nmr-processing 9.1.0 → 9.2.0

package/lib-esm/prediction/predictAllSpectra.js

@@ -11,8 +11,8 @@ export async function predictAllSpectra(molecule, options = {}) {
         ...{
             proton: { from: 0, to: 14 },
             carbon: { from: 0, to: 200 },
-            nbPoints: 4098,
-            lineWidth: 0.03,
+            nbPoints: 65536,
+            lineWidth: 1,
         },
         ...(simulationOptions.oneD || {}),
     };

package/lib-esm/prediction/predictAllSpectra.js.map

@@ -1 +1 @@
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package/lib-esm/prediction/predictCOSY.js.map

@@ -1 +1 @@
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package/lib-esm/prediction/predictHMBC.js.map

@@ -1 +1 @@
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package/lib-esm/prediction/predictHSQC.js.map

@@ -1 +1 @@
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+{"version":3,"file":"predictHSQC.js","sourceRoot":"","sources":["../../src/prediction/predictHSQC.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,aAAa,EAAwB,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAE,aAAa,EAAwB,MAAM,iBAAiB,CAAC;AACtE,OAAO,EAAE,SAAS,EAAa,MAAM,mBAAmB,CAAC;AAwCzD;;;GAGG;AAEH,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,QAAkB,EAClB,UAA8B,EAAE;IAEhC,IAAI,EACF,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,EAAE,CAAC,EAAE,aAAa,EAAE,CAAC,EAAE,aAAa,EAAE,EAClD,WAAW,EACX,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,cAAc,GACf,GAAG,OAAO,CAAC;IAEZ,OAAO,SAAS,CAAC,QAAQ,EAAE;QACzB,IAAI,EAAE,GAAG;QACT,EAAE,EAAE,GAAG;QACP,SAAS;QACT,SAAS;QACT,SAAS;QACT,WAAW;QACX,cAAc;QACd,YAAY;KACb,CAAC,CAAC;AACL,CAAC"}

package/lib-esm/prediction/utils/predict2D.js

@@ -2,9 +2,9 @@ import { v4 as generateID } from '@lukeed/uuid';
 import { agnes } from 'ml-hclust';
 import { Matrix } from 'ml-matrix';
 import { getGroupedDiastereotopicAtomIDs, getPathsInfo, } from 'openchemlib-utils';
+import { setIDs } from '../../peaks/util/setIDs';
 import { getNuclei } from './getNuclei';
 import { getPredictions } from './getPredictions';
-import { setIDs } from '../../peaks/util/setIDs';
 function checkFromTo(options) {
     if (!options.from || !options.to) {
         throw new Error('options from and to are mandatory');

package/lib-esm/prediction/utils/predict2D.js.map

@@ -1 +1 @@
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package/lib-esm/signals/Jcoupling.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=Jcoupling.js.map

package/lib-esm/signals/Jcoupling.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Jcoupling.js","sourceRoot":"","sources":["../../src/signals/Jcoupling.ts"],"names":[],"mappings":""}

package/lib-esm/signals/addDummySignals.js

@@ -1,9 +1,15 @@
 import { couplingPatterns } from '../constants/couplingPatterns';
 export function addDummySignals(signals) {
     let newSignals = JSON.parse(JSON.stringify(signals));
+    let nextAtomToAssign = signals.reduce((nextAtomToAssign, signal) => {
+        const { atoms = [] } = signal;
+        return Math.max(...atoms) > nextAtomToAssign
+            ? Math.max(...atoms)
+            : nextAtomToAssign;
+    }, 0) + 1;
     signals.forEach((signal, s) => {
-        const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
-        let { newCouplings, tempSignals } = checkCouplings(jCouplings, newSignals, signalAssignment);
+        const { js: jCouplings = [], atoms: signalAssignment = [nextAtomToAssign++], } = signal;
+        let { newCouplings, tempSignals } = checkCouplings(jCouplings, newSignals, signalAssignment, nextAtomToAssign + signals.length);
         if (tempSignals.length > 0)
             newSignals.push(...tempSignals);
         newSignals[s].js = newCouplings;
@@ -11,8 +17,7 @@ export function addDummySignals(signals) {
     });
     return newSignals.sort((a, b) => a.delta - b.delta);
 }
-function checkCouplings(jCouplings, signals, signalAssignment) {
-    let newSignalAssignment = signals.length - 1;
+function checkCouplings(jCouplings, signals, signalAssignment, nextAtomToAssign) {
     let tempSignals = [];
     const newCouplings = jCouplings.reduce((newCouplings, jCoupling) => {
         const { atoms = [], multiplicity, coupling } = jCoupling;
@@ -21,12 +26,12 @@ function checkCouplings(jCouplings, signals, signalAssignment) {
                 let tempCouplings = [];
                 const nbLinks = couplingPatterns.indexOf(multiplicity);
                 for (let i = 0; i < nbLinks; i++) {
-                    newSignalAssignment++;
+                    nextAtomToAssign++;
                     tempCouplings.push({
                         coupling,
-                        atoms: [newSignalAssignment],
+                        atoms: [nextAtomToAssign],
                     });
-                    tempSignals.push(formatSignal(coupling, [newSignalAssignment], signalAssignment));
+                    tempSignals.push(formatSignal(coupling, [nextAtomToAssign], signalAssignment));
                 }
             }
             else {

package/lib-esm/signals/addDummySignals.js.map

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package/lib-esm/signals/optimization/defaultParameters.js

@@ -0,0 +1,33 @@
+export const defaultParameters = {
+    delta: {
+        init: (data) => data.signal.delta,
+        min: (data) => data.signal.delta - data.shape.fwhm * 2,
+        max: (data) => data.signal.delta + data.shape.fwhm * 2,
+        gradientDifference: () => 2e-3,
+    },
+    intensity: {
+        init: (data) => data.signal.intensity || 1,
+        min: () => 0,
+        max: () => 1.5,
+        gradientDifference: () => 1e-3,
+    },
+    fwhm: {
+        init: (data) => data.shape.fwhm,
+        min: (data) => data.shape.fwhm * 0.25,
+        max: (data) => data.shape.fwhm * 4,
+        gradientDifference: (data) => data.shape.fwhm * 2e-3,
+    },
+    mu: {
+        init: (data) => data.shape.mu || 0.5,
+        min: () => 0,
+        max: () => 1,
+        gradientDifference: () => 0.01,
+    },
+    coupling: {
+        init: (data) => data.jCoupling.coupling,
+        min: (data) => data.jCoupling.coupling * 0.8,
+        max: (data) => data.jCoupling.coupling * 1.2,
+        gradientDifference: () => 0.01,
+    },
+};
+//# sourceMappingURL=defaultParameters.js.map

package/lib-esm/signals/optimization/defaultParameters.js.map

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package/lib-esm/signals/optimization/directOptimization.js

@@ -0,0 +1,25 @@
+import direct from 'ml-direct';
+export function directOptimization(data, sumOfShapes, options) {
+    const { minValues, maxValues, directOptions = {} } = options;
+    const objectiveFunction = getObjectiveFunction(data, sumOfShapes);
+    const result = direct(objectiveFunction, minValues, maxValues, directOptions);
+    const { optima } = result;
+    return {
+        error: result.minFunctionValue,
+        iterations: result.iterations,
+        parameterValues: optima[0],
+    };
+}
+function getObjectiveFunction(data, sumOfShapes) {
+    const { x, y } = data;
+    const nbPoints = x.length;
+    return (parameters) => {
+        const fct = sumOfShapes(parameters);
+        let error = 0;
+        for (let i = 0; i < nbPoints; i++) {
+            error += Math.pow(y[i] - fct(x[i]), 2);
+        }
+        return error;
+    };
+}
+//# sourceMappingURL=directOptimization.js.map

package/lib-esm/signals/optimization/directOptimization.js.map

@@ -0,0 +1 @@
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package/lib-esm/signals/optimization/getInternalSignals.js

@@ -0,0 +1,146 @@
+import { getShape1D } from 'ml-peak-shape-generator';
+import { xyFindClosestPoint } from 'ml-spectra-processing';
+import { defaultParameters } from './defaultParameters';
+import { signalsToPointXY } from './signalsToPointXY';
+const properties = ['init', 'min', 'max', 'gradientDifference'];
+export function getInternalSignals(data, signals, minMaxY, options) {
+    var _a, _b;
+    let index = 0;
+    let internalSignals = [];
+    const { shape: shapeAsOption = { kind: 'gaussian' }, baseline: shiftValue = minMaxY.min, lineWidth = 1, frequency, } = options;
+    const normalizedSignals = normalizeSignals({
+        signals,
+        data,
+        shiftValue,
+        frequency,
+        range: minMaxY.range,
+    });
+    for (const signal of normalizedSignals) {
+        const { shape = { ...shapeAsOption } } = signal;
+        if (!shape.fwhm) {
+            shape.fwhm = lineWidth;
+        }
+        shape.fwhm /= frequency;
+        const shapeFct = getShape1D(shape);
+        const parameters = [
+            'delta',
+            'intensity',
+            ...shapeFct.getParameters(),
+        ];
+        const propertiesValues = {
+            min: [],
+            max: [],
+            init: [],
+            gradientDifference: [],
+        };
+        for (const parameter of parameters) {
+            for (const property of properties) {
+                propertiesValues[property].push(getPropertyValue({
+                    signal,
+                    frequency,
+                    parameter,
+                    property,
+                    minMaxY,
+                    shapeFct,
+                }));
+            }
+        }
+        for (const jCoupling of signal.js || []) {
+            for (const property of properties) {
+                const parameter = 'coupling';
+                let generalParameterValue = (_b = (_a = options === null || options === void 0 ? void 0 : options.parameters) === null || _a === void 0 ? void 0 : _a[parameter]) === null || _b === void 0 ? void 0 : _b[property];
+                if (generalParameterValue) {
+                    if (typeof generalParameterValue === 'number') {
+                        propertiesValues[property].push(getNormalizedValue(generalParameterValue, parameter, property, minMaxY, frequency, options.baseline));
+                    }
+                    else {
+                        let value = generalParameterValue({ jCoupling });
+                        propertiesValues[property].push(getNormalizedValue(value, parameter, property, minMaxY, frequency, options.baseline));
+                    }
+                }
+                if (!defaultParameters[parameter]) {
+                    throw new Error(`No default parameter for ${parameter}`);
+                }
+                const defaultParameterValues = defaultParameters[parameter][property];
+                propertiesValues[property].push(defaultParameterValues({ jCoupling }));
+            }
+        }
+        const fromIndex = index;
+        const toIndex = fromIndex + parameters.length - 1;
+        const fromIndexCoupling = toIndex + 1;
+        const toIndexCoupling = fromIndexCoupling + signal.js.length - 1;
+        index += toIndexCoupling - fromIndex + 1;
+        internalSignals.push({
+            shape: shape,
+            shapeFct,
+            signal,
+            parameters,
+            propertiesValues,
+            fromIndex,
+            toIndex,
+            fromIndexCoupling,
+            toIndexCoupling,
+        });
+    }
+    return internalSignals;
+}
+function normalizeSignals(options) {
+    const { signals, data, frequency, shiftValue, range } = options;
+    const getMaxIntensity = (signal) => {
+        const peaks = signalsToPointXY([signal], { frequency, maxClusterSize: 1 });
+        const biggestPeak = peaks.reduce((biggest, peak) => (peak.y > biggest.y ? peak : biggest), peaks[0]);
+        const { y: maxIntensity } = xyFindClosestPoint(data, biggestPeak.x);
+        return maxIntensity;
+    };
+    return signals.map((signal) => {
+        const { intensity = getMaxIntensity(signal) } = signal;
+        return {
+            ...signal,
+            js: signal.js || [],
+            intensity: (intensity - shiftValue) / range,
+        };
+    });
+}
+function getPropertyValue(options) {
+    var _a, _b, _c, _d;
+    const { signal, frequency, parameter, property, minMaxY, shapeFct } = options;
+    // check if the property is specified in the signal
+    let propertyValue = (_b = (_a = signal === null || signal === void 0 ? void 0 : signal.parameters) === null || _a === void 0 ? void 0 : _a[parameter]) === null || _b === void 0 ? void 0 : _b[property];
+    if (propertyValue) {
+        return getNormalizedValue(propertyValue, parameter, property, minMaxY, frequency, options.baseline);
+    }
+    // check if there are some global option, it could be a number or a callback
+    let generalParameterValue = (_d = (_c = options === null || options === void 0 ? void 0 : options.parameters) === null || _c === void 0 ? void 0 : _c[parameter]) === null || _d === void 0 ? void 0 : _d[property];
+    if (generalParameterValue) {
+        if (typeof generalParameterValue === 'number') {
+            return getNormalizedValue(generalParameterValue, parameter, property, minMaxY, frequency, options.baseline);
+        }
+        else {
+            let value = generalParameterValue(signal);
+            return getNormalizedValue(value, parameter, property, minMaxY, frequency, options.baseline);
+        }
+    }
+    // we just need to take the default parameters
+    if (!defaultParameters[parameter]) {
+        throw new Error(`No default parameter for ${parameter}`);
+    }
+    const defaultParameterValues = defaultParameters[parameter][property];
+    return defaultParameterValues({ signal, shape: shapeFct });
+}
+function getNormalizedValue(value, parameter, property, minMaxY, frequency, baseline) {
+    if (parameter === 'intensity') {
+        if (property === 'gradientDifference') {
+            return value;
+        }
+        else {
+            return baseline !== undefined
+                ? (value - baseline) / minMaxY.range
+                : (value - minMaxY.min) / minMaxY.range;
+        }
+    }
+    else if (parameter === 'fwhm') {
+        return value / frequency;
+    }
+    return value;
+}
+//# sourceMappingURL=getInternalSignals.js.map

package/lib-esm/signals/optimization/getInternalSignals.js.map

@@ -0,0 +1 @@
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package/lib-esm/signals/optimization/getSumOfShapes.js

@@ -0,0 +1,42 @@
+import { signalsToPointXY } from './signalsToPointXY';
+const defaultSimulationOptions = {
+    maxClusterSize: 1,
+};
+export function getSumOfShapes(internalSignals, options) {
+    const simulationOptions = { ...defaultSimulationOptions, ...options };
+    return function sumOfShapes(parameters) {
+        const peaks = [];
+        for (const internalSignal of internalSignals) {
+            const delta = parameters[internalSignal.fromIndex];
+            const intensity = parameters[internalSignal.fromIndex + 1];
+            for (let i = 2; i < internalSignal.parameters.length; i++) {
+                //@ts-expect-error Not simply to solve the issue
+                internalSignal.shapeFct[internalSignal.parameters[i]] =
+                    parameters[internalSignal.fromIndex + i];
+            }
+            const couplings = internalSignal.signal.js;
+            for (let i = 0; i < couplings.length; i++) {
+                couplings[i].coupling =
+                    parameters[internalSignal.fromIndexCoupling + i];
+            }
+            const currentPeaks = signalsToPointXY([
+                {
+                    delta,
+                    js: couplings,
+                },
+            ], simulationOptions);
+            peaks.push(...currentPeaks.map((peak) => {
+                return { intensity, shape: internalSignal.shapeFct, ...peak };
+            }));
+        }
+        return (currentX) => {
+            let totalY = 0;
+            for (let peak of peaks) {
+                const { x, y, intensity, shape } = peak;
+                totalY += y * intensity * shape.fct(currentX - x);
+            }
+            return totalY;
+        };
+    };
+}
+//# sourceMappingURL=getSumOfShapes.js.map

package/lib-esm/signals/optimization/getSumOfShapes.js.map

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package/lib-esm/signals/optimization/signalsToPointXY.js

@@ -0,0 +1,20 @@
+import { addDummySignals } from '../addDummySignals';
+import { signalsToSpinSystem } from '../simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from '../simulation/simulateXYPeaks';
+import { splitSpinSystem } from '../simulation/splitSpinSystem';
+export function signalsToPointXY(signals, options) {
+    const { frequency, maxClusterSize = 1 } = options;
+    const completeSignalSet = addDummySignals(signals);
+    const spinSystem = signalsToSpinSystem(completeSignalSet);
+    spinSystem.clusters = splitSpinSystem(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const pointsXY = simulateXYPeaks(spinSystem, options).filter((point) => point.x < 1000);
+    const maxIntensity = pointsXY.reduce((max, peak) => (peak.y > max ? peak.y : max), Number.MIN_SAFE_INTEGER);
+    for (const point of pointsXY) {
+        point.y /= maxIntensity;
+    }
+    return pointsXY;
+}
+//# sourceMappingURL=signalsToPointXY.js.map

package/lib-esm/signals/optimization/signalsToPointXY.js.map

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

@@ -0,0 +1,104 @@
+import { v4 } from '@lukeed/uuid';
+import { levenbergMarquardt } from 'ml-levenberg-marquardt';
+import { getShape1D } from 'ml-peak-shape-generator';
+import { xMinMaxValues } from 'ml-spectra-processing';
+import { directOptimization } from './optimization/directOptimization';
+import { getInternalSignals, } from './optimization/getInternalSignals';
+import { getSumOfShapes } from './optimization/getSumOfShapes';
+import { signalsToPointXY, } from './optimization/signalsToPointXY';
+const defaultLMOptimizationOptions = {
+    damping: 1.5,
+    maxIterations: 100,
+    errorTolerance: 1e-8,
+};
+const defaultDirectOptimizationOptions = {
+    iterations: 25,
+};
+export function optimizeSignals(data, signals, options) {
+    const { optimization = {}, simulation: simulationOptions, ...restOptions } = options;
+    let temp = xMinMaxValues(data.y);
+    const minMaxY = { ...temp, range: temp.max - temp.min };
+    const internalSignals = getInternalSignals(data, signals, minMaxY, {
+        frequency: simulationOptions.frequency,
+        ...restOptions,
+    });
+    const { baseline: shiftValue = minMaxY.min } = options;
+    let normalizedY = new Float64Array(data.y.length);
+    for (let i = 0; i < data.y.length; i++) {
+        normalizedY[i] = (data.y[i] - shiftValue) / minMaxY.range;
+    }
+    const nbParams = internalSignals[internalSignals.length - 1].toIndexCoupling + 1;
+    const minValues = new Float64Array(nbParams);
+    const maxValues = new Float64Array(nbParams);
+    const initialValues = new Float64Array(nbParams);
+    const gradientDifferences = new Float64Array(nbParams);
+    let index = 0;
+    for (const internalSignal of internalSignals) {
+        for (let i = 0; i < internalSignal.parameters.length; i++) {
+            minValues[index] = internalSignal.propertiesValues.min[i];
+            maxValues[index] = internalSignal.propertiesValues.max[i];
+            initialValues[index] = internalSignal.propertiesValues.init[i];
+            gradientDifferences[index++] =
+                internalSignal.propertiesValues.gradientDifference[i];
+        }
+        for (let i = internalSignal.parameters.length; i < internalSignal.parameters.length + internalSignal.signal.js.length; i++) {
+            minValues[index] = internalSignal.propertiesValues.min[i];
+            maxValues[index] = internalSignal.propertiesValues.max[i];
+            initialValues[index] = internalSignal.propertiesValues.init[i];
+            gradientDifferences[index++] =
+                internalSignal.propertiesValues.gradientDifference[i];
+        }
+    }
+    const sumOfShapes = getSumOfShapes(internalSignals, simulationOptions);
+    const { kind, options: optimizationOptions } = optimization;
+    const [algorithm, defaultOptimizationOptions] = kind === 'direct'
+        ? [directOptimization, defaultDirectOptimizationOptions]
+        : [levenbergMarquardt, defaultLMOptimizationOptions];
+    let fitted = algorithm({ x: data.x, y: normalizedY }, sumOfShapes, {
+        minValues,
+        maxValues,
+        initialValues,
+        gradientDifference: gradientDifferences,
+        ...defaultOptimizationOptions,
+        ...optimizationOptions,
+    });
+    const fittedValues = fitted.parameterValues;
+    const newSignals = [];
+    for (const internalSignal of internalSignals) {
+        const { fromIndexCoupling } = internalSignal;
+        const js = internalSignal.signal.js.map((jCoupling, i) => {
+            jCoupling.coupling = fittedValues[fromIndexCoupling + i];
+            return jCoupling;
+        });
+        const delta = fittedValues[internalSignal.fromIndex];
+        const pointXYs = signalsToPointXY([{ delta, js }], simulationOptions);
+        const intensity = fittedValues[internalSignal.fromIndex + 1] * minMaxY.range + shiftValue;
+        const newPeaks = [];
+        for (const { x, y } of pointXYs) {
+            const peak = {
+                id: v4(),
+                x,
+                y: intensity * y,
+                width: 0,
+                shape: { ...internalSignal.shape },
+            };
+            for (let i = 2; i < internalSignal.parameters.length; i++) {
+                //@ts-expect-error should be fixed once
+                peak.shape[internalSignal.parameters[i]] =
+                    fittedValues[internalSignal.fromIndex + i];
+            }
+            peak.shape.fwhm *= simulationOptions.frequency;
+            peak.width = getShape1D(peak.shape).fwhmToWidth(peak.shape.fwhm);
+            newPeaks.push(peak);
+        }
+        newSignals.push({
+            delta,
+            js,
+            shape: { ...newPeaks[0].shape },
+            intensity,
+            peaks: newPeaks,
+        });
+    }
+    return newSignals;
+}
+//# sourceMappingURL=optimizeSignals.js.map

package/lib-esm/signals/optimizeSignals.js.map

@@ -0,0 +1 @@
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package/lib-esm/signals/simulation/simulateXYPeaks.js

@@ -162,7 +162,7 @@ spinSystem, options = {}) {
             });
         }
     }
-    return xyPeaks;
+    return xyPeaks.filter((peak) => peak.x < 1000);
 }
 function triuTimesAbs(A, val) {
     A.forEachNonZero((i, j, v) => {