nmr-processing 8.1.0 → 8.3.1

package/README.md

@@ -5,7 +5,25 @@
 [![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
 
-.
+## Introduction
+
+The goal is to have [pure functions](https://medium.com/@jamesjefferyuk/javascript-what-are-pure-functions-4d4d5392d49c) allowing to process NMR spectra.
+
+All the functions use only native javascript object and will not use any classes.
+
+The functions are sorted by category on which they apply. Currently the categories are:
+
+- xy
+- xyz
+- peaks
+- signals
+- ranges
+- prediction
+- assignment
+
+## Debug
+
+A viewer for xy data is available in `/web`
 
 ## Installation
 
@@ -14,12 +32,14 @@
 ## Usage
 
 ```js
-import { myModule } from 'nmr-processing';
+import { library } from 'nmr-processing';
 
-const result = myModule(args);
+const result = library(args);
 // result is ...
 ```
 
+## [API Documentation](https://cheminfo.github.io/nmr-processing/)
+
 ## License
 
 [MIT](./LICENSE)

package/lib/apodization/apodization.d.ts

@@ -0,0 +1,22 @@
+import { DoubleArray } from 'cheminfo-types';
+import { ShapeOptions } from './compose';
+export interface DataReIm {
+    /** Array of re values */
+    re: DoubleArray;
+    /** Array of im values */
+    im: DoubleArray;
+}
+interface ApodizationOptions {
+    /**
+     * number of points at the end of the shape to apply the window function inverted
+     * @default 0
+     */
+    pointsToShift?: number;
+    compose: ShapeOptions;
+}
+export declare function apodization(data: DataReIm, options: ApodizationOptions): {
+    re: DoubleArray;
+    im: DoubleArray;
+    windowData: Float64Array;
+};
+export {};

package/lib/apodization/apodization.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.apodization = void 0;
+const applyWindow_1 = require("./applyWindow");
+const compose_1 = require("./compose");
+function apodization(data, options) {
+    const { compose: composeOptions, pointsToShift } = options;
+    const windowData = (0, compose_1.compose)(composeOptions);
+    const applyWindowOptions = {
+        windowData,
+        pointsToShift,
+    };
+    const re = (0, applyWindow_1.applyWindow)(data.re, applyWindowOptions);
+    const im = (0, applyWindow_1.applyWindow)(data.im, applyWindowOptions);
+    return { re, im, windowData };
+}
+exports.apodization = apodization;
+//# sourceMappingURL=apodization.js.map

package/lib/apodization/apodization.js.map

@@ -0,0 +1 @@
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package/lib/apodization/applyWindow.d.ts

@@ -0,0 +1,28 @@
+import { DoubleArray } from 'cheminfo-types';
+export interface ApplyWindowOptions {
+    /**
+     * data of a window function it should be scaled to max = 1 to ensure compatibility with new apodizations.
+     */
+    windowData: DoubleArray;
+    /**
+     * Start Location for Applying Apodize Window
+     */
+    start?: number;
+    /**
+     * length of the window function
+     */
+    length?: number;
+    /**
+     * number of points at the end of the shape to apply the window function inverted
+     * @default 0
+     */
+    pointsToShift?: number;
+    /**
+     * output array
+     */
+    output?: DoubleArray;
+}
+/**
+ * pure function that applies a window function to the input data.
+ */
+export declare function applyWindow(data: DoubleArray, options: ApplyWindowOptions): DoubleArray;

package/lib/apodization/applyWindow.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.applyWindow = void 0;
+/**
+ * pure function that applies a window function to the input data.
+ */
+function applyWindow(data, options) {
+    const dataLength = data.length;
+    const { windowData, start = 0, length = dataLength, pointsToShift = 0, output = new Float64Array(data), } = options;
+    const firstEndPoint = Math.min(start + length, dataLength - pointsToShift);
+    for (let i = start, j = 0; i < firstEndPoint; i++) {
+        output[i] *= windowData[j++];
+    }
+    for (let i = dataLength - 1, j = 0; i > dataLength - pointsToShift - 1; i--) {
+        output[i] *= windowData[j++];
+    }
+    return output;
+}
+exports.applyWindow = applyWindow;
+//# sourceMappingURL=applyWindow.js.map

package/lib/apodization/applyWindow.js.map

@@ -0,0 +1 @@
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package/lib/apodization/compose.d.ts

@@ -0,0 +1,23 @@
+import type { WindowFunctions } from './shapes/WindowFunctions';
+interface ShapeToAdd {
+    /**
+     * Start Location for Applying Apodize Window
+     */
+    start?: number;
+    /**
+     * parameters of the shape plus the kind of shape to identify
+     */
+    shape: WindowFunctions;
+}
+export interface ShapeOptions {
+    /**
+     * length of the window shape
+     */
+    length: number;
+    /**
+     * parameters of the shape plus the kind of shape to identify
+     */
+    shapes?: ShapeToAdd[];
+}
+export declare function compose(shapeOptions: ShapeOptions): Float64Array;
+export {};

package/lib/apodization/compose.js

@@ -0,0 +1,25 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.compose = void 0;
+const applyWindow_1 = require("./applyWindow");
+const getFunction_1 = require("./getFunction");
+const getData_1 = require("./utils/getData");
+function compose(shapeOptions) {
+    const { length: dataLength, shapes = [] } = shapeOptions;
+    let data = new Float64Array(dataLength).fill(1);
+    shapes.forEach((options) => {
+        const { shape, start = 0 } = options;
+        const { options: shapeOptions } = shape;
+        const length = 'length' in shapeOptions ? shapeOptions.length : dataLength - start;
+        const windowData = (0, getData_1.getData)((0, getFunction_1.getFunction)(shape), length);
+        (0, applyWindow_1.applyWindow)(data, {
+            windowData,
+            length,
+            start,
+            output: data,
+        });
+    });
+    return data;
+}
+exports.compose = compose;
+//# sourceMappingURL=compose.js.map

package/lib/apodization/compose.js.map

@@ -0,0 +1 @@
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package/lib/apodization/getFunction.d.ts

@@ -0,0 +1,2 @@
+import type { WindowFunctions } from './shapes/WindowFunctions';
+export declare function getFunction(shape: WindowFunctions): (i: number) => number;

package/lib/apodization/getFunction.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getFunction = void 0;
+const exponential_1 = require("./shapes/exponential");
+const lorentzToGauss_1 = require("./shapes/lorentzToGauss");
+function getFunction(shape) {
+    const { kind, options } = shape;
+    switch (kind) {
+        case 'exponential':
+            return (0, exponential_1.exponential)(options);
+        case 'lorentzToGauss':
+            return (0, lorentzToGauss_1.lorentzToGauss)(options);
+        default:
+            throw Error(`Unknown distribution ${kind}`);
+    }
+}
+exports.getFunction = getFunction;
+//# sourceMappingURL=getFunction.js.map

package/lib/apodization/getFunction.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"getFunction.js","sourceRoot":"","sources":["../../src/apodization/getFunction.ts"],"names":[],"mappings":";;;AACA,sDAAmD;AACnD,4DAAyD;AAEzD,SAAgB,WAAW,CAAC,KAAsB;IAChD,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,KAAK,CAAC;IAChC,QAAQ,IAAI,EAAE;QACZ,KAAK,aAAa;YAChB,OAAO,IAAA,yBAAW,EAAC,OAAO,CAAC,CAAC;QAC9B,KAAK,gBAAgB;YACnB,OAAO,IAAA,+BAAc,EAAC,OAAO,CAAC,CAAC;QACjC;YACE,MAAM,KAAK,CAAC,wBAAwB,IAAc,EAAE,CAAC,CAAC;KACzD;AACH,CAAC;AAVD,kCAUC"}

package/lib/apodization/shapes/WindowFunctions.d.ts

@@ -0,0 +1,12 @@
+import type { ExponentialOptions } from './exponential';
+import type { LorentzToGaussOptions } from './lorentzToGauss';
+interface Exponential {
+    kind: 'exponential';
+    options: ExponentialOptions;
+}
+interface LorentToGauss {
+    kind: 'lorentzToGauss';
+    options: LorentzToGaussOptions;
+}
+export declare type WindowFunctions = Exponential | LorentToGauss;
+export {};

package/lib/apodization/shapes/WindowFunctions.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=WindowFunctions.js.map

package/lib/apodization/shapes/WindowFunctions.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"WindowFunctions.js","sourceRoot":"","sources":["../../../src/apodization/shapes/WindowFunctions.ts"],"names":[],"mappings":""}

package/lib/apodization/shapes/exponential.d.ts

@@ -0,0 +1,11 @@
+export interface ExponentialOptions {
+    /**
+     * line broadening value in Hz, a negative value will invert the shape
+     */
+    lb: number;
+    /**
+     * increment value in time or the independent value
+     */
+    dw: number;
+}
+export declare function exponential(options: ExponentialOptions): (i: number) => number;

package/lib/apodization/shapes/exponential.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.exponential = void 0;
+function exponential(options) {
+    const { lb, dw } = options;
+    const coefExp = -lb * Math.PI * dw;
+    return (i) => Math.exp(coefExp * i);
+}
+exports.exponential = exponential;
+//# sourceMappingURL=exponential.js.map

package/lib/apodization/shapes/exponential.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"exponential.js","sourceRoot":"","sources":["../../../src/apodization/shapes/exponential.ts"],"names":[],"mappings":";;;AAWA,SAAgB,WAAW,CAAC,OAA2B;IACrD,MAAM,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,OAAO,CAAC;IAC3B,MAAM,OAAO,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,EAAE,GAAG,EAAE,CAAC;IACnC,OAAO,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC;AAC9C,CAAC;AAJD,kCAIC"}

package/lib/apodization/shapes/lorentzToGauss.d.ts

@@ -0,0 +1,26 @@
+export interface LorentzToGaussOptions {
+    /**
+     * size of the shape function
+     */
+    length: number;
+    /**
+     * increment value in time or the independent value
+     */
+    dw: number;
+    /**
+     * Gaussian Broaden Width, Hz
+     * @default 0
+     */
+    gaussianHz?: number;
+    /**
+     * Inverse Exponential Width, Hz
+     * @default 0
+     */
+    exponentialHz?: number;
+    /**
+     * Location of Gauss Maximum, this value should be between 0 to 1
+     * @default 0
+     */
+    center?: number;
+}
+export declare function lorentzToGauss(options: LorentzToGaussOptions): (i: number) => number;

package/lib/apodization/shapes/lorentzToGauss.js

@@ -0,0 +1,15 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.lorentzToGauss = void 0;
+function lorentzToGauss(options) {
+    const { dw, length, gaussianHz = 0, exponentialHz = 0, center = 0 } = options;
+    if (center > 1 || center < 0) {
+        throw new Error('The center of gaussian shape should be inside of the window function: 0 - 1');
+    }
+    const C5 = Math.pow(0.6 * Math.PI * gaussianHz * dw, 2);
+    const C2 = center * (length - 1);
+    const C6 = Math.PI * dw * exponentialHz;
+    return (i) => Math.exp(i * C6 - Math.pow(C2 - i, 2) * C5);
+}
+exports.lorentzToGauss = lorentzToGauss;
+//# sourceMappingURL=lorentzToGauss.js.map

package/lib/apodization/shapes/lorentzToGauss.js.map

@@ -0,0 +1 @@
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package/lib/apodization/utils/getData.d.ts

@@ -0,0 +1,4 @@
+/**
+ * generate and scale the data of a window function
+ */
+export declare function getData(func: (i: number) => number, length: number): Float64Array;

package/lib/apodization/utils/getData.js

@@ -0,0 +1,21 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getData = void 0;
+/**
+ * generate and scale the data of a window function
+ */
+function getData(func, length) {
+    const data = new Float64Array(length);
+    let max = Number.MIN_SAFE_INTEGER;
+    for (let i = 0; i < length; i++) {
+        const value = func(i);
+        data[i] = value;
+        if (value > max)
+            max = value;
+    }
+    for (let i = 0; i < length; i++)
+        data[i] /= max;
+    return data;
+}
+exports.getData = getData;
+//# sourceMappingURL=getData.js.map

package/lib/apodization/utils/getData.js.map

@@ -0,0 +1 @@
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package/lib/assignment/utils/buildAssignments.d.ts

@@ -1,4 +1,4 @@
-import treeSet from 'ml-tree-set';
+import TreeSet from 'ml-tree-set';
 import { Targets, NMRSignal1DWithAtomsAndDiaIDs } from '../get1HAssignments';
 export interface RestrictionByCS1D {
     chemicalShiftRestriction: boolean;
@@ -24,7 +24,7 @@ export interface Predictions1Dassignments {
     [key: string]: Signals1DAssignment;
 }
 export interface StoreAssignments {
-    solutions: treeSet;
+    solutions: TreeSet;
     nSolutions: number;
 }
 export declare function buildAssignments(props: BuildAssignmentsProps): Promise<{

package/lib/assignment/utils/exploreTreeRec.js

@@ -55,7 +55,7 @@ function addSolution(store, props) {
     store.nSolutions++;
     let solution = {
         assignment: JSON.parse(JSON.stringify(partial)),
-        score: score,
+        score,
     };
     if (store.nSolutions >= maxSolutions) {
         if (solution.score > store.solutions.last().score) {

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

@@ -1 +1 @@
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package/lib/assignment/utils/getAssignment/checkIDs.d.ts

@@ -3,4 +3,4 @@ import type { SpectraData } from '../../getAssignments';
 import type { SpectraDataWithIds, NMRRangeWithIds, NMRZoneWithIds } from '../../nmrAssigment';
 export declare function checkIDs(input?: SpectraData[]): SpectraDataWithIds[];
 export declare function hasIDs(data: NMRRange[] | NMRZone[]): asserts data is NMRRangeWithIds[] | NMRZoneWithIds[];
-export declare function addIDs(data: NMRRange[] | NMRZone[]): NMRRangeWithIds[] | NMRZoneWithIds[];
+export declare function addIDs<T extends NMRRange[] | NMRZone[]>(data: T): T & (NMRRangeWithIds[] | NMRZoneWithIds[]);

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

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package/lib/databases/DatabaseNMREntry.d.ts

@@ -1,5 +1,7 @@
+import { OCLMolecule } from 'cheminfo-types';
 import { NMRRange } from '../xy/NMRRange';
 export interface DatabaseNMREntry {
+    ocl?: OCLMolecule;
     smiles?: string;
     solvent: string;
     nucleus: string;

package/lib/index.d.ts

@@ -27,6 +27,9 @@ 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 type { NMRSignal1D } from './signals/NMRSignal1D';
 export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';

package/lib/index.js

@@ -43,4 +43,7 @@ __exportStar(require("./xyz/xyzJResAnalyzer"), exports);
 __exportStar(require("./databases/getDatabase"), exports);
 __exportStar(require("./databases/carbonImpurities"), exports);
 __exportStar(require("./databases/protonImpurities"), exports);
+__exportStar(require("./peaks/solventSuppression"), exports);
+__exportStar(require("./ranges/markSolventSignal"), exports);
+__exportStar(require("./apodization/apodization"), exports);
 //# sourceMappingURL=index.js.map

package/lib/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,qDAAmC;AACnC,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;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C;AAE7C,6DAA2C;AAC3C,6DAA2C;AAE3C,4DAA0C"}

package/lib/peaks/peaksToRanges.d.ts

@@ -1,6 +1,7 @@
 import type { DataXY } from 'cheminfo-types';
 import type { NMRRange } from '../xy/NMRRange';
 import type { NMRPeak1D } from './NMRPeak1D';
+import type { SignalIntern } from './util/jAnalyzer';
 export interface OptionsPeaksToRanges {
     /**
      * Number of hydrogens or some number to normalize the integration data. If it's zero return the absolute integration value
@@ -59,4 +60,19 @@ 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: NMRPeak1DIntern[], options?: OptionsPeaksToRanges): NMRRange[];
+/**
+ * Extract the signals from the peakList and the given spectrum.
+ * @param {object} data - spectra data
+ * @param {array} peakList - nmr signals
+ * @param {object} [options = {}]
+ * @param {number} [options.integrationSum='100'] - Number of hydrogens or some number to normalize the integration data, If it's zero return the absolute integration value
+ * @param {string} [options.integralType='sum'] - option to chose between approx area with peaks or the sum of the points of given range
+ * @param {number} [options.frequencyCluster=16] - distance limit to clustering the peaks.
+ * range = frequencyCluster / observeFrequency -> Peaks withing this range are considered to belongs to the same signal1D
+ * @param {string} [options.nucleus='1H'] - - Nucleus
+ * @param {String} [options.frequency = 400] - Observed frequency
+ * @return {array} nmr signals
+ * @private
+ */
+export declare function detectSignals(data: DataXY, peakList: NMRPeak1DIntern[], options?: OptionsDetectSignals): SignalIntern[];
 export {};

package/lib/peaks/peaksToRanges.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.peaksToRanges = void 0;
+exports.detectSignals = exports.peaksToRanges = void 0;
 const ml_spectra_processing_1 = require("ml-spectra-processing");
 const jAnalyzer_1 = __importDefault(require("./util/jAnalyzer"));
 const joinRanges_1 = require("./util/joinRanges");
@@ -82,7 +82,7 @@ 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,
@@ -246,6 +246,7 @@ function detectSignals(data, peakList, options = {}) {
     }
     return signals;
 }
+exports.detectSignals = detectSignals;
 /**
  * Return the area of a Lorentzian function
  * @param {object} peak - object with peak information

package/lib/peaks/peaksToRanges.js.map

@@ -1 +1 @@
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package/lib/peaks/solventSuppression.d.ts

@@ -1,3 +1,6 @@
 import { NMRSignal1D } from '../signals/NMRSignal1D';
 import { NMRPeak1D } from './NMRPeak1D';
-export declare function solventSuppression(peakList: NMRPeak1D[], solvent: NMRSignal1D[], options?: any): NMRPeak1D[];
+export declare function solventSuppression<T extends NMRPeak1D>(peakList: T[], solvent: NMRSignal1D[], options?: {
+    markSolventPeaks?: boolean;
+    solventZoneExtension?: number;
+}): T[];