nmr-processing 3.3.4 → 5.0.0

package/CHANGELOG.md

@@ -1,5 +1,47 @@
 # Changelog
 
+## [5.0.0](https://www.github.com/cheminfo/nmr-processing/compare/v4.0.0...v5.0.0) (2021-11-26)
+
+
+### ⚠ BREAKING CHANGES
+
+* xyzAutoPeaksPicking change structure NMRSignal2D
+
+### Features
+
+* xyzAutoPeaksPicking change structure NMRSignal2D ([bc5192f](https://www.github.com/cheminfo/nmr-processing/commit/bc5192f1155743c225b92353c2750519a8eaf1ab))
+
+## [4.0.0](https://www.github.com/cheminfo/nmr-processing/compare/v3.4.1...v4.0.0) (2021-11-23)
+
+
+### ⚠ BREAKING CHANGES
+
+* change shape1D n NMRPeak1D structure (#119)
+
+### Features
+
+* change shape1D n NMRPeak1D structure ([#119](https://www.github.com/cheminfo/nmr-processing/issues/119)) ([0255510](https://www.github.com/cheminfo/nmr-processing/commit/02555100407fe2ff80a4c41fff1ddd66d97fbaef))
+
+### [3.4.1](https://www.github.com/cheminfo/nmr-processing/compare/v3.4.0...v3.4.1) (2021-11-06)
+
+
+### Bug Fixes
+
+* **rangesToXY:** draw massive ranges ([#117](https://www.github.com/cheminfo/nmr-processing/issues/117)) ([a80025a](https://www.github.com/cheminfo/nmr-processing/commit/a80025a5b5805625f036b478ed9d24f269cfa2b7))
+
+## [3.4.0](https://www.github.com/cheminfo/nmr-processing/compare/v3.3.4...v3.4.0) (2021-11-04)
+
+
+### Features
+
+* add get13CAssignments function ([#116](https://www.github.com/cheminfo/nmr-processing/issues/116)) ([73f9df6](https://www.github.com/cheminfo/nmr-processing/commit/73f9df6c1d88599828409f8194fb58c1323e0ae9))
+* automatic assignment for proton ([#114](https://www.github.com/cheminfo/nmr-processing/issues/114)) ([f50932e](https://www.github.com/cheminfo/nmr-processing/commit/f50932e78f93db5a4c8dd0c798240a4b18df153a))
+
+
+### Bug Fixes
+
+* export get1HAssignment ([7753e7f](https://www.github.com/cheminfo/nmr-processing/commit/7753e7fbb1e3927b1d32746ab0f4f3b380d98dca))
+
 ### [3.3.4](https://www.github.com/cheminfo/nmr-processing/compare/v3.3.3...v3.3.4) (2021-10-26)
 
 

package/lib/assignment/get13CAssignments.d.ts

@@ -0,0 +1,35 @@
+import { Molecule } from 'openchemlib';
+import { NMRRange } from '..';
+import { PredictCarbonOptions } from '../prediction/predictCarbon';
+import { RestrictionByCS } from './utils/buildAssignments';
+export interface Get13CAssignmentsOptions {
+    restrictionByCS?: Partial<RestrictionByCS>;
+    /**
+     * min score to accept an assignment
+     * @default 1
+     */
+    minScore?: number;
+    /**
+     * maximal number of assignments to return
+     * @default 10
+     */
+    maxSolutions?: number;
+    /**
+     * number of allowed unassignment signals
+     * @default 0
+     */
+    nbAllowedUnAssigned?: number;
+    /**
+     * time limit in miliseconds to finish the assignment procedure.
+     * @default 6000
+     */
+    timeout?: number;
+    /**
+     * prediction options
+     */
+    predictionOptions?: PredictCarbonOptions;
+}
+export declare function get13CAssignments(ranges: NMRRange[], molecule: Molecule, options?: Get13CAssignmentsOptions): Promise<{
+    score: any;
+    assignment: unknown[];
+}[]>;

package/lib/assignment/get13CAssignments.js

@@ -0,0 +1,54 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.get13CAssignments = void 0;
+const openchemlib_utils_1 = require("openchemlib-utils");
+const predictCarbon_1 = require("../prediction/predictCarbon");
+const buildAssignments_1 = require("./utils/buildAssignments");
+const generateID_1 = __importDefault(require("./utils/generateID"));
+function checkAtomsAndDiaIDs(signals) {
+    for (const signal of signals) {
+        if (!signal.atoms)
+            throw new Error('signal has not atoms property');
+        if (!signal.diaIDs)
+            throw new Error('signal has not diaIDs property');
+        if (!signal.nbAtoms)
+            throw new Error('signal has not nbAtoms property');
+    }
+}
+function checkIntegration(ranges) {
+    for (let range of ranges) {
+        if (range.integration === undefined)
+            range.integration = 0;
+    }
+    return ranges;
+}
+async function get13CAssignments(ranges, molecule, options = {}) {
+    let { restrictionByCS = {}, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
+    if (!molecule) {
+        throw new Error('It is needed a OCL molecule instance to assign');
+    }
+    (0, openchemlib_utils_1.addDiastereotopicMissingChirality)(molecule);
+    const { joinedSignals } = await (0, predictCarbon_1.predictCarbon)(molecule, predictionOptions);
+    checkAtomsAndDiaIDs(joinedSignals);
+    const copyRanges = checkIntegration(ranges);
+    const targets = {};
+    for (const range of copyRanges) {
+        const { id = (0, generateID_1.default)() } = range;
+        targets[id] = JSON.parse(JSON.stringify(range));
+    }
+    return (0, buildAssignments_1.buildAssignments)({
+        restrictionByCS,
+        timeout,
+        minScore,
+        nbAllowedUnAssigned,
+        maxSolutions,
+        targets,
+        joinedSignals,
+        useIntegrationRestriction: false,
+    });
+}
+exports.get13CAssignments = get13CAssignments;
+//# sourceMappingURL=get13CAssignments.js.map

package/lib/assignment/get13CAssignments.js.map

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package/lib/assignment/get1HAssignments.d.ts

@@ -0,0 +1,42 @@
+import { Molecule } from 'openchemlib';
+import { NMRRange } from '..';
+import { PredictProtonOptions } from '../prediction/predictProton';
+import { MakeMandatory } from '../types/MakeMandatory';
+import type { NMRSignal1D } from '../types/NMRSignal1D';
+import { RestrictionByCS } from './utils/buildAssignments';
+export declare type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<NMRSignal1D, 'atoms' | 'diaIDs' | 'nbAtoms'>;
+export declare type NMRRangeWithIntegration = MakeMandatory<NMRRange, 'integration'>;
+export interface Get1HAssignmentsOptions {
+    restrictionByCS?: Partial<RestrictionByCS>;
+    /**
+     * min score to accept an assignment
+     * @default 1
+     */
+    minScore?: number;
+    /**
+     * maximal number of assignments to return
+     * @default 10
+     */
+    maxSolutions?: number;
+    /**
+     * number of allowed unassignment signals
+     * @default 0
+     */
+    nbAllowedUnAssigned?: number;
+    /**
+     * time limit in miliseconds to finish the assignment procedure.
+     * @default 6000
+     */
+    timeout?: number;
+    /**
+     * prediction options
+     */
+    predictionOptions?: PredictProtonOptions;
+}
+export interface Targets {
+    [key: string]: NMRRangeWithIntegration;
+}
+export declare function get1HAssignments(ranges: NMRRange[], molecule: Molecule, options?: Get1HAssignmentsOptions): Promise<{
+    score: any;
+    assignment: unknown[];
+}[]>;

package/lib/assignment/get1HAssignments.js

@@ -0,0 +1,55 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.get1HAssignments = void 0;
+const openchemlib_utils_1 = require("openchemlib-utils");
+const predictProton_1 = require("../prediction/predictProton");
+const buildAssignments_1 = require("./utils/buildAssignments");
+const generateID_1 = __importDefault(require("./utils/generateID"));
+function checkAtomsAndDiaIDs(signals) {
+    for (const signal of signals) {
+        if (!signal.atoms)
+            throw new Error('signal has not atoms property');
+        if (!signal.diaIDs)
+            throw new Error('signal has not diaIDs property');
+        if (!signal.nbAtoms)
+            throw new Error('signal has not nbAtoms property');
+    }
+}
+function checkForIntegration(ranges) {
+    for (let range of ranges) {
+        if (range.integration === undefined) {
+            throw new Error('ranges has not integration property');
+        }
+    }
+}
+async function get1HAssignments(ranges, molecule, options = {}) {
+    let { restrictionByCS, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned = 0, timeout = 6000, predictionOptions = {}, } = options;
+    if (!molecule) {
+        throw new Error('It is needed a OCL molecule instance to assign');
+    }
+    molecule.addImplicitHydrogens();
+    (0, openchemlib_utils_1.addDiastereotopicMissingChirality)(molecule);
+    const { joinedSignals } = await (0, predictProton_1.predictProton)(molecule, predictionOptions);
+    checkForIntegration(ranges);
+    checkAtomsAndDiaIDs(joinedSignals);
+    const targets = {};
+    for (const range of ranges) {
+        const { id = (0, generateID_1.default)() } = range;
+        targets[id] = JSON.parse(JSON.stringify(range));
+    }
+    return (0, buildAssignments_1.buildAssignments)({
+        restrictionByCS,
+        timeout,
+        minScore,
+        nbAllowedUnAssigned,
+        maxSolutions,
+        targets,
+        joinedSignals,
+        useIntegrationRestriction: true,
+    });
+}
+exports.get1HAssignments = get1HAssignments;
+//# sourceMappingURL=get1HAssignments.js.map

package/lib/assignment/get1HAssignments.js.map

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

@@ -0,0 +1,33 @@
+import treeSet from 'ml-tree-set';
+import { Targets, NMRSignal1DWithAtomsAndDiaIDs } from '../get1HAssignments';
+export interface RestrictionByCS {
+    chemicalShiftRestriction: boolean;
+    tolerance: number;
+    useChemicalShiftScore: boolean;
+}
+export interface BuildAssignmentsProps {
+    restrictionByCS?: Partial<RestrictionByCS>;
+    timeout: number;
+    minScore: number;
+    useIntegrationRestriction: boolean;
+    nbAllowedUnAssigned: number;
+    maxSolutions: number;
+    targets: Targets;
+    joinedSignals: NMRSignal1DWithAtomsAndDiaIDs[];
+}
+export interface Signals1DAssignment extends NMRSignal1DWithAtomsAndDiaIDs {
+    diaIDIndex: number;
+    allHydrogens: number;
+    error?: number;
+}
+export interface Predictions1Dassignments {
+    [key: string]: Signals1DAssignment;
+}
+export interface StoreAssignments1D {
+    solutions: treeSet;
+    nSolutions: number;
+}
+export declare function buildAssignments(props: BuildAssignmentsProps): Promise<{
+    score: any;
+    assignment: unknown[];
+}[]>;

package/lib/assignment/utils/buildAssignments.js

@@ -0,0 +1,93 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.buildAssignments = void 0;
+const ml_tree_set_1 = __importDefault(require("ml-tree-set"));
+const createMapPossibleAssignments_1 = require("./createMapPossibleAssignments");
+const exploreTreeRec_1 = require("./exploreTreeRec");
+const comparator = (a, b) => {
+    return b.score - a.score;
+};
+async function buildAssignments(props) {
+    const { restrictionByCS = {}, useIntegrationRestriction, timeout, minScore, nbAllowedUnAssigned, maxSolutions, targets, joinedSignals, } = props;
+    const { tolerance = 1, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
+    let date = new Date();
+    let timeStart = date.getTime();
+    let store = {
+        solutions: new ml_tree_set_1.default(comparator),
+        nSolutions: 0,
+    };
+    let nSources = joinedSignals.length;
+    const predictions = {};
+    for (let prediction of joinedSignals) {
+        const diaID = prediction.diaIDs[0];
+        const index = prediction.atoms[0];
+        predictions[diaID] = {
+            ...prediction,
+            diaIDIndex: index,
+            allHydrogens: prediction.nbAtoms,
+        };
+    }
+    const possibleAssignmentMap = (0, createMapPossibleAssignments_1.createMapPossibleAssignments)({
+        restrictionByCS: {
+            tolerance,
+            useChemicalShiftScore,
+            chemicalShiftRestriction,
+        },
+        useIntegrationRestriction,
+        predictions,
+        targets,
+    });
+    const diaIDPeerPossibleAssignment = Object.keys(possibleAssignmentMap);
+    let partial = fillPartial(nSources);
+    store = {
+        solutions: new ml_tree_set_1.default(comparator),
+        nSolutions: 0,
+    };
+    (0, exploreTreeRec_1.exploreTreeRec)({
+        nSources,
+        restrictionByCS: {
+            tolerance,
+            useChemicalShiftScore,
+            chemicalShiftRestriction,
+        },
+        timeout,
+        timeStart,
+        targets,
+        predictions,
+        maxSolutions,
+        lowerBoundScore: minScore,
+        nbAllowedUnAssigned,
+        possibleAssignmentMap,
+        diaIDPeerPossibleAssignment,
+        useIntegrationRestriction,
+    }, 0, partial, store);
+    const assignments = [];
+    for (const solution of store.solutions.elements) {
+        const { assignment, score } = solution;
+        const currentAssignment = JSON.parse(JSON.stringify(targets));
+        for (let i = 0; i < assignment.length; i++) {
+            let range = currentAssignment[assignment[i]];
+            if (!range.diaIDs)
+                range.diaIDs = [];
+            if (assignment[i])
+                range.diaIDs.push(diaIDPeerPossibleAssignment[i]);
+        }
+        assignments.push({
+            score,
+            assignment: Object.values(currentAssignment),
+        });
+    }
+    return assignments;
+}
+exports.buildAssignments = buildAssignments;
+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/assignment/utils/buildAssignments.js.map

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

@@ -0,0 +1,15 @@
+import { MakeMandatory } from '../../types/MakeMandatory';
+import type { Targets } from '../get1HAssignments';
+import type { RestrictionByCS, Predictions1Dassignments } from './buildAssignments';
+declare type RestrictionByCSMandatory = MakeMandatory<RestrictionByCS, 'chemicalShiftRestriction' | 'tolerance' | 'useChemicalShiftScore'>;
+interface CreateMapPossibleAssignments {
+    predictions: Predictions1Dassignments;
+    restrictionByCS: RestrictionByCSMandatory;
+    targets: Targets;
+    useIntegrationRestriction: boolean;
+}
+export interface PossibleAssignmentMap {
+    [key: string]: string[];
+}
+export declare function createMapPossibleAssignments(props: CreateMapPossibleAssignments): PossibleAssignmentMap;
+export {};

package/lib/assignment/utils/createMapPossibleAssignments.js

@@ -0,0 +1,51 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createMapPossibleAssignments = void 0;
+function createMapPossibleAssignments(props) {
+    const { restrictionByCS, predictions, targets, useIntegrationRestriction } = props;
+    const { tolerance: toleranceCS, chemicalShiftRestriction } = restrictionByCS;
+    let errorAbs = Math.abs(toleranceCS);
+    const expandMap = {};
+    for (const diaID in predictions) {
+        let prediction = predictions[diaID];
+        if (prediction.error)
+            prediction.error = Math.abs(prediction.error);
+        expandMap[diaID] = [];
+        if (targets) {
+            for (const targetID in targets) {
+                let target = targets[targetID];
+                const { nbAtoms } = prediction;
+                const { integration } = target;
+                const couldBeAssigned = useIntegrationRestriction
+                    ? integration > 0
+                        ? nbAtoms - integration < 1
+                        : true
+                    : true;
+                if (couldBeAssigned) {
+                    if (!chemicalShiftRestriction ||
+                        typeof prediction.delta === 'undefined') {
+                        // Chemical shift is not a restriction
+                        expandMap[diaID].push(targetID);
+                    }
+                    else {
+                        let error = errorAbs;
+                        if (prediction.error) {
+                            error = Math.max(error, prediction.error);
+                        }
+                        const delta = target.signals && target.signals.length > 0
+                            ? target.signals[0].delta
+                            : (target.to + target.from) / 2;
+                        let distAfterLimit = Math.abs(prediction.delta - delta - errorAbs);
+                        if (distAfterLimit < 4 * errorAbs) {
+                            expandMap[diaID].push(targetID);
+                        }
+                    }
+                }
+            }
+        }
+        expandMap[diaID].push('*');
+    }
+    return expandMap;
+}
+exports.createMapPossibleAssignments = createMapPossibleAssignments;
+//# sourceMappingURL=createMapPossibleAssignments.js.map

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

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

@@ -0,0 +1,22 @@
+import type { Targets } from '../get1HAssignments';
+import type { RestrictionByCS, StoreAssignments1D, Predictions1Dassignments } from './buildAssignments';
+import type { PossibleAssignmentMap } from './createMapPossibleAssignments';
+export interface ExploreTreeRecProps {
+    nSources: number;
+    restrictionByCS: RestrictionByCS;
+    timeout: number;
+    timeStart: number;
+    maxSolutions: number;
+    targets: Targets;
+    useIntegrationRestriction: boolean;
+    predictions: Predictions1Dassignments;
+    lowerBoundScore: number;
+    nbAllowedUnAssigned: number;
+    possibleAssignmentMap: PossibleAssignmentMap;
+    diaIDPeerPossibleAssignment: string[];
+}
+export declare function exploreTreeRec(props: ExploreTreeRecProps, currentIndex: number, partial: Array<string | null>, store: StoreAssignments1D): StoreAssignments1D | undefined;
+export interface SolutionAssignment {
+    assignment: string[];
+    score: number;
+}

package/lib/assignment/utils/exploreTreeRec.js

@@ -0,0 +1,77 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.exploreTreeRec = void 0;
+const partialScore_1 = require("./partialScore");
+function exploreTreeRec(props, currentIndex, partial, store) {
+    const { nSources, restrictionByCS, timeout, timeStart, maxSolutions, targets, predictions, lowerBoundScore, nbAllowedUnAssigned, possibleAssignmentMap, useIntegrationRestriction, diaIDPeerPossibleAssignment, } = props;
+    const currentDate = new Date();
+    if (currentDate.getTime() - timeStart > timeout) {
+        new Error('timeout expired');
+        return store;
+    }
+    const diaID = diaIDPeerPossibleAssignment[currentIndex];
+    const possibleAssignments = possibleAssignmentMap[diaID];
+    for (let targetID of possibleAssignments) {
+        partial[currentIndex] = targetID;
+        let score = (0, partialScore_1.partialScore)(partial, {
+            useIntegrationRestriction,
+            diaIDPeerPossibleAssignment,
+            nbAllowedUnAssigned,
+            restrictionByCS,
+            predictions,
+            targets,
+        });
+        if (score === 0) {
+            if (targetID === '*') {
+                partial[currentIndex] = null;
+            }
+            continue;
+        }
+        if (currentIndex === nSources - 1 && score >= lowerBoundScore) {
+            addSolution(store, { predictions, partial, score, maxSolutions });
+        }
+        else if (currentIndex < nSources - 1) {
+            exploreTreeRec({
+                nSources,
+                restrictionByCS,
+                timeout,
+                timeStart,
+                maxSolutions,
+                targets,
+                predictions,
+                lowerBoundScore,
+                nbAllowedUnAssigned,
+                possibleAssignmentMap,
+                useIntegrationRestriction,
+                diaIDPeerPossibleAssignment,
+            }, currentIndex + 1, JSON.parse(JSON.stringify(partial)), store);
+        }
+    }
+}
+exports.exploreTreeRec = exploreTreeRec;
+function addSolution(store, props) {
+    let { score, maxSolutions, partial, predictions } = props;
+    score /= doubleAssignmentPenalty(partial, predictions);
+    store.nSolutions++;
+    let solution = {
+        assignment: JSON.parse(JSON.stringify(partial)),
+        score: 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 doubleAssignmentPenalty(partial, predictions) {
+    const nbSources = Object.keys(predictions).length;
+    let assignments = new Set(partial);
+    let nbDoubleAssignment = nbSources - assignments.size;
+    return nbDoubleAssignment > 0 ? 2 * nbDoubleAssignment : 1;
+}
+//# sourceMappingURL=exploreTreeRec.js.map

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

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

@@ -0,0 +1 @@
+export default function generateID(): string;

package/lib/assignment/utils/generateID.js

@@ -0,0 +1,13 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const BASE62 = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
+const LENGTH = 8;
+function generateID() {
+    let id = '';
+    for (let i = 0; i < LENGTH; i++) {
+        id += BASE62.charAt(Math.floor(Math.random() * 62));
+    }
+    return id;
+}
+exports.default = generateID;
+//# sourceMappingURL=generateID.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"generateID.js","sourceRoot":"","sources":["../../../src/assignment/utils/generateID.ts"],"names":[],"mappings":";;AAAA,MAAM,MAAM,GAAG,gEAAgE,CAAC;AAEhF,MAAM,MAAM,GAAG,CAAC,CAAC;AAEjB,SAAwB,UAAU;IAChC,IAAI,EAAE,GAAG,EAAE,CAAC;IACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,EAAE,IAAI,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAC;KACrD;IACD,OAAO,EAAE,CAAC;AACZ,CAAC;AAND,6BAMC"}

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

@@ -0,0 +1,16 @@
+import { Targets } from '../get1HAssignments';
+import type { Predictions1Dassignments, RestrictionByCS } from './buildAssignments';
+interface PartialScoreOptions {
+    restrictionByCS: RestrictionByCS;
+    /**
+     * number of allowed unassignment signals
+     * @default 0
+     */
+    useIntegrationRestriction: boolean;
+    nbAllowedUnAssigned: number;
+    diaIDPeerPossibleAssignment: string[];
+    predictions: Predictions1Dassignments;
+    targets: Targets;
+}
+export declare function partialScore(partial: Array<string | null>, options: PartialScoreOptions): number;
+export {};