nmr-processing 7.4.3 → 8.2.0

package/lib/prediction/predictAllSpectra.js

@@ -1,40 +1,126 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.predictAllSpectra = void 0;
+const signals2DToZ_1 = require("../signals/signals2DToZ");
 const signalsToXY_1 = require("../signals/signalsToXY");
+const getFrequency_1 = require("../utilities/getFrequency");
 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 { simulation: simulationOptions = { oneD: {}, twoD: {} }, prediction: predictionOptions = {}, } = options;
+    const predictions = await (0, predictAll_1.predictAll)(molecule, predictionOptions);
     const spectra = [];
     const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
-    spectra.push(getProton(predictions.proton, options.simulation));
+    const oneDOptions = {
+        ...{
+            proton: { from: 0, to: 14 },
+            carbon: { from: 0, to: 200 },
+            nbPoints: 4098,
+            lineWidth: 0.03,
+        },
+        ...(simulationOptions.oneD || {}),
+    };
+    const twoDOptions = {
+        ...{
+            from: { x: oneDOptions.proton.from, y: oneDOptions.carbon.from },
+            to: { x: oneDOptions.proton.to, y: oneDOptions.carbon.to },
+            nbPoints: { x: 1024, y: 1024 },
+        },
+        ...(simulationOptions.twoD || {}),
+    };
+    for (const experiment in predictions) {
+        switch (experiment) {
+            case 'carbon':
+            case 'proton': {
+                spectra.push(get1DSpectrum(predictions[experiment], {
+                    nbPoints: oneDOptions.nbPoints,
+                    lineWidth: oneDOptions.lineWidth,
+                    ...oneDOptions[experiment],
+                    experiment,
+                    frequency: simulationOptions.frequency,
+                }));
+                break;
+            }
+            case 'cosy':
+            case 'hsqc':
+            case 'hmbc': {
+                spectra.push(get2DSpectrum(predictions[experiment], {
+                    ...twoDOptions,
+                    experiment,
+                    frequency: simulationOptions.frequency,
+                }));
+                break;
+            }
+            default:
+                break;
+        }
+    }
     return result;
 }
 exports.predictAllSpectra = predictAllSpectra;
-function getProton(prediction, options) {
-    const { x, y } = (0, signalsToXY_1.signalsToXY)(prediction.signals, options);
+function get2DSpectrum(prediction, options) {
+    const { signals, zones, nuclei } = prediction;
+    const { frequency: baseFrequency, experiment } = options;
+    const width = get2DWidth(nuclei);
+    const frequency = calculateFrequency(nuclei, baseFrequency);
+    const spectrumData = (0, signals2DToZ_1.signals2DToZ)(signals, {
+        ...options,
+        width,
+        factor: 3,
+    });
+    const spectrum = {
+        data: { ...spectrumData, noise: 0.01 },
+        info: {
+            nucleus: nuclei,
+            originFrequency: frequency,
+            baseFrequency: frequency,
+            pulseSequence: experiment,
+            experiment: '2d',
+        },
+        zones: { values: zones },
+    };
+    return spectrum;
+}
+function get2DWidth(nucleus) {
+    return nucleus[0] === nucleus[1] ? 0.02 : { x: 0.02, y: 0.2133 };
+}
+function get1DSpectrum(prediction, options) {
+    const { frequency = 400, experiment } = options;
+    const { signals, nucleus } = prediction;
+    const realFrequency = calculateFrequency(nucleus, frequency);
+    const { x, y } = (0, signalsToXY_1.signalsToXY)(signals, {
+        ...options,
+        frequency: realFrequency,
+    });
     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,
+            originFrequency: realFrequency,
+            baseFrequency: realFrequency,
             pulseSequence: 'prediction',
-            experiment: 'proton',
+            experiment,
             isFt: true,
         },
-        // todo: currently we disable the ranges because there is no ID
-        //ranges: { values: prediction.ranges },
+        ranges: { values: prediction.ranges },
     };
     return spectrum;
 }
+function calculateFrequency(nucleus, frequency) {
+    if (typeof nucleus === 'string') {
+        return (0, getFrequency_1.getFrequency)(nucleus, { nucleus: '1H', frequency });
+    }
+    else {
+        if (nucleus[0] === nucleus[1]) {
+            return `${frequency},${frequency}`;
+        }
+        else {
+            return `${frequency},${(0, getFrequency_1.getFrequency)(nucleus[1], {
+                nucleus: nucleus[0],
+                frequency,
+            })}`;
+        }
+    }
+}
 //# sourceMappingURL=predictAllSpectra.js.map

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package/lib/ranges/markSolventSignal.d.ts

@@ -0,0 +1,3 @@
+import { NMRSignal1D } from '../signals/NMRSignal1D';
+import { NMRRange } from '../xy/NMRRange';
+export declare function markSolventPeaks<T extends NMRRange>(input: T[], solventSignals: NMRSignal1D[], options?: any): T[];

package/lib/ranges/markSolventSignal.js

@@ -0,0 +1,107 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.markSolventPeaks = void 0;
+const generateID_1 = __importDefault(require("../assignment/utils/generateID"));
+const checkIDs_1 = require("../assignment/utils/getAssignment/checkIDs");
+const peaksToRanges_1 = require("../peaks/peaksToRanges");
+const solventSuppression_1 = require("../peaks/solventSuppression");
+function markSolventPeaks(input, solventSignals, options = {}) {
+    const { frequency = 400 } = options;
+    const ranges = (0, checkIDs_1.addIDs)([...input]);
+    let peakList = [];
+    for (const range of ranges) {
+        const rangeID = range.id;
+        for (const signal of range.signals || []) {
+            const signalID = signal.id;
+            for (let peak of signal.peaks || []) {
+                peakList.push({
+                    ...peak,
+                    rangeID,
+                    signalID,
+                });
+            }
+        }
+    }
+    const peaks = (0, solventSuppression_1.solventSuppression)(peakList, solventSignals, {
+        markSolventPeaks: true,
+    });
+    const signalsWithSolvent = getSignalIDsWithSolvent(peaks);
+    for (let range of ranges) {
+        if (!range.signals)
+            continue;
+        for (let signal of range.signals) {
+            if (!signalsWithSolvent.includes(signal.id))
+                continue;
+            const signalPeaks = [];
+            const solventSignalPeaks = [];
+            for (let peak of peaks) {
+                if (peak.signalID === signal.id) {
+                    const { signalID, rangeID, ...newPeak } = peak;
+                    if (peak.kind === 'solvent') {
+                        solventSignalPeaks.push(newPeak);
+                    }
+                    else {
+                        signalPeaks.push(newPeak);
+                    }
+                }
+            }
+            const newSignals = signalPeaks.length > 0
+                ? (0, peaksToRanges_1.detectSignals)({ x: [], y: [] }, signalPeaks, {
+                    integralType: 'peak',
+                    frequency,
+                })
+                : [];
+            solventSignalPeaks.sort((a, b) => a.x - b.x);
+            const lowPPMValue = solventSignalPeaks[0].x;
+            const highPPMValue = solventSignalPeaks[solventSignalPeaks.length - 1].x;
+            const newSolventSignals = (0, peaksToRanges_1.detectSignals)({ x: [], y: [] }, solventSignalPeaks, {
+                integralType: 'peak',
+                frequencyCluster: (highPPMValue - lowPPMValue) * frequency,
+                frequency,
+            });
+            range.signals = [
+                ...adaptSignals(newSignals),
+                ...adaptSignals(newSolventSignals),
+                ...range.signals.filter((currSignal) => currSignal.id !== signal.id),
+            ];
+        }
+    }
+    return ranges;
+}
+exports.markSolventPeaks = markSolventPeaks;
+function getSignalIDsWithSolvent(solventPeaks) {
+    const uniqueSignalID = new Set();
+    for (let peak of solventPeaks) {
+        if (peak.kind !== 'solvent')
+            continue;
+        uniqueSignalID.add(peak.signalID);
+    }
+    return Array.from(uniqueSignalID);
+}
+function adaptSignals(signals) {
+    const newSignals = [];
+    for (let signal of signals) {
+        const signalResult = {
+            id: (0, generateID_1.default)(),
+            delta: signal.delta,
+            kind: signal.kind || 'signal',
+            multiplicity: signal.multiplicity,
+            integration: signal.integralData.value,
+        };
+        signalResult.peaks = signal.peaks.map((peak) => {
+            const newResult = {
+                y: peak.intensity,
+                ...peak,
+            };
+            delete newResult.intensity;
+            return newResult;
+        });
+        signalResult.js = signal.nmrJs || [];
+        newSignals.push(signalResult);
+    }
+    return newSignals;
+}
+//# sourceMappingURL=markSolventSignal.js.map

package/lib/ranges/markSolventSignal.js.map

@@ -0,0 +1 @@
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package/lib/ranges/rangesToXY.js

@@ -13,17 +13,26 @@ function checkForSignals(ranges) {
             throw new Error('range has not signals');
     }
 }
+const defaultFromTo = (nucleus = '') => {
+    switch (nucleus.toUpperCase()) {
+        case '13C':
+            return { from: -5, to: 206 };
+        default:
+            return { from: -0.5, to: 10.5 };
+    }
+};
 function rangesToXY(ranges, options = {}) {
     checkForSignals(ranges);
-    let { frequency = 400, lineWidth = 1, from = 0, to = 10, nbPoints = 16 * 1024, shape = { kind: 'gaussian' }, } = options;
+    let { frequency = 400, lineWidth = 1, nbPoints = 16 * 1024, shape = { kind: 'gaussian' }, } = options;
     const addSpectrum = (a, b) => {
         for (let i = 0; i < nbPoints; i++) {
             a[i] += b[i];
         }
     };
+    const { from, to } = getFromTo(ranges, options);
     const spectrumOptions = {
-        from,
         to,
+        from,
         nbPoints,
         shape,
         lineWidth,
@@ -84,7 +93,7 @@ function broadPeakOrMultipletSpectrum(signals, options = {}) {
     return spectrumGenerator.getSpectrum();
 }
 function peaksOfMultiplet(delta, options) {
-    const { frequency, lineWidth, intensities = [1, 2, 5, 4, 5, 3, 4, 2, 1], } = options;
+    const { frequency, lineWidth, intensities = [1, 2, 5, 4, 5, 7, 5, 4, 5, 2, 1], } = options;
     const lineWidthPpm = lineWidth / frequency;
     const spaceBetweenPeaks = lineWidthPpm * 1.5;
     const peaks = [];
@@ -111,4 +120,19 @@ function normalizeSpectrum(spectrum, signals, options = {}) {
         }
     }
 }
+function getFromTo(ranges, options) {
+    const { from: defaultFrom, to: defaultTo } = defaultFromTo(options.nucleus);
+    let rangesFrom = Number.MAX_SAFE_INTEGER;
+    let rangesTo = Number.MIN_SAFE_INTEGER;
+    for (const range of ranges) {
+        for (const signal of range.signals || []) {
+            if (rangesFrom > signal.delta)
+                rangesFrom = signal.delta;
+            if (rangesTo < signal.delta)
+                rangesTo = signal.delta;
+        }
+    }
+    const { from = Math.min(rangesFrom - 0.5, defaultFrom), to = Math.max(rangesTo + 0.5, defaultTo), } = options;
+    return { from, to };
+}
 //# sourceMappingURL=rangesToXY.js.map

package/lib/ranges/rangesToXY.js.map

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package/lib/signals/addDummySignals.d.ts

@@ -0,0 +1,2 @@
+import { NMRSignal1D } from './NMRSignal1D';
+export declare function addDummySignals(signals: NMRSignal1D[]): NMRSignal1D[];

package/lib/signals/addDummySignals.js

@@ -0,0 +1,56 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.addDummySignals = void 0;
+const couplingPatterns_1 = require("../constants/couplingPatterns");
+function addDummySignals(signals) {
+    let newSignals = JSON.parse(JSON.stringify(signals));
+    signals.forEach((signal, s) => {
+        const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
+        let { newCouplings, tempSignals } = checkCouplings(jCouplings, newSignals, signalAssignment);
+        if (tempSignals.length > 0)
+            newSignals.push(...tempSignals);
+        newSignals[s].js = newCouplings;
+        newSignals[s].atoms = signalAssignment;
+    });
+    return newSignals.sort((a, b) => a.delta - b.delta);
+}
+exports.addDummySignals = addDummySignals;
+function checkCouplings(jCouplings, signals, signalAssignment) {
+    let newSignalAssignment = signals.length - 1;
+    let tempSignals = [];
+    const newCouplings = jCouplings.reduce((newCouplings, jCoupling) => {
+        const { atoms = [], multiplicity, coupling } = jCoupling;
+        if (atoms.length === 0) {
+            if (coupling && multiplicity) {
+                let tempCouplings = [];
+                const nbLinks = couplingPatterns_1.couplingPatterns.indexOf(multiplicity);
+                for (let i = 0; i < nbLinks; i++) {
+                    newSignalAssignment++;
+                    tempCouplings.push({
+                        coupling,
+                        atoms: [newSignalAssignment],
+                    });
+                    tempSignals.push(formatSignal(coupling, [newSignalAssignment], signalAssignment));
+                }
+            }
+            else {
+                newCouplings.push(jCoupling);
+            }
+        }
+        return newCouplings;
+    }, []);
+    return { newCouplings, tempSignals };
+}
+function formatSignal(coupling, newSignalAssignment, signalAssignment) {
+    return {
+        delta: 100000,
+        atoms: newSignalAssignment,
+        js: [
+            {
+                coupling,
+                atoms: signalAssignment,
+            },
+        ],
+    };
+}
+//# sourceMappingURL=addDummySignals.js.map

package/lib/signals/addDummySignals.js.map

@@ -0,0 +1 @@
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package/lib/signals/hackSignalsToXY.js

@@ -1,61 +1,15 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.hackSignalsToXY = void 0;
-const couplingPatterns_1 = require("../constants/couplingPatterns");
+const addDummySignals_1 = require("./addDummySignals");
 const signalsToXY_1 = require("./signalsToXY");
 /**
  * Create the xy object from an array of 1D signals.
  * @param signals Array of signals with assigned or unassigned couplings.
  */
 function hackSignalsToXY(signals, options = {}) {
-    let newSignals = JSON.parse(JSON.stringify(signals));
-    signals.forEach((signal, s) => {
-        const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
-        let { newCouplings, tempSignals } = checkCouplings(jCouplings, newSignals, signalAssignment);
-        if (tempSignals.length > 0)
-            newSignals.push(...tempSignals);
-        newSignals[s].js = newCouplings;
-        newSignals[s].atoms = signalAssignment;
-    });
+    let newSignals = (0, addDummySignals_1.addDummySignals)(signals);
     return (0, signalsToXY_1.signalsToXY)(newSignals, options);
 }
 exports.hackSignalsToXY = hackSignalsToXY;
-function checkCouplings(jCouplings, signals, signalAssignment) {
-    let newSignalAssignment = signals.length - 1;
-    let tempSignals = [];
-    const newCouplings = jCouplings.reduce((newCouplings, jCoupling) => {
-        const { atoms = [], multiplicity, coupling } = jCoupling;
-        if (atoms.length === 0) {
-            if (coupling && multiplicity) {
-                let tempCouplings = [];
-                const nbLinks = couplingPatterns_1.couplingPatterns.indexOf(multiplicity);
-                for (let i = 0; i < nbLinks; i++) {
-                    newSignalAssignment++;
-                    tempCouplings.push({
-                        coupling,
-                        atoms: [newSignalAssignment],
-                    });
-                    tempSignals.push(formatSignal(coupling, [newSignalAssignment], signalAssignment));
-                }
-            }
-            else {
-                newCouplings.push(jCoupling);
-            }
-        }
-        return newCouplings;
-    }, []);
-    return { newCouplings, tempSignals };
-}
-function formatSignal(coupling, newSignalAssignment, signalAssignment) {
-    return {
-        delta: 100000,
-        atoms: newSignalAssignment,
-        js: [
-            {
-                coupling,
-                atoms: signalAssignment,
-            },
-        ],
-    };
-}
 //# sourceMappingURL=hackSignalsToXY.js.map

package/lib/signals/hackSignalsToXY.js.map

@@ -1 +1 @@
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+{"version":3,"file":"hackSignalsToXY.js","sourceRoot":"","sources":["../../src/signals/hackSignalsToXY.ts"],"names":[],"mappings":";;;AACA,uDAAoD;AACpD,+CAAgE;AAEhE;;;GAGG;AAEH,SAAgB,eAAe,CAC7B,OAAsB,EACtB,UAA8B,EAAE;IAEhC,IAAI,UAAU,GAAG,IAAA,iCAAe,EAAC,OAAO,CAAC,CAAC;IAC1C,OAAO,IAAA,yBAAW,EAAC,UAAU,EAAE,OAAO,CAAC,CAAC;AAC1C,CAAC;AAND,0CAMC"}

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

@@ -1,43 +1,6 @@
 import { DataXY } from 'cheminfo-types';
-import type { Shape1D } from 'ml-peak-shape-generator';
 import type { SpinSystem } from '../spinSystem';
-interface Simulate1DOptions {
-    /**
-     * The linewidth of the output spectrum, expresed in Hz.
-     * @default 1
-     */
-    lineWidth?: number;
-    /**
-     * Maximum number of atoms on each cluster that can be considered to be simulated together. It affects the the quality and speed of the simulation.
-     * @default 8
-     */
-    maxClusterSize?: number;
-    /**
-     * The frequency in Mhz of the fake spectrometer that records the spectrum.
-     * @default 400
-     */
-    frequency?: number;
-    /**
-     * The low limit of the ordinate variable.
-     * @default 0
-     */
-    from?: number;
-    /**
-     * The upper limit of the ordinate variable.
-     * @default 10
-     */
-    to?: number;
-    /**
-     * Number of points of the output spectrum.
-     * @default 16K
-     */
-    nbPoints?: number;
-    /**
-     * Shape options
-     * @default {kind:'gaussian'}
-     */
-    shape?: Shape1D;
-}
+import type { Simulate1DOptions } from './simulateXYPeaks';
 /**
  * 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).
  */
@@ -46,4 +9,3 @@ export default function simulate1D(
  * The SpinSystem object to be simulated
  */
 spinSystem: SpinSystem, options?: Simulate1DOptions): DataXY;
-export {};