npm - nmr-processing - Versions diffs - 6.0.8 → 7.1.0 - Mend

nmr-processing 6.0.8 → 7.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (38) hide show

package/lib/index.d.ts +1 -0
package/lib/index.js +6 -1
package/lib/index.js.map +1 -1
package/lib/peaks/NMRPeak1D.d.ts +5 -2
package/lib/peaks/peaksToRanges.d.ts +3 -1
package/lib/peaks/peaksToRanges.js.map +1 -1
package/lib/peaks/util/jAnalyzer.d.ts +1 -1
package/lib/peaks/util/jAnalyzer.js.map +1 -1
package/lib/prediction/predictAllSpectra.d.ts +18 -0
package/lib/prediction/predictAllSpectra.js +40 -0
package/lib/prediction/predictAllSpectra.js.map +1 -0
package/lib/prediction/utils/getFilteredIDiaIDs.d.ts +1 -1
package/lib/utilities/resurrectRange.js +12 -16
package/lib/utilities/resurrectRange.js.map +1 -1
package/lib/xy/xyAutoPeaksPicking.d.ts +5 -4
package/lib/xy/xyAutoPeaksPicking.js +14 -23
package/lib/xy/xyAutoPeaksPicking.js.map +1 -1
package/lib/xyz/xyzAutoZonesPicking.js +5 -1
package/lib/xyz/xyzAutoZonesPicking.js.map +1 -1
package/lib-esm/index.js +1 -0
package/lib-esm/index.js.map +1 -1
package/lib-esm/peaks/peaksToRanges.js.map +1 -1
package/lib-esm/peaks/util/jAnalyzer.js.map +1 -1
package/lib-esm/prediction/predictAllSpectra.js +36 -0
package/lib-esm/prediction/predictAllSpectra.js.map +1 -0
package/lib-esm/utilities/resurrectRange.js +12 -16
package/lib-esm/utilities/resurrectRange.js.map +1 -1
package/lib-esm/xy/xyAutoPeaksPicking.js +15 -24
package/lib-esm/xy/xyAutoPeaksPicking.js.map +1 -1
package/package.json +14 -15
package/src/index.ts +1 -0
package/src/{openchemlib.d.ts → openchemlib-utils.d.ts} +0 -1
package/src/peaks/NMRPeak1D.ts +5 -2
package/src/peaks/peaksToRanges.ts +5 -3
package/src/peaks/util/jAnalyzer.ts +3 -1
package/src/prediction/predictAllSpectra.ts +48 -0
package/src/utilities/resurrectRange.ts +17 -17
package/src/xy/xyAutoPeaksPicking.ts +25 -36

package/lib/index.d.ts CHANGED Viewed

@@ -8,6 +8,7 @@ export * from './prediction/predictCOSY';
 export * from './prediction/predictHSQC';
 export * from './prediction/predictHMBC';
 export * from './prediction/predictAll';
+export * from './prediction/predictAllSpectra';
 export * from './assignment/get1HAssignments';
 export * from './assignment/get13CAssignments';
 export * from './ranges/rangesToACS';

package/lib/index.js CHANGED Viewed

@@ -1,7 +1,11 @@
 "use strict";
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
-    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
 }) : (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     o[k2] = m[k];
@@ -20,6 +24,7 @@ __exportStar(require("./prediction/predictCOSY"), exports);
 __exportStar(require("./prediction/predictHSQC"), exports);
 __exportStar(require("./prediction/predictHMBC"), exports);
 __exportStar(require("./prediction/predictAll"), exports);
+__exportStar(require("./prediction/predictAllSpectra"), exports);
 __exportStar(require("./assignment/get1HAssignments"), exports);
 __exportStar(require("./assignment/get13CAssignments"), exports);
 __exportStar(require("./ranges/rangesToACS"), exports);

package/lib/index.js.map CHANGED Viewed

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

package/lib/peaks/NMRPeak1D.d.ts CHANGED Viewed

@@ -1,4 +1,7 @@
-import type { Peak1D } from 'ml-gsd';
-export interface NMRPeak1D extends Peak1D {
+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/peaksToRanges.d.ts CHANGED Viewed

@@ -54,7 +54,9 @@ export interface OptionsDetectSignals {
     frequency?: number;
     nucleus?: string;
 }
+declare type NMRPeak1DIntern = Omit<NMRPeak1D, 'fwhm' | 'shape'>;
 /**
  * This function clustering peaks and calculate the integration value for each range from the peak list returned from extractPeaks function.
  */
-export declare function peaksToRanges(data: DataXY, peakList: NMRPeak1D[], options?: OptionsPeaksToRanges): NMRRange[];
+export declare function peaksToRanges(data: DataXY, peakList: NMRPeak1DIntern[], options?: OptionsPeaksToRanges): NMRRange[];
+export {};

package/lib/peaks/peaksToRanges.js.map CHANGED Viewed

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package/lib/peaks/util/jAnalyzer.d.ts CHANGED Viewed

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

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

	@@ -1 +1 @@
1	- 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package/lib/prediction/predictAllSpectra.d.ts ADDED Viewed

@@ -0,0 +1,18 @@
+import type { Molecule } from 'openchemlib';
+import { OptionsSignalsToXY } from '../signals/signalsToXY';
+import { PredictAllOptions } from './predictAll';
+/**
+ * This function will generate an object compatible with NMR-ium
+ *
+ * @param molecule
+ * @param options
+ */
+export declare function predictAllSpectra(molecule: Molecule, options?: {
+    prediction?: PredictAllOptions;
+    simulation?: OptionsSignalsToXY;
+}): Promise<{
+    spectra: any[];
+    molecules: {
+        molfile: any;
+    }[];
+}>;

package/lib/prediction/predictAllSpectra.js ADDED Viewed

@@ -0,0 +1,40 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.predictAllSpectra = void 0;
+const signalsToXY_1 = require("../signals/signalsToXY");
+const predictAll_1 = require("./predictAll");
+/**
+ * This function will generate an object compatible with NMR-ium
+ *
+ * @param molecule
+ * @param options
+ */
+async function predictAllSpectra(molecule, options = {}) {
+    const predictions = await (0, predictAll_1.predictAll)(molecule, options.prediction);
+    const spectra = [];
+    const result = { spectra, molecules: [{ molfile: predictions.molfile }] };
+    spectra.push(getProton(predictions.proton, options.simulation));
+    return result;
+}
+exports.predictAllSpectra = predictAllSpectra;
+function getProton(prediction, options) {
+    const { x, y } = (0, signalsToXY_1.signalsToXY)(prediction.signals, options);
+    const spectrum = {
+        id: '',
+        // todo Array.from is temporary for the developement
+        data: { x: Array.from(x), re: Array.from(y), im: null },
+        info: {
+            nucleus: prediction.nucleus,
+            dimension: 1,
+            originFrequency: 400,
+            baseFrequency: 400,
+            pulseSequence: 'prediction',
+            experiment: 'proton',
+            isFt: true,
+        },
+        // todo: currently we disable the ranges because there is no ID
+        //ranges: { values: prediction.ranges },
+    };
+    return spectrum;
+}
+//# sourceMappingURL=predictAllSpectra.js.map

package/lib/prediction/predictAllSpectra.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"predictAllSpectra.js","sourceRoot":"","sources":["../../src/prediction/predictAllSpectra.ts"],"names":[],"mappings":";;;AAEA,wDAAyE;AAEzE,6CAA6D;AAC7D;;;;;GAKG;AAEI,KAAK,UAAU,iBAAiB,CACrC,QAAkB,EAClB,UAGI,EAAE;IAEN,MAAM,WAAW,GAAG,MAAM,IAAA,uBAAU,EAAC,QAAQ,EAAE,OAAO,CAAC,UAAU,CAAC,CAAC;IACnE,MAAM,OAAO,GAAU,EAAE,CAAC;IAC1B,MAAM,MAAM,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,CAAC,EAAE,OAAO,EAAE,WAAW,CAAC,OAAO,EAAE,CAAC,EAAE,CAAC;IAC1E,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,MAAM,EAAE,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC;IAEhE,OAAO,MAAM,CAAC;AAChB,CAAC;AAbD,8CAaC;AAED,SAAS,SAAS,CAAC,UAAe,EAAE,OAA4B;IAC9D,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,IAAA,yBAAW,EAAC,UAAU,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;IAC1D,MAAM,QAAQ,GAAG;QACf,EAAE,EAAE,EAAE;QACN,oDAAoD;QACpD,IAAI,EAAE,EAAE,CAAC,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE;QACvD,IAAI,EAAE;YACJ,OAAO,EAAE,UAAU,CAAC,OAAO;YAC3B,SAAS,EAAE,CAAC;YACZ,eAAe,EAAE,GAAG;YACpB,aAAa,EAAE,GAAG;YAClB,aAAa,EAAE,YAAY;YAC3B,UAAU,EAAE,QAAQ;YACpB,IAAI,EAAE,IAAI;SACX;QACD,+DAA+D;QAC/D,wCAAwC;KACzC,CAAC;IAEF,OAAO,QAAQ,CAAC;AAClB,CAAC"}

package/lib/prediction/utils/getFilteredIDiaIDs.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-/// <reference path="../../../src/openchemlib.d.ts" />
+/// <reference path="../../../src/openchemlib-utils.d.ts" />
 import type { Molecule } from 'openchemlib';
 import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
 export interface GroupDiaIDsWithHose extends GroupDiastereotopicAtomIDs {

package/lib/utilities/resurrectRange.js CHANGED Viewed

@@ -9,16 +9,12 @@ function resurrectRange(part, options = {}) {
     const split = (0, splitParenthesis_1.splitParenthesis)(part);
     if (!split.before)
         return;
-    // before parenthesis there should be only numbers but we will still split with space
-    const beforeParts = split.before
-        .split(/(?: |(?<=[0-9])-)/)
-        .map((part) => Number(part))
-        .filter((part) => !Number.isNaN(part));
-    if (beforeParts.length < 1 || beforeParts.length > 2) {
+    const beforeMatch = /.*?(?<from>-?[0-9.]+)-?(?<to>-?[0-9.]*).*/.exec(split.before);
+    if (!beforeMatch || !beforeMatch.groups)
         return;
-    }
-    const from = beforeParts[0];
-    const to = beforeParts.length > 1 ? beforeParts[1] : beforeParts[0];
+    const isARange = beforeMatch.groups.to !== '';
+    const from = Number(beforeMatch.groups.from);
+    const to = isARange ? Number(beforeMatch.groups.to) : from;
     const insideParts = split.inside.split(/ *, */);
     let signal = { delta: NaN, js: [] };
     let range = { from, to, signals: [signal] };
@@ -30,22 +26,22 @@ function resurrectRange(part, options = {}) {
     if (multiplicityParts.length === 1) {
         const multiplicity = multiplicityParts[0];
         if (multiplicity === 'm') {
-            if (beforeParts.length === 1) {
-                // a complex signal
-                signal.delta = beforeParts[0];
+            if (isARange) {
+                // a real range
+                signal.delta = (from + to) / 2;
                 signal.multiplicity = multiplicity;
             }
             else {
-                // a real range
-                signal.delta = (beforeParts[0] + beforeParts[1]) / 2;
+                // a complex signal
+                signal.delta = from;
                 signal.multiplicity = multiplicity;
             }
         }
         else {
             // looks like a real multiplicity, s, d, dd, etc..
-            if (beforeParts.length === 1) {
+            if (!isARange) {
                 // a complex signal
-                signal.delta = beforeParts[0];
+                signal.delta = from;
                 signal.multiplicity = multiplicity;
             }
         }

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

	@@ -1 +1 @@
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package/lib/xy/xyAutoPeaksPicking.d.ts CHANGED Viewed

@@ -1,13 +1,14 @@
 import { DataXY } from 'cheminfo-types';
-import type { Peak1D, GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions } from 'ml-gsd';
-export interface IGetPeakListOptions extends GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions {
+import type { GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions } from 'ml-gsd';
+import { NMRPeak1D } from '..';
+export interface GetPeakListOptions extends GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions {
     /**
      * If it is true, the peaks parameters will be optimized.
      * @default false
      */
     optimize: boolean;
 }
-export interface OptionsXYAutoPeaksPicking extends Partial<IGetPeakListOptions> {
+export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
     /**
      * Low limit value in the x axis to extract a sub set of points from the input data.
      */
@@ -32,4 +33,4 @@ export interface OptionsXYAutoPeaksPicking extends Partial<IGetPeakListOptions>
      */
     useSanPlot?: boolean;
 }
-export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): Peak1D[];
+export declare function xyAutoPeaksPicking(data: DataXY, options?: OptionsXYAutoPeaksPicking): NMRPeak1D[];

package/lib/xy/xyAutoPeaksPicking.js CHANGED Viewed

@@ -4,19 +4,21 @@ exports.xyAutoPeaksPicking = void 0;
 const ml_gsd_1 = require("ml-gsd");
 const ml_spectra_processing_1 = require("ml-spectra-processing");
 function xyAutoPeaksPicking(data, options = {}) {
-    const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorWidth = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, lookNegative = false, sgOptions = { windowSize: 9, polynomial: 3 }, } = options;
+    const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, lookNegative = false, } = options;
+    const { windowSize = 9, polynomial = 3 } = sgOptions;
     if (from !== undefined && to !== undefined) {
         data = (0, ml_spectra_processing_1.xyExtract)(data, { zones: [{ from, to }] });
     }
-    if (data.x.length < sgOptions.windowSize)
+    if (data.x.length < windowSize)
         return [];
     const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
     let getPeakOptions = {
         shape,
         broadWidth,
         optimize,
-        factorWidth,
-        sgOptions,
+        factorLimits,
+        maxCriteria: true,
+        sgOptions: { windowSize, polynomial },
         minMaxRatio,
         broadRatio,
         noiseLevel: cutOff.positive,
@@ -27,23 +29,24 @@ function xyAutoPeaksPicking(data, options = {}) {
     let peaks = getPeakList(data, getPeakOptions);
     if (lookNegative) {
         getPeakOptions.noiseLevel = cutOff.negative;
-        peaks.push(...getNegativePeaks(data, getPeakOptions));
+        getPeakOptions.maxCriteria = false;
+        peaks.push(...getPeakList(data, getPeakOptions));
     }
     return peaks;
 }
 exports.xyAutoPeaksPicking = xyAutoPeaksPicking;
 function getPeakList(data, options) {
-    const { shape, broadWidth, optimize, factorWidth, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
+    const { shape, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
     let peakList = (0, ml_gsd_1.gsd)(data, {
-        shape,
         sgOptions,
+        maxCriteria,
         minMaxRatio,
         noiseLevel,
         smoothY,
         realTopDetection,
     });
     if (broadWidth) {
-        peakList = (0, ml_gsd_1.joinBroadPeaks)(data, peakList, {
+        peakList = (0, ml_gsd_1.joinBroadPeaks)(peakList, {
             broadRatio,
             broadWidth,
             shape,
@@ -51,25 +54,13 @@ function getPeakList(data, options) {
         });
     }
     if (optimize) {
-        peakList = (0, ml_gsd_1.optimizePeaks)(data, peakList, {
+        return (0, ml_gsd_1.optimizePeaks)(data, peakList, {
             shape,
-            factorWidth,
+            factorLimits,
             optimization,
         });
     }
-    return peakList;
-}
-function getNegativePeaks(data, options) {
-    let { x, y } = data;
-    let negativeDataY = new Float64Array(data.y.length);
-    for (let i = 0; i < negativeDataY.length; i++) {
-        negativeDataY[i] = -1 * y[i];
-    }
-    let peakList = getPeakList({ x, y: negativeDataY }, options);
-    for (const peak of peakList) {
-        peak.y *= -1;
-    }
-    return peakList;
+    return (0, ml_gsd_1.appendShapeAndFWHM)(peakList, { shape });
 }
 function getCutOff(data, options) {
     const { noiseLevel, useSanPlot, thresholdFactor } = options;

package/lib/xy/xyAutoPeaksPicking.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/xyz/xyzAutoZonesPicking.js CHANGED Viewed

@@ -1,7 +1,11 @@
 "use strict";
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
-    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
 }) : (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     o[k2] = m[k];

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

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package/lib-esm/index.js CHANGED Viewed

@@ -8,6 +8,7 @@ export * from './prediction/predictCOSY';
 export * from './prediction/predictHSQC';
 export * from './prediction/predictHMBC';
 export * from './prediction/predictAll';
+export * from './prediction/predictAllSpectra';
 export * from './assignment/get1HAssignments';
 export * from './assignment/get13CAssignments';
 export * from './ranges/rangesToACS';

package/lib-esm/index.js.map CHANGED Viewed

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

	@@ -1 +1 @@
1	- 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