nmr-processing 7.1.0 → 7.4.0

package/lib/utilities/getFrequency.js

@@ -0,0 +1,30 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getFrequency = void 0;
+const gyromagneticRatio_1 = require("../constants/gyromagneticRatio");
+/**
+ * calculate the frequency of a nucleus with respect to a reference nucleus
+ */
+function getFrequency(
+/**
+ * nucleus to calculate the frequency
+ */
+nucleus, observedNucleusData) {
+    const { nucleus: obsNucleus, frequency } = observedNucleusData;
+    checkExistence(nucleus, obsNucleus);
+    return ((frequency * gyromagneticRatio_1.GYROMAGNETIC_RATIO[nucleus]) /
+        gyromagneticRatio_1.GYROMAGNETIC_RATIO[obsNucleus]);
+}
+exports.getFrequency = getFrequency;
+function checkExistence(...nucleus) {
+    let nuclei = [];
+    for (const n of nucleus) {
+        if (!(n in gyromagneticRatio_1.GYROMAGNETIC_RATIO)) {
+            nuclei.push(n);
+        }
+    }
+    if (nuclei.length !== 0) {
+        throw new Error(`${nuclei.join(' , ')} is not supported`);
+    }
+}
+//# sourceMappingURL=getFrequency.js.map

package/lib/utilities/getFrequency.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/get13CAssignments.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/get1HAssignments.js.map

@@ -1 +1 @@
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package/lib-esm/assignment/getAssignments.js

@@ -0,0 +1,37 @@
+import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
+import { buildAssignments, } from './utils/getAssignment/buildAssignments';
+import { checkIDs } from './utils/getAssignment/checkIDs';
+import { getTargetsAndCorrelations } from './utils/getAssignment/getTargetsAndCorrelations';
+import getWorkFlow from './utils/getAssignment/getWorkFlow';
+export async function getAssignments(input, options = {}) {
+    let { restrictionByCS = {}, justAssign, minScore = 1, 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)
+        throw new Error('It is needed a molecule to assign');
+    molecule.addImplicitHydrogens();
+    addDiastereotopicMissingChirality(molecule);
+    const spectra = checkIDs(input.spectra);
+    const { targets, correlations } = getTargetsAndCorrelations(spectra, correlationOptions);
+    const { assignmentOrder } = getWorkFlow(correlations, justAssign);
+    const solutions = await buildAssignments({
+        restrictionByCS: {
+            tolerance,
+            useChemicalShiftScore,
+            chemicalShiftRestriction,
+        },
+        spectra,
+        molecule,
+        timeout,
+        minScore,
+        maxSolutions,
+        assignmentOrder,
+        nbAllowedUnAssigned,
+        correlations,
+        targets,
+        predictionOptions,
+        predictions,
+    });
+    return solutions;
+}
+//# sourceMappingURL=getAssignments.js.map

package/lib-esm/assignment/getAssignments.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/utils/buildAssignments.js.map

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

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package/lib-esm/assignment/utils/getAssignment/buildAssignments.js

@@ -0,0 +1,198 @@
+import treeSet from 'ml-tree-set';
+import { getConnectivityMatrix } from 'openchemlib-utils';
+import { predictCarbon } from '../../../prediction/predictCarbon';
+import { predictProton } from '../../../prediction/predictProton';
+import { createMapPossibleAssignment, } from './createMapPossibleAssignment';
+import { exploreTree } from './exploreTree';
+import { isSpectraData1D } from './isSpectraData1D';
+import { searchIndices } from './searchIndices';
+const comparator = (a, b) => {
+    return b.score - a.score;
+};
+const predictor = { H: predictProton, C: predictCarbon };
+function checkNMRSignal1D(signals) {
+    const keys = [
+        'nbAtoms',
+        'diaIDs',
+        'atoms',
+    ];
+    for (const signal of signals) {
+        for (let key of keys) {
+            if (!signal[key])
+                throw new Error(`property ${key} does not exist`);
+        }
+    }
+}
+export const getAllHydrogens = {
+    C: (m, i) => m.getAllHydrogens(i),
+    H: () => 1,
+};
+export async function buildAssignments(props) {
+    const { spectra, molecule, restrictionByCS, timeout, minScore, nbAllowedUnAssigned = {}, maxSolutions, correlations, assignmentOrder, predictionOptions, predictions: inputPrediction = {}, targets, } = props;
+    let date = new Date();
+    let timeStart = date.getTime();
+    let lowerBoundScore = minScore;
+    let store = {
+        solutions: new treeSet(comparator),
+        nSolutions: 0,
+    };
+    const pathLengthMatrix = getConnectivityMatrix(molecule, {
+        pathLength: true,
+    });
+    let infoByAtomType = {};
+    const predictions = {};
+    let possibleAssignmentMap = {};
+    let diaIDPeerPossibleAssignment = {};
+    for (const atomTypesToPredict of assignmentOrder) {
+        for (const atomType of atomTypesToPredict) {
+            const options = predictionOptions[atomType];
+            const predictedSignals = inputPrediction[atomType];
+            let { joinedSignals } = predictedSignals
+                ? { joinedSignals: predictedSignals }
+                : await predictor[atomType](molecule, options);
+            checkNMRSignal1D(joinedSignals);
+            if (!predictions[atomType])
+                predictions[atomType] = {};
+            for (let prediction of joinedSignals) {
+                const diaID = prediction.diaIDs[0];
+                const index = prediction.atoms[0];
+                const allHydrogens = getAllHydrogens[atomType](molecule, index);
+                predictions[atomType][diaID] = {
+                    ...prediction,
+                    diaIDIndex: index,
+                    allHydrogens: prediction.nbAtoms * allHydrogens,
+                    protonsCount: allHydrogens,
+                    pathLength: pathLengthMatrix[index],
+                };
+            }
+            infoByAtomType[atomType] = {
+                nSources: joinedSignals.length,
+                currentIndex: 0,
+                nbAllowedUnAssigned: nbAllowedUnAssigned[atomType] || 0,
+            };
+        }
+        possibleAssignmentMap = createMapPossibleAssignment(possibleAssignmentMap, {
+            restrictionByCS,
+            predictions,
+            targets,
+        });
+        diaIDPeerPossibleAssignment = {};
+        for (const atomType in possibleAssignmentMap) {
+            diaIDPeerPossibleAssignment[atomType] = Object.keys(possibleAssignmentMap[atomType]);
+        }
+        let sourceOfPartials = getSourceOfPartials(store, infoByAtomType, atomTypesToPredict);
+        store = {
+            solutions: new treeSet(comparator),
+            nSolutions: 0,
+        };
+        for (let partial of sourceOfPartials) {
+            exploreTree({
+                currentAtomTypes: atomTypesToPredict,
+                restrictionByCS,
+                timeout,
+                timeStart,
+                targets,
+                predictions,
+                correlations,
+                maxSolutions,
+                lowerBoundScore,
+                possibleAssignmentMap,
+                diaIDPeerPossibleAssignment,
+            }, infoByAtomType, partial, store);
+        }
+    }
+    return annotateSpectraData({
+        store,
+        spectra,
+        diaIDPeerPossibleAssignment,
+        targets,
+    });
+}
+function annotateSpectraData(input) {
+    var _a;
+    const { store, spectra, diaIDPeerPossibleAssignment, targets } = input;
+    const { solutions } = store;
+    const mapSignalId = {};
+    const atomTypes = Object.keys(targets);
+    for (const atomType of atomTypes) {
+        const targetByAtomType = targets[atomType];
+        for (const targetId in targetByAtomType) {
+            let target = targetByAtomType[targetId];
+            for (const link of target.link) {
+                const signalId = link.signal.id;
+                if (mapSignalId[signalId])
+                    continue;
+                mapSignalId[link.signal.id] = searchIndices(signalId, spectra);
+            }
+        }
+    }
+    const result = [];
+    for (let solution of solutions.elements) {
+        const spectraResult = JSON.parse(JSON.stringify(spectra));
+        const { assignment, score } = solution;
+        const atomTypes = Object.keys(assignment);
+        for (const atomType of atomTypes) {
+            const targetByAtomType = targets[atomType];
+            const assignmentPeerAtomType = assignment[atomType];
+            for (let index = 0; index < assignmentPeerAtomType.length; index++) {
+                const targetID = assignmentPeerAtomType[index];
+                if (targetID === '*' || !targetID)
+                    continue;
+                const target = targetByAtomType[targetID];
+                const diaId = diaIDPeerPossibleAssignment[atomType][index];
+                for (let 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];
+                        if (!signal.diaIDs)
+                            signal.diaIDs = [];
+                        signal.diaIDs.push(diaId);
+                    }
+                    else {
+                        const axis = link.axis;
+                        const signal = spectrum.zones[elementIndex].signals[signalIndex];
+                        if (!signal[axis].diaIDs)
+                            signal[axis].diaIDs = [];
+                        (_a = signal[axis].diaIDs) === null || _a === void 0 ? void 0 : _a.push(diaId);
+                    }
+                }
+            }
+        }
+        result.push({
+            score,
+            assignment: spectraResult,
+        });
+    }
+    return result;
+}
+function getSourceOfPartials(store, infoByAtomType, currentAtoms) {
+    return store.nSolutions > 0
+        ? store.solutions.elements.map((e) => {
+            let currentAssignment = e.assignment;
+            for (const atom of currentAtoms) {
+                currentAssignment[atom] = fillPartial(infoByAtomType[atom].nSources);
+            }
+            return currentAssignment;
+        })
+        : initializePartials(infoByAtomType, currentAtoms);
+}
+function initializePartials(infoByAtomType, currentAtoms) {
+    const partial = {};
+    const atomsType = Object.keys(infoByAtomType);
+    for (const atom of atomsType) {
+        const value = currentAtoms.includes(atom) ? null : '*';
+        partial[atom] = fillPartial(infoByAtomType[atom].nSources, value);
+    }
+    return [partial];
+}
+function fillPartial(nSources, value = null) {
+    const partial = new Array(nSources);
+    for (let i = 0; i < nSources; i++) {
+        partial[i] = value;
+    }
+    return partial;
+}
+//# sourceMappingURL=buildAssignments.js.map

package/lib-esm/assignment/utils/getAssignment/buildAssignments.js.map

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package/lib-esm/assignment/utils/getAssignment/checkIDs.js

@@ -0,0 +1,48 @@
+import generateID from '../generateID';
+import { isSpectraData1D } from './isSpectraData1D';
+export function checkIDs(input = []) {
+    let inputClone = JSON.parse(JSON.stringify(input));
+    let spectra = [];
+    for (const spectraData of inputClone) {
+        const { info, id } = spectraData;
+        if (isSpectraData1D(spectraData)) {
+            let data = addIDs(spectraData.ranges);
+            for (const element of data) {
+                const { integration } = element;
+                for (let signal of element.signals || []) {
+                    if (!signal.integration)
+                        signal.integration = integration;
+                }
+            }
+            spectra.push({ id, info, ranges: data });
+        }
+        else {
+            let data = addIDs(spectraData.zones);
+            spectra.push({ id, info, zones: data });
+        }
+    }
+    return spectra;
+}
+export 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 || []) {
+            if (!signal.id)
+                throw new Error('A signal has not an ID');
+        }
+    }
+}
+export function addIDs(data) {
+    for (const element of data) {
+        if (!element.id)
+            element.id = generateID();
+        for (let signal of element.signals || []) {
+            if (!signal.id)
+                signal.id = generateID();
+        }
+    }
+    hasIDs(data);
+    return data;
+}
+//# sourceMappingURL=checkIDs.js.map

package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/utils/getAssignment/createMapPossibleAssignment.js

@@ -0,0 +1,51 @@
+import { getCorrelationDelta } from 'nmr-correlation';
+export function createMapPossibleAssignment(expandMap, props) {
+    const { restrictionByCS, predictions, targets } = 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];
+        if (!expandMap[atomType])
+            expandMap[atomType] = {};
+        for (const diaID in predictionByAtomType) {
+            let prediction = predictionByAtomType[diaID];
+            expandMap[atomType][diaID] = [];
+            if (targetByAtomType) {
+                for (const targetID in targetByAtomType) {
+                    let target = targetByAtomType[targetID];
+                    const { nbAtoms, protonsCount: protonsCountFromPrediction } = prediction;
+                    const { integration, protonsCount } = target;
+                    const couldBeAssigned = !integration
+                        ? true
+                        : atomType === 'H'
+                            ? nbAtoms - integration < 1
+                            : protonsCount.length > 0
+                                ? protonsCount.some((count) => protonsCountFromPrediction === count)
+                                : true;
+                    if (couldBeAssigned) {
+                        if (!chemicalShiftRestriction ||
+                            typeof prediction.delta === 'undefined') {
+                            // Chemical shift is not a restriction
+                            expandMap[atomType][diaID].push(targetID);
+                        }
+                        else {
+                            let targetDelta = getCorrelationDelta(target);
+                            if (targetDelta === undefined) {
+                                throw new Error(`Correlation has not delta`);
+                            }
+                            let distAfterLimit = Math.abs(prediction.delta - targetDelta - errorAbs);
+                            if (distAfterLimit < 4 * errorAbs) {
+                                expandMap[atomType][diaID].push(targetID);
+                            }
+                        }
+                    }
+                }
+            }
+            expandMap[atomType][diaID].push('*');
+        }
+    }
+    return expandMap;
+}
+//# sourceMappingURL=createMapPossibleAssignment.js.map

package/lib-esm/assignment/utils/getAssignment/createMapPossibleAssignment.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/utils/getAssignment/exploreTree.js

@@ -0,0 +1,89 @@
+import { partialScore } from './partialScore';
+export function exploreTree(props, infoByAtomTypes, partial, store) {
+    const { currentAtomTypes, restrictionByCS, timeout, timeStart, maxSolutions, targets, predictions, correlations, lowerBoundScore, possibleAssignmentMap, diaIDPeerPossibleAssignment, } = props;
+    const currentDate = new Date();
+    if (currentDate.getTime() - timeStart > timeout) {
+        new Error('timeout expired');
+        return store;
+    }
+    for (const atomType of currentAtomTypes) {
+        const { currentIndex, nSources } = infoByAtomTypes[atomType];
+        if (currentIndex >= nSources - 1 &&
+            partial[atomType][currentIndex] !== null) {
+            continue;
+        }
+        const diaID = diaIDPeerPossibleAssignment[atomType][currentIndex];
+        const possibleAssignments = possibleAssignmentMap[atomType][diaID];
+        for (let targetID of possibleAssignments) {
+            partial[atomType][currentIndex] = targetID;
+            let score = partialScore(partial, {
+                diaIDPeerPossibleAssignment,
+                infoByAtomTypes,
+                restrictionByCS,
+                predictions,
+                correlations,
+                targets,
+            });
+            if (score === 0) {
+                continue;
+            }
+            if (isLastOne(currentAtomTypes, infoByAtomTypes) &&
+                score >= lowerBoundScore) {
+                addSolution(store, { predictions, partial, score, maxSolutions });
+            }
+            else {
+                const newInfo = JSON.parse(JSON.stringify(infoByAtomTypes));
+                newInfo[atomType].currentIndex += 1;
+                exploreTree({
+                    currentAtomTypes,
+                    restrictionByCS,
+                    timeout,
+                    timeStart,
+                    maxSolutions,
+                    targets,
+                    predictions,
+                    correlations,
+                    lowerBoundScore,
+                    possibleAssignmentMap,
+                    diaIDPeerPossibleAssignment,
+                }, newInfo, JSON.parse(JSON.stringify(partial)), store);
+            }
+        }
+    }
+}
+function addSolution(store, props) {
+    let { score, maxSolutions, partial, predictions } = props;
+    score /= doubleAssignmentPenalty(partial, predictions);
+    let solution = {
+        assignment: JSON.parse(JSON.stringify(partial)),
+        score,
+    };
+    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 isLastOne(currentAtomTypes, infoByAtomTypes) {
+    let lastOne = true;
+    for (const atomType of currentAtomTypes) {
+        const { currentIndex, nSources } = infoByAtomTypes[atomType];
+        lastOne = lastOne && currentIndex >= nSources - 1;
+    }
+    return lastOne;
+}
+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]);
+        nbDoubleAssignment += nbSources - assignments.size;
+    }
+    return nbDoubleAssignment > 0 ? 2 * nbDoubleAssignment : 1;
+}
+//# sourceMappingURL=exploreTree.js.map

package/lib-esm/assignment/utils/getAssignment/exploreTree.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/utils/getAssignment/formatData.js

@@ -0,0 +1,16 @@
+import { isSpectraData1D } from './isSpectraData1D';
+export function formatData(input = []) {
+    let inputClone = JSON.parse(JSON.stringify(input));
+    let spectra = [];
+    for (const spectraData of inputClone) {
+        const { info } = spectraData;
+        if (isSpectraData1D(spectraData)) {
+            spectra.push({ info, ranges: { values: spectraData.ranges } });
+        }
+        else {
+            spectra.push({ info, zones: { values: spectraData.zones } });
+        }
+    }
+    return spectra;
+}
+//# sourceMappingURL=formatData.js.map

package/lib-esm/assignment/utils/getAssignment/formatData.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/utils/getAssignment/getIntegrationOfAttachedProtons.js

@@ -0,0 +1,10 @@
+export function getIntegrationOfAttachedProtons(target, correlations) {
+    const { H: attachment = [] } = target.attachment;
+    let integration = 0;
+    for (const match of attachment) {
+        const correlation = correlations[match];
+        integration += Number(correlation.link[0].signal.integration);
+    }
+    return integration;
+}
+//# sourceMappingURL=getIntegrationOfAttachedProtons.js.map

package/lib-esm/assignment/utils/getAssignment/getIntegrationOfAttachedProtons.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/utils/getAssignment/getTargetsAndCorrelations.js

@@ -0,0 +1,33 @@
+import { buildCorrelationData } from 'nmr-correlation';
+import { formatData } from './formatData';
+import { getIntegrationOfAttachedProtons } from './getIntegrationOfAttachedProtons';
+export function getTargetsAndCorrelations(spectra, options = {}) {
+    //add indirect links, if a carbon C1 is attached to a proton H1 that correlating
+    //with carbon C2, so the carbon C1 and C2 are also correlating
+    const { tolerance = { C: 0.25, H: 0.05 } } = options;
+    const spectraData = formatData(spectra);
+    const { values: correlations } = buildCorrelationData(spectraData, {
+        tolerance,
+    });
+    let targets = {};
+    for (const correlation of correlations) {
+        if (correlation.pseudo)
+            continue;
+        const { id: targetID, atomType } = correlation;
+        if (!targets[atomType])
+            targets[atomType] = {};
+        targets[atomType][targetID] = correlation;
+        if (atomType === 'H') {
+            targets[atomType][targetID].integration =
+                correlation.link[0].signal.integration;
+        }
+        else {
+            targets[atomType][targetID].integration = getIntegrationOfAttachedProtons(correlation, correlations);
+        }
+    }
+    return {
+        targets,
+        correlations,
+    };
+}
+//# sourceMappingURL=getTargetsAndCorrelations.js.map

package/lib-esm/assignment/utils/getAssignment/getTargetsAndCorrelations.js.map

@@ -0,0 +1 @@
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