrictionByCS1D } from './utils/oneDimensionalAssignment/buildAssignments';
 export interface Get13CAssignmentsOptions {
     restrictionByCS?: Partial<RestrictionByCS1D>;
     /**

package/lib/assignment/get13CAssignments.js

@@ -4,7 +4,7 @@ exports.get13CAssignments = void 0;
 const uuid_1 = require("@lukeed/uuid");
 const openchemlib_utils_1 = require("openchemlib-utils");
 const predictCarbon_1 = require("../prediction/predictCarbon");
-const buildAssignments_1 = require("./utils/buildAssignments");
+const buildAssignments_1 = require("./utils/oneDimensionalAssignment/buildAssignments");
 function checkAtomsAndDiaIDs(signals) {
     for (const signal of signals) {
         if (!signal.atoms)
@@ -16,14 +16,14 @@ function checkAtomsAndDiaIDs(signals) {
     }
 }
 function checkIntegration(ranges) {
-    for (let range of ranges) {
+    for (const range of ranges) {
         if (range.integration === undefined)
             range.integration = 0;
     }
     return ranges;
 }
 async function get13CAssignments(ranges, molecule, options = {}) {
-    let { restrictionByCS = {}, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
+    const { restrictionByCS = {}, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
     if (!molecule) {
         throw new Error('It is needed a OCL molecule instance to assign');
     }

package/lib/assignment/get13CAssignments.js.map

@@ -1 +1 @@
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+{"version":3,"file":"get13CAssignments.js","sourceRoot":"","sources":["../../src/assignment/get13CAssignments.ts"],"names":[],"mappings":";;;AAAA,uCAAgD;AAEhD,yDAAsE;AAGtE,+DAGqC;AAOrC,wFAG2D;AAE3D,SAAS,mBAAmB,CAC1B,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAC;QACpE,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;QACtE,IAAI,CAAC,MAAM,CAAC,OAAO;YAAE,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACzE;AACH,CAAC;AAED,SAAS,gBAAgB,CAAC,MAAkB;IAC1C,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,IAAI,KAAK,CAAC,WAAW,KAAK,SAAS;YAAE,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC;KAC5D;IACD,OAAO,MAAmC,CAAC;AAC7C,CAAC;AA8BM,KAAK,UAAU,iBAAiB,CACrC,MAAkB,EAClB,QAAkB,EAClB,UAAoC,EAAE;IAEtC,MAAM,EACJ,eAAe,GAAG,EAAE,EACpB,QAAQ,GAAG,CAAC,EACZ,YAAY,GAAG,EAAE,EACjB,mBAAmB,GAAG,CAAC,EACvB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,GACvB,GAAG,OAAO,CAAC;IAEZ,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,gDAAgD,CAAC,CAAC;KACnE;IAED,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAC5C,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,IAAA,6BAAa,EAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC;IAE3E,mBAAmB,CAAC,aAAa,CAAC,CAAC;IACnC,MAAM,UAAU,GAAG,gBAAgB,CAAC,MAAM,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAY,EAAE,CAAC;IAC5B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE;QAC9B,MAAM,EAAE,EAAE,GAAG,IAAA,SAAU,GAAE,EAAE,GAAG,KAAK,CAAC;QACpC,OAAO,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC;KACjD;IAED,OAAO,IAAA,mCAAgB,EAAC;QACtB,eAAe;QACf,OAAO;QACP,QAAQ;QACR,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,aAAa;QACb,yBAAyB,EAAE,KAAK;KACjC,CAAC,CAAC;AACL,CAAC;AAxCD,8CAwCC"}

package/lib/assignment/get1HAssignments.d.ts

@@ -3,7 +3,7 @@ import { NMRRange } from '..';
 import { PredictProtonOptions } from '../prediction/predictProton';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { MakeMandatory } from '../utilities/MakeMandatory';
-import { RestrictionByCS1D } from './utils/buildAssignments';
+import { RestrictionByCS1D } from './utils/oneDimensionalAssignment/buildAssignments';
 export type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<NMRSignal1D, 'atoms' | 'diaIDs' | 'nbAtoms'>;
 export type NMRRangeWithIntegration = MakeMandatory<NMRRange, 'integration'>;
 export interface Get1HAssignmentsOptions {
@@ -33,9 +33,7 @@ export interface Get1HAssignmentsOptions {
      */
     predictionOptions?: PredictProtonOptions;
 }
-export interface Targets {
-    [key: string]: NMRRangeWithIntegration;
-}
+export type Targets = Record<string, NMRRangeWithIntegration>;
 export declare function get1HAssignments(ranges: NMRRange[], molecule: Molecule, options?: Get1HAssignmentsOptions): Promise<{
     score: w;
     assignment: unknown[];

package/lib/assignment/get1HAssignments.js

@@ -4,7 +4,7 @@ exports.get1HAssignments = void 0;
 const uuid_1 = require("@lukeed/uuid");
 const openchemlib_utils_1 = require("openchemlib-utils");
 const predictProton_1 = require("../prediction/predictProton");
-const buildAssignments_1 = require("./utils/buildAssignments");
+const buildAssignments_1 = require("./utils/oneDimensionalAssignment/buildAssignments");
 function checkAtomsAndDiaIDs(signals) {
     for (const signal of signals) {
         if (!signal.atoms)
@@ -16,14 +16,14 @@ function checkAtomsAndDiaIDs(signals) {
     }
 }
 function checkForIntegration(ranges) {
-    for (let range of ranges) {
+    for (const range of ranges) {
         if (range.integration === undefined) {
             throw new Error('ranges has not integration property');
         }
     }
 }
 async function get1HAssignments(ranges, molecule, options = {}) {
-    let { restrictionByCS, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
+    const { restrictionByCS, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
     if (!molecule) {
         throw new Error('It is needed a OCL molecule instance to assign');
     }

package/lib/assignment/get1HAssignments.js.map

@@ -1 +1 @@
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+{"version":3,"file":"get1HAssignments.js","sourceRoot":"","sources":["../../src/assignment/get1HAssignments.ts"],"names":[],"mappings":";;;AAAA,uCAAgD;AAEhD,yDAAsE;AAGtE,+DAGqC;AAIrC,wFAG2D;AAO3D,SAAS,mBAAmB,CAC1B,OAAsB;IAEtB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,IAAI,CAAC,MAAM,CAAC,KAAK;YAAE,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAC;QACpE,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;QACtE,IAAI,CAAC,MAAM,CAAC,OAAO;YAAE,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAC;KACzE;AACH,CAAC;AAID,SAAS,mBAAmB,CAC1B,MAAkB;IAElB,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,IAAI,KAAK,CAAC,WAAW,KAAK,SAAS,EAAE;YACnC,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAC;SACxD;KACF;AACH,CAAC;AAgCM,KAAK,UAAU,gBAAgB,CACpC,MAAkB,EAClB,QAAkB,EAClB,UAAmC,EAAE;IAErC,MAAM,EACJ,eAAe,EACf,QAAQ,GAAG,CAAC,EACZ,YAAY,GAAG,EAAE,EACjB,mBAAmB,GAAG,CAAC,EACvB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,GACvB,GAAG,OAAO,CAAC;IAEZ,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,gDAAgD,CAAC,CAAC;KACnE;IAED,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,IAAA,6BAAa,EAAC,QAAQ,EAAE,iBAAiB,CAAC,CAAC;IAE3E,mBAAmB,CAAC,MAAM,CAAC,CAAC;IAC5B,mBAAmB,CAAC,aAAa,CAAC,CAAC;IAEnC,MAAM,OAAO,GAAY,EAAE,CAAC;IAC5B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE;QAC1B,MAAM,EAAE,EAAE,GAAG,IAAA,SAAU,GAAE,EAAE,GAAG,KAAK,CAAC;QACpC,OAAO,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC;KACjD;IAED,OAAO,IAAA,mCAAgB,EAAC;QACtB,eAAe;QACf,OAAO;QACP,QAAQ;QACR,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,aAAa;QACb,yBAAyB,EAAE,IAAI;KAChC,CAAC,CAAC;AACL,CAAC;AA1CD,4CA0CC"}

package/lib/assignment/getAssignments.d.ts

@@ -4,7 +4,7 @@ import type { PredictCarbonOptions } from '../prediction/predictCarbon';
 import type { PredictProtonOptions } from '../prediction/predictProton';
 import { NMRRange } from '../xy/NMRRange';
 import { NMRZone } from '../xyz/NMRZone';
-import { AtomTypes, RestrictionByCS } from './utils/getAssignment/buildAssignments';
+import { AtomTypes, RestrictionByCS } from './utils/generalAssignment/buildAssignments';
 export interface SpectraData1D {
     id?: string;
     ranges: NMRRange[];
@@ -28,7 +28,7 @@ export interface GetAutoAssignmentInput {
     molecule: Molecule;
 }
 export interface GetAssignmentsOptions {
-    justAssign?: Array<AtomTypes[]>;
+    justAssign?: AtomTypes[][];
     restrictionByCS?: Partial<RestrictionByCS>;
     /**
      * min score to accept an assignment
@@ -44,9 +44,7 @@ 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

package/lib/assignment/getAssignments.js

@@ -5,12 +5,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getAssignments = void 0;
 const openchemlib_utils_1 = require("openchemlib-utils");
-const buildAssignments_1 = require("./utils/getAssignment/buildAssignments");
-const checkIDs_1 = require("./utils/getAssignment/checkIDs");
-const getTargetsAndCorrelations_1 = require("./utils/getAssignment/getTargetsAndCorrelations");
-const getWorkFlow_1 = __importDefault(require("./utils/getAssignment/getWorkFlow"));
+const buildAssignments_1 = require("./utils/generalAssignment/buildAssignments");
+const checkIDs_1 = require("./utils/generalAssignment/checkIDs");
+const getTargetsAndCorrelations_1 = require("./utils/generalAssignment/getTargetsAndCorrelations");
+const getWorkFlow_1 = __importDefault(require("./utils/generalAssignment/getWorkFlow"));
 async function getAssignments(input, options = {}) {
-    let { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
+    const { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
     const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
     const molecule = input.molecule;
     if (!molecule)

package/lib/assignment/getAssignments.js.map

@@ -1 +1 @@
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package/lib/assignment/nmrAssigment.d.ts

@@ -5,11 +5,11 @@ export type NMRSignal1DWithId = MakeMandatory<NMRSignal1D, 'id'>;
 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'> {
     ranges: NMRRangeWithIds[];

package/lib/assignment/utils/addSolution.d.ts

@@ -0,0 +1,13 @@
+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 declare function addSolution(store: StoreAssignments, props: AddSolutionProps): void;
+export {};

package/lib/assignment/utils/addSolution.js

@@ -0,0 +1,29 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.addSolution = void 0;
+function addSolution(store, props) {
+    const { score, maxSolutions, partial, predictions } = props;
+    store.nSolutions++;
+    const solution = {
+        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++;
+    }
+}
+exports.addSolution = addSolution;
+function doubleAssignmentPenalty(partial, predictions) {
+    const nbSources = Object.keys(predictions).length;
+    const assignments = new Set(partial);
+    const nbDoubleAssignment = nbSources - assignments.size;
+    return nbDoubleAssignment > 0 ? 2 * nbDoubleAssignment : 1;
+}
+//# sourceMappingURL=addSolution.js.map

package/lib/assignment/utils/addSolution.js.map

@@ -0,0 +1 @@
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package/lib/assignment/utils/{getAssignment → generalAssignment}/buildAssignments.d.ts

@@ -5,18 +5,12 @@ import { MakeMandatory } from '../../../utilities/MakeMandatory';
 import { SpectraDataWithIds } from '../../nmrAssigment';
 import { TargetsByAtomType } from './getTargetsAndCorrelations';
 export type AtomTypes = 'H' | 'C';
-export type CurrentAtoms = Array<AtomTypes>;
-export interface Partial {
-    [key: string]: Array<string | null>;
-}
-export interface DiaIDPeerPossibleAssignment {
-    [key: string]: string[];
-}
+export type CurrentAtoms = AtomTypes[];
+export type Partial = Record<string, Array<string | null>>;
+export type DiaIDPeerPossibleAssignment = Record<string, string[]>;
 export interface RestrictionByCS {
     chemicalShiftRestriction: boolean;
-    tolerance: {
-        [key: string]: number;
-    };
+    tolerance: Record<string, number>;
     useChemicalShiftScore: boolean;
 }
 export interface BuildAssignmentInput {
@@ -25,12 +19,10 @@ 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[];
@@ -48,19 +40,13 @@ export interface Prediction extends NMRSignal1DFromPrediction {
     protonsCount: number;
     pathLength: number[];
 }
-export interface Predictions {
-    [key: string]: Prediction;
-}
-export interface PredictionsByAtomType {
-    [key: string]: Predictions;
-}
-export interface InfoByAtomType {
-    [key: string]: {
-        nSources: number;
-        currentIndex: number;
-        nbAllowedUnAssigned: number;
-    };
-}
+export type Predictions = Record<string, Prediction>;
+export type PredictionsByAtomType = Record<string, Predictions>;
+export type InfoByAtomType = Record<string, {
+    nSources: number;
+    currentIndex: number;
+    nbAllowedUnAssigned: number;
+}>;
 export declare const getAllHydrogens: {
     C: (m: Molecule, i: number) => number;
     H: () => number;

package/lib/assignment/utils/{getAssignment → generalAssignment}/buildAssignments.js

@@ -23,7 +23,7 @@ function checkNMRSignal1D(signals) {
         '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`);
         }
@@ -35,7 +35,7 @@ exports.getAllHydrogens = {
 };
 async function buildAssignments(props) {
     const { spectra, molecule, restrictionByCS, timeout, minScore, nbAllowedUnAssigned = {}, maxSolutions, correlations, assignmentOrder, predictionOptions, predictions: inputPrediction = {}, targets, } = props;
-    let lowerBoundScore = minScore;
+    const lowerBoundScore = minScore;
     let store = {
         solutions: new ml_tree_set_1.default(comparator),
         nSolutions: 0,
@@ -43,7 +43,7 @@ async function buildAssignments(props) {
     const pathLengthMatrix = (0, openchemlib_utils_1.getConnectivityMatrix)(molecule, {
         pathLength: true,
     });
-    let infoByAtomType = {};
+    const infoByAtomType = {};
     const predictions = {};
     let possibleAssignmentMap = {};
     let diaIDPeerPossibleAssignment = {};
@@ -51,14 +51,14 @@ async function buildAssignments(props) {
         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);
             checkNMRSignal1D(joinedSignals);
             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 = exports.getAllHydrogens[atomType](molecule, index);
@@ -71,7 +71,7 @@ async function buildAssignments(props) {
                     pathLength: pathLengthMatrix[index],
                 };
             }
-            for (let diaID in predictions[atomType]) {
+            for (const diaID in predictions[atomType]) {
                 predictions[atomType][diaID].allHydrogens *= 100 / totalHydrogens;
             }
             infoByAtomType[atomType] = {
@@ -89,13 +89,13 @@ async function buildAssignments(props) {
         for (const atomType in possibleAssignmentMap) {
             diaIDPeerPossibleAssignment[atomType] = Object.keys(possibleAssignmentMap[atomType]);
         }
-        let sourceOfPartials = getSourceOfPartials(store, infoByAtomType, atomTypesToPredict);
+        const sourceOfPartials = getSourceOfPartials(store, infoByAtomType, atomTypesToPredict);
         store = {
             solutions: new ml_tree_set_1.default(comparator),
             nSolutions: 0,
         };
         const timeStart = Date.now();
-        for (let partial of sourceOfPartials) {
+        for (const partial of sourceOfPartials) {
             (0, exploreTree_1.exploreTree)({
                 currentAtomTypes: atomTypesToPredict,
                 restrictionByCS,
@@ -127,7 +127,7 @@ function annotateSpectraData(input) {
     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])
@@ -137,7 +137,7 @@ function annotateSpectraData(input) {
         }
     }
     const result = [];
-    for (let solution of solutions.elements) {
+    for (const solution of solutions.elements) {
         const spectraResult = JSON.parse(JSON.stringify(spectra));
         const { assignment, score } = solution;
         const atomTypes = Object.keys(assignment);
@@ -150,13 +150,13 @@ function annotateSpectraData(input) {
                     continue;
                 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 ((0, isSpectraData1D_1.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))
@@ -185,7 +185,7 @@ function annotateSpectraData(input) {
 function getSourceOfPartials(store, infoByAtomType, currentAtoms) {
     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/lib/assignment/utils/generalAssignment/buildAssignments.js.map

@@ -0,0 +1 @@
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package/lib/assignment/utils/{getAssignment → generalAssignment}/checkIDs.js

@@ -4,19 +4,19 @@ exports.addIDs = exports.hasIDs = exports.checkIDs = void 0;
 const uuid_1 = require("@lukeed/uuid");
 const isSpectraData1D_1 = require("./isSpectraData1D");
 function checkIDs(input = []) {
-    let inputClone = JSON.parse(JSON.stringify(input));
-    let spectra = [];
+    const inputClone = JSON.parse(JSON.stringify(input));
+    const spectra = [];
     for (const spectraData of inputClone) {
         if (!('info' in spectraData)) {
             throw new Error('each spectrum should contain info properties with nucleus information');
         }
         const { info, id } = spectraData;
         if ((0, isSpectraData1D_1.isSpectraData1D)(spectraData)) {
-            let ranges = addIDs(spectraData.ranges);
+            const ranges = addIDs(spectraData.ranges);
             spectra.push({ id, info, ranges });
         }
         else {
-            let data = addIDs(spectraData.zones);
+            const data = addIDs(spectraData.zones);
             spectra.push({ id, info, zones: data });
         }
     }
@@ -27,7 +27,7 @@ function hasIDs(data) {
     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');
         }
@@ -38,7 +38,7 @@ function addIDs(data) {
     for (const element of data) {
         if (!element.id)
             element.id = (0, uuid_1.v4)();
-        for (let signal of element.signals || []) {
+        for (const signal of element.signals || []) {
             if (!signal.id)
                 signal.id = (0, uuid_1.v4)();
         }

package/lib/assignment/utils/generalAssignment/checkIDs.js.map

@@ -0,0 +1 @@
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package/lib/assignment/utils/{getAssignment → generalAssignment}/createMapPossibleAssignment.d.ts

@@ -1,12 +1,8 @@
-import { PossibleAssignmentMap } from '../createMapPossibleAssignments';
+import { PossibleAssignmentMap } from '../oneDimensionalAssignment/createMapPossibleAssignments';
 import { PredictionsByAtomType, RestrictionByCS } from './buildAssignments';
 import { TargetsByAtomType } from './getTargetsAndCorrelations';
-export interface PossibleAssignments {
-    [key: string]: string[];
-}
-export interface MapPossibleAssignments {
-    [key: string]: PossibleAssignmentMap;
-}
+export type PossibleAssignments = Record<string, string[]>;
+export type MapPossibleAssignments = Record<string, PossibleAssignmentMap>;
 export interface CreateMapPossibleAssignmentOptions {
     restrictionByCS: RestrictionByCS;
     predictions: PredictionsByAtomType;

package/lib/assignment/utils/{getAssignment → generalAssignment}/createMapPossibleAssignment.js

@@ -7,17 +7,17 @@ function createMapPossibleAssignment(expandMap, props) {
     const { tolerance: toleranceCS, chemicalShiftRestriction } = restrictionByCS;
     const atomTypes = Object.keys(predictions);
     for (const atomType of atomTypes) {
-        let errorAbs = toleranceCS[atomType];
-        let predictionByAtomType = predictions[atomType];
-        let targetByAtomType = targets[atomType];
+        const errorAbs = toleranceCS[atomType];
+        const predictionByAtomType = predictions[atomType];
+        const targetByAtomType = targets[atomType];
         if (!expandMap[atomType])
             expandMap[atomType] = {};
         for (const diaID in predictionByAtomType) {
-            let prediction = predictionByAtomType[diaID];
+            const prediction = predictionByAtomType[diaID];
             expandMap[atomType][diaID] = [];
             if (targetByAtomType) {
                 for (const targetID in targetByAtomType) {
-                    let target = targetByAtomType[targetID];
+                    const target = targetByAtomType[targetID];
                     const { nbAtoms, protonsCount: protonsCountFromPrediction } = prediction;
                     const { integration, protonsCount } = target;
                     const couldBeAssigned = !integration
@@ -34,11 +34,11 @@ function createMapPossibleAssignment(expandMap, props) {
                             expandMap[atomType][diaID].push(targetID);
                         }
                         else {
-                            let targetDelta = (0, nmr_correlation_1.getCorrelationDelta)(target);
+                            const targetDelta = (0, nmr_correlation_1.getCorrelationDelta)(target);
                             if (targetDelta === undefined) {
                                 throw new Error(`Correlation has not delta`);
                             }
-                            let distAfterLimit = Math.abs(prediction.delta - targetDelta - errorAbs);
+                            const distAfterLimit = Math.abs(prediction.delta - targetDelta - errorAbs);
                             if (distAfterLimit < 4 * errorAbs) {
                                 expandMap[atomType][diaID].push(targetID);
                             }

package/lib/assignment/utils/generalAssignment/createMapPossibleAssignment.js.map

@@ -0,0 +1 @@
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package/lib/assignment/utils/{getAssignment → generalAssignment}/exploreTree.d.ts

@@ -1,4 +1,4 @@
-import { StoreAssignments } from '../buildAssignments';
+import { StoreAssignments } from '../oneDimensionalAssignment/buildAssignments';
 import { RestrictionByCS, DiaIDPeerPossibleAssignment, InfoByAtomType, Partial, CurrentAtoms, PredictionsByAtomType } from './buildAssignments';
 import { MapPossibleAssignments } from './createMapPossibleAssignment';
 import { CorrelationWithIntegration, TargetsByAtomType } from './getTargetsAndCorrelations';

package/lib/assignment/utils/{getAssignment → generalAssignment}/exploreTree.js

@@ -16,9 +16,9 @@ function exploreTree(props, infoByAtomTypes, partial, store) {
         }
         const diaID = diaIDPeerPossibleAssignment[atomType][currentIndex];
         const possibleAssignments = possibleAssignmentMap[atomType][diaID];
-        for (let targetID of possibleAssignments) {
+        for (const targetID of possibleAssignments) {
             partial[atomType][currentIndex] = targetID;
-            let score = (0, partialScore_1.partialScore)(partial, {
+            const score = (0, partialScore_1.partialScore)(partial, {
                 diaIDPeerPossibleAssignment,
                 infoByAtomTypes,
                 restrictionByCS,
@@ -55,11 +55,10 @@ function exploreTree(props, infoByAtomTypes, partial, store) {
 }
 exports.exploreTree = exploreTree;
 function addSolution(store, props) {
-    let { score, maxSolutions, partial, predictions } = props;
-    score /= doubleAssignmentPenalty(partial, predictions);
-    let solution = {
+    const { score, maxSolutions, partial, predictions } = props;
+    const solution = {
         assignment: JSON.parse(JSON.stringify(partial)),
-        score,
+        score: score / doubleAssignmentPenalty(partial, predictions),
     };
     if (store.nSolutions >= maxSolutions) {
         if (solution.score > store.solutions.last().score) {
@@ -84,7 +83,7 @@ function doubleAssignmentPenalty(partial, predictions) {
     let nbDoubleAssignment = 0;
     for (const atomType in predictions) {
         const nbSources = Object.keys(predictions[atomType]).length;
-        let assignments = new Set(partial[atomType]);
+        const assignments = new Set(partial[atomType]);
         nbDoubleAssignment += nbSources - assignments.size;
     }
     return nbDoubleAssignment > 0 ? 2 * nbDoubleAssignment : 1;

package/lib/assignment/utils/generalAssignment/exploreTree.js.map

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