nmr-processing 8.0.0 → 8.3.0

package/lib-esm/assignment/utils/getAssignment/buildAssignments.js

@@ -1,4 +1,4 @@
-import treeSet from 'ml-tree-set';
+import TreeSet from 'ml-tree-set';
 import { getConnectivityMatrix } from 'openchemlib-utils';
 import { predictCarbon } from '../../../prediction/predictCarbon';
 import { predictProton } from '../../../prediction/predictProton';
@@ -33,7 +33,7 @@ export async function buildAssignments(props) {
     let timeStart = date.getTime();
     let lowerBoundScore = minScore;
     let store = {
-        solutions: new treeSet(comparator),
+        solutions: new TreeSet(comparator),
         nSolutions: 0,
     };
     const pathLengthMatrix = getConnectivityMatrix(molecule, {
@@ -87,7 +87,7 @@ export async function buildAssignments(props) {
         }
         let sourceOfPartials = getSourceOfPartials(store, infoByAtomType, atomTypesToPredict);
         store = {
-            solutions: new treeSet(comparator),
+            solutions: new TreeSet(comparator),
             nSolutions: 0,
         };
         for (let partial of sourceOfPartials) {

package/lib-esm/assignment/utils/getAssignment/checkIDs.js.map

@@ -1 +1 @@
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package/lib-esm/index.js

@@ -1,4 +1,4 @@
-export * from './constants/gyromagneticRatio';
+export * from 'gyromagnetic-ratio';
 export * from './constants/impurities';
 export * from './constants/couplingPatterns';
 export * from './peaks/peaksFilterImpurities';
@@ -27,4 +27,8 @@ export * from './xyz/xyzJResAnalyzer';
 export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
+export * from './peaks/solventSuppression';
+export * from './ranges/markSolventSignal';
+export * from './apodization/apodization';
+export * from './apodization/compose';
 //# sourceMappingURL=index.js.map

package/lib-esm/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAE7C,cAAc,+BAA+B,CAAC;AAE9C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAE/C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,6BAA6B,CAAC;AAE5C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,0BAA0B,CAAC;AAEzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AAEtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,8BAA8B,CAAC;AAE7C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAE3C,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC"}

package/lib-esm/peaks/peaksToRanges.js

@@ -76,7 +76,7 @@ export function peaksToRanges(data, peakList, options = {}) {
                 let peaksO = [];
                 for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
                     sum += computeArea(signal.peaks[j]);
-                    if (signal.maskPattern[j] === false) {
+                    if (!signal.maskPattern[j]) {
                         let peakR = signal.peaks.splice(j, 1)[0];
                         peaksO.push({
                             x: peakR.x,
@@ -176,7 +176,7 @@ export function peaksToRanges(data, peakList, options = {}) {
  * @return {array} nmr signals
  * @private
  */
-function detectSignals(data, peakList, options = {}) {
+export function detectSignals(data, peakList, options = {}) {
     let { integrationSum = 100, integralType = 'sum', frequencyCluster = 16, frequency = 400, nucleus = '1H', } = options;
     let signal1D = assignSignal(peakList[0], frequency, nucleus);
     let peaks;

package/lib-esm/peaks/peaksToRanges.js.map

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package/lib-esm/peaks/solventSuppression.js

@@ -0,0 +1,154 @@
+import { linearSumAssignment } from 'linear-sum-assignment';
+import { Matrix } from 'ml-matrix';
+import { gaussianFct } from 'ml-peak-shape-generator';
+import { xFindClosestIndex, xMaxValue } from 'ml-spectra-processing';
+import { addDummySignals } from '../signals/addDummySignals';
+import { signalsToSpinSystem } from '../signals/simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from '../signals/simulation/simulateXYPeaks';
+import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
+export function solventSuppression(peakList, solvent, options = {}) {
+    const peaks = [...peakList].sort((a, b) => a.x - b.x);
+    const xValues = peaks.map((peak) => peak.x);
+    const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;
+    for (const solventSignal of solvent) {
+        let solventXYPeaks = solventSignal.peaks
+            ? solventSignal.peaks
+            : getSolventPeaks(solventSignal);
+        solventXYPeaks.sort((a, b) => a.x - b.x);
+        let upIndex = xFindClosestIndex(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension);
+        let lowIndex = xFindClosestIndex(xValues, solventXYPeaks[0].x - solventZoneExtension);
+        const nearPeaks = peaks.filter((peak, index) => index >= lowIndex && index <= upIndex);
+        const amplitudeResiduals = [];
+        const deltaResiduals = [];
+        const positionResiduals = [];
+        for (let peak of nearPeaks) {
+            const { peaks: shiftedSolventPeaks, delta: currentDelta } = 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 = gaussianFct(Math.abs(solventSignal.delta - currentDelta), 0.5);
+            }
+            amplitudeResiduals.push(amplitudeResidual);
+            deltaResiduals.push(deltaResidual);
+            positionResiduals.push(positionResidual);
+        }
+        const [maxAmplitude, maxDelta, maxPosition] = [
+            amplitudeResiduals,
+            deltaResiduals,
+            positionResiduals,
+        ].map((data) => {
+            const max = xMaxValue(data);
+            return max === 0 ? 1 : max;
+        });
+        let minIndex = -1;
+        let minScore = Number.MAX_SAFE_INTEGER;
+        let score = [];
+        for (let i = 0; i < deltaResiduals.length; i++) {
+            const value = (amplitudeResiduals[i] / maxAmplitude +
+                deltaResiduals[i] / maxDelta +
+                1 -
+                positionResiduals[i] / maxPosition) /
+                3;
+            score.push(value);
+            if (minScore > value) {
+                minIndex = i;
+                minScore = value;
+            }
+        }
+        if (minScore < 0 || minIndex < 0) {
+            new Error('There is not a correct match with the pattern');
+            return peaks;
+        }
+        const { peaks: shiftedSolventPeaks } = getShiftedSolventPeaks(nearPeaks[minIndex], solventSignal, solventXYPeaks);
+        const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+        const { rowAssignments, gain } = linearSumAssignment(diff, {
+            maximaze: false,
+        });
+        if (gain < 0) {
+            new Error('The gain is below to zero');
+            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;
+}
+function getSolventPeaks(signal, options = {}) {
+    let signals = addDummySignals([signal]);
+    let spinSystem = signalsToSpinSystem(signals);
+    const { frequency = 400, maxClusterSize = 8 } = options;
+    spinSystem.clusters = splitSpinSystem(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = 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.
+    let deltaPPM = peak.x - solventSignal.delta;
+    if (solventXYPeaks.length > 1 && solventXYPeaks.length % 2 === 0) {
+        deltaPPM += solventXYPeaks[0].x;
+    }
+    const maxIntensity = shiftedSolventPeaks.reduce((max, current) => (current.y > max ? current.y : max), shiftedSolventPeaks[0].y);
+    let currentDelta = 0;
+    for (let shiftedSolventPeak of shiftedSolventPeaks) {
+        shiftedSolventPeak.x += deltaPPM;
+        shiftedSolventPeak.y /= maxIntensity;
+        currentDelta += shiftedSolventPeak.x;
+    }
+    return {
+        peaks: shiftedSolventPeaks,
+        delta: currentDelta / shiftedSolventPeaks.length,
+    };
+}
+function getClosestPeaks(shiftedSolventPeaks, nearPeaks) {
+    const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+    const { rowAssignments, gain } = linearSumAssignment(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 getDiffMatrix(rows, columns) {
+    const nbColumns = columns.length;
+    const nbRows = rows.length;
+    const diff = new 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-esm/peaks/solventSuppression.js.map

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package/lib-esm/peaks/util/jAnalyzer.js

@@ -8,11 +8,12 @@ let maxErrorIter1 = 2.5; // Hz
 let maxErrorIter2 = 1; // Hz
 let jAxisKeys = { jAxis: 'x', intensity: 'intensity' };
 function checkSignalForCompilePattern(signal) {
-    if (!signal.symRank) {
+    if (!('symRank' in signal)) {
         throw new Error('Internal error, symRank was not calculated');
     }
-    if (!signal.mask)
+    if (!('mask' in signal)) {
         throw new Error('Internal Error, mask was not added');
+    }
 }
 export default {
     /**
@@ -52,10 +53,8 @@ export default {
                 if (peaks.length === 1 && n === 0) {
                     validPattern = true;
                 }
-                else {
-                    if (peaks.length <= 1) {
-                        continue;
-                    }
+                else if (peaks.length <= 1) {
+                    continue;
                 }
                 // 1.3 Establish a range for the Heights Hi [peaks.intensity*0.85,peaks.intensity*1.15];
                 let ranges = getRanges(peaks);
@@ -320,7 +319,7 @@ function getRanges(peaks) {
         }
         currentIndex[i] = 0;
     }
-    return { values: ranges, currentIndex: currentIndex, active: 0 };
+    return { values: ranges, currentIndex, active: 0 };
 }
 /**
  * Performs a symmetrization of the signal by using different aproximations to the center.
@@ -437,22 +436,22 @@ function symmetrize(signalInput, maxError, iteration, key) {
                 if (Math.abs(diffL - diffR) < maxError) {
                     avg = Math.min(peaks[left].intensity, peaks[right].intensity);
                     avgWidth = Math.min(peaks[left].width, peaks[right].width);
-                    peaks[left].intensity = peaks[right].intensity = avg;
-                    peaks[left].width = peaks[right].width = avgWidth;
+                    peaks[left].intensity = avg;
+                    peaks[right].intensity = avg;
+                    peaks[left].width = avgWidth;
+                    peaks[right].width = avgWidth;
                     middle = [
                         middle[0] + (peaks[right].x + peaks[left].x) / 2,
                         middle[1] + 1,
                     ];
                 }
+                else if (Math.max(diffL, diffR) === diffR) {
+                    mask[right] = false;
+                    left--;
+                }
                 else {
-                    if (Math.max(diffL, diffR) === diffR) {
-                        mask[right] = false;
-                        left--;
-                    }
-                    else {
-                        mask[left] = false;
-                        right++;
-                    }
+                    mask[left] = false;
+                    right++;
                 }
             }
         }
@@ -496,10 +495,8 @@ function symmetrize(signalInput, maxError, iteration, key) {
         }
         symFactor /= weight;
     }
-    else {
-        if (peaks.length === 1) {
-            symFactor = 1;
-        }
+    else if (peaks.length === 1) {
+        symFactor = 1;
     }
     let newSumHeights = 0;
     for (const peak of peaks) {
@@ -510,15 +507,13 @@ function symmetrize(signalInput, maxError, iteration, key) {
     if (symFactor > 0.8 && symFactor < 0.97 && iteration < 2) {
         return symmetrize(newSignal, maxErrorIter2, 2, key);
     }
-    else {
+    else if (peaks.length > 1) {
         // Center the given pattern at cs and symmetrize x
-        if (peaks.length > 1) {
-            let dxi;
-            for (let i = Math.ceil(peaks.length / 2) - 1; i >= 0; i--) {
-                dxi = (peaks[i].x - peaks[peaks.length - 1 - i].x) / 2.0;
-                peaks[i].x = cs + dxi;
-                peaks[peaks.length - 1 - i].x = cs - dxi;
-            }
+        let dxi;
+        for (let i = Math.ceil(peaks.length / 2) - 1; i >= 0; i--) {
+            dxi = (peaks[i].x - peaks[peaks.length - 1 - i].x) / 2.0;
+            peaks[i].x = cs + dxi;
+            peaks[peaks.length - 1 - i].x = cs - dxi;
         }
     }
     newSignal.symRank = symFactor;
@@ -561,7 +556,7 @@ function normalize(signal, n) {
     let index = signal.mask2.length - 1;
     for (let i = peaks.length - 1; i >= 0; i--) {
         peaks[i].intensity *= norm;
-        while (index >= 0 && signal.mask2[index] === false) {
+        while (index >= 0 && !signal.mask2[index]) {
             index--;
         }
         if (peaks[i].intensity < 0.75) {
@@ -592,7 +587,7 @@ function chemicalShift(peaks, mask = []) {
     let area;
     if (mask.length > 0) {
         for (let i = 0; i < peaks.length; i++) {
-            if (mask[i] === true) {
+            if (mask[i]) {
                 area = getArea(peaks[i]);
                 sum += area;
                 cs += area * peaks[i].x;

package/lib-esm/peaks/util/jAnalyzer.js.map

@@ -1 +1 @@
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package/lib-esm/peaks/util/peakOptimizer.js

@@ -115,7 +115,7 @@ function completeMissingIfNeeded(output, properties, thisSignal, thisProp) {
             }
         }
     }
-    if (diagX === false) {
+    if (!diagX) {
         newSignal = {
             x: {
                 delta: thisSignal.y.delta,
@@ -135,7 +135,7 @@ function completeMissingIfNeeded(output, properties, thisSignal, thisProp) {
         properties.push(tmpProp);
         addedPeaks++;
     }
-    if (diagY === false) {
+    if (!diagY) {
         newSignal = {
             x: {
                 delta: thisSignal.y.delta,
@@ -174,15 +174,13 @@ function checkCrossPeaks(output, properties, signal, updateProperties) {
                 crossPeaksX.push(i);
                 shift += cross.x.delta;
             }
-            else {
-                if (Math.abs(cross.y.delta - signal.y.delta) < diagonalError) {
-                    hits++;
-                    if (updateProperties) {
-                        properties[i][1]++;
-                    }
-                    crossPeaksY.push(i);
-                    shift += cross.y.delta;
+            else if (Math.abs(cross.y.delta - signal.y.delta) < diagonalError) {
+                hits++;
+                if (updateProperties) {
+                    properties[i][1]++;
                 }
+                crossPeaksY.push(i);
+                shift += cross.y.delta;
             }
         }
     }
@@ -245,13 +243,11 @@ function initializeProperties(signals) {
             signals[i].x.delta = shift;
             signals[i].y.delta = shift;
         }
+        else if (signals[i].x.delta - signals[i].y.delta > 0) {
+            signalsProperties[i][0] = 1;
+        }
         else {
-            if (signals[i].x.delta - signals[i].y.delta > 0) {
-                signalsProperties[i][0] = 1;
-            }
-            else {
-                signalsProperties[i][0] = -1;
-            }
+            signalsProperties[i][0] = -1;
         }
     }
     return signalsProperties;

package/lib-esm/peaks/util/peakOptimizer.js.map

@@ -1 +1 @@
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