nmr-processing 7.0.1 → 7.3.0

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

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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 @@
+{"version":3,"file":"searchIndices.js","sourceRoot":"","sources":["../../../../src/assignment/utils/getAssignment/searchIndices.ts"],"names":[],"mappings":";;;AAEA,uDAAoD;AAEpD,SAAgB,aAAa,CAAC,QAAgB,EAAE,OAAsB;IACpE,KAAK,IAAI,aAAa,GAAG,CAAC,EAAE,aAAa,GAAG,OAAO,CAAC,MAAM,EAAE,aAAa,EAAE,EAAE;QAC3E,MAAM,QAAQ,GAAG,OAAO,CAAC,aAAa,CAAC,CAAC;QACxC,MAAM,IAAI,GAAG,IAAA,iCAAe,EAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC;QAC1E,KAAK,IAAI,YAAY,GAAG,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC,MAAM,EAAE,YAAY,EAAE,EAAE;YACrE,MAAM,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,CAAC,OAAO,IAAI,EAAE,CAAC;YACjD,KAAK,IAAI,WAAW,GAAG,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,EAAE,WAAW,EAAE,EAAE;gBACrE,IAAI,QAAQ,KAAK,OAAO,CAAC,WAAW,CAAC,CAAC,EAAE,EAAE;oBACxC,OAAO,EAAE,aAAa,EAAE,WAAW,EAAE,YAAY,EAAE,CAAC;iBACrD;aACF;SACF;KACF;IACD,MAAM,IAAI,KAAK,CAAC,8BAA8B,QAAQ,KAAK,CAAC,CAAC;AAC/D,CAAC;AAdD,sCAcC"}

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/index.d.ts

@@ -8,8 +8,10 @@ export * from './prediction/predictCOSY';
 export * from './prediction/predictHSQC';
 export * from './prediction/predictHMBC';
 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';

package/lib/index.js

@@ -1,7 +1,11 @@
 "use strict";
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
-    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
 }) : (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     o[k2] = m[k];
@@ -20,8 +24,10 @@ __exportStar(require("./prediction/predictCOSY"), exports);
 __exportStar(require("./prediction/predictHSQC"), exports);
 __exportStar(require("./prediction/predictHMBC"), exports);
 __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);

package/lib/index.js.map

@@ -1 +1 @@
-{"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;AAExC,gEAA8C;AAC9C,iEAA+C;AAE/C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAE5C,0DAAwC;AACxC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C"}
+{"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;AAE5C,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/predictAllSpectra.d.ts

@@ -0,0 +1,18 @@
+import type { Molecule } from 'openchemlib';
+import { OptionsSignalsToXY } from '../signals/signalsToXY';
+import { PredictAllOptions } from './predictAll';
+/**
+ * This function will generate an object compatible with NMR-ium
+ *
+ * @param molecule
+ * @param options
+ */
+export declare function predictAllSpectra(molecule: Molecule, options?: {
+    prediction?: PredictAllOptions;
+    simulation?: OptionsSignalsToXY;
+}): Promise<{
+    spectra: any[];
+    molecules: {
+        molfile: any;
+    }[];
+}>;

package/lib/prediction/predictAllSpectra.js

@@ -0,0 +1,40 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.predictAllSpectra = void 0;
+const signalsToXY_1 = require("../signals/signalsToXY");
+const predictAll_1 = require("./predictAll");
+/**
+ * This function will generate an object compatible with NMR-ium
+ *
+ * @param molecule
+ * @param options
+ */
+async function predictAllSpectra(molecule, options = {}) {
+    const predictions = await (0, predictAll_1.predictAll)(molecule, options.prediction);
+    const spectra = [];
+    const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
+    spectra.push(getProton(predictions.proton, options.simulation));
+    return result;
+}
+exports.predictAllSpectra = predictAllSpectra;
+function getProton(prediction, options) {
+    const { x, y } = (0, signalsToXY_1.signalsToXY)(prediction.signals, options);
+    const spectrum = {
+        id: '',
+        // todo Array.from is temporary for the developement
+        data: { x: Array.from(x), re: Array.from(y), im: null },
+        info: {
+            nucleus: prediction.nucleus,
+            dimension: 1,
+            originFrequency: 400,
+            baseFrequency: 400,
+            pulseSequence: 'prediction',
+            experiment: 'proton',
+            isFt: true,
+        },
+        // todo: currently we disable the ranges because there is no ID
+        //ranges: { values: prediction.ranges },
+    };
+    return spectrum;
+}
+//# sourceMappingURL=predictAllSpectra.js.map

package/lib/prediction/predictAllSpectra.js.map

@@ -0,0 +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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package/lib/xyz/xyzAutoZonesPicking.js

@@ -1,7 +1,11 @@
 "use strict";
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
-    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
 }) : (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     o[k2] = m[k];

package/lib/xyz/xyzAutoZonesPicking.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/get13CAssignments.js.map

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