New Case Study:See how Anthropic automated 95% of dependency reviews with Socket.Learn More →
Socket
Sign inDemoInstall
Socket
Sign inDemoInstall

nmr-processing

Package Overview
Dependencies
Maintainers
4
Versions
278
Alerts
File Explorer

Advanced tools

License
Socket logo

Install Socket

Detect and block malicious and high-risk dependencies

Install

nmr-processing - npm Package Compare versions

Comparing version

9.0.3-pre.1660735983
to
9.0.3-pre.1661572417

lib-esm/peaks/util/addMissingIDs.js
lib-esm/peaks/util/addMissingIDs.js.map
lib-esm/utilities/clone.js
lib-esm/utilities/clone.js.map
lib/peaks/util/addMissingIDs.d.ts
lib/peaks/util/addMissingIDs.js
lib/peaks/util/addMissingIDs.js.map
lib/utilities/clone.d.ts
lib/utilities/clone.js
lib/utilities/clone.js.map
src/peaks/util/addMissingIDs.ts
src/utilities/clone.ts

2

lib-esm/assignment/get13CAssignments.js

@@ -0,5 +1,5 @@

import { v4 as generateID } from '@lukeed/uuid';
import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
import { predictCarbon, } from '../prediction/predictCarbon';
import { buildAssignments } from './utils/buildAssignments';
import generateID from './utils/generateID';
function checkAtomsAndDiaIDs(signals) {

@@ -6,0 +6,0 @@ for (const signal of signals) {

2

lib-esm/assignment/get1HAssignments.js

@@ -0,5 +1,5 @@

import { v4 as generateID } from '@lukeed/uuid';
import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
import { predictProton, } from '../prediction/predictProton';
import { buildAssignments } from './utils/buildAssignments';
import generateID from './utils/generateID';
function checkAtomsAndDiaIDs(signals) {

@@ -6,0 +6,0 @@ for (const signal of signals) {

2

lib-esm/assignment/utils/getAssignment/checkIDs.js

@@ -1,2 +0,2 @@

import generateID from '../generateID';
import { v4 as generateID } from '@lukeed/uuid';
import { isSpectraData1D } from './isSpectraData1D';

@@ -3,0 +3,0 @@ export function checkIDs(input = []) {

3

lib-esm/peaks/peaksToRanges.js

@@ -0,1 +1,2 @@

import { v4 as generateID } from '@lukeed/uuid';
import { xyIntegration } from 'ml-spectra-processing';

@@ -17,2 +18,3 @@ import { joinRanges } from '../ranges/utils/joinRanges';

return {
id: generateID(),
delta: NaN,

@@ -136,2 +138,3 @@ nbPeaks: 1,

const range = {
id: generateID(),
from: signal.integralData.from,

@@ -138,0 +141,0 @@ to: signal.integralData.to,

2

lib-esm/peaks/peaksToXY.js

@@ -27,3 +27,3 @@ import { generateSpectrum } from 'spectrum-generator';

const lastPeak = newPeaks[newPeaks.length - 1];
const { from = firstPeak.x - firstPeak.width * 2, to = lastPeak.x + lastPeak.width * 2, } = options;
const { from = firstPeak.x - (firstPeak.width * 2) / options.frequency, to = lastPeak.x + (lastPeak.width * 2) / options.frequency, } = options;
return {

@@ -30,0 +30,0 @@ from,

2

lib-esm/peaks/peakToXY.js

@@ -7,5 +7,5 @@ import { addMissingShape } from 'ml-gsd';

const factor = getShape1D(newPeak.shape).getFactor();
const { from = newPeak.x - peak.width * factor, to = newPeak.x + peak.width * factor, } = options;
const { from = newPeak.x - (peak.width * factor) / options.frequency, to = newPeak.x + (peak.width * factor) / options.frequency, } = options;
return peaksToXY([peak], { ...options, from, to });
}
//# sourceMappingURL=peakToXY.js.map

3

lib-esm/peaks/solventSuppression.js

@@ -9,4 +9,5 @@ import { linearSumAssignment } from 'linear-sum-assignment';

import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
import { cloneArray } from '../utilities/clone';
export function solventSuppression(peakList, solvent, options = {}) {
const peaks = [...peakList].sort((a, b) => a.x - b.x);
const peaks = cloneArray(peakList).sort((a, b) => a.x - b.x);
const xValues = peaks.map((peak) => peak.x);

@@ -13,0 +14,0 @@ const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;

8

lib-esm/peaks/util/convertWidth.js
import { hasProperty } from '../../utilities/hasProperty';
const { parse, stringify } = JSON;
/**

@@ -6,3 +7,3 @@ * convert width and fwhm to ppm

export function convertWidth(peaks, options) {
const { frequency, convertTo, output = JSON.parse(JSON.stringify(peaks)), } = options;
const { frequency, convertTo, output = parse(stringify(peaks)), } = options;
const convert = getConverter(convertTo, frequency);

@@ -12,4 +13,5 @@ for (const peak of output) {

if (hasProperty(peak, 'shape')) {
if (peak.shape.fwhm) {
peak.shape.fwhm = convert(peak.shape.fwhm);
const shape = peak.shape;
if (shape.fwhm) {
shape.fwhm = convert(shape.fwhm);
}

@@ -16,0 +18,0 @@ }

5

lib-esm/ranges/markSolventSignal.js

@@ -1,8 +0,9 @@

import generateID from '../assignment/utils/generateID';
import { v4 as generateID } from '@lukeed/uuid';
import { addIDs } from '../assignment/utils/getAssignment/checkIDs';
import { detectSignals } from '../peaks/peaksToRanges';
import { solventSuppression } from '../peaks/solventSuppression';
import { cloneArray } from '../utilities/clone';
export function markSolventPeaks(input, solventSignals, options = {}) {
const { frequency = 400 } = options;
const ranges = addIDs([...input]);
const ranges = addIDs(cloneArray(input));
let peakList = [];

@@ -9,0 +10,0 @@ for (const range of ranges) {

2

lib-esm/ranges/utils/joinRanges.js

@@ -0,1 +1,2 @@

import { v4 as generateID } from '@lukeed/uuid';
export function joinRanges(ranges) {

@@ -7,2 +8,3 @@ ranges.sort((a, b) => a.from - b.from);

if (currentRange.to > nextRange.from) {
currentRange.id = generateID();
currentRange.to = Math.max(nextRange.to, currentRange.to);

@@ -9,0 +11,0 @@ if (currentRange.signals && nextRange.signals) {

26

lib-esm/xy/xyAutoPeaksPicking.js

@@ -1,2 +0,2 @@

import { gsd, optimizePeaks, joinBroadPeaks } from 'ml-gsd';
import { gsd, optimizePeaks, joinBroadPeaks, } from 'ml-gsd';
import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';

@@ -64,4 +64,4 @@ import { convertWidthToHz } from '../peaks/util/convertWidthToHz';

});
if (broadWidth) {
peakList = joinBroadPeaks(peakList, {
const newPeaks = broadWidth
? joinBroadPeaks(peakList, {
broadRatio,

@@ -71,11 +71,11 @@ broadWidth,

optimization,
});
}
}).map(toNMRPeak1DStructure)
: peakList.map(toNMRPeak1DStructure);
return convertWidthToHz(optimize
? optimizePeaks(data, peakList, {
? optimizePeaks(data, newPeaks, {
shape,
factorLimits,
optimization,
})
: peakList, { frequency });
}).map(toNMRPeak1DStructure)
: newPeaks, { frequency });
}

@@ -96,2 +96,12 @@ function getCutOff(data, options) {

}
function toNMRPeak1DStructure(peak) {
const { id, shape, x, y, width } = peak;
return {
id,
x,
y,
width,
shape,
};
}
//# sourceMappingURL=xyAutoPeaksPicking.js.map

2

lib-esm/xyz/util/formatZone.js

@@ -0,1 +1,2 @@

import { v4 as generateID } from '@lukeed/uuid';
export function formatZones(signals) {

@@ -21,2 +22,3 @@ let zones = [];

zones.push({
id: generateID(),
x: {

@@ -23,0 +25,0 @@ from: minMax1[0],

13

lib-esm/xyz/xyzAutoZonesPicking.js

@@ -0,1 +1,2 @@

import { v4 as generateID } from '@lukeed/uuid';
import { Matrix } from 'ml-matrix';

@@ -5,2 +6,3 @@ import * as convolution from 'ml-matrix-convolution';

import simpleClustering from 'ml-simple-clustering';
import { addMissingIDs } from '../peaks/util/addMissingIDs';
import { determineRealTop } from '../peaks/util/determineRealTop';

@@ -66,3 +68,3 @@ import { getKernel } from '../peaks/util/getKernel';

}
let signals = createSignals2D(peaksMC1, {
let signals = createSignals2D(addMissingIDs(peaksMC1), {
nRows: nbSubSpectra,

@@ -86,3 +88,3 @@ nCols: nbPoints,

}
const createSignals2D = (peaks, options) => {
function createSignals2D(peaks, options) {
let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;

@@ -135,2 +137,3 @@ let [nucleusX, nucleusY] = nuclei;

let signal = {
id: generateID(),
x: {

@@ -164,4 +167,4 @@ delta: 0,

return signals;
};
const padData = (spectraData, options) => {
}
function padData(spectraData, options) {
let { minX, maxX, minY, maxY } = spectraData;

@@ -194,3 +197,3 @@ const width = options.width;

};
};
}
//# sourceMappingURL=xyzAutoZonesPicking.js.map

11

lib-esm/xyz/xyzJResAnalyzer.js

@@ -0,4 +1,7 @@

import { v4 as generateID } from '@lukeed/uuid';
import simpleClustering from 'ml-simple-clustering';
import { addMissingIDs } from '../peaks/util/addMissingIDs';
import jAnalyzer from '../signals/utils/jAnalyzer';
import { formatZones } from './util/formatZone';
const { parse, stringify } = JSON;
export function xyzJResAnalyzer(signals, options = {}) {

@@ -8,3 +11,3 @@ let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {

}, } = options;
let temporalSignals = compilePattern([...signals], {
let temporalSignals = compilePattern(signals, {
observedFrequencies,

@@ -23,2 +26,3 @@ tolerances,

}
signals2D = addMissingIDs(signals2D);
return getZones ? formatZones(signals2D) : signals2D;

@@ -36,3 +40,3 @@ }

const defaultWidth = 0.02 * observedFrequencies[0];
const newSignals = JSON.parse(JSON.stringify(signals));
const newSignals = parse(stringify(signals));
//adapt to 1D jAnalyzer

@@ -89,3 +93,3 @@ for (const signal of newSignals) {

let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
const peaks = JSON.parse(JSON.stringify(peaksInput));
const peaks = parse(stringify(peaksInput));
let [nucleusX, nucleusY] = nuclei;

@@ -114,2 +118,3 @@ let [toleranceX, toleranceY] = tolerances;

let signal = {
id: generateID(),
nucleusX,

@@ -116,0 +121,0 @@ nucleusY,

7

lib/assignment/get13CAssignments.js
"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.get13CAssignments = void 0;
const uuid_1 = require("@lukeed/uuid");
const openchemlib_utils_1 = require("openchemlib-utils");
const predictCarbon_1 = require("../prediction/predictCarbon");
const buildAssignments_1 = require("./utils/buildAssignments");
const generateID_1 = __importDefault(require("./utils/generateID"));
function checkAtomsAndDiaIDs(signals) {

@@ -39,3 +36,3 @@ for (const signal of signals) {

for (const range of copyRanges) {
const { id = (0, generateID_1.default)() } = range;
const { id = (0, uuid_1.v4)() } = range;
targets[id] = JSON.parse(JSON.stringify(range));

@@ -42,0 +39,0 @@ }

7

lib/assignment/get1HAssignments.js
"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.get1HAssignments = void 0;
const uuid_1 = require("@lukeed/uuid");
const openchemlib_utils_1 = require("openchemlib-utils");
const predictProton_1 = require("../prediction/predictProton");
const buildAssignments_1 = require("./utils/buildAssignments");
const generateID_1 = __importDefault(require("./utils/generateID"));
function checkAtomsAndDiaIDs(signals) {

@@ -40,3 +37,3 @@ for (const signal of signals) {

for (const range of ranges) {
const { id = (0, generateID_1.default)() } = range;
const { id = (0, uuid_1.v4)() } = range;
targets[id] = JSON.parse(JSON.stringify(range));

@@ -43,0 +40,0 @@ }

2

lib/assignment/utils/getAssignment/checkIDs.d.ts

@@ -6,2 +6,2 @@ import type { NMRRange, NMRZone } from '../../..';

export declare function hasIDs(data: NMRRange[] | NMRZone[]): asserts data is NMRRangeWithIds[] | NMRZoneWithIds[];
export declare function addIDs<T extends NMRRange[] | NMRZone[]>(data: T): T & (NMRRangeWithIds[] | NMRZoneWithIds[]);
export declare function addIDs<T extends NMRRange[] | NMRZone[]>(data: T): (T & NMRRangeWithIds[]) | (T & NMRZoneWithIds[]);

9

lib/assignment/utils/getAssignment/checkIDs.js
"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.addIDs = exports.hasIDs = exports.checkIDs = void 0;
const generateID_1 = __importDefault(require("../generateID"));
const uuid_1 = require("@lukeed/uuid");
const isSpectraData1D_1 = require("./isSpectraData1D");

@@ -43,6 +40,6 @@ function checkIDs(input = []) {

if (!element.id)
element.id = (0, generateID_1.default)();
element.id = (0, uuid_1.v4)();
for (let signal of element.signals || []) {
if (!signal.id)
signal.id = (0, generateID_1.default)();
signal.id = (0, uuid_1.v4)();
}

@@ -49,0 +46,0 @@ }

1

lib/peaks/NMRPeak1D.d.ts
import type { PeakXYWidth } from 'cheminfo-types';
import type { Shape1D } from 'ml-peak-shape-generator';
export interface NMRPeak1D extends PeakXYWidth {
id?: string;
kind?: string;
shape?: Shape1D;
}

2

lib/peaks/peaksFilterImpurities.d.ts

@@ -23,3 +23,3 @@ import { impurities } from '../constants/impurities';

*/
export declare function peaksFilterImpurities(peakList: NMRPeak1D[], options?: OptionsPeaksFilterImpurities): NMRPeak1D[];
export declare function peaksFilterImpurities<T extends NMRPeak1D>(peakList: T[], options?: OptionsPeaksFilterImpurities): T[];
export {};

3

lib/peaks/peaksToRanges.js

@@ -7,2 +7,3 @@ "use strict";

exports.detectSignals = exports.peaksToRanges = void 0;
const uuid_1 = require("@lukeed/uuid");
const ml_spectra_processing_1 = require("ml-spectra-processing");

@@ -24,2 +25,3 @@ const joinRanges_1 = require("../ranges/utils/joinRanges");

return {
id: (0, uuid_1.v4)(),
delta: NaN,

@@ -143,2 +145,3 @@ nbPeaks: 1,

const range = {
id: (0, uuid_1.v4)(),
from: signal.integralData.from,

@@ -145,0 +148,0 @@ to: signal.integralData.to,

2

lib/peaks/peaksToXY.js

@@ -31,3 +31,3 @@ "use strict";

const lastPeak = newPeaks[newPeaks.length - 1];
const { from = firstPeak.x - firstPeak.width * 2, to = lastPeak.x + lastPeak.width * 2, } = options;
const { from = firstPeak.x - (firstPeak.width * 2) / options.frequency, to = lastPeak.x + (lastPeak.width * 2) / options.frequency, } = options;
return {

@@ -34,0 +34,0 @@ from,

2

lib/peaks/peakToXY.js

@@ -10,3 +10,3 @@ "use strict";

const factor = (0, ml_peak_shape_generator_1.getShape1D)(newPeak.shape).getFactor();
const { from = newPeak.x - peak.width * factor, to = newPeak.x + peak.width * factor, } = options;
const { from = newPeak.x - (peak.width * factor) / options.frequency, to = newPeak.x + (peak.width * factor) / options.frequency, } = options;
return (0, peaksToXY_1.peaksToXY)([peak], { ...options, from, to });

@@ -13,0 +13,0 @@ }

3

lib/peaks/solventSuppression.js

@@ -12,4 +12,5 @@ "use strict";

const splitSpinSystem_1 = require("../signals/simulation/splitSpinSystem");
const clone_1 = require("../utilities/clone");
function solventSuppression(peakList, solvent, options = {}) {
const peaks = [...peakList].sort((a, b) => a.x - b.x);
const peaks = (0, clone_1.cloneArray)(peakList).sort((a, b) => a.x - b.x);
const xValues = peaks.map((peak) => peak.x);

@@ -16,0 +17,0 @@ const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;

6

lib/peaks/util/convertWidth.d.ts
import { MakeMandatory } from '../../utilities/MakeMandatory';
import { NMRPeak1D } from '../NMRPeak1D';
export declare type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
export interface ConvertWidthOptions {
export interface ConvertWidthOptions<T> {
convertTo: string & {

@@ -9,3 +9,3 @@ _kind?: 'hz' | 'ppm';

frequency: number;
output?: NMRPeak1D[];
output?: T[];
}

@@ -15,2 +15,2 @@ /**

*/
export declare function convertWidth(peaks: NMRPeak1D[], options: ConvertWidthOptions): NMRPeak1D[];
export declare function convertWidth<T extends NMRPeak1D>(peaks: T[], options: ConvertWidthOptions<T>): T[];

8

lib/peaks/util/convertWidth.js

@@ -5,2 +5,3 @@ "use strict";

const hasProperty_1 = require("../../utilities/hasProperty");
const { parse, stringify } = JSON;
/**

@@ -10,3 +11,3 @@ * convert width and fwhm to ppm

function convertWidth(peaks, options) {
const { frequency, convertTo, output = JSON.parse(JSON.stringify(peaks)), } = options;
const { frequency, convertTo, output = parse(stringify(peaks)), } = options;
const convert = getConverter(convertTo, frequency);

@@ -16,4 +17,5 @@ for (const peak of output) {

if ((0, hasProperty_1.hasProperty)(peak, 'shape')) {
if (peak.shape.fwhm) {
peak.shape.fwhm = convert(peak.shape.fwhm);
const shape = peak.shape;
if (shape.fwhm) {
shape.fwhm = convert(shape.fwhm);
}

@@ -20,0 +22,0 @@ }

4

lib/peaks/util/convertWidthToHz.d.ts
import { NMRPeak1D } from '../NMRPeak1D';
import { ConvertWidthOptions } from './convertWidth';
export declare type ConvertWidthTo = Omit<ConvertWidthOptions, 'convertTo'>;
export declare function convertWidthToHz(peaks: NMRPeak1D[], options: ConvertWidthTo): NMRPeak1D[];
export declare type ConvertWidthTo<T> = Omit<ConvertWidthOptions<T>, 'convertTo'>;
export declare function convertWidthToHz<T extends NMRPeak1D>(peaks: T[], options: ConvertWidthTo<T>): T[];

2

lib/peaks/util/convertWidthToPPM.d.ts
import { NMRPeak1D } from '../NMRPeak1D';
import { ConvertWidthTo } from './convertWidthToHz';
export declare function convertWidthToPPM(peaks: NMRPeak1D[], options: ConvertWidthTo): NMRPeak1D[];
export declare function convertWidthToPPM<T extends NMRPeak1D>(peaks: T[], options: ConvertWidthTo<T>): T[];

2

lib/peaks/util/determineRealTop.d.ts
import type { Peak2D } from 'ml-matrix-peaks-finder';
export declare function determineRealTop(peaks: Peak2D[], options: any): Peak2D[];
export declare function determineRealTop<T extends Peak2D>(peaks: T[], options: any): T[];

5

lib/prediction/predictCOSY.d.ts

@@ -0,1 +1,2 @@

/// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
import { Molecule } from 'openchemlib';

@@ -62,6 +63,6 @@ import { PredictProtonOptions } from './predictProton';

nuclei: string[];
joinedSignals: import("..").NMRSignal2D[];
joinedSignals: import("..").NMRSignal2D<import("ml-matrix-peaks-finder").Peak2D>[];
signals: any[];
zones: {
signals: import("..").NMRSignal2D[];
signals: import("..").NMRSignal2D<import("ml-matrix-peaks-finder").Peak2D>[];
x: {

@@ -68,0 +69,0 @@ from: number;

5

lib/prediction/predictHMBC.d.ts

@@ -0,1 +1,2 @@

/// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
import { Molecule } from 'openchemlib';

@@ -61,6 +62,6 @@ import type { PredictCarbonOptions } from './predictCarbon';

nuclei: string[];
joinedSignals: import("..").NMRSignal2D[];
joinedSignals: import("..").NMRSignal2D<import("ml-matrix-peaks-finder").Peak2D>[];
signals: any[];
zones: {
signals: import("..").NMRSignal2D[];
signals: import("..").NMRSignal2D<import("ml-matrix-peaks-finder").Peak2D>[];
x: {

@@ -67,0 +68,0 @@ from: number;

5

lib/prediction/predictHSQC.d.ts

@@ -0,1 +1,2 @@

/// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
import { Molecule } from 'openchemlib';

@@ -61,6 +62,6 @@ import { PredictCarbonOptions } from './predictCarbon';

nuclei: string[];
joinedSignals: import("..").NMRSignal2D[];
joinedSignals: import("..").NMRSignal2D<import("ml-matrix-peaks-finder").Peak2D>[];
signals: any[];
zones: {
signals: import("..").NMRSignal2D[];
signals: import("..").NMRSignal2D<import("ml-matrix-peaks-finder").Peak2D>[];
x: {

@@ -67,0 +68,0 @@ from: number;

5

lib/prediction/utils/predict2D.d.ts

@@ -0,1 +1,2 @@

/// <reference path="../../../src/ml-matrix-peaks-finder.d.ts" />
import { Molecule } from 'openchemlib';

@@ -78,6 +79,6 @@ import type { NMRSignal2D } from '../../xyz/NMRSignal2D';

nuclei: string[];
joinedSignals: NMRSignal2D[];
joinedSignals: NMRSignal2D<import("ml-matrix-peaks-finder").Peak2D>[];
signals: any[];
zones: {
signals: NMRSignal2D[];
signals: NMRSignal2D<import("ml-matrix-peaks-finder").Peak2D>[];
x: {

@@ -84,0 +85,0 @@ from: number;

10

lib/ranges/markSolventSignal.js
"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.markSolventPeaks = void 0;
const generateID_1 = __importDefault(require("../assignment/utils/generateID"));
const uuid_1 = require("@lukeed/uuid");
const checkIDs_1 = require("../assignment/utils/getAssignment/checkIDs");
const peaksToRanges_1 = require("../peaks/peaksToRanges");
const solventSuppression_1 = require("../peaks/solventSuppression");
const clone_1 = require("../utilities/clone");
function markSolventPeaks(input, solventSignals, options = {}) {
const { frequency = 400 } = options;
const ranges = (0, checkIDs_1.addIDs)([...input]);
const ranges = (0, checkIDs_1.addIDs)((0, clone_1.cloneArray)(input));
let peakList = [];

@@ -88,3 +86,3 @@ for (const range of ranges) {

const signalResult = {
id: (0, generateID_1.default)(),
id: (0, uuid_1.v4)(),
delta: signal.delta,

@@ -91,0 +89,0 @@ kind: signal.kind || 'signal',

2

lib/ranges/utils/joinRanges.js
"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.joinRanges = void 0;
const uuid_1 = require("@lukeed/uuid");
function joinRanges(ranges) {

@@ -10,2 +11,3 @@ ranges.sort((a, b) => a.from - b.from);

if (currentRange.to > nextRange.from) {
currentRange.id = (0, uuid_1.v4)();
currentRange.to = Math.max(nextRange.to, currentRange.to);

@@ -12,0 +14,0 @@ if (currentRange.signals && nextRange.signals) {

1

lib/signals/utils/jAnalyzer.d.ts

@@ -17,2 +17,3 @@ import type { NMRPeak1D } from '../../peaks/NMRPeak1D';

export interface SignalIntern {
id: string;
delta: number;

@@ -19,0 +20,0 @@ nbPeaks: number;

6

lib/xy/xyAutoPeaksPicking.d.ts
import { DataXY } from 'cheminfo-types';
import type { GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions } from 'ml-gsd';
import { GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions } from 'ml-gsd';
import { NMRPeak1D } from '..';
import { MakeMandatory } from '../utilities/MakeMandatory';
export interface GetPeakListOptions extends GSDOptions, OptimizePeaksOptions, JoinBroadPeaksOptions {

@@ -44,2 +45,3 @@ /**

}
export declare function xyAutoPeaksPicking(data: DataXY, options: OptionsXYAutoPeaksPicking): NMRPeak1D[];
export declare type NMRPeak1DWithID = MakeMandatory<NMRPeak1D, 'id'>;
export declare function xyAutoPeaksPicking(data: DataXY, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithID[];

24

lib/xy/xyAutoPeaksPicking.js

@@ -68,4 +68,4 @@ "use strict";

});
if (broadWidth) {
peakList = (0, ml_gsd_1.joinBroadPeaks)(peakList, {
const newPeaks = broadWidth
? (0, ml_gsd_1.joinBroadPeaks)(peakList, {
broadRatio,

@@ -75,11 +75,11 @@ broadWidth,

optimization,
});
}
}).map(toNMRPeak1DStructure)
: peakList.map(toNMRPeak1DStructure);
return (0, convertWidthToHz_1.convertWidthToHz)(optimize
? (0, ml_gsd_1.optimizePeaks)(data, peakList, {
? (0, ml_gsd_1.optimizePeaks)(data, newPeaks, {
shape,
factorLimits,
optimization,
})
: peakList, { frequency });
}).map(toNMRPeak1DStructure)
: newPeaks, { frequency });
}

@@ -100,2 +100,12 @@ function getCutOff(data, options) {

}
function toNMRPeak1DStructure(peak) {
const { id, shape, x, y, width } = peak;
return {
id,
x,
y,
width,
shape,
};
}
//# sourceMappingURL=xyAutoPeaksPicking.js.map

4

lib/xy/xyPeaksOptimization.d.ts

@@ -9,2 +9,4 @@ import { DataXY, PeakXYWidth } from 'cheminfo-types';

}
export declare function xyPeaksOptimization(data: DataXY, peaks: PeakXYWidth[], options: XYPeaksOptimizationOptions): import("..").NMRPeak1D[];
export declare function xyPeaksOptimization<T extends PeakXYWidth>(data: DataXY, peaks: T[], options: XYPeaksOptimizationOptions): (T extends {
id: string;
} ? import("ml-gsd").GSDPeakOptimizedID : import("ml-gsd").GSDPeakOptimized)[];

4

lib/xyz/NMRSignal2D.d.ts

@@ -10,3 +10,3 @@ import type { FromTo } from 'cheminfo-types';

}
export interface NMRSignal2D {
export interface NMRSignal2D<T extends Peak2D = Peak2D> {
x: Signal2DProjection;

@@ -18,4 +18,4 @@ y: Signal2DProjection;

id?: string;
peaks?: Peak2D[];
peaks?: T[];
kind?: string;
}

5

lib/xyz/util/formatZone.d.ts

@@ -1,3 +0,2 @@

import { NMRSignal2D } from '../NMRSignal2D';
import { NMRZone } from '../NMRZone';
export declare function formatZones(signals: NMRSignal2D[]): NMRZone[];
import { NMRSignal2DWithID, NMRZoneWithID } from '../xyzAutoZonesPicking';
export declare function formatZones(signals: NMRSignal2DWithID[]): NMRZoneWithID[];

2

lib/xyz/util/formatZone.js
"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.formatZones = void 0;
const uuid_1 = require("@lukeed/uuid");
function formatZones(signals) {

@@ -24,2 +25,3 @@ let zones = [];

zones.push({
id: (0, uuid_1.v4)(),
x: {

@@ -26,0 +28,0 @@ from: minMax1[0],

8

lib/xyz/xyzAutoZonesPicking.d.ts

@@ -0,2 +1,6 @@

import type { Peak2D } from 'ml-matrix-peaks-finder';
import type { GetKernelOptions } from '../peaks/util/getKernel';
import { MakeMandatory } from '../utilities/MakeMandatory';
import type { NMRSignal2D } from './NMRSignal2D';
import { NMRZone } from './NMRZone';
export interface Data2D {

@@ -64,3 +68,5 @@ z: number[][] | Float64Array[];

}
export declare function xyzAutoZonesPicking(spectraData: Data2D, options: XYZAutoZonesPickingOptions): import("./NMRZone").NMRZone[];
export declare type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<NMRSignal2D<T>, 'id'>;
export declare type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
export declare function xyzAutoZonesPicking(spectraData: Data2D, options: XYZAutoZonesPickingOptions): NMRZoneWithID[];
/**

@@ -67,0 +73,0 @@ * This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed

13

lib/xyz/xyzAutoZonesPicking.js

@@ -30,2 +30,3 @@ "use strict";

exports.xyzAutoZonesPicking = void 0;
const uuid_1 = require("@lukeed/uuid");
const ml_matrix_1 = require("ml-matrix");

@@ -35,2 +36,3 @@ const convolution = __importStar(require("ml-matrix-convolution"));

const ml_simple_clustering_1 = __importDefault(require("ml-simple-clustering"));
const addMissingIDs_1 = require("../peaks/util/addMissingIDs");
const determineRealTop_1 = require("../peaks/util/determineRealTop");

@@ -96,3 +98,3 @@ const getKernel_1 = require("../peaks/util/getKernel");

}
let signals = createSignals2D(peaksMC1, {
let signals = createSignals2D((0, addMissingIDs_1.addMissingIDs)(peaksMC1), {
nRows: nbSubSpectra,

@@ -117,3 +119,3 @@ nCols: nbPoints,

exports.xyzAutoZonesPicking = xyzAutoZonesPicking;
const createSignals2D = (peaks, options) => {
function createSignals2D(peaks, options) {
let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;

@@ -166,2 +168,3 @@ let [nucleusX, nucleusY] = nuclei;

let signal = {
id: (0, uuid_1.v4)(),
x: {

@@ -195,4 +198,4 @@ delta: 0,

return signals;
};
const padData = (spectraData, options) => {
}
function padData(spectraData, options) {
let { minX, maxX, minY, maxY } = spectraData;

@@ -225,3 +228,3 @@ const width = options.width;

};
};
}
//# sourceMappingURL=xyzAutoZonesPicking.js.map

5

lib/xyz/xyzJResAnalyzer.d.ts

@@ -0,1 +1,2 @@

import type { Peak2D } from 'ml-matrix-peaks-finder';
import type { JAxisKeys } from '../signals/utils/jAnalyzer';

@@ -28,3 +29,5 @@ import type { NMRSignal2D } from './NMRSignal2D';

}
export declare function xyzJResAnalyzer(signals: NMRSignal2D[], options?: XYZJResAnalyzerOptions): NMRSignal2D[] | import("./NMRZone").NMRZone[];
export declare function xyzJResAnalyzer(signals: NMRSignal2D[], options?: XYZJResAnalyzerOptions): import("./xyzAutoZonesPicking").NMRZoneWithID[] | (NMRSignal2D<Peak2D> & {
id: string;
})[];
export {};

11

lib/xyz/xyzJResAnalyzer.js

@@ -7,5 +7,8 @@ "use strict";

exports.xyzJResAnalyzer = void 0;
const uuid_1 = require("@lukeed/uuid");
const ml_simple_clustering_1 = __importDefault(require("ml-simple-clustering"));
const addMissingIDs_1 = require("../peaks/util/addMissingIDs");
const jAnalyzer_1 = __importDefault(require("../signals/utils/jAnalyzer"));
const formatZone_1 = require("./util/formatZone");
const { parse, stringify } = JSON;
function xyzJResAnalyzer(signals, options = {}) {

@@ -15,3 +18,3 @@ let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {

}, } = options;
let temporalSignals = compilePattern([...signals], {
let temporalSignals = compilePattern(signals, {
observedFrequencies,

@@ -30,2 +33,3 @@ tolerances,

}
signals2D = (0, addMissingIDs_1.addMissingIDs)(signals2D);
return getZones ? (0, formatZone_1.formatZones)(signals2D) : signals2D;

@@ -44,3 +48,3 @@ }

const defaultWidth = 0.02 * observedFrequencies[0];
const newSignals = JSON.parse(JSON.stringify(signals));
const newSignals = parse(stringify(signals));
//adapt to 1D jAnalyzer

@@ -97,3 +101,3 @@ for (const signal of newSignals) {

let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
const peaks = JSON.parse(JSON.stringify(peaksInput));
const peaks = parse(stringify(peaksInput));
let [nucleusX, nucleusY] = nuclei;

@@ -122,2 +126,3 @@ let [toleranceX, toleranceY] = tolerances;

let signal = {
id: (0, uuid_1.v4)(),
nucleusX,

@@ -124,0 +129,0 @@ nucleusY,

5

package.json
{
"name": "nmr-processing",
"version": "9.0.3-pre.1660735983",
"version": "9.0.3-pre.1661572417",
"description": "Pure functions allowing to process NMR spectra.",

@@ -57,2 +57,3 @@ "main": "./lib/index.js",

"dependencies": {
"@lukeed/uuid": "^2.0.0",
"binary-search": "^1.3.6",

@@ -67,3 +68,3 @@ "cross-fetch": "^3.1.5",

"ml-array-sum": "^1.1.6",
"ml-gsd": "^12.0.0",
"ml-gsd": "12.0.0-pre.1661543950",
"ml-hclust": "^3.1.0",

@@ -70,0 +71,0 @@ "ml-levenberg-marquardt": "^4.1.0",

2

src/assignment/get13CAssignments.ts

@@ -0,1 +1,2 @@

import { v4 as generateID } from '@lukeed/uuid';
import { Molecule } from 'openchemlib';

@@ -16,3 +17,2 @@ import { addDiastereotopicMissingChirality } from 'openchemlib-utils';

import { RestrictionByCS1D, buildAssignments } from './utils/buildAssignments';
import generateID from './utils/generateID';

@@ -19,0 +19,0 @@ function checkAtomsAndDiaIDs(

2

src/assignment/get1HAssignments.ts

@@ -0,1 +1,2 @@

import { v4 as generateID } from '@lukeed/uuid';
import { Molecule } from 'openchemlib';

@@ -13,3 +14,2 @@ import { addDiastereotopicMissingChirality } from 'openchemlib-utils';

import { buildAssignments, RestrictionByCS1D } from './utils/buildAssignments';
import generateID from './utils/generateID';

@@ -16,0 +16,0 @@ export type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<

3

src/assignment/utils/getAssignment/checkIDs.ts

@@ -0,1 +1,3 @@

import { v4 as generateID } from '@lukeed/uuid';
import type { NMRRange, NMRZone } from '../../..';

@@ -8,3 +10,2 @@ import type { SpectraData } from '../../getAssignments';

} from '../../nmrAssigment';
import generateID from '../generateID';

@@ -11,0 +12,0 @@ import { isSpectraData1D } from './isSpectraData1D';

1

src/ml-matrix-peaks-finder.d.ts

@@ -12,2 +12,3 @@ declare module 'ml-matrix-peaks-finder' {

interface Peak2D {
id?: string;
x: number;

@@ -14,0 +15,0 @@ y: number;

1

src/peaks/NMRPeak1D.ts

@@ -5,4 +5,5 @@ import type { PeakXYWidth } from 'cheminfo-types';

export interface NMRPeak1D extends PeakXYWidth {
id?: string;
kind?: string;
shape?: Shape1D;
}

8

src/peaks/peaksFilterImpurities.ts

@@ -37,4 +37,4 @@ import { impurities } from '../constants/impurities';

export function peaksFilterImpurities(
peakList: NMRPeak1D[],
export function peaksFilterImpurities<T extends NMRPeak1D>(
peakList: T[],
options: OptionsPeaksFilterImpurities = {},

@@ -60,4 +60,4 @@ ) {

function checkImpurity(
peakList: NMRPeak1D[],
function checkImpurity<T extends NMRPeak1D>(
peakList: T[],
impurity: ImpuritySignal[],

@@ -64,0 +64,0 @@ options: OptionsCheckImpurity,

3

src/peaks/peaksToRanges.ts

@@ -0,1 +1,2 @@

import { v4 as generateID } from '@lukeed/uuid';
import type { DataXY } from 'cheminfo-types';

@@ -93,2 +94,3 @@ import { xyIntegration } from 'ml-spectra-processing';

return {
id: generateID(),
delta: NaN,

@@ -236,2 +238,3 @@ nbPeaks: 1,

const range: NMRRange = {
id: generateID(),
from: signal.integralData.from,

@@ -238,0 +241,0 @@ to: signal.integralData.to,

4

src/peaks/peaksToXY.ts

@@ -56,4 +56,4 @@ import { generateSpectrum, OptionsSG1D } from 'spectrum-generator';

const {
from = firstPeak.x - firstPeak.width * 2,
to = lastPeak.x + lastPeak.width * 2,
from = firstPeak.x - (firstPeak.width * 2) / options.frequency,
to = lastPeak.x + (lastPeak.width * 2) / options.frequency,
} = options;

@@ -60,0 +60,0 @@

4

src/peaks/peakToXY.ts

@@ -12,4 +12,4 @@ import { addMissingShape } from 'ml-gsd';

const {
from = newPeak.x - peak.width * factor,
to = newPeak.x + peak.width * factor,
from = newPeak.x - (peak.width * factor) / options.frequency,
to = newPeak.x + (peak.width * factor) / options.frequency,
} = options;

@@ -16,0 +16,0 @@

3

src/peaks/solventSuppression.ts

@@ -12,2 +12,3 @@ import { PointXY } from 'cheminfo-types';

import { splitSpinSystem } from '../signals/simulation/splitSpinSystem';
import { cloneArray } from '../utilities/clone';

@@ -21,3 +22,3 @@ import { NMRPeak1D } from './NMRPeak1D';

) {
const peaks = [...peakList].sort((a, b) => a.x - b.x);
const peaks = cloneArray(peakList).sort((a, b) => a.x - b.x);

@@ -24,0 +25,0 @@ const xValues = peaks.map((peak) => peak.x);

20

src/peaks/util/convertWidth.ts

@@ -0,1 +1,3 @@

import { Shape1D } from 'ml-peak-shape-generator';
import { MakeMandatory } from '../../utilities/MakeMandatory';

@@ -5,8 +7,10 @@ import { hasProperty } from '../../utilities/hasProperty';

const { parse, stringify } = JSON;
export type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
export interface ConvertWidthOptions {
export interface ConvertWidthOptions<T> {
convertTo: string & { _kind?: 'hz' | 'ppm' };
frequency: number;
output?: NMRPeak1D[];
output?: T[];
}

@@ -16,7 +20,10 @@ /**

*/
export function convertWidth(peaks: NMRPeak1D[], options: ConvertWidthOptions) {
export function convertWidth<T extends NMRPeak1D>(
peaks: T[],
options: ConvertWidthOptions<T>,
): T[] {
const {
frequency,
convertTo,
output = JSON.parse(JSON.stringify(peaks)) as NMRPeak1D[],
output = parse(stringify(peaks)) as T[],
} = options;

@@ -29,4 +36,5 @@

if (hasProperty(peak, 'shape')) {
if (peak.shape.fwhm) {
peak.shape.fwhm = convert(peak.shape.fwhm);
const shape = peak.shape as Shape1D;
if (shape.fwhm) {
shape.fwhm = convert(shape.fwhm);
}

@@ -33,0 +41,0 @@ }

7

src/peaks/util/convertWidthToHz.ts

@@ -5,6 +5,9 @@ import { NMRPeak1D } from '../NMRPeak1D';

export type ConvertWidthTo = Omit<ConvertWidthOptions, 'convertTo'>;
export type ConvertWidthTo<T> = Omit<ConvertWidthOptions<T>, 'convertTo'>;
export function convertWidthToHz(peaks: NMRPeak1D[], options: ConvertWidthTo) {
export function convertWidthToHz<T extends NMRPeak1D>(
peaks: T[],
options: ConvertWidthTo<T>,
): T[] {
return convertWidth(peaks, { ...options, convertTo: 'hz' });
}

5

src/peaks/util/convertWidthToPPM.ts

@@ -6,4 +6,7 @@ import { NMRPeak1D } from '../NMRPeak1D';

export function convertWidthToPPM(peaks: NMRPeak1D[], options: ConvertWidthTo) {
export function convertWidthToPPM<T extends NMRPeak1D>(
peaks: T[],
options: ConvertWidthTo<T>,
) {
return convertWidth(peaks, { ...options, convertTo: 'ppm' });
}

2

src/peaks/util/determineRealTop.ts

@@ -12,3 +12,3 @@ import { levenbergMarquardt } from 'ml-levenberg-marquardt';

export function determineRealTop(peaks: Peak2D[], options: any) {
export function determineRealTop<T extends Peak2D>(peaks: T[], options: any) {
let { nCols, absoluteData, originalData, minX, maxX, minY, maxY } = options;

@@ -15,0 +15,0 @@ for (let i = 0; i < peaks.length; i++) {

6

src/ranges/markSolventSignal.ts

@@ -0,3 +1,4 @@

import { v4 as generateID } from '@lukeed/uuid';
import { NMRRangeWithIds, NMRSignal1DWithId } from '../assignment/nmrAssigment';
import generateID from '../assignment/utils/generateID';
import { addIDs } from '../assignment/utils/getAssignment/checkIDs';

@@ -9,2 +10,3 @@ import { NMRPeak1D } from '../peaks/NMRPeak1D';

import { SignalIntern } from '../signals/utils/jAnalyzer';
import { cloneArray } from '../utilities/clone';
import { NMRRange } from '../xy/NMRRange';

@@ -23,3 +25,3 @@

const { frequency = 400 } = options;
const ranges = addIDs([...input]) as NMRRangeWithIds[];
const ranges = addIDs(cloneArray(input)) as NMRRangeWithIds[];

@@ -26,0 +28,0 @@ let peakList: NMRPeak1DWithSignalID[] = [];

3

src/ranges/utils/joinRanges.ts

@@ -0,1 +1,3 @@

import { v4 as generateID } from '@lukeed/uuid';
import type { NMRRange } from '../../xy/NMRRange';

@@ -11,2 +13,3 @@

if (currentRange.to > nextRange.from) {
currentRange.id = generateID();
currentRange.to = Math.max(nextRange.to, currentRange.to);

@@ -13,0 +16,0 @@ if (currentRange.signals && nextRange.signals) {

1

src/signals/utils/jAnalyzer.ts

@@ -37,2 +37,3 @@ import type { NMRPeak1D } from '../../peaks/NMRPeak1D';

export interface SignalIntern {
id: string;
delta: number;

@@ -39,0 +40,0 @@ nbPeaks: number;

48

src/xy/xyAutoPeaksPicking.ts
import { DataXY } from 'cheminfo-types';
import { gsd, optimizePeaks, joinBroadPeaks } from 'ml-gsd';
import type {
import {
gsd,
optimizePeaks,
joinBroadPeaks,
GSDPeakID,
GSDOptions,
OptimizePeaksOptions,
JoinBroadPeaksOptions,
GSDPeakOptimizedID,
} from 'ml-gsd';

@@ -16,2 +20,3 @@ import {

import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
import { MakeMandatory } from '../utilities/MakeMandatory';

@@ -76,6 +81,8 @@ /**

export type NMRPeak1DWithID = MakeMandatory<NMRPeak1D, 'id'>;
export function xyAutoPeaksPicking(
data: DataXY,
options: OptionsXYAutoPeaksPicking,
): NMRPeak1D[] {
): NMRPeak1DWithID[] {
const {

@@ -185,19 +192,19 @@ from,

if (broadWidth) {
peakList = joinBroadPeaks(peakList, {
broadRatio,
broadWidth,
shape,
optimization,
});
}
const newPeaks = broadWidth
? joinBroadPeaks(peakList, {
broadRatio,
broadWidth,
shape,
optimization,
}).map(toNMRPeak1DStructure)
: peakList.map(toNMRPeak1DStructure);
return convertWidthToHz(
optimize
? optimizePeaks(data, peakList, {
? optimizePeaks(data, newPeaks, {
shape,
factorLimits,
optimization,
})
: peakList,
}).map(toNMRPeak1DStructure)
: newPeaks,
{ frequency },

@@ -223,1 +230,14 @@ );

}
function toNMRPeak1DStructure(
peak: GSDPeakID | GSDPeakOptimizedID,
): NMRPeak1DWithID {
const { id, shape, x, y, width } = peak;
return {
id,
x,
y,
width,
shape,
};
}

4

src/xy/xyPeaksOptimization.ts

@@ -13,5 +13,5 @@ import { DataXY, PeakXYWidth } from 'cheminfo-types';

}
export function xyPeaksOptimization(
export function xyPeaksOptimization<T extends PeakXYWidth>(
data: DataXY,
peaks: PeakXYWidth[],
peaks: T[],
options: XYPeaksOptimizationOptions,

@@ -18,0 +18,0 @@ ) {

4

src/xyz/NMRSignal2D.ts

@@ -11,3 +11,3 @@ import type { FromTo } from 'cheminfo-types';

}
export interface NMRSignal2D {
export interface NMRSignal2D<T extends Peak2D = Peak2D> {
x: Signal2DProjection;

@@ -19,4 +19,4 @@ y: Signal2DProjection;

id?: string;
peaks?: Peak2D[];
peaks?: T[];
kind?: string;
}

10

src/xyz/util/formatZone.ts

@@ -1,6 +0,7 @@

import { NMRSignal2D } from '../NMRSignal2D';
import { NMRZone } from '../NMRZone';
import { v4 as generateID } from '@lukeed/uuid';
export function formatZones(signals: NMRSignal2D[]) {
let zones: NMRZone[] = [];
import { NMRSignal2DWithID, NMRZoneWithID } from '../xyzAutoZonesPicking';
export function formatZones(signals: NMRSignal2DWithID[]) {
let zones: NMRZoneWithID[] = [];
for (const signal of signals) {

@@ -24,2 +25,3 @@ let minMax1 = [Number.MAX_VALUE, 0];

zones.push({
id: generateID(),
x: {

@@ -26,0 +28,0 @@ from: minMax1[0],

33

src/xyz/xyzAutoZonesPicking.ts

@@ -0,1 +1,2 @@

import { v4 as generateID } from '@lukeed/uuid';
import { Matrix } from 'ml-matrix';

@@ -7,2 +8,3 @@ import * as convolution from 'ml-matrix-convolution';

import { addMissingIDs } from '../peaks/util/addMissingIDs';
import { determineRealTop } from '../peaks/util/determineRealTop';

@@ -12,4 +14,6 @@ import { getKernel } from '../peaks/util/getKernel';

import * as PeakOptimizer from '../peaks/util/peakOptimizer';
import { MakeMandatory } from '../utilities/MakeMandatory';
import type { NMRSignal2D } from './NMRSignal2D';
import { NMRZone } from './NMRZone';
import { formatZones } from './util/formatZone';

@@ -93,6 +97,12 @@

export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<
NMRSignal2D<T>,
'id'
>;
export type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
export function xyzAutoZonesPicking(
spectraData: Data2D,
options: XYZAutoZonesPickingOptions,
) {
): NMRZoneWithID[] {
let {

@@ -167,3 +177,3 @@ sizeToPad = 14,

let signals = createSignals2D(peaksMC1, {
let signals = createSignals2D(addMissingIDs(peaksMC1), {
nRows: nbSubSpectra,

@@ -210,3 +220,7 @@ nCols: nbPoints,

}
const createSignals2D = (peaks: Peak2D[], options: CreateSignals2DOptions) => {
function createSignals2D<T extends Peak2D>(
peaks: T[],
options: CreateSignals2DOptions,
) {
let {

@@ -275,6 +289,7 @@ nCols,

let signals: NMRSignal2D[] = [];
let signals: NMRSignal2DWithID<T>[] = [];
if (clusters) {
for (const cluster of clusters) {
let signal: any = {
id: generateID(),
x: {

@@ -291,3 +306,3 @@ delta: 0,

};
let peaks2D: Peak2D[] = [];
let peaks2D: T[] = [];
let sumZ = 0;

@@ -307,9 +322,9 @@

signal.peaks = peaks2D;
signals.push(signal as NMRSignal2D);
signals.push(signal as NMRSignal2DWithID<T>);
}
}
return signals;
};
}
const padData = (spectraData: Data2D, options: { width: number }) => {
function padData(spectraData: Data2D, options: { width: number }) {
let { minX, maxX, minY, maxY } = spectraData;

@@ -346,2 +361,2 @@

};
};
}

40

src/xyz/xyzJResAnalyzer.ts

@@ -0,4 +1,6 @@

import { v4 as generateID } from '@lukeed/uuid';
import type { Peak2D } from 'ml-matrix-peaks-finder';
import simpleClustering from 'ml-simple-clustering';
import { addMissingIDs } from '../peaks/util/addMissingIDs';
import type { JAxisKeys } from '../signals/utils/jAnalyzer';

@@ -11,2 +13,4 @@ import jAnalyzer from '../signals/utils/jAnalyzer';

const { parse, stringify } = JSON;
interface CompilePatternOptions {

@@ -37,2 +41,14 @@ observedFrequencies?: number[] | Float64Array;

interface Peak2DInternalCompiler extends Peak2D {
width?: number;
}
type Signal2DInternalCompiler = Omit<NMRSignal2D, 'peaks'> & {
peaks: Peak2DInternalCompiler[];
integralData: { from: number; to: number };
nbPeaks: number;
multiplicity: string;
pattern: string;
observe: number;
};
type CompilePatternOptionsMandatory = MakeMandatory<

@@ -58,3 +74,3 @@ CompilePatternOptions,

} = options;
let temporalSignals = compilePattern([...signals], {
let temporalSignals = compilePattern(signals, {
observedFrequencies,

@@ -72,2 +88,5 @@ tolerances,

}
signals2D = addMissingIDs(signals2D);
return getZones ? formatZones(signals2D) : signals2D;

@@ -96,3 +115,3 @@ }

const defaultWidth = 0.02 * observedFrequencies[0];
const newSignals = JSON.parse(JSON.stringify(signals));
const newSignals = parse(stringify(signals));
//adapt to 1D jAnalyzer

@@ -154,18 +173,6 @@ for (const signal of newSignals) {

interface Peak2DHack extends Peak2D {
width?: number;
}
type Signal2DHack = Omit<NMRSignal2D, 'peaks'> & {
peaks: Peak2DHack[];
integralData: { from: number; to: number };
nbPeaks: number;
multiplicity: string;
pattern: string;
observe: number;
};
function createSignals2D(peaksInput: Peak2D[], options: any) {
let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
const peaks: Peak2DHack[] = JSON.parse(JSON.stringify(peaksInput));
const peaks: Peak2DInternalCompiler[] = parse(stringify(peaksInput));

@@ -198,2 +205,3 @@ let [nucleusX, nucleusY] = nuclei;

let signal: any = {
id: generateID(),
nucleusX,

@@ -249,3 +257,3 @@ nucleusY,

signal.peaks = peaks2D;
signals.push(signal as Signal2DHack);
signals.push(signal as Signal2DInternalCompiler);
}

@@ -252,0 +260,0 @@ }

lib-esm/assignment/utils/generateID.js
lib-esm/assignment/utils/generateID.js.map
lib/assignment/utils/generateID.d.ts
lib/assignment/utils/generateID.js
lib/assignment/utils/generateID.js.map
src/assignment/utils/generateID.ts
lib-esm/assignment/get13CAssignments.js.map

Sorry, the diff of this file is not supported yet

lib-esm/assignment/get1HAssignments.js.map

Sorry, the diff of this file is not supported yet

lib-esm/assignment/utils/getAssignment/checkIDs.js.map

Sorry, the diff of this file is not supported yet

lib-esm/peaks/peaksFilterImpurities.js.map

Sorry, the diff of this file is not supported yet

lib-esm/peaks/peaksToRanges.js.map

Sorry, the diff of this file is not supported yet

lib-esm/peaks/peaksToXY.js.map

Sorry, the diff of this file is not supported yet

lib-esm/peaks/peakToXY.js.map

Sorry, the diff of this file is not supported yet

lib-esm/peaks/solventSuppression.js.map

Sorry, the diff of this file is not supported yet

lib-esm/peaks/util/convertWidth.js.map

Sorry, the diff of this file is not supported yet

lib-esm/peaks/util/convertWidthToHz.js.map

Sorry, the diff of this file is not supported yet

lib-esm/peaks/util/convertWidthToPPM.js.map

Sorry, the diff of this file is not supported yet

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

Sorry, the diff of this file is not supported yet

lib-esm/ranges/markSolventSignal.js.map

Sorry, the diff of this file is not supported yet

lib-esm/ranges/utils/joinRanges.js.map

Sorry, the diff of this file is not supported yet

lib-esm/signals/utils/jAnalyzer.js.map

Sorry, the diff of this file is not supported yet

lib-esm/xy/xyAutoPeaksPicking.js.map

Sorry, the diff of this file is not supported yet

lib-esm/xy/xyPeaksOptimization.js.map

Sorry, the diff of this file is not supported yet

lib-esm/xyz/util/formatZone.js.map

Sorry, the diff of this file is not supported yet

lib-esm/xyz/xyzAutoZonesPicking.js.map

Sorry, the diff of this file is not supported yet

lib-esm/xyz/xyzJResAnalyzer.js.map

Sorry, the diff of this file is not supported yet

lib/assignment/get13CAssignments.js.map

Sorry, the diff of this file is not supported yet

lib/assignment/get1HAssignments.js.map

Sorry, the diff of this file is not supported yet

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

Sorry, the diff of this file is not supported yet

lib/peaks/peaksFilterImpurities.js.map

Sorry, the diff of this file is not supported yet

lib/peaks/peaksToRanges.js.map

Sorry, the diff of this file is not supported yet

lib/peaks/peaksToXY.js.map

Sorry, the diff of this file is not supported yet

lib/peaks/peakToXY.js.map

Sorry, the diff of this file is not supported yet

lib/peaks/solventSuppression.js.map

Sorry, the diff of this file is not supported yet

lib/peaks/util/convertWidth.js.map

Sorry, the diff of this file is not supported yet

lib/peaks/util/convertWidthToHz.js.map

Sorry, the diff of this file is not supported yet

lib/peaks/util/convertWidthToPPM.js.map

Sorry, the diff of this file is not supported yet

lib/peaks/util/determineRealTop.js.map

Sorry, the diff of this file is not supported yet

lib/ranges/markSolventSignal.js.map

Sorry, the diff of this file is not supported yet

lib/ranges/utils/joinRanges.js.map

Sorry, the diff of this file is not supported yet

lib/signals/utils/jAnalyzer.js.map

Sorry, the diff of this file is not supported yet

lib/xy/xyAutoPeaksPicking.js.map

Sorry, the diff of this file is not supported yet

lib/xy/xyPeaksOptimization.js.map

Sorry, the diff of this file is not supported yet

lib/xyz/util/formatZone.js.map

Sorry, the diff of this file is not supported yet

lib/xyz/xyzAutoZonesPicking.js.map

Sorry, the diff of this file is not supported yet

lib/xyz/xyzJResAnalyzer.js.map

Sorry, the diff of this file is not supported yet