nmr-processing 3.3.3 → 4.0.0

package/lib/ranges/rangesToXY.d.ts

@@ -1,4 +1,4 @@
-import type { Shape1DOptions } from 'spectrum-generator';
+import type { Shape1D } from 'ml-peak-shape-generator';
 import type { NMRRange } from '../types/NMRRange';
 export interface RangeToXYOptions {
     /**
@@ -30,7 +30,7 @@ export interface RangeToXYOptions {
      * options of signals.
      * @default { kind: 'gaussian' }
      */
-    shape: Shape1DOptions;
+    shape: Shape1D;
 }
 export declare function rangesToXY(ranges: NMRRange[], options?: any): {
     x: number[];

package/lib/ranges/rangesToXY.js

@@ -31,7 +31,15 @@ function rangesToXY(ranges, options = {}) {
     };
     let spectrum = new Float64Array(nbPoints);
     for (const range of ranges) {
-        const { integration, signals } = range;
+        const { integration, signals = [] } = range;
+        const { multiplicity: rangeMulplicity = '' } = range;
+        if (rangeMulplicity === 'm' && signals.length < 1) {
+            const { from, to } = range;
+            signals.push({
+                delta: (from + to) / 2,
+                multiplicity: 'm',
+            });
+        }
         let rangeSpectrum = new Float64Array(nbPoints);
         for (const signal of signals) {
             const { multiplicity } = signal;
@@ -96,8 +104,8 @@ function normalizeSpectrum(spectrum, signals, options = {}) {
         return acc + integration;
     }, 0), } = options;
     const sum = spectrum.reduce((acc, element) => acc + element, 0);
-    const norma = (integration / sum) * 1e6;
     if (sum !== 0) {
+        const norma = (integration / sum) * 1e6;
         for (let i = 0; i < spectrum.length; i++) {
             spectrum[i] *= norma;
         }

package/lib/ranges/rangesToXY.js.map

@@ -1 +1 @@
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package/lib/signals/signals2DToZ.d.ts

@@ -1,6 +1,6 @@
 import type { XYNumber } from 'spectrum-generator';
 import type { NMRSignal2D } from '../types/NMRSignal2D';
-interface signals2DToZOptions {
+interface Signals2DToZOptions {
     /**
      * lower limit in the spectrum, if it is a number the value will be defined for both axes
      * @default -1
@@ -29,5 +29,5 @@ export interface Peak2DSeries {
     y: number[];
     z: number[];
 }
-export declare function signals2DToZ(signals: NMRSignal2D[], options?: signals2DToZOptions): import("spectrum-generator").Spectrum2D;
+export declare function signals2DToZ(signals: NMRSignal2D[], options?: Signals2DToZOptions): import("spectrum-generator").Spectrum2D;
 export {};

package/lib/signals/signalsToXY.d.ts

@@ -1,4 +1,4 @@
-import type { Shape1DOptions } from 'spectrum-generator';
+import type { Shape1D } from 'ml-peak-shape-generator';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
 export interface OptionsSignalsToXY {
     frequency?: number;
@@ -15,7 +15,7 @@ export interface OptionsSignalsToXY {
     /**
      * Shape options for ml-spectrum-generator
      */
-    shape?: Shape1DOptions;
+    shape?: Shape1D;
     /**
      * The linewidth of the output spectrum, expresed in Hz.
      * @default 1

package/lib/signals/simulation/simulate1D.d.ts

@@ -1,4 +1,5 @@
-import type { Shape1DOptions } from 'spectrum-generator';
+import { DataXY } from 'cheminfo-types';
+import type { Shape1D } from 'ml-peak-shape-generator';
 import type { SpinSystem } from '../../types/spinSystem';
 interface Simulate1DOptions {
     /**
@@ -35,7 +36,7 @@ interface Simulate1DOptions {
      * Shape options
      * @default {kind:'gaussian'}
      */
-    shape?: Shape1DOptions;
+    shape?: Shape1D;
 }
 /**
  * This function simulates a one dimensional nmr spectrum. This function returns an array containing the relative intensities of the spectrum in the specified simulation window (from-to).
@@ -44,5 +45,5 @@ export default function simulate1D(
 /**
  * The SpinSystem object to be simulated
  */
-spinSystem: SpinSystem, options?: Simulate1DOptions): import("cheminfo-types").DataXY<import("cheminfo-types").DoubleArray>;
+spinSystem: SpinSystem, options?: Simulate1DOptions): DataXY;
 export {};

package/lib/signals/simulation/simulate1D.js.map

@@ -1 +1 @@
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package/lib/types/NMRPeak1D.d.ts

@@ -1,11 +1,4 @@
-export interface NMRPeak1D {
+import type { Peak1D } from 'ml-gsd';
+export interface NMRPeak1D extends Peak1D {
     kind?: string;
-    x: number;
-    y: number;
-    shape: {
-        width: number;
-        noiseLevel?: number;
-        soft?: boolean;
-        kind?: string;
-    };
 }

package/lib/types/NMRRange.d.ts

@@ -2,6 +2,7 @@ import type { NMRSignal1D } from './NMRSignal1D';
 export interface NMRRange {
     from: number;
     to: number;
+    id?: string;
     diaIDs?: string[];
     kind?: string;
     pubIntegral?: number;

package/lib/types/NMRSignal1D.d.ts

@@ -1,7 +1,8 @@
-import type { GSDPeak } from 'ml-gsd';
+import type { NMRPeak1D } from './NMRPeak1D';
 import type { Jcoupling } from './jcoupling';
 export interface NMRSignal1D {
     delta: number;
+    id?: string;
     js?: Jcoupling[];
     atoms?: number[];
     assignment?: string;
@@ -10,7 +11,7 @@ export interface NMRSignal1D {
     diaIDs?: string[];
     nbAtoms?: number;
     integration?: number;
-    peaks?: GSDPeak[];
+    peaks?: NMRPeak1D[];
     statistic?: {
         mean: number;
         sd: number;

package/lib/types/NMRSignal2D.d.ts

@@ -13,6 +13,7 @@ export interface Signal2DAxisData {
 export interface NMRSignal2D {
     x: Signal2DAxisData;
     y: Signal2DAxisData;
+    id?: string;
     peaks?: MPFPeak[];
     kind?: string;
     _highlight?: (number | string)[];

package/lib/types/NMRZone.d.ts

@@ -1,11 +1,12 @@
 import type { NMRSignal2D } from "./NMRSignal2D";
-interface fromTo {
+interface FromTo {
     from: number;
     to: number;
 }
 export interface NMRZone {
-    x: fromTo;
-    y: fromTo;
+    x: FromTo;
+    y: FromTo;
+    id?: string;
     signals: NMRSignal2D;
 }
 export {};

package/lib/xy/xyAutoPeaksPicking.d.ts

@@ -1,68 +1,13 @@
 import { DataXY } from 'cheminfo-types';
-import type { NMRPeak1D } from '../types/NMRPeak1D';
-interface OptionsGetPeakList {
-    /**
-     * Noise threshold in spectrum y units. Default is three/thresholdFactor times the absolute median of data.y.
-     * @default `median(data.y) * (options.thresholdFactor || 3)`
-     */
-    noiseLevel?: number;
-    /**
-     * Threshold to determine if a given peak should be considered as a noise, bases on its relative height compared to the highest peak.
-     * @default 0.01
-     */
-    minMaxRatio: number;
-    /**
-     * If broadRatio is higher than 0, then all the peaks which second derivative smaller than broadRatio * maxAbsSecondDerivative will be marked with the soft mask equal to true.
-     * @default 0.00025
-     */
-    broadRatio: number;
-    /**
-     * Select the peak intensities from a smoothed version of the independent variables.
-     * @default true
-     */
-    smoothY: boolean;
+import type { Peak1D, IGSDOptions, IOptimizePeaksOptions, IJoinBroadPeaksOptions } from 'ml-gsd';
+export interface IGetPeakListOptions extends IGSDOptions, IOptimizePeaksOptions, IJoinBroadPeaksOptions {
     /**
      * If it is true, the peaks parameters will be optimized.
      * @default false
      */
     optimize: boolean;
-    /**
-     * factor to determine the width at the moment to group the peaks in signals in 'GSD.optimizePeaks' function.
-     * @default 4
-     */
-    factorWidth: number;
-    /**
-     * if it is true, it optimizes the x and intensity by extrapolation.
-     */
-    realTopDetection: boolean;
-    /**
-     * options to shape used to adapt the FWHM
-     * @default {kind:'gaussian'}
-     */
-    shape: {
-        kind: string;
-    };
-    /**
-     * options for optimization step, kind represent the algorithm
-     * @default {kind:'lm'}
-     */
-    optimization: {
-        kind: string;
-    };
-    /**
-     * Threshold to determine if some peak is candidate to clustering into range.
-     * @default 0.25
-     */
-    broadWidth: number;
-    /**
-     * Options for savitz Golay
-     */
-    sgOptions: {
-        windowSize: number;
-        polynomial: number;
-    };
 }
-export interface OptionsXYAutoPeaksPicking extends Partial<OptionsGetPeakList> {
+export interface OptionsXYAutoPeaksPicking extends Partial<IGetPeakListOptions> {
     /**
      * Low limit value in the x axis to extract a sub set of points from the input data.
      */
@@ -87,5 +32,4 @@ export interface OptionsXYAutoPeaksPicking extends Partial<OptionsGetPeakList> {
      */
     useSanPlot?: boolean;
 }
-export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): NMRPeak1D[];
-export {};
+export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): Peak1D[];

package/lib/xy/xyAutoPeaksPicking.js

@@ -36,14 +36,14 @@ function getPeakList(data, options) {
         shape,
         sgOptions,
         minMaxRatio,
-        broadRatio,
         noiseLevel,
         smoothY,
         realTopDetection,
     });
     if (broadWidth) {
-        peakList = (0, ml_gsd_1.joinBroadPeaks)(peakList, {
-            width: broadWidth,
+        peakList = (0, ml_gsd_1.joinBroadPeaks)(data, peakList, {
+            broadRatio,
+            broadWidth,
             shape,
             optimization,
         });

package/lib/xy/xyAutoPeaksPicking.js.map

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

@@ -0,0 +1,47 @@
+import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
+import { predictCarbon, } from '../prediction/predictCarbon';
+import { buildAssignments } from './utils/buildAssignments';
+import generateID from './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;
+}
+export 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');
+    }
+    addDiastereotopicMissingChirality(molecule);
+    const { joinedSignals } = await predictCarbon(molecule, predictionOptions);
+    checkAtomsAndDiaIDs(joinedSignals);
+    const copyRanges = checkIntegration(ranges);
+    const targets = {};
+    for (const range of copyRanges) {
+        const { id = generateID() } = range;
+        targets[id] = JSON.parse(JSON.stringify(range));
+    }
+    return buildAssignments({
+        restrictionByCS,
+        timeout,
+        minScore,
+        nbAllowedUnAssigned,
+        maxSolutions,
+        targets,
+        joinedSignals,
+        useIntegrationRestriction: false,
+    });
+}
+//# sourceMappingURL=get13CAssignments.js.map

package/lib-esm/assignment/get13CAssignments.js.map

@@ -0,0 +1 @@
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package/lib-esm/assignment/get1HAssignments.js

@@ -0,0 +1,48 @@
+import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
+import { predictProton, } from '../prediction/predictProton';
+import { buildAssignments } from './utils/buildAssignments';
+import generateID from './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');
+        }
+    }
+}
+export 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();
+    addDiastereotopicMissingChirality(molecule);
+    const { joinedSignals } = await predictProton(molecule, predictionOptions);
+    checkForIntegration(ranges);
+    checkAtomsAndDiaIDs(joinedSignals);
+    const targets = {};
+    for (const range of ranges) {
+        const { id = generateID() } = range;
+        targets[id] = JSON.parse(JSON.stringify(range));
+    }
+    return buildAssignments({
+        restrictionByCS,
+        timeout,
+        minScore,
+        nbAllowedUnAssigned,
+        maxSolutions,
+        targets,
+        joinedSignals,
+        useIntegrationRestriction: true,
+    });
+}
+//# sourceMappingURL=get1HAssignments.js.map

package/lib-esm/assignment/get1HAssignments.js.map

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

@@ -0,0 +1,86 @@
+import treeSet from 'ml-tree-set';
+import { createMapPossibleAssignments } from './createMapPossibleAssignments';
+import { exploreTreeRec } from './exploreTreeRec';
+const comparator = (a, b) => {
+    return b.score - a.score;
+};
+export 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 treeSet(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 = createMapPossibleAssignments({
+        restrictionByCS: {
+            tolerance,
+            useChemicalShiftScore,
+            chemicalShiftRestriction,
+        },
+        useIntegrationRestriction,
+        predictions,
+        targets,
+    });
+    const diaIDPeerPossibleAssignment = Object.keys(possibleAssignmentMap);
+    let partial = fillPartial(nSources);
+    store = {
+        solutions: new treeSet(comparator),
+        nSolutions: 0,
+    };
+    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;
+}
+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/buildAssignments.js.map

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package/lib-esm/assignment/utils/createMapPossibleAssignments.js

@@ -0,0 +1,47 @@
+export 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;
+}
+//# sourceMappingURL=createMapPossibleAssignments.js.map

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

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