nmr-processing 7.1.0 → 7.4.0

package/lib/assignment/utils/getAssignment/partialScore.js

@@ -0,0 +1,221 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.partialScore = void 0;
+const nmr_correlation_1 = require("nmr-correlation");
+const groupCarbonTargetByIntegrationZone_1 = __importDefault(require("./groupCarbonTargetByIntegrationZone"));
+function partialScore(partial, props) {
+    const { diaIDPeerPossibleAssignment, infoByAtomTypes, restrictionByCS, predictions, targets, correlations, } = props;
+    const { tolerance: toleranceCS, useChemicalShiftScore } = restrictionByCS;
+    let totalStarts = 0;
+    let totalPartial = 0;
+    let partialInverse = {};
+    let activeDomainOnPrediction = {};
+    const atomTypes = Object.keys(partial);
+    for (const atomType of atomTypes) {
+        let countStars = 0;
+        const { nbAllowedUnAssigned } = infoByAtomTypes[atomType];
+        const currentPartialInverse = {};
+        const partialAssignment = partial[atomType] || [];
+        partialInverse[atomType] = currentPartialInverse;
+        activeDomainOnPrediction[atomType] = [];
+        totalPartial += partialAssignment.length;
+        for (let i = 0; i < partialAssignment.length; i++) {
+            const targetID = partialAssignment[i];
+            if (targetID && targetID !== '*') {
+                activeDomainOnPrediction[atomType].push(i);
+                if (!currentPartialInverse[targetID]) {
+                    currentPartialInverse[targetID] = [];
+                }
+                currentPartialInverse[targetID].push(diaIDPeerPossibleAssignment[atomType][i]);
+            }
+            if (targetID === '*')
+                countStars++;
+        }
+        if (countStars > nbAllowedUnAssigned)
+            return 0;
+        totalStarts += countStars;
+    }
+    const activeDomainOnTarget = {};
+    for (const atomType in partialInverse) {
+        activeDomainOnTarget[atomType] = Object.keys(partialInverse[atomType]);
+    }
+    const valuesActiveDomainOnTarget = Object.values(activeDomainOnTarget);
+    if (valuesActiveDomainOnTarget.reduce((sum, e) => (e.length === 0 ? sum + 1 : sum), 0) === valuesActiveDomainOnTarget.length) {
+        return 0;
+    }
+    const getPredictionByDiaID = getPrediction.bind({}, predictions);
+    // check the integration
+    const targetByIntegral = [];
+    for (const atomType in partial) {
+        if (atomType === 'C' && activeDomainOnTarget[atomType].length > 0) {
+            targetByIntegral.push(...(0, groupCarbonTargetByIntegrationZone_1.default)(activeDomainOnTarget[atomType], targets[atomType], correlations));
+        }
+        else {
+            for (let targetID of activeDomainOnTarget[atomType]) {
+                targetByIntegral.push({
+                    atomType,
+                    targetIDs: [targetID],
+                    integration: targets.H[targetID].integration,
+                });
+            }
+        }
+    }
+    for (const group of targetByIntegral) {
+        const { integration, atomType } = group;
+        if (integration === undefined || isNaN(integration))
+            continue;
+        let total = 0;
+        for (let targetID of group.targetIDs) {
+            let targetToSource = partialInverse[atomType][targetID];
+            for (const diaID of targetToSource) {
+                const { prediction, atomType: atomOfPrediction } = getPredictionByDiaID(diaID);
+                if (atomType === atomOfPrediction)
+                    total += prediction.allHydrogens;
+            }
+        }
+        if (total - integration >= 0.5) {
+            return 0;
+        }
+    }
+    //chemical shift score
+    let count = 1;
+    let chemicalShiftScore = 1;
+    if (useChemicalShiftScore) {
+        chemicalShiftScore = 0;
+        count = 0;
+        for (const atomType of Object.keys(partial)) {
+            const partialPeerAtomType = partial[atomType];
+            const targetsPeerAtomType = targets[atomType];
+            for (let index = 0; index < partialPeerAtomType.length; index++) {
+                const targetID = partialPeerAtomType[index];
+                if (targetID && targetID !== '*') {
+                    count++;
+                    let diaID = diaIDPeerPossibleAssignment[atomType][index];
+                    let source = predictions[atomType][diaID];
+                    let target = targetsPeerAtomType[targetID];
+                    let error = toleranceCS[atomType];
+                    // if (source.error) {
+                    //   error = Math.max(source.error, toleranceCS);
+                    // }
+                    if (typeof source.delta === 'undefined') {
+                        // Chemical shift is not a restriction
+                        chemicalShiftScore += 1;
+                    }
+                    else {
+                        const targetDelta = (0, nmr_correlation_1.getCorrelationDelta)(target);
+                        if (targetDelta === undefined) {
+                            throw new Error('correlation has not delta');
+                        }
+                        let diff = Math.abs(source.delta - targetDelta);
+                        if (diff < error) {
+                            //@TODO: check for a better discriminant
+                            chemicalShiftScore += 1;
+                        }
+                        else {
+                            diff = Math.abs(diff - error);
+                            chemicalShiftScore += (-0.25 / error) * diff + 1;
+                        }
+                    }
+                }
+            }
+        }
+        if (count > 0) {
+            chemicalShiftScore /= count;
+        }
+    }
+    let scoreOn2D = 0;
+    if (howManyActived(activeDomainOnTarget) > 1) {
+        let andConstrains = {};
+        let activeDomain = [];
+        for (const atomType of Object.keys(activeDomainOnPrediction)) {
+            activeDomain = activeDomain.concat(activeDomainOnPrediction[atomType].map((e) => ({ index: e, atomType })));
+        }
+        for (let i = 0; i < activeDomain.length; i++) {
+            const { atomType: atomTypeI, index: indexI } = activeDomain[i];
+            const predictionI = predictions[atomTypeI][diaIDPeerPossibleAssignment[atomTypeI][indexI]];
+            for (let j = i + 1; j < activeDomain.length; j++) {
+                const { atomType: atomTypeJ, index: indexJ } = activeDomain[j];
+                const predictionJ = predictions[atomTypeJ][diaIDPeerPossibleAssignment[atomTypeJ][indexJ]];
+                let pathLength = predictionI.pathLength[predictionJ.diaIDIndex];
+                let isPossible = pathLength < 5;
+                let partialI = partial[atomTypeI][indexI];
+                let partialJ = partial[atomTypeJ][indexJ];
+                if (!partialI || !partialJ)
+                    continue;
+                let keyOnTargertMap = partialI > partialJ
+                    ? `${partialJ} ${partialI}`
+                    : `${partialI} ${partialJ}`;
+                let areLinked = checkLinking({
+                    from: {
+                        targetID: partialI,
+                        atomType: atomTypeI,
+                    },
+                    to: {
+                        targetID: partialJ,
+                        atomType: atomTypeJ,
+                    },
+                }, targets);
+                let partialScore2D = isPossible
+                    ? areLinked
+                        ? 1
+                        : 0
+                    : !areLinked
+                        ? 1
+                        : 0;
+                andConstrains[keyOnTargertMap] = andConstrains[keyOnTargertMap]
+                    ? Math.max(andConstrains[keyOnTargertMap], partialScore2D)
+                    : partialScore2D;
+            }
+        }
+        let sumAnd = 0;
+        for (let key in andConstrains) {
+            sumAnd += andConstrains[key];
+        }
+        scoreOn2D =
+            sumAnd / ((activeDomain.length * (activeDomain.length - 1)) / 2);
+    }
+    const penaltyByStarts = totalStarts / totalPartial;
+    if (chemicalShiftScore === 0)
+        return scoreOn2D - penaltyByStarts;
+    if (scoreOn2D === 0)
+        return chemicalShiftScore - penaltyByStarts;
+    return (chemicalShiftScore + scoreOn2D) / 2 - penaltyByStarts;
+}
+exports.partialScore = partialScore;
+function checkLinking(partials, correlations) {
+    const { from, to } = partials;
+    if (from.targetID === to.targetID)
+        return true;
+    let correlationI = correlations[from.atomType][from.targetID];
+    let correlationJ = correlations[to.atomType][to.targetID];
+    for (const linkJ of correlationJ.link) {
+        for (const link of correlationI.link) {
+            if (link.signal.id === linkJ.signal.id)
+                return true;
+        }
+    }
+    return false;
+}
+function getPrediction(predictions, diaID) {
+    const atomTypes = Object.keys(predictions);
+    for (const atomType of atomTypes) {
+        const predictionByAtomType = predictions[atomType];
+        if (!predictionByAtomType)
+            throw new Error(`prediction by ${atomType}`);
+        if (predictionByAtomType[diaID]) {
+            return { atomType, prediction: predictionByAtomType[diaID] };
+        }
+    }
+    throw new Error(`There is not prediction for ${diaID}`);
+}
+function howManyActived(actived) {
+    let sum = 0;
+    for (const atom in actived) {
+        sum += actived[atom].length;
+    }
+    return sum;
+}
+//# sourceMappingURL=partialScore.js.map

package/lib/assignment/utils/getAssignment/partialScore.js.map

@@ -0,0 +1 @@
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package/lib/assignment/utils/getAssignment/searchIndices.d.ts

@@ -0,0 +1,6 @@
+import { SpectraData } from '../../getAssignments';
+export declare function searchIndices(signalId: string, spectra: SpectraData[]): {
+    spectrumIndex: number;
+    signalIndex: number;
+    elementIndex: number;
+};

package/lib/assignment/utils/getAssignment/searchIndices.js

@@ -0,0 +1,21 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.searchIndices = void 0;
+const isSpectraData1D_1 = require("./isSpectraData1D");
+function searchIndices(signalId, spectra) {
+    for (let spectrumIndex = 0; spectrumIndex < spectra.length; spectrumIndex++) {
+        const spectrum = spectra[spectrumIndex];
+        const data = (0, isSpectraData1D_1.isSpectraData1D)(spectrum) ? spectrum.ranges : spectrum.zones;
+        for (let elementIndex = 0; elementIndex < data.length; elementIndex++) {
+            const signals = data[elementIndex].signals || [];
+            for (let signalIndex = 0; signalIndex < signals.length; signalIndex++) {
+                if (signalId === signals[signalIndex].id) {
+                    return { spectrumIndex, signalIndex, elementIndex };
+                }
+            }
+        }
+    }
+    throw new Error(`There is not a signal with ${signalId} ID`);
+}
+exports.searchIndices = searchIndices;
+//# sourceMappingURL=searchIndices.js.map

package/lib/assignment/utils/getAssignment/searchIndices.js.map

@@ -0,0 +1 @@
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package/lib/assignment/utils/partialScore.d.ts

@@ -1,7 +1,7 @@
 import { Targets } from '../get1HAssignments';
-import type { Predictions1Dassignments, RestrictionByCS } from './buildAssignments';
+import type { Predictions1Dassignments, RestrictionByCS1D } from './buildAssignments';
 interface PartialScoreOptions {
-    restrictionByCS: RestrictionByCS;
+    restrictionByCS: RestrictionByCS1D;
     /**
      * number of allowed unassignment signals
      * @default 0

package/lib/constants/gyromagneticRatio.d.ts

@@ -1,20 +1,6 @@
-export declare const gyromagneticRatio: {
-    '1H': number;
-    '2H': number;
-    '3H': number;
-    '3He': number;
-    '7Li': number;
-    '13C': number;
-    '14N': number;
-    '15N': number;
-    '17O': number;
-    '19F': number;
-    '23Na': number;
-    '27Al': number;
-    '29Si': number;
-    '31P': number;
-    '57Fe': number;
-    '63Cu': number;
-    '67Zn': number;
-    '129Xe': number;
+export declare type Nuclei = '1H' | '2H' | '3H' | '3He' | '7Li' | '13C' | '14N' | '15N' | '17O' | '19F' | '23Na' | '27Al' | '29Si' | '31P' | '57Fe' | '63Cu' | '67Zn' | '129Xe';
+declare type GyromagneticRatio = {
+    [key in Nuclei]: number;
 };
+export declare const GYROMAGNETIC_RATIO: GyromagneticRatio;
+export {};

package/lib/constants/gyromagneticRatio.js

@@ -2,9 +2,8 @@
 // sources:
 // https://en.wikipedia.org/wiki/Gyromagnetic_ratio
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.gyromagneticRatio = void 0;
-// TODO: #13 can we have a better source and more digits ? @jwist
-exports.gyromagneticRatio = {
+exports.GYROMAGNETIC_RATIO = void 0;
+exports.GYROMAGNETIC_RATIO = {
     '1H': 267.52218744e6,
     '2H': 41.065e6,
     '3H': 285.3508e6,

package/lib/constants/gyromagneticRatio.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":";AAAA,WAAW;AACX,mDAAmD;;;AA4BtC,QAAA,kBAAkB,GAAsB;IACnD,IAAI,EAAE,cAAc;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,CAAC,SAAS;IACjB,KAAK,EAAE,SAAS;IAChB,KAAK,EAAE,UAAU;IACjB,KAAK,EAAE,QAAQ;IACf,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,CAAC,OAAO;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,OAAO;IACf,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,OAAO,EAAE,CAAC,QAAQ;CACnB,CAAC"}

package/lib/index.d.ts

@@ -11,6 +11,7 @@ export * from './prediction/predictAll';
 export * from './prediction/predictAllSpectra';
 export * from './assignment/get1HAssignments';
 export * from './assignment/get13CAssignments';
+export * from './assignment/getAssignments';
 export * from './ranges/rangesToACS';
 export * from './ranges/rangesToXY';
 export * from './signals/signalsToRanges';
@@ -18,6 +19,7 @@ export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
+export * from './utilities/getFrequency';
 export * from './xy/xyAutoPeaksPicking';
 export * from './xy/xyAutoRangesPicking';
 export * from './xyz/xyzAutoZonesPicking';

package/lib/index.js

@@ -27,6 +27,7 @@ __exportStar(require("./prediction/predictAll"), exports);
 __exportStar(require("./prediction/predictAllSpectra"), exports);
 __exportStar(require("./assignment/get1HAssignments"), exports);
 __exportStar(require("./assignment/get13CAssignments"), exports);
+__exportStar(require("./assignment/getAssignments"), exports);
 __exportStar(require("./ranges/rangesToACS"), exports);
 __exportStar(require("./ranges/rangesToXY"), exports);
 __exportStar(require("./signals/signalsToRanges"), exports);
@@ -34,6 +35,7 @@ __exportStar(require("./signals/signalsToXY"), exports);
 __exportStar(require("./signals/signals2DToZ"), exports);
 __exportStar(require("./utilities/resurrect"), exports);
 __exportStar(require("./utilities/rangeFromSignal"), exports);
+__exportStar(require("./utilities/getFrequency"), exports);
 __exportStar(require("./xy/xyAutoPeaksPicking"), exports);
 __exportStar(require("./xy/xyAutoRangesPicking"), exports);
 __exportStar(require("./xyz/xyzAutoZonesPicking"), exports);

package/lib/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,gEAA8C;AAC9C,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAE9C,6DAA2C;AAC3C,6DAA2C;AAC3C,2DAAyC;AACzC,2DAAyC;AACzC,2DAAyC;AACzC,0DAAwC;AACxC,iEAA+C;AAE/C,gEAA8C;AAC9C,iEAA+C;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C"}

package/lib/peaks/peaksToRanges.js

@@ -146,6 +146,7 @@ function peaksToRanges(data, peakList, options = {}) {
             delta: signal.delta,
             kind: signal.kind || 'signal',
             multiplicity: signal.multiplicity,
+            integration: signal.integralData.value,
         };
         if (keepPeaks) {
             signalResult.peaks = signal.peaks.map((peak) => {

package/lib/peaks/peaksToRanges.js.map

@@ -1 +1 @@
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package/lib/prediction/utils/predict2D.d.ts

@@ -70,8 +70,6 @@ export interface PredictOptions {
 }
 export interface Predictions {
     [key: string]: Prediction1D | undefined;
-    H?: Prediction1D;
-    C?: Prediction1D;
 }
 export declare function predict2D(molecule: Molecule, options?: Predict2DOptions): Promise<{
     molfile: string;

package/lib/prediction/utils/predict2D.js

@@ -16,7 +16,7 @@ async function predict2D(molecule, options = {}) {
     let { from, to, minLength = 0, maxLength, predictOptions = {}, predictions, predictor, joinDistance = { H: 0.05, C: 0.5 }, includeDiagonal = false, } = options;
     molecule.addImplicitHydrogens();
     let diaIDs = (0, openchemlib_utils_1.getGroupedDiastereotopicAtomIDs)(molecule);
-    const paths = (0, openchemlib_utils_1.getPathsInfo)(molecule, {
+    const pathsInfo = (0, openchemlib_utils_1.getPathsInfo)(molecule, {
         fromLabel: from,
         toLabel: to,
         minLength,
@@ -26,7 +26,7 @@ async function predict2D(molecule, options = {}) {
     for (let diaID of diaIDs) {
         diaIDswithAtomInfo.push({
             ...diaID,
-            atomInfo: JSON.parse(JSON.stringify(paths[diaID.atoms[0]])),
+            pathInfo: JSON.parse(JSON.stringify(pathsInfo[diaID.atoms[0]])),
         });
     }
     const xPrediction = await (0, getPredictions_1.getPredictions)(from, molecule, predictOptions, predictor, predictions);
@@ -53,21 +53,21 @@ async function predict2D(molecule, options = {}) {
     }
     let group = {};
     for (const diaID of diaIDswithAtomInfo) {
-        const atom = diaID.atomInfo;
-        if (atom.paths.length < 1)
+        const pathInfo = diaID.pathInfo;
+        if (pathInfo.paths.length < 1)
             continue;
-        if (!signalsByDiaID.x[atom.oclID])
+        if (!signalsByDiaID.x[pathInfo.oclID])
             continue;
-        const currentPaths = atom.paths;
+        const currentPaths = pathInfo.paths;
         for (const path of currentPaths) {
-            if (!signalsByDiaID.y[paths[path.to].oclID])
+            if (!signalsByDiaID.y[pathsInfo[path.to].oclID])
                 continue;
             let fromToDiaID = {
-                x: atom,
-                y: paths[path.to],
+                x: pathInfo,
+                y: pathsInfo[path.to],
             };
             const key = `${fromToDiaID.x.oclID}-${fromToDiaID.y.oclID}`;
-            if (key === `${atom.oclID}-${atom.oclID}` || group[key]) {
+            if (key === `${pathInfo.oclID}-${pathInfo.oclID}` || group[key]) {
                 continue;
             }
             let peak = { z: 100 };
@@ -83,8 +83,9 @@ async function predict2D(molecule, options = {}) {
             group[key] = signal;
         }
     }
-    if (includeDiagonal)
-        addSelftCorrelation(group, { paths, signalsByDiaID });
+    if (includeDiagonal) {
+        addSelftCorrelation(group, { paths: pathsInfo, signalsByDiaID });
+    }
     // clusterize signals by distance
     const joinedSignals = Object.values(group);
     const zones = createZones(joinedSignals, { joinDistance, from, to });

package/lib/prediction/utils/predict2D.js.map

@@ -1 +1 @@
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+{"version":3,"file":"predict2D.js","sourceRoot":"","sources":["../../../src/prediction/utils/predict2D.ts"],"names":[],"mappings":";;;AAAA,yCAA2C;AAC3C,yCAAmC;AAEnC,yDAG2B;AAc3B,2CAAwC;AACxC,qDAAkD;AAsFlD,SAAS,WAAW,CAClB,OAAyB;IAEzB,IAAI,CAAC,OAAO,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;KACtD;AACH,CAAC;AAMM,KAAK,UAAU,SAAS,CAC7B,QAAkB,EAClB,UAA4B,EAAE;IAE9B,WAAW,CAAC,OAAO,CAAC,CAAC;IAErB,IAAI,EACF,IAAI,EACJ,EAAE,EACF,SAAS,GAAG,CAAC,EACb,SAAS,EACT,cAAc,GAAG,EAAE,EACnB,WAAW,EACX,SAAS,EACT,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,eAAe,GAAG,KAAK,GACxB,GAAG,OAAO,CAAC;IAEZ,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAEhC,IAAI,MAAM,GAAG,IAAA,mDAA+B,EAAC,QAAQ,CAAC,CAAC;IAEvD,MAAM,SAAS,GAAG,IAAA,gCAAY,EAAC,QAAQ,EAAE;QACvC,SAAS,EAAE,IAAI;QACf,OAAO,EAAE,EAAE;QACX,SAAS;QACT,SAAS;KACV,CAAC,CAAC;IAEH,IAAI,kBAAkB,GAA6C,EAAE,CAAC;IACtE,KAAK,IAAI,KAAK,IAAI,MAAM,EAAE;QACxB,kBAAkB,CAAC,IAAI,CAAC;YACtB,GAAG,KAAK;YACR,QAAQ,EAAE,IAAI,CAAC,KAAK,CAClB,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAC9B;SACd,CAAC,CAAC;KACJ;IAED,MAAM,WAAW,GAAG,MAAM,IAAA,+BAAc,EACtC,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAEF,MAAM,WAAW,GACf,IAAI,KAAK,EAAE;QACT,CAAC,CAAC,WAAW;QACb,CAAC,CAAC,MAAM,IAAA,+BAAc,EAClB,EAAE,EACF,QAAQ,EACR,cAAc,EACd,SAAS,EACT,WAAW,CACZ,CAAC;IAER,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,EAAE;QAChC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAC;KACnD;IAED,MAAM,OAAO,GAAoC;QAC/C,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;KACf,CAAC;IAEF,MAAM,cAAc,GAAoB;QACtC,CAAC,EAAE,EAAE;QACL,CAAC,EAAE,EAAE;KACN,CAAC;IACF,KAAK,MAAM,IAAI,IAAI,cAAc,EAAE;QACjC,KAAK,MAAM,MAAM,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,aAAa,EAAE;YAChD,IAAI,CAAC,MAAM,CAAC,MAAM;gBAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;YAC7D,cAAc,CAAC,IAAI,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC;SACjD;KACF;IACD,IAAI,KAAK,GAAmC,EAAE,CAAC;IAC/C,KAAK,MAAM,KAAK,IAAI,kBAAkB,EAAE;QACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;QAChC,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAExC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC;YAAE,SAAS;QAEhD,MAAM,YAAY,GAAG,QAAQ,CAAC,KAAK,CAAC;QACpC,KAAK,MAAM,IAAI,IAAI,YAAY,EAAE;YAC/B,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC;gBAAE,SAAS;YAE1D,IAAI,WAAW,GAAgC;gBAC7C,CAAC,EAAE,QAAQ;gBACX,CAAC,EAAE,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;aACtB,CAAC;YAEF,MAAM,GAAG,GAAG,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,IAAI,WAAW,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC;YAE5D,IAAI,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,IAAI,QAAQ,CAAC,KAAK,EAAE,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE;gBAC/D,SAAS;aACV;YAED,IAAI,IAAI,GAAQ,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC;YAC3B,IAAI,MAAM,GAAQ,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;YACnC,KAAK,IAAI,IAAI,IAAI,WAAW,EAAE;gBAC5B,IAAI,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC;gBACpC,IAAI,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;gBAC/C,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;gBACvD,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;aACxD;YAED,MAAM,CAAC,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC;YACtB,KAAK,CAAC,GAAG,CAAC,GAAG,MAAqB,CAAC;SACpC;KACF;IAED,IAAI,eAAe,EAAE;QACnB,mBAAmB,CAAC,KAAK,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,cAAc,EAAE,CAAC,CAAC;KAClE;IAED,iCAAiC;IACjC,MAAM,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;IAC3C,MAAM,KAAK,GAAG,WAAW,CAAC,aAAa,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC;IAErE,OAAO;QACL,OAAO,EAAE,QAAQ,CAAC,SAAS,EAAE;QAC7B,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,MAAM;QACxB,MAAM,EAAE,IAAA,qBAAS,EAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC;QAC/B,aAAa;QACb,OAAO,EAAE,YAAY,CAAC,aAAa,CAAC;QACpC,KAAK;QACL,QAAQ;KACT,CAAC;AACJ,CAAC;AAnID,8BAmIC;AAED,SAAS,YAAY,CAAC,aAA4B;IAChD,IAAI,OAAO,GAAG,EAAE,CAAC;IACjB,KAAK,MAAM,MAAM,IAAI,aAAa,EAAE;QAClC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;YACxC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,EAAE;gBACxC,IAAI,SAAS,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC;gBACnD,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,KAAK,CAAC,CAAC;gBAC5B,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;aACzB;SACF;KACF;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAMD,SAAS,mBAAmB,CAC1B,KAAqC,EACrC,OAAmC;IAEnC,MAAM,EAAE,KAAK,GAAG,EAAE,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAC/C,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,IAAI,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,SAAS;QAEpC,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC;QACvB,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,CAAC;YAAE,SAAS;QACvC,IAAI,KAAK,CAAC,GAAG,KAAK,IAAI,KAAK,EAAE,CAAC;YAAE,SAAS;QAEzC,IAAI,MAAM,GAAQ,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;QAEnC,IAAI,IAAI,GAAQ,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC;QACzB,KAAK,IAAI,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE;YAC3B,IAAI,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;YAC/C,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC;YACvD,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC;YAC9B,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,cAAc,CAAC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package/lib/signals/signals2DToZ.d.ts

@@ -23,6 +23,7 @@ interface Signals2DToZOptions {
      * @default 0.02
      */
     width?: number | XYNumber;
+    factor?: number | XYNumber;
 }
 export interface Peak2DSeries {
     x: number[];

package/lib/signals/signals2DToZ.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.signals2DToZ = void 0;
 const spectrum_generator_1 = require("spectrum-generator");
 function signals2DToZ(signals, options = {}) {
-    let { from = -1, to = 12, nbPoints = 512, width = 0.02 } = options;
+    let { from = -1, to = 12, nbPoints = 512, width = 0.02, factor = 3, } = options;
     const peaks = signals.reduce((acc, { x, y }) => {
         acc.x.push(x.delta);
         acc.y.push(y.delta);
@@ -11,7 +11,7 @@ function signals2DToZ(signals, options = {}) {
         return acc;
     }, { x: [], y: [], z: [] });
     width = ensureXYNumber(width);
-    return (0, spectrum_generator_1.generateSpectrum2D)(peaks, {
+    return (0, spectrum_generator_1.generateSpectrum2D)(mergeClosePeaks(peaks), {
         generator: {
             from: ensureXYNumber(from),
             to: ensureXYNumber(to),
@@ -19,12 +19,27 @@ function signals2DToZ(signals, options = {}) {
         },
         peaks: {
             width,
+            factor,
         },
     });
 }
 exports.signals2DToZ = signals2DToZ;
 function ensureXYNumber(input) {
-    let result = typeof input !== 'object' ? { x: input, y: input } : input;
-    return result;
+    return typeof input !== 'object' ? { x: input, y: input } : { ...input };
+}
+function mergeClosePeaks(peaksIn) {
+    let peaks = JSON.parse(JSON.stringify(peaksIn));
+    for (let i = 0; i < peaks.x.length; i++) {
+        for (let j = i + 1; j < peaks.x.length; j++) {
+            if (peaks.x[i] === peaks.x[j] && peaks.y[i] === peaks.y[j]) {
+                peaks.z[i] += peaks.z[j];
+                peaks.x.splice(j, 1);
+                peaks.y.splice(j, 1);
+                peaks.z.splice(j, 1);
+                j--;
+            }
+        }
+    }
+    return peaks;
 }
 //# sourceMappingURL=signals2DToZ.js.map

package/lib/signals/signals2DToZ.js.map

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package/lib/utilities/getFrequency.d.ts

@@ -0,0 +1,21 @@
+import { Nuclei } from '../constants/gyromagneticRatio';
+export interface ObjervedNucleusData {
+    /**
+     * nucleus to use as reference in the calculation of frequency
+     */
+    nucleus: Nucleus;
+    /**
+     * frequency of the reference nucleus
+     */
+    frequency: number;
+}
+declare type Nucleus = Nuclei | (string & Record<never, never>);
+/**
+ * calculate the frequency of a nucleus with respect to a reference nucleus
+ */
+export declare function getFrequency(
+/**
+ * nucleus to calculate the frequency
+ */
+nucleus: Nucleus, observedNucleusData: ObjervedNucleusData): number;
+export {};