nmr-processing 7.1.0 → 7.4.0

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

@@ -0,0 +1,57 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.addIDs = exports.hasIDs = exports.checkIDs = void 0;
+const generateID_1 = __importDefault(require("../generateID"));
+const isSpectraData1D_1 = require("./isSpectraData1D");
+function checkIDs(input = []) {
+    let inputClone = JSON.parse(JSON.stringify(input));
+    let spectra = [];
+    for (const spectraData of inputClone) {
+        const { info, id } = spectraData;
+        if ((0, isSpectraData1D_1.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;
+}
+exports.checkIDs = checkIDs;
+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');
+        }
+    }
+}
+exports.hasIDs = hasIDs;
+function addIDs(data) {
+    for (const element of data) {
+        if (!element.id)
+            element.id = (0, generateID_1.default)();
+        for (let signal of element.signals || []) {
+            if (!signal.id)
+                signal.id = (0, generateID_1.default)();
+        }
+    }
+    hasIDs(data);
+    return data;
+}
+exports.addIDs = addIDs;
+//# sourceMappingURL=checkIDs.js.map

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

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

@@ -0,0 +1,15 @@
+import { PossibleAssignmentMap } from '../createMapPossibleAssignments';
+import { PredictionsByAtomType, RestrictionByCS } from './buildAssignments';
+import { TargetsByAtomType } from './getTargetsAndCorrelations';
+export interface PossibleAssignments {
+    [key: string]: string[];
+}
+export interface MapPossibleAssignments {
+    [key: string]: PossibleAssignmentMap;
+}
+export interface CreateMapPossibleAssignmentOptions {
+    restrictionByCS: RestrictionByCS;
+    predictions: PredictionsByAtomType;
+    targets: TargetsByAtomType;
+}
+export declare function createMapPossibleAssignment(expandMap: MapPossibleAssignments, props: CreateMapPossibleAssignmentOptions): MapPossibleAssignments;

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

@@ -0,0 +1,55 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createMapPossibleAssignment = void 0;
+const nmr_correlation_1 = require("nmr-correlation");
+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 = (0, nmr_correlation_1.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;
+}
+exports.createMapPossibleAssignment = createMapPossibleAssignment;
+//# sourceMappingURL=createMapPossibleAssignment.js.map

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

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

@@ -0,0 +1,22 @@
+import { StoreAssignments } from '../buildAssignments';
+import { RestrictionByCS, DiaIDPeerPossibleAssignment, InfoByAtomType, Partial, CurrentAtoms, PredictionsByAtomType } from './buildAssignments';
+import { MapPossibleAssignments } from './createMapPossibleAssignment';
+import { CorrelationWithIntegration, TargetsByAtomType } from './getTargetsAndCorrelations';
+export interface ExploreTreeRecOptions {
+    currentAtomTypes: CurrentAtoms;
+    restrictionByCS: RestrictionByCS;
+    timeout: number;
+    timeStart: number;
+    maxSolutions: number;
+    targets: TargetsByAtomType;
+    predictions: PredictionsByAtomType;
+    correlations: CorrelationWithIntegration[];
+    lowerBoundScore: number;
+    possibleAssignmentMap: MapPossibleAssignments;
+    diaIDPeerPossibleAssignment: DiaIDPeerPossibleAssignment;
+}
+export declare function exploreTree(props: ExploreTreeRecOptions, infoByAtomTypes: InfoByAtomType, partial: Partial, store: StoreAssignments): StoreAssignments | undefined;
+export interface AssignmentSolution {
+    assignment: string[];
+    score: number;
+}

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

@@ -0,0 +1,93 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.exploreTree = void 0;
+const partialScore_1 = require("./partialScore");
+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 = (0, partialScore_1.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);
+            }
+        }
+    }
+}
+exports.exploreTree = exploreTree;
+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

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package/lib/assignment/utils/getAssignment/formatData.d.ts

@@ -0,0 +1,14 @@
+import { NMRRangeWithIds, NMRZoneWithIds, SpectraData1DWithIds, SpectraData2DWithIds, SpectraDataWithIds } from './checkIDs';
+interface SpectraData1DFormatted extends Omit<SpectraData1DWithIds, 'ranges'> {
+    ranges: {
+        values: NMRRangeWithIds[];
+    };
+}
+interface SpectraData2DFormatted extends Omit<SpectraData2DWithIds, 'zones'> {
+    zones: {
+        values: NMRZoneWithIds[];
+    };
+}
+export declare type SpectraDataFormatted = SpectraData1DFormatted | SpectraData2DFormatted;
+export declare function formatData(input?: SpectraDataWithIds[]): SpectraDataFormatted[];
+export {};

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

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.formatData = void 0;
+const isSpectraData1D_1 = require("./isSpectraData1D");
+function formatData(input = []) {
+    let inputClone = JSON.parse(JSON.stringify(input));
+    let spectra = [];
+    for (const spectraData of inputClone) {
+        const { info } = spectraData;
+        if ((0, isSpectraData1D_1.isSpectraData1D)(spectraData)) {
+            spectra.push({ info, ranges: { values: spectraData.ranges } });
+        }
+        else {
+            spectra.push({ info, zones: { values: spectraData.zones } });
+        }
+    }
+    return spectra;
+}
+exports.formatData = formatData;
+//# sourceMappingURL=formatData.js.map

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

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

@@ -0,0 +1,3 @@
+import { Values } from 'nmr-correlation';
+import type { CorrelationWithIntegration } from './getTargetsAndCorrelations';
+export declare function getIntegrationOfAttachedProtons(target: CorrelationWithIntegration, correlations: Values): number;

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

@@ -0,0 +1,14 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getIntegrationOfAttachedProtons = void 0;
+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;
+}
+exports.getIntegrationOfAttachedProtons = getIntegrationOfAttachedProtons;
+//# sourceMappingURL=getIntegrationOfAttachedProtons.js.map

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

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

@@ -0,0 +1,18 @@
+import type { Correlation, Link } from 'nmr-correlation';
+import { SpectraDataWithIds } from './checkIDs';
+export interface CorrelationWithIntegration extends Pick<Correlation, 'link' | 'atomType' | 'label' | 'attachment' | 'protonsCount'> {
+    integration: number;
+    indirectLinks: Array<Link>;
+}
+export interface Targets {
+    [key: string]: CorrelationWithIntegration;
+}
+export interface TargetsByAtomType {
+    H: Targets;
+    C: Targets;
+}
+export interface TargetsAndCorrelations {
+    targets: TargetsByAtomType;
+    correlations: CorrelationWithIntegration[];
+}
+export declare function getTargetsAndCorrelations(spectra: SpectraDataWithIds[], options?: any): TargetsAndCorrelations;

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

@@ -0,0 +1,37 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getTargetsAndCorrelations = void 0;
+const nmr_correlation_1 = require("nmr-correlation");
+const formatData_1 = require("./formatData");
+const getIntegrationOfAttachedProtons_1 = require("./getIntegrationOfAttachedProtons");
+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 = (0, formatData_1.formatData)(spectra);
+    const { values: correlations } = (0, nmr_correlation_1.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 = (0, getIntegrationOfAttachedProtons_1.getIntegrationOfAttachedProtons)(correlation, correlations);
+        }
+    }
+    return {
+        targets,
+        correlations,
+    };
+}
+exports.getTargetsAndCorrelations = getTargetsAndCorrelations;
+//# sourceMappingURL=getTargetsAndCorrelations.js.map

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

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

@@ -0,0 +1,19 @@
+import { Values } from 'nmr-correlation';
+import { AtomTypes } from './buildAssignments';
+/**
+ * if hsqc is present in experimentTypes we can just predict 13C
+ * spectrum and try to assign the carbons first.
+ * @param {*} correlations
+ * @param {*} justAssign
+ */
+declare function getWorkFlow(correlations: Values, justAssign?: Array<AtomTypes[]>): {
+    assignmentOrder: AtomTypes[][];
+    experimentTypes: ExperimentTypes;
+};
+export default getWorkFlow;
+interface ExperimentTypes {
+    types: string[];
+    hasProton: boolean;
+    hasCarbon: boolean;
+    hasHSQC: boolean;
+}

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

@@ -0,0 +1,52 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+/**
+ * if hsqc is present in experimentTypes we can just predict 13C
+ * spectrum and try to assign the carbons first.
+ * @param {*} correlations
+ * @param {*} justAssign
+ */
+function getWorkFlow(correlations, justAssign = []) {
+    const experimentTypes = extractExperimentType(correlations);
+    const { hasHSQC, types } = experimentTypes;
+    if (justAssign.length > 0) {
+        return { assignmentOrder: justAssign, experimentTypes };
+    }
+    const assignmentOrder = [];
+    if (hasHSQC) {
+        assignmentOrder.push(['C'], ['H']);
+    }
+    else {
+        assignmentOrder.push(types.filter((type) => type === 'H' || type === 'C'));
+    }
+    return { assignmentOrder, experimentTypes };
+}
+exports.default = getWorkFlow;
+function extractExperimentType(correlations) {
+    const types = [];
+    for (const correlation of correlations) {
+        let experimentType = correlation.experimentType;
+        if (experimentType === '1d') {
+            experimentType = `${correlation.atomType.toUpperCase()}`;
+        }
+        if (!types.includes(experimentType)) {
+            types.push(experimentType);
+        }
+        for (const link of correlation.link) {
+            experimentType = link.experimentType;
+            if (experimentType === '1d') {
+                experimentType = `${link.atomType[0].toUpperCase()}`;
+            }
+            if (!types.includes(experimentType)) {
+                types.push(experimentType);
+            }
+        }
+    }
+    return {
+        types,
+        hasProton: types.includes('H'),
+        hasCarbon: types.includes('C'),
+        hasHSQC: types.includes('hsqc'),
+    };
+}
+//# sourceMappingURL=getWorkFlow.js.map

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

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package/lib/assignment/utils/getAssignment/groupCarbonTargetByIntegrationZone.d.ts

@@ -0,0 +1,7 @@
+import { CorrelationWithIntegration, Targets } from './getTargetsAndCorrelations';
+declare function groupCarbonTargetByIntegrationZone(activeDomainOnTarget: string[], targets: Targets, correlations: CorrelationWithIntegration[]): {
+    atomType: string;
+    targetIDs: string[];
+    integration: number;
+}[];
+export default groupCarbonTargetByIntegrationZone;

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

@@ -0,0 +1,43 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+function groupCarbonTargetByIntegrationZone(activeDomainOnTarget, targets, correlations) {
+    let targetID = activeDomainOnTarget[0];
+    let { H: attachments = [] } = targets[targetID].attachment;
+    let targetByIntegral = [
+        { targetIDs: [targetID], attachments: new Set(attachments) },
+    ];
+    for (let i = 1; i < activeDomainOnTarget.length; i++) {
+        let targetID = activeDomainOnTarget[i];
+        let target = targets[targetID];
+        let { H: attachments = [] } = target.attachment;
+        let alone = true;
+        for (let group of targetByIntegral) {
+            const pertain = attachments.some((attachment) => group.attachments.has(attachment));
+            if (pertain) {
+                alone = false;
+                group.targetIDs.push(targetID);
+                for (let attachment of attachments) {
+                    group.attachments.add(attachment);
+                }
+                break;
+            }
+        }
+        if (alone) {
+            targetByIntegral.push({
+                targetIDs: [targetID],
+                attachments: new Set(attachments),
+            });
+        }
+    }
+    return targetByIntegral.map((t) => ({
+        atomType: 'C',
+        targetIDs: t.targetIDs,
+        integration: correlations
+            ? Array.from(t.attachments).reduce((sum, index) => {
+                return correlations[index].integration + sum;
+            }, 0)
+            : 0,
+    }));
+}
+exports.default = groupCarbonTargetByIntegrationZone;
+//# sourceMappingURL=groupCarbonTargetByIntegrationZone.js.map

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

@@ -0,0 +1 @@
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package/lib/assignment/utils/getAssignment/isSpectraData1D.d.ts

@@ -0,0 +1,2 @@
+import { SpectraData, SpectraData1D } from '../../getAssignments';
+export declare function isSpectraData1D(spectrum: SpectraData): spectrum is SpectraData1D;

package/lib/assignment/utils/getAssignment/isSpectraData1D.js

@@ -0,0 +1,8 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isSpectraData1D = void 0;
+function isSpectraData1D(spectrum) {
+    return 'ranges' in spectrum;
+}
+exports.isSpectraData1D = isSpectraData1D;
+//# sourceMappingURL=isSpectraData1D.js.map

package/lib/assignment/utils/getAssignment/isSpectraData1D.js.map

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

@@ -0,0 +1,13 @@
+import { InfoByAtomType, Partial, PredictionsByAtomType, RestrictionByCS } from './buildAssignments';
+import { CorrelationWithIntegration, TargetsByAtomType } from './getTargetsAndCorrelations';
+export interface PartialScoreOptions {
+    diaIDPeerPossibleAssignment: {
+        [key: string]: string[];
+    };
+    restrictionByCS: RestrictionByCS;
+    infoByAtomTypes: InfoByAtomType;
+    correlations: CorrelationWithIntegration[];
+    predictions: PredictionsByAtomType;
+    targets: TargetsByAtomType;
+}
+export declare function partialScore(partial: Partial, props: PartialScoreOptions): number;