nmr-processing 3.3.3 → 4.0.0

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

@@ -0,0 +1,73 @@
+import { partialScore } from './partialScore';
+export function exploreTreeRec(props, currentIndex, partial, store) {
+    const { nSources, restrictionByCS, timeout, timeStart, maxSolutions, targets, predictions, lowerBoundScore, nbAllowedUnAssigned, possibleAssignmentMap, useIntegrationRestriction, diaIDPeerPossibleAssignment, } = props;
+    const currentDate = new Date();
+    if (currentDate.getTime() - timeStart > timeout) {
+        new Error('timeout expired');
+        return store;
+    }
+    const diaID = diaIDPeerPossibleAssignment[currentIndex];
+    const possibleAssignments = possibleAssignmentMap[diaID];
+    for (let targetID of possibleAssignments) {
+        partial[currentIndex] = targetID;
+        let score = partialScore(partial, {
+            useIntegrationRestriction,
+            diaIDPeerPossibleAssignment,
+            nbAllowedUnAssigned,
+            restrictionByCS,
+            predictions,
+            targets,
+        });
+        if (score === 0) {
+            if (targetID === '*') {
+                partial[currentIndex] = null;
+            }
+            continue;
+        }
+        if (currentIndex === nSources - 1 && score >= lowerBoundScore) {
+            addSolution(store, { predictions, partial, score, maxSolutions });
+        }
+        else if (currentIndex < nSources - 1) {
+            exploreTreeRec({
+                nSources,
+                restrictionByCS,
+                timeout,
+                timeStart,
+                maxSolutions,
+                targets,
+                predictions,
+                lowerBoundScore,
+                nbAllowedUnAssigned,
+                possibleAssignmentMap,
+                useIntegrationRestriction,
+                diaIDPeerPossibleAssignment,
+            }, currentIndex + 1, JSON.parse(JSON.stringify(partial)), store);
+        }
+    }
+}
+function addSolution(store, props) {
+    let { score, maxSolutions, partial, predictions } = props;
+    score /= doubleAssignmentPenalty(partial, predictions);
+    store.nSolutions++;
+    let solution = {
+        assignment: JSON.parse(JSON.stringify(partial)),
+        score: score,
+    };
+    if (store.nSolutions >= maxSolutions) {
+        if (solution.score > store.solutions.last().score) {
+            store.solutions.pollLast();
+            store.solutions.add(solution);
+        }
+    }
+    else {
+        store.solutions.add(solution);
+        store.nSolutions++;
+    }
+}
+function doubleAssignmentPenalty(partial, predictions) {
+    const nbSources = Object.keys(predictions).length;
+    let assignments = new Set(partial);
+    let nbDoubleAssignment = nbSources - assignments.size;
+    return nbDoubleAssignment > 0 ? 2 * nbDoubleAssignment : 1;
+}
+//# sourceMappingURL=exploreTreeRec.js.map

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

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

@@ -0,0 +1,10 @@
+const BASE62 = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
+const LENGTH = 8;
+export default function generateID() {
+    let id = '';
+    for (let i = 0; i < LENGTH; i++) {
+        id += BASE62.charAt(Math.floor(Math.random() * 62));
+    }
+    return id;
+}
+//# sourceMappingURL=generateID.js.map

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

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

@@ -0,0 +1,87 @@
+export function partialScore(partial, options) {
+    const { useIntegrationRestriction, diaIDPeerPossibleAssignment, nbAllowedUnAssigned, restrictionByCS, predictions, targets, } = options;
+    const { useChemicalShiftScore } = restrictionByCS;
+    let countStars = 0;
+    let totalPartial = partial.length;
+    let partialInverse = {};
+    let activeDomainOnPrediction = [];
+    for (let i = 0; i < partial.length; i++) {
+        const targetID = partial[i];
+        if (targetID && targetID !== '*') {
+            activeDomainOnPrediction.push(i);
+            if (!partialInverse[targetID]) {
+                partialInverse[targetID] = [];
+            }
+            partialInverse[targetID].push(diaIDPeerPossibleAssignment[i]);
+        }
+        if (targetID === '*')
+            countStars++;
+    }
+    if (countStars > nbAllowedUnAssigned)
+        return 0;
+    const activeDomainOnTarget = Object.keys(partialInverse);
+    if (activeDomainOnTarget.length === 0) {
+        return 0;
+    }
+    if (useIntegrationRestriction) {
+        for (let targetID of activeDomainOnTarget) {
+            let targetToSource = partialInverse[targetID];
+            let total = 0;
+            for (const diaID of targetToSource) {
+                const prediction = predictions[diaID];
+                total += prediction.allHydrogens;
+            }
+            const { integration } = targets[targetID];
+            if (total - integration >= 0.5) {
+                return 0;
+            }
+        }
+    }
+    //chemical shift score
+    let chemicalShiftScore = useChemicalShiftScore
+        ? chemicalShiftScoring(partial, options)
+        : 1;
+    const penaltyByStarts = countStars / totalPartial;
+    return chemicalShiftScore - penaltyByStarts;
+}
+function chemicalShiftScoring(partial, options) {
+    const { tolerance } = options.restrictionByCS;
+    const { diaIDPeerPossibleAssignment, predictions, targets } = options;
+    let chemicalShiftScore = 0;
+    let count = 0;
+    for (let index = 0; index < partial.length; index++) {
+        const targetID = partial[index];
+        if (targetID && targetID !== '*') {
+            count++;
+            let diaID = diaIDPeerPossibleAssignment[index];
+            let source = predictions[diaID];
+            let target = targets[targetID];
+            let error = tolerance;
+            if (source.error) {
+                error = Math.max(source.error, tolerance);
+            }
+            if (typeof source.delta === 'undefined') {
+                // Chemical shift is not a restriction
+                chemicalShiftScore += 1;
+            }
+            else {
+                const delta = target.signals && target.signals.length > 0
+                    ? target.signals[0].delta
+                    : (target.to + target.from) / 2;
+                let diff = Math.abs(source.delta - delta);
+                if (diff < error) {
+                    chemicalShiftScore += 1;
+                }
+                else {
+                    diff = Math.abs(diff - error);
+                    chemicalShiftScore += (-0.25 / error) * diff + 1;
+                }
+            }
+        }
+    }
+    if (count > 0) {
+        chemicalShiftScore /= count;
+    }
+    return chemicalShiftScore;
+}
+//# sourceMappingURL=partialScore.js.map

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

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

@@ -1,8 +1,3 @@
-/**
- * @typedef {Object} DataXY
- * @property {Array<Number>} x Array of x values
- * @property {Array<Number>} y Array of y values
- */
 export * from './constants/gyromagneticRatio';
 export * from './constants/impurities';
 export * from './constants/couplingPatterns';
@@ -13,6 +8,8 @@ export * from './prediction/predictCOSY';
 export * from './prediction/predictHSQC';
 export * from './prediction/predictHMBC';
 export * from './prediction/predictAll';
+export * from './assignment/get1HAssignments';
+export * from './assignment/get13CAssignments';
 export * from './ranges/rangesToACS';
 export * from './ranges/rangesToXY';
 export * from './signals/signalsToRanges';

package/lib-esm/index.js.map

@@ -1 +1 @@
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package/lib-esm/peaks/peaksFilterImpurities.js

@@ -29,7 +29,7 @@ function checkImpurity(peakList, impurity, options) {
     while (i--) {
         j = peakList.length;
         while (j--) {
-            tolerance = error + peakList[j].shape.width;
+            tolerance = error + peakList[j].width;
             difference = Math.abs(impurity[i].shift - peakList[j].x);
             if (difference < tolerance) {
                 // && (impurity[i].multiplicity === '' || (impurity[i].multiplicity.indexOf(peakList[j].multiplicity)) { // some impurities has multiplicities like 'bs' but at presents it is unsupported

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

@@ -1 +1 @@
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package/lib-esm/peaks/peaksToRanges.js

@@ -17,22 +17,20 @@ const assignSignal = (peak, frequency, nucleus) => {
         delta: NaN,
         nbPeaks: 1,
         kind: 'signal',
-        startX: peak.x - peak.shape.width,
-        stopX: peak.x + peak.shape.width,
+        startX: peak.x - peak.width,
+        stopX: peak.x + peak.width,
         observe: frequency,
         nucleus,
         integralData: {
-            from: peak.x - peak.shape.width * 3,
-            to: peak.x + peak.shape.width * 3,
+            from: peak.x - peak.width * 3,
+            to: peak.x + peak.width * 3,
             value: 0,
         },
         peaks: [
             {
                 x: peak.x,
                 intensity: peak.y,
-                shape: {
-                    width: peak.shape.width,
-                },
+                width: peak.width,
             },
         ],
     };
@@ -81,9 +79,7 @@ export function peaksToRanges(data, peakList, options = {}) {
                         peaksO.push({
                             x: peakR.x,
                             y: peakR.intensity,
-                            shape: {
-                                width: peakR.shape.width,
-                            },
+                            width: peakR.width,
                         });
                         signal.mask.splice(j, 1);
                         signal.mask2.splice(j, 1);
@@ -194,19 +190,17 @@ function detectSignals(data, peakList, options = {}) {
             signals.push(signal1D);
         }
         else {
-            let tmp = peak.x + peak.shape.width;
+            let tmp = peak.x + peak.width;
             signal1D.stopX = Math.max(signal1D.stopX, tmp);
             signal1D.startX = Math.min(signal1D.startX, tmp);
             signal1D.nbPeaks++;
             signal1D.peaks.push({
                 x: peak.x,
                 intensity: peak.y,
-                shape: {
-                    width: peak.shape.width,
-                },
+                width: peak.width,
             });
-            signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.shape.width * 3);
-            signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.shape.width * 3);
+            signal1D.integralData.from = Math.min(signal1D.integralData.from, peak.x - peak.width * 3);
+            signal1D.integralData.to = Math.max(signal1D.integralData.to, peak.x + peak.width * 3);
             if (peak.kind)
                 signal1D.kind = peak.kind;
         }
@@ -250,6 +244,6 @@ function detectSignals(data, peakList, options = {}) {
  * @private
  */
 function computeArea(peak) {
-    return Math.abs(peak.intensity * peak.shape.width * 1.57); // todo add an option with this value: 1.772453851
+    return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
 }
 //# sourceMappingURL=peaksToRanges.js.map

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

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

@@ -1,6 +1,5 @@
 import LM from 'ml-levenberg-marquardt';
-import { gaussian2D } from 'ml-peak-shape-generator';
-const { fct: gaussian2DFct } = gaussian2D;
+import { Gaussian2D } from 'ml-peak-shape-generator';
 const direction8X = [-1, -1, -1, 0, 0, 1, 1, 1];
 const direction8Y = [-1, 0, 1, -1, 1, -1, 0, 1];
 const direction16X = [-2, -2, -2, -2, -2, -1, -1, 0, 0, 1, 1, 2, 2, 2, 2, 2];
@@ -106,6 +105,7 @@ function fitGaussian(data, options) {
     };
 }
 function paramGaussian2D(intervalX, intervalY, nCols) {
+    const gaussian2D = new Gaussian2D();
     return (p) => {
         return (t) => {
             let nL = p.length / 5;
@@ -113,9 +113,10 @@ function paramGaussian2D(intervalX, intervalY, nCols) {
             let xIndex = t % nCols;
             let yIndex = (t - xIndex) / nCols;
             for (let i = 0; i < nL; i++) {
+                gaussian2D.fwhm = { x: p[i + 3 * nL], y: p[i + 4 * nL] };
                 result +=
                     p[i + 2 * nL] *
-                        gaussian2DFct((xIndex - p[i]) * intervalX, (yIndex - p[i + nL]) * intervalY, p[i + 3 * nL], p[i + 4 * nL]);
+                        gaussian2D.fct((xIndex - p[i]) * intervalX, (yIndex - p[i + nL]) * intervalY);
             }
             return result;
         };

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

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

@@ -42,7 +42,7 @@ export default {
             signal.asymmetric = false;
             let P1, n2, maxFlagged;
             let k = 1;
-            let Jc = [];
+            let jCouplings = [];
             // Loop over the possible number of coupling contributing to the multiplet
             for (let n = 0; n < 9; n++) {
                 // 1.2 Normalize. It makes a deep copy of the peaks before to modify them.
@@ -76,17 +76,17 @@ export default {
                             numbering[i][j] = k++;
                         }
                     }
-                    Jc = []; // The array to store the detected j-coupling
+                    jCouplings = []; // The array to store the detected j-coupling
                     // 2.2 Set j = 1; J1 = P2 - P1. Flag components 1 and 2 as accounted for.
                     let j = 1;
-                    Jc.push(peaks[1].x - peaks[0].x);
+                    jCouplings.push(peaks[1].x - peaks[0].x);
                     P1 = peaks[0].x;
                     numbering[0].splice(0, 1); // Flagged
                     numbering[1].splice(0, 1); // Flagged
                     k = 1;
                     let nFlagged = 2;
                     maxFlagged = Math.pow(2, n) - 1;
-                    while (Jc.length < n && nFlagged < maxFlagged && k < peaks.length) {
+                    while (jCouplings.length < n && nFlagged < maxFlagged && k < peaks.length) {
                         counter += 1;
                         // 4.1. Increment j. Set k to the number of the first unflagged component.
                         j++;
@@ -95,7 +95,7 @@ export default {
                         }
                         if (k < peaks.length) {
                             // 4.2 Jj = Pk - P1.
-                            Jc.push(peaks[k].x - peaks[0].x);
+                            jCouplings.push(peaks[k].x - peaks[0].x);
                             // Flag component k and, for each sum of the...
                             numbering[k].splice(0, 1); // Flageed
                             nFlagged++;
@@ -103,7 +103,7 @@ export default {
                             for (let u = 2; u <= j; u++) {
                                 let jSum = 0;
                                 for (let i = 0; i < u; i++) {
-                                    jSum += Jc[i];
+                                    jSum += jCouplings[i];
                                 }
                                 for (let i = 1; i < numbering.length; i++) {
                                     // Maybe 0.25 Hz is too much?
@@ -117,7 +117,7 @@ export default {
                         }
                     }
                     // Calculate the ideal patter by using the extracted j-couplings
-                    let pattern = idealPattern(Jc);
+                    let pattern = idealPattern(jCouplings);
                     // Compare the ideal pattern with the proposed intensities.
                     // All the intensities have to match to accept the multiplet
                     validPattern = true;
@@ -129,7 +129,7 @@ export default {
                 }
                 // If we found a valid pattern we should inform about the pattern.
                 if (validPattern) {
-                    updateSignal(signal, Jc);
+                    updateSignal(signal, jCouplings);
                 }
             }
         }
@@ -144,56 +144,56 @@ export default {
  * @private
  * update the signal
  * @param {*} signal
- * @param {*} Jc
+ * @param {*} jCouplings
  */
-function updateSignal(signal, Jc) {
+function updateSignal(signal, jCouplings) {
     // Update the limits of the signal
     let peaks = signal.peaksComp; // Always in Hz
     let nbPeaks = peaks.length;
-    signal.startX = peaks[0].x / signal.observe - peaks[0].shape.width;
+    signal.startX = peaks[0].x / signal.observe - peaks[0].width;
     signal.stopX =
-        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width;
+        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width;
     signal.integralData.from =
-        peaks[0].x / signal.observe - peaks[0].shape.width * 3;
+        peaks[0].x / signal.observe - peaks[0].width * 3;
     signal.integralData.to =
-        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].shape.width * 3;
+        peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
     // Compile the pattern and format the constant couplings
     signal.maskPattern = signal.mask2;
-    signal.multiplicity = abstractPattern(signal, Jc);
+    signal.multiplicity = abstractPattern(signal, jCouplings);
     signal.pattern = signal.multiplicity; // Our library depends on this parameter, but it is old
 }
 /**
  * Returns the multiplet in the compact format
  * @param {object} signal
- * @param {object} Jc
+ * @param {object} jCouplings
  * @return {String}
  * @private
  */
-function abstractPattern(signal, Jc) {
+function abstractPattern(signal, jCouplings) {
     let tol = 0.05;
     let pattern = '';
     let cont = 1;
     let newNmrJs = [];
-    if (Jc && Jc.length > 0) {
-        Jc.sort((a, b) => {
+    if (jCouplings && jCouplings.length > 0) {
+        jCouplings.sort((a, b) => {
             return b - a;
         });
-        for (let i = 0; i < Jc.length - 1; i++) {
-            if (Math.abs(Jc[i] - Jc[i + 1]) < tol) {
+        for (let i = 0; i < jCouplings.length - 1; i++) {
+            if (Math.abs(jCouplings[i] - jCouplings[i + 1]) < tol) {
                 cont++;
             }
             else {
                 newNmrJs.push({
-                    coupling: Math.abs(Jc[i]),
+                    coupling: Math.abs(jCouplings[i]),
                     multiplicity: patterns[cont],
                 });
                 pattern += patterns[cont];
                 cont = 1;
             }
         }
-        let index = Jc.length - 1;
+        let index = jCouplings.length - 1;
         newNmrJs.push({
-            coupling: Math.abs(Jc[index]),
+            coupling: Math.abs(jCouplings[index]),
             multiplicity: patterns[cont],
         });
         pattern += patterns[cont];
@@ -210,15 +210,15 @@ function abstractPattern(signal, Jc) {
 /**
  * This function creates an ideal pattern from the given J-couplings
  * @private
- * @param {Array} Jc
+ * @param {Array} jCouplings
  * @return {*[]}
  * @private
  */
-function idealPattern(Jc) {
-    let hsum = Math.pow(2, Jc.length);
+function idealPattern(jCouplings) {
+    let hsum = Math.pow(2, jCouplings.length);
     let pattern = [{ x: 0, intensity: hsum }];
     // To split the initial height
-    for (const jc of Jc) {
+    for (const jc of jCouplings) {
         for (let j = pattern.length - 1; j >= 0; j--) {
             pattern.push({
                 x: pattern[j].x + jc / 2,
@@ -375,9 +375,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
         peaks[i] = {
             x: peak[jAxis] * newSignal.observe,
             intensity: peak[intensity],
-            shape: {
-                width: peak.shape.width,
-            },
+            width: peak.width,
         };
     }
     // Join the peaks that are closer than 0.25 Hz
@@ -389,7 +387,7 @@ function symmetrize(signalInput, maxError, iteration, key) {
             peaks[i].intensity = peaks[i].intensity + peaks[i + 1].intensity;
             peaks[i].x /= peaks[i].intensity;
             peaks[i].intensity /= 2;
-            peaks[i].shape.width += peaks[i + 1].shape.width;
+            peaks[i].width += peaks[i + 1].width;
             peaks.splice(i + 1, 1);
         }
     }
@@ -437,9 +435,9 @@ function symmetrize(signalInput, maxError, iteration, key) {
                 let diffR = Math.abs(peaks[right].x - cs);
                 if (Math.abs(diffL - diffR) < maxError) {
                     avg = Math.min(peaks[left].intensity, peaks[right].intensity);
-                    avgWidth = Math.min(peaks[left].shape.width, peaks[right].shape.width);
+                    avgWidth = Math.min(peaks[left].width, peaks[right].width);
                     peaks[left].intensity = peaks[right].intensity = avg;
-                    peaks[left].shape.width = peaks[right].shape.width = avgWidth;
+                    peaks[left].width = peaks[right].width = avgWidth;
                     middle = [
                         middle[0] + (peaks[right].x + peaks[left].x) / 2,
                         middle[1] + 1,
@@ -616,6 +614,6 @@ function chemicalShift(peaks, mask = []) {
  * @private
  */
 function getArea(peak) {
-    return Math.abs(peak.intensity * peak.shape.width * 1.57); // 1.772453851);
+    return Math.abs(peak.intensity * peak.width * 1.57); // 1.772453851);
 }
 //# sourceMappingURL=jAnalyzer.js.map