npm - nmr-processing - Versions diffs - 5.0.0 → 6.0.0 - Mend

nmr-processing 5.0.0 → 6.0.0

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Files changed (114) hide show

package/lib/assignment/get13CAssignments.js.map +1 -1
package/lib/assignment/utils/buildAssignments.js.map +1 -1
package/lib/assignment/utils/createMapPossibleAssignments.js.map +1 -1
package/lib/constants/couplingValues.js.map +1 -1
package/lib/index.d.ts +1 -1
package/lib/index.js +1 -1
package/lib/peaks/util/determineRealTop.d.ts +2 -2
package/lib/peaks/util/determineRealTop.js.map +1 -1
package/lib/peaks/util/jAnalyzer.js +4 -3
package/lib/peaks/util/jAnalyzer.js.map +1 -1
package/lib/peaks/util/peakOptimizer.d.ts +2 -2
package/lib/peaks/util/peakOptimizer.js.map +1 -1
package/lib/prediction/predictAll.js +1 -1
package/lib/prediction/predictAll.js.map +1 -1
package/lib/prediction/predictHSQC.js.map +1 -1
package/lib/prediction/predictProton.js +1 -1
package/lib/prediction/predictProton.js.map +1 -1
package/lib/prediction/utils/getFilteredIDiaIDs.js.map +1 -1
package/lib/prediction/utils/getNuclei.js +1 -1
package/lib/prediction/utils/getNuclei.js.map +1 -1
package/lib/prediction/utils/getPredictions.d.ts +2 -2
package/lib/prediction/utils/queryByHOSE.js.map +1 -1
package/lib/signal/signalJoinCouplings.d.ts +1 -1
package/lib/signal/signalJoinCouplings.js +3 -3
package/lib/signal/signalJoinCouplings.js.map +1 -1
package/lib/signals/signalsJoin.d.ts +1 -1
package/lib/signals/signalsJoin.js +7 -7
package/lib/signals/signalsJoin.js.map +1 -1
package/lib/signals/simulation/splitSpinSystem.js.map +1 -1
package/lib/types/NMRSignal2D.d.ts +6 -4
package/lib/types/NMRZone.d.ts +3 -7
package/lib/types/jcoupling.d.ts +1 -1
package/lib/types/modules/nmr-parser.d.ts +11 -0
package/lib/types/modules/nmr-parser.js +2 -0
package/lib/types/modules/nmr-parser.js.map +1 -0
package/lib/types/prediction1D.d.ts +2 -2
package/lib/utilities/joinPatterns.js.map +1 -1
package/lib/xy/xyAutoPeaksPicking.d.ts +2 -2
package/lib/xyz/{xyzAutoPeaksPicking.d.ts → xyzAutoZonesPicking.d.ts} +2 -2
package/lib/xyz/{xyzAutoPeaksPicking.js → xyzAutoZonesPicking.js} +38 -26
package/lib/xyz/xyzAutoZonesPicking.js.map +1 -0
package/lib/xyz/xyzJResAnalyzer.js.map +1 -1
package/lib-esm/assignment/get13CAssignments.js.map +1 -1
package/lib-esm/assignment/utils/buildAssignments.js.map +1 -1
package/lib-esm/assignment/utils/createMapPossibleAssignments.js.map +1 -1
package/lib-esm/constants/couplingValues.js.map +1 -1
package/lib-esm/index.js +1 -1
package/lib-esm/peaks/util/determineRealTop.js.map +1 -1
package/lib-esm/peaks/util/jAnalyzer.js +4 -3
package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
package/lib-esm/peaks/util/peakOptimizer.js.map +1 -1
package/lib-esm/prediction/predictAll.js +1 -1
package/lib-esm/prediction/predictAll.js.map +1 -1
package/lib-esm/prediction/predictHSQC.js.map +1 -1
package/lib-esm/prediction/predictProton.js +1 -1
package/lib-esm/prediction/predictProton.js.map +1 -1
package/lib-esm/prediction/utils/getFilteredIDiaIDs.js.map +1 -1
package/lib-esm/prediction/utils/getNuclei.js +1 -1
package/lib-esm/prediction/utils/getNuclei.js.map +1 -1
package/lib-esm/prediction/utils/queryByHOSE.js.map +1 -1
package/lib-esm/signal/signalJoinCouplings.js +3 -3
package/lib-esm/signal/signalJoinCouplings.js.map +1 -1
package/lib-esm/signals/signalsJoin.js +7 -7
package/lib-esm/signals/signalsJoin.js.map +1 -1
package/lib-esm/signals/simulation/splitSpinSystem.js.map +1 -1
package/lib-esm/types/modules/nmr-parser.js +2 -0
package/lib-esm/types/modules/nmr-parser.js.map +1 -0
package/lib-esm/utilities/joinPatterns.js.map +1 -1
package/lib-esm/xyz/{xyzAutoPeaksPicking.js → xyzAutoZonesPicking.js} +36 -24
package/lib-esm/xyz/xyzAutoZonesPicking.js.map +1 -0
package/lib-esm/xyz/xyzJResAnalyzer.js.map +1 -1
package/package.json +19 -16
package/src/assignment/get13CAssignments.ts +4 -1
package/src/assignment/utils/buildAssignments.ts +1 -4
package/src/assignment/utils/createMapPossibleAssignments.ts +4 -1
package/src/constants/couplingValues.ts +1 -1
package/src/index.ts +1 -1
package/src/peaks/util/determineRealTop.ts +3 -4
package/src/peaks/util/jAnalyzer.ts +7 -7
package/src/peaks/util/peakOptimizer.ts +4 -3
package/src/prediction/predictAll.ts +5 -5
package/src/prediction/predictHSQC.ts +4 -1
package/src/prediction/predictProton.ts +1 -1
package/src/prediction/utils/getFilteredIDiaIDs.ts +1 -2
package/src/prediction/utils/getNuclei.ts +3 -3
package/src/prediction/utils/getPredictions.ts +3 -3
package/src/prediction/utils/queryByHOSE.ts +1 -1
package/src/signal/signalJoinCouplings.ts +3 -3
package/src/signals/signalsJoin.ts +7 -7
package/src/signals/signalsToXY.ts +1 -1
package/src/signals/simulation/splitSpinSystem.ts +10 -2
package/src/types/NMRSignal2D.ts +7 -5
package/src/types/NMRZone.ts +6 -6
package/src/types/dataStructure.ts +1 -1
package/src/types/jcoupling.ts +1 -1
package/src/types/ml-matrix-peaks-finder/index.d.ts +2 -2
package/src/types/ml-simple-clustering/index.d.ts +1 -1
package/src/types/ml-spectra-processing/index.d.ts +8 -2
package/src/types/modules/nmr-parser.ts +17 -0
package/src/types/openchemlib-utils/index..d.ts +17 -6
package/src/types/prediction1D.ts +2 -2
package/src/utilities/joinPatterns.ts +0 -1
package/src/xy/xyAutoPeaksPicking.ts +6 -6
package/src/xyz/{xyzAutoPeaksPicking.ts → xyzAutoZonesPicking.ts} +40 -26
package/src/xyz/xyzJResAnalyzer.ts +4 -4
package/CHANGELOG.md +0 -572
package/lib/types/MPFPeak.d.ts +0 -9
package/lib/types/MPFPeak.js +0 -3
package/lib/types/MPFPeak.js.map +0 -1
package/lib/xyz/xyzAutoPeaksPicking.js.map +0 -1
package/lib-esm/types/MPFPeak.js +0 -2
package/lib-esm/types/MPFPeak.js.map +0 -1
package/lib-esm/xyz/xyzAutoPeaksPicking.js.map +0 -1
package/src/types/MPFPeak.ts +0 -9

package/lib/types/jcoupling.d.ts CHANGED Viewed

@@ -4,5 +4,5 @@ export interface Jcoupling {
     assignment?: string | string[];
     diaIDs?: string[];
     multiplicity?: string;
-    distance?: number;
+    pathLength?: number;
 }

package/lib/types/modules/nmr-parser.d.ts ADDED Viewed

@@ -0,0 +1,11 @@
+declare module 'nmr-parser' {
+    interface FromBrukerOptions {
+        base64?: boolean;
+        shiftX?: number;
+        info?: any;
+        name?: string;
+    }
+    function fromBruker(zipFile: ArrayBuffer | string, options?: Partial<FromBrukerOptions>): Promise<Array<any>>;
+    function fromJCAMP(buffer: string | ArrayBuffer, options?: any): Array<any>;
+    function fromJEOL(buffer: ArrayBuffer): any;
+}

package/lib/types/modules/nmr-parser.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ "use strict";
2	+ //# sourceMappingURL=nmr-parser.js.map

package/lib/types/modules/nmr-parser.js.map ADDED Viewed

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

package/lib/types/prediction1D.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 import type { Molecule } from 'openchemlib';
-import type { NMRRange } from "./NMRRange";
-import type { NMRSignal1D } from "./NMRSignal1D";
+import type { NMRRange } from './NMRRange';
+import type { NMRSignal1D } from './NMRSignal1D';
 export interface Prediction1D {
     molfile: string;
     diaIDs: string[];

package/lib/utilities/joinPatterns.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"joinPatterns.js","sourceRoot":"","sources":["../../src/utilities/joinPatterns.ts"],"names":[],"mappings":";;;AAAA,oEAAiE;AACjE,gEAA6D;~~AAG7D~~,SAAgB,YAAY,CAAC,QAAkB;IAC7C,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE;QAC3C,IAAI,KAAK,CAAC,+BAAc,CAAC,OAAO,CAAC,CAAC,EAAE;YAClC,MAAM,IAAI,KAAK,CACb,WAAW,OAAO,cAAc,MAAM,CAAC,IAAI,CAAC,+BAAc,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CACxE,CAAC;SACH;QACD,OAAO,GAAG,GAAG,+BAAc,CAAC,OAAO,CAAC,CAAC;IACvC,CAAC,EAAE,CAAC,CAAC,CAAC;IAEN,IAAI,CAAC,mCAAgB,CAAC,GAAG,CAAC,EAAE;QAC1B,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAC;KACrD;IAED,OAAO,mCAAgB,CAAC,GAAG,CAAC,CAAC;AAC/B,CAAC;AAfD,oCAeC"}
1	+ {"version":3,"file":"joinPatterns.js","sourceRoot":"","sources":["../../src/utilities/joinPatterns.ts"],"names":[],"mappings":";;;AAAA,oEAAiE;AACjE,gEAA6D;AAE7D,SAAgB,YAAY,CAAC,QAAkB;IAC7C,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE;QAC3C,IAAI,KAAK,CAAC,+BAAc,CAAC,OAAO,CAAC,CAAC,EAAE;YAClC,MAAM,IAAI,KAAK,CACb,WAAW,OAAO,cAAc,MAAM,CAAC,IAAI,CAAC,+BAAc,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CACxE,CAAC;SACH;QACD,OAAO,GAAG,GAAG,+BAAc,CAAC,OAAO,CAAC,CAAC;IACvC,CAAC,EAAE,CAAC,CAAC,CAAC;IAEN,IAAI,CAAC,mCAAgB,CAAC,GAAG,CAAC,EAAE;QAC1B,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAC;KACrD;IAED,OAAO,mCAAgB,CAAC,GAAG,CAAC,CAAC;AAC/B,CAAC;AAfD,oCAeC"}

package/lib/xy/xyAutoPeaksPicking.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 import { DataXY } from 'cheminfo-types';
-import type { Peak1D, IGSDOptions, IOptimizePeaksOptions, IJoinBroadPeaksOptions } from 'ml-gsd';
-export interface IGetPeakListOptions extends IGSDOptions, IOptimizePeaksOptions, IJoinBroadPeaksOptions {
+import type { Peak1D, GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions } from 'ml-gsd';
+export interface IGetPeakListOptions extends GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions {
     /**
      * If it is true, the peaks parameters will be optimized.
      * @default false

package/lib/xyz/{xyzAutoPeaksPicking.d.ts → xyzAutoZonesPicking.d.ts} RENAMED Viewed

@@ -1,5 +1,5 @@
+import { NMRZone } from '..';
 import type { GetKernelOptions } from '../peaks/util/getKernel';
-import type { NMRSignal2D } from '../types/NMRSignal2D';
 export interface Data2D {
     z: number[][] | Float64Array[];
     minX: number;
@@ -62,7 +62,7 @@ export interface XYZAutoPeaksPickingOptions {
      */
     kernel?: GetKernelOptions;
 }
-export declare function xyzAutoPeaksPicking(spectraData: Data2D, options: XYZAutoPeaksPickingOptions): NMRSignal2D[];
+export declare function xyzAutoZonesPicking(spectraData: Data2D, options: XYZAutoPeaksPickingOptions): NMRZone[];
 /**
  * This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed
  * of many 2D-peaks, and it has some additional information related to the NMR spectrum.

package/lib/xyz/{xyzAutoPeaksPicking.js → xyzAutoZonesPicking.js} RENAMED Viewed

@@ -22,7 +22,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.xyzAutoPeaksPicking = void 0;
+exports.xyzAutoZonesPicking = void 0;
 const ml_matrix_1 = require("ml-matrix");
 const convolution = __importStar(require("ml-matrix-convolution"));
 const matrixPeakFinders = __importStar(require("ml-matrix-peaks-finder"));
@@ -41,7 +41,7 @@ const smallFilter = [
     [0, 1, 3, 7, 7, 7, 3, 1, 0],
     [0, 0, 1, 2, 2, 2, 1, 0, 0],
 ];
-function xyzAutoPeaksPicking(spectraData, options) {
+function xyzAutoZonesPicking(spectraData, options) {
     let { sizeToPad = 14, realTopDetection = true, thresholdFactor = 0.5, nuclei = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
     if (!Array.isArray(observedFrequencies) &&
         !ArrayBuffer.isView(observedFrequencies)) {
@@ -103,9 +103,42 @@ function xyzAutoPeaksPicking(spectraData, options) {
     if (enhanceSymmetry) {
         signals = PeakOptimizer.enhanceSymmetry(signals);
     }
-    return signals;
+    return formatZones(signals);
+}
+exports.xyzAutoZonesPicking = xyzAutoZonesPicking;
+function formatZones(signals) {
+    let zones = [];
+    for (const signal of signals) {
+        let minMax1 = [Number.MAX_VALUE, 0];
+        let minMax2 = [Number.MAX_VALUE, 0];
+        for (const peak of signal.peaks || []) {
+            if (peak.minX < minMax1[0]) {
+                minMax1[0] = peak.minX;
+            }
+            if (peak.maxX > minMax1[1]) {
+                minMax1[1] = peak.maxX;
+            }
+            if (peak.minY < minMax2[0]) {
+                minMax2[0] = peak.minY;
+            }
+            if (peak.maxY > minMax2[1]) {
+                minMax2[1] = peak.maxY;
+            }
+        }
+        zones.push({
+            x: {
+                from: minMax1[0],
+                to: minMax1[1],
+            },
+            y: {
+                from: minMax2[0],
+                to: minMax2[1],
+            },
+            signals: [signal],
+        });
+    }
+    return zones;
 }
-exports.xyzAutoPeaksPicking = xyzAutoPeaksPicking;
 const createSignals2D = (peaks, options) => {
     let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
     let [nucleusX, nucleusY] = nuclei;
@@ -133,9 +166,6 @@ const createSignals2D = (peaks, options) => {
         peaks[i].maxX = minX + dx * peaks[i].maxX;
         peaks[i].maxY = minY + dy * peaks[i].maxY;
         // Still having problems to correctly detect peaks on those areas. So I'm removing everything there.
-        if (peaks[i].y < -1 || peaks[i].y >= 210) {
-            peaks.splice(i, 1);
-        }
     }
     // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
     // array like form
@@ -169,8 +199,6 @@ const createSignals2D = (peaks, options) => {
                 },
             };
             let peaks2D = [];
-            let minMax1 = [Number.MAX_VALUE, 0];
-            let minMax2 = [Number.MAX_VALUE, 0];
             let sumZ = 0;
             for (let jPeak = 0; jPeak < cluster.length; jPeak++) {
                 if (cluster[jPeak] === 1) {
@@ -178,24 +206,8 @@ const createSignals2D = (peaks, options) => {
                     signal.x.delta += peaks[jPeak].x * peaks[jPeak].z;
                     signal.y.delta += peaks[jPeak].y * peaks[jPeak].z;
                     sumZ += peaks[jPeak].z;
-                    if (peaks[jPeak].minX < minMax1[0]) {
-                        minMax1[0] = peaks[jPeak].minX;
-                    }
-                    if (peaks[jPeak].maxX > minMax1[1]) {
-                        minMax1[1] = peaks[jPeak].maxX;
-                    }
-                    if (peaks[jPeak].minY < minMax2[0]) {
-                        minMax2[0] = peaks[jPeak].minY;
-                    }
-                    if (peaks[jPeak].maxY > minMax2[1]) {
-                        minMax2[1] = peaks[jPeak].maxY;
-                    }
                 }
             }
-            signal.x.from = minMax1[0];
-            signal.y.from = minMax2[0];
-            signal.x.to = minMax1[1];
-            signal.y.to = minMax2[1];
             signal.x.delta /= sumZ;
             signal.y.delta /= sumZ;
             signal.peaks = peaks2D;
@@ -233,4 +245,4 @@ const padData = (spectraData, options) => {
         maxY: maxY + yOffset * yInterval,
     };
 };
-//# sourceMappingURL=xyzAutoPeaksPicking.js.map
+//# sourceMappingURL=xyzAutoZonesPicking.js.map

package/lib/xyz/xyzAutoZonesPicking.js.map ADDED Viewed

@@ -0,0 +1 @@

+ 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package/lib/xyz/xyzJResAnalyzer.js.map CHANGED Viewed

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package/lib-esm/assignment/utils/createMapPossibleAssignments.js.map CHANGED Viewed

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package/lib-esm/constants/couplingValues.js.map CHANGED Viewed

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

@@ -19,7 +19,7 @@ export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
 export * from './xy/xyAutoPeaksPicking';
 export * from './xy/xyAutoRangesPicking';
-export * from './xyz/xyzAutoPeaksPicking';
+export * from './xyz/xyzAutoZonesPicking';
 export * from './xyz/xyzJResAnalyzer';
 export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';

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

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

@@ -86,7 +86,9 @@ export default {
                     k = 1;
                     let nFlagged = 2;
                     maxFlagged = Math.pow(2, n) - 1;
-                    while (jCouplings.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++;
@@ -153,8 +155,7 @@ function updateSignal(signal, jCouplings) {
     signal.startX = peaks[0].x / signal.observe - peaks[0].width;
     signal.stopX =
         peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width;
-    signal.integralData.from =
-        peaks[0].x / signal.observe - peaks[0].width * 3;
+    signal.integralData.from = peaks[0].x / signal.observe - peaks[0].width * 3;
     signal.integralData.to =
         peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
     // Compile the pattern and format the constant couplings

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

	@@ -1 +1 @@
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package/lib-esm/prediction/predictAll.js CHANGED Viewed

@@ -17,7 +17,7 @@ export async function predictAll(molecule, options = {}) {
     }
     predictions = {
         H: xPrediction,
-        C: yPrediction
+        C: yPrediction,
     };
     const { molfile, diaIDs } = xPrediction;
     const spectra = {

package/lib-esm/prediction/predictAll.js.map CHANGED Viewed

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

	@@ -1 +1 @@
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package/lib-esm/prediction/predictProton.js CHANGED Viewed

@@ -69,7 +69,7 @@ function protonParser(result, molecule, diaIDs) {
                 atoms: [linked],
                 diaIDs: [diaIDs[linked]],
                 multiplicity: 'd',
-                distance: distanceMatrix[atom][linked],
+                pathLength: distanceMatrix[atom][linked],
             });
             signal.js.sort((a, b) => b.coupling - a.coupling);
         }

package/lib-esm/prediction/predictProton.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/prediction/utils/getFilteredIDiaIDs.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib-esm/prediction/utils/getNuclei.js CHANGED Viewed

@@ -3,6 +3,6 @@ const nucleusMap = {
     c: '13C',
 };
 export function getNuclei(input) {
-    return Object.values(input).map((e) => (nucleusMap[e.toLowerCase()]));
+    return Object.values(input).map((e) => nucleusMap[e.toLowerCase()]);
 }
 //# sourceMappingURL=getNuclei.js.map

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