nmr-processing 6.0.8 → 7.1.0

package/lib/index.d.ts

@@ -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

@@ -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

@@ -1 +1 @@
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+{"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

@@ -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

@@ -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

@@ -1 +1 @@
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package/lib/peaks/util/jAnalyzer.d.ts

@@ -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

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

@@ -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

@@ -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

@@ -0,0 +1 @@
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package/lib/prediction/utils/getFilteredIDiaIDs.d.ts

@@ -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

@@ -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

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

@@ -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

@@ -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

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

@@ -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

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package/lib-esm/index.js

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,+BAA+B,CAAC;AAC9C,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;AAE/C,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;AAE5C,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"}

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

@@ -1 +1 @@
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