nmr-processing 8.0.0 → 8.1.0

package/lib/index.d.ts

@@ -1,4 +1,4 @@
-export * from './constants/gyromagneticRatio';
+export * from 'gyromagnetic-ratio';
 export * from './constants/impurities';
 export * from './constants/couplingPatterns';
 export * from './peaks/peaksFilterImpurities';

package/lib/index.js

@@ -14,7 +14,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-__exportStar(require("./constants/gyromagneticRatio"), exports);
+__exportStar(require("gyromagnetic-ratio"), exports);
 __exportStar(require("./constants/impurities"), exports);
 __exportStar(require("./constants/couplingPatterns"), exports);
 __exportStar(require("./peaks/peaksFilterImpurities"), exports);

package/lib/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,qDAAmC;AACnC,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAE9C,6DAA2C;AAC3C,6DAA2C;AAC3C,2DAAyC;AACzC,2DAAyC;AACzC,2DAAyC;AACzC,0DAAwC;AACxC,iEAA+C;AAE/C,gEAA8C;AAC9C,iEAA+C;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C"}

package/lib/peaks/NMRPeak1D.d.ts

@@ -2,6 +2,5 @@ import type { PeakXYWidth } from 'cheminfo-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
 export interface NMRPeak1D extends PeakXYWidth {
     kind?: string;
-    fwhm?: number;
     shape?: Shape1D;
 }

package/lib/peaks/solventSuppression.d.ts

@@ -0,0 +1,3 @@
+import { NMRSignal1D } from '../signals/NMRSignal1D';
+import { NMRPeak1D } from './NMRPeak1D';
+export declare function solventSuppression(peakList: NMRPeak1D[], solvent: NMRSignal1D[], options?: any): NMRPeak1D[];

package/lib/peaks/solventSuppression.js

@@ -0,0 +1,147 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.solventSuppression = void 0;
+const linear_sum_assignment_1 = __importDefault(require("linear-sum-assignment"));
+const ml_matrix_1 = require("ml-matrix");
+const ml_peak_shape_generator_1 = require("ml-peak-shape-generator");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const addDummySignals_1 = require("../signals/addDummySignals");
+const signalsToSpinSystem_1 = require("../signals/simulation/signalsToSpinSystem");
+const simulateXYPeaks_1 = require("../signals/simulation/simulateXYPeaks");
+const splitSpinSystem_1 = require("../signals/simulation/splitSpinSystem");
+function solventSuppression(peakList, solvent, options = {}) {
+    const peaks = [...peakList];
+    sortAscending(peaks);
+    const xValues = peaks.map((peak) => peak.x);
+    const { markSolventPeaks = false } = options;
+    let solventSignals = solvent; //addDummySignals(solvent);
+    // solventSignals = solventSignals.slice(0, solventSignals.findIndex((signal) => signal.delta > 400));
+    for (const solventSignal of solventSignals) {
+        const solventXYPeaks = solventSignal.peaks
+            ? solventSignal.peaks
+            : getSolventPeaks(solventSignal);
+        sortAscending(solventXYPeaks);
+        let upIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + 1);
+        let lowIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[0].x - 1);
+        if (upIndex === lowIndex)
+            continue;
+        const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
+        const amplitudeResiduals = [];
+        const deltaResiduals = [];
+        const positionResiduals = [];
+        for (let peak of nearPeaks) {
+            const shiftedSolventPeaks = getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks);
+            const closestPeaks = getClosestPeaks(shiftedSolventPeaks, nearPeaks);
+            let deltaResidual = 0;
+            let amplitudeResidual = 0;
+            let positionResidual = 0;
+            for (let i = 0; i < closestPeaks.length; i++) {
+                amplitudeResidual += Math.abs(shiftedSolventPeaks[i].y - closestPeaks[i].y);
+                deltaResidual += Math.abs(shiftedSolventPeaks[i].x - closestPeaks[i].x);
+            }
+            if (closestPeaks.length === 0) {
+                deltaResidual = Number.MAX_SAFE_INTEGER;
+                amplitudeResidual = Number.MAX_SAFE_INTEGER;
+                positionResidual = Number.MAX_SAFE_INTEGER;
+            }
+            else {
+                positionResidual = (0, ml_peak_shape_generator_1.gaussianFct)(solventSignal.delta - peak.x, 0.5);
+            }
+            amplitudeResiduals.push(amplitudeResidual);
+            deltaResiduals.push(deltaResidual);
+            positionResiduals.push(positionResidual);
+        }
+        const maxAmplitude = (0, ml_spectra_processing_1.xMaxValue)(amplitudeResiduals);
+        const maxDelta = (0, ml_spectra_processing_1.xMaxValue)(deltaResiduals);
+        const maxPosition = (0, ml_spectra_processing_1.xMaxValue)(positionResiduals);
+        let minIndex = -1;
+        let minScore = Number.MAX_SAFE_INTEGER;
+        for (let i = 0; i < deltaResiduals.length; i++) {
+            const value = (amplitudeResiduals[i] / maxAmplitude +
+                deltaResiduals[i] / maxDelta +
+                (1 - positionResiduals[i]) / maxPosition) /
+                3;
+            if (minScore > value) {
+                minIndex = i;
+                minScore = value;
+            }
+        }
+        const shiftedSolventPeaks = getShiftedSolventPeaks(nearPeaks[minIndex], solventSignal, solventXYPeaks);
+        const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+        const { rowAssignments, gain } = (0, linear_sum_assignment_1.default)(diff, {
+            maximaze: false,
+        });
+        if (gain === -1)
+            return peaks;
+        if (markSolventPeaks) {
+            for (let index of rowAssignments) {
+                peaks[index + lowIndex].kind = 'solvent';
+            }
+        }
+        else {
+            rowAssignments.sort((a, b) => b - a);
+            for (let index of rowAssignments) {
+                peaks.splice(index + lowIndex, 1);
+            }
+        }
+    }
+    return peaks;
+}
+exports.solventSuppression = solventSuppression;
+function getSolventPeaks(signal, options = {}) {
+    let signals = (0, addDummySignals_1.addDummySignals)([signal]);
+    let spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(signals);
+    const { frequency = 400, maxClusterSize = 8 } = options;
+    spinSystem.clusters = (0, splitSpinSystem_1.splitSpinSystem)(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = (0, simulateXYPeaks_1.simulateXYPeaks)(spinSystem);
+    return peaks.filter((peak) => peak.x < 1000);
+}
+function getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks) {
+    const shiftedSolventPeaks = JSON.parse(JSON.stringify(solventXYPeaks));
+    // shift x values of solventPeaks to center it to the current peak.
+    const deltaPPM = peak.x - solventSignal.delta;
+    const maxIntensity = shiftedSolventPeaks.reduce((max, current) => (current.y > max ? current.y : max), shiftedSolventPeaks[0].y);
+    for (let shiftedSolventPeak of shiftedSolventPeaks) {
+        shiftedSolventPeak.x += deltaPPM;
+        shiftedSolventPeak.y /= maxIntensity;
+    }
+    return shiftedSolventPeaks;
+}
+function getClosestPeaks(shiftedSolventPeaks, nearPeaks) {
+    const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+    const { rowAssignments, gain } = (0, linear_sum_assignment_1.default)(diff, {
+        maximaze: false,
+    });
+    if (gain === -1)
+        return [];
+    const assignmentPeaks = [];
+    let maxValue = Number.MIN_SAFE_INTEGER;
+    for (let index of rowAssignments) {
+        if (maxValue < nearPeaks[index].y)
+            maxValue = nearPeaks[index].y;
+        assignmentPeaks.push({ ...nearPeaks[index] });
+    }
+    assignmentPeaks.forEach((peak, i, arr) => (arr[i].y /= maxValue));
+    return assignmentPeaks;
+}
+function sortAscending(peaks) {
+    return peaks[0].x > peaks[1].x ? peaks.sort((a, b) => a.x - b.x) : peaks;
+}
+function getDiffMatrix(rows, columns) {
+    const nbColumns = columns.length;
+    const nbRows = rows.length;
+    const diff = new ml_matrix_1.Matrix(nbRows, nbColumns);
+    for (let r = 0; r < nbRows; r++) {
+        for (let c = 0; c < nbColumns; c++) {
+            diff.set(r, c, Math.abs(rows[r].x - columns[c].x));
+        }
+    }
+    return diff;
+}
+//# sourceMappingURL=solventSuppression.js.map

package/lib/peaks/solventSuppression.js.map

@@ -0,0 +1 @@
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package/lib/peaks/util/jAnalyzer.d.ts

@@ -10,7 +10,7 @@ interface IntergralData {
     from: number;
     to: number;
 }
-export declare type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape' | 'fwhm'> & {
+export declare type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
     intensity: number;
 };
 export interface SignalIntern {

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

@@ -1 +1 @@
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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 {};