nmr-processing 9.1.0 → 9.2.0

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

@@ -1 +1 @@
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package/lib/index.d.ts

@@ -19,6 +19,7 @@ export * from './ranges/rangesToXY';
 export * from './signals/signalsToRanges';
 export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
+export * from './signals/optimizeSignals';
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
 export * from './utilities/getFrequency';
@@ -38,8 +39,8 @@ export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';
 export type { NMRZone } from './xyz/NMRZone';
 export type { NMRPeak1D } from './peaks/NMRPeak1D';
-export type { Prediction1D } from './prediction/prediction1D';
-export type { Jcoupling } from './signals/jcoupling';
+export type { Prediction1D } from './prediction/Prediction1D';
+export type { Jcoupling } from './signals/Jcoupling';
 export type { DatabaseNMREntry } from './databases/DatabaseNMREntry';
 export type { DataBaseLevelStructure, DataBaseStructure, } from './prediction/dataStructure';
 export type { NMRSignal1DWithId, NMRSignal2DWithId, SpectraData1DWithIds, SpectraData2DWithIds, SpectraDataWithIds, } from './assignment/nmrAssigment';

package/lib/index.js

@@ -35,6 +35,7 @@ __exportStar(require("./ranges/rangesToXY"), exports);
 __exportStar(require("./signals/signalsToRanges"), exports);
 __exportStar(require("./signals/signalsToXY"), exports);
 __exportStar(require("./signals/signals2DToZ"), exports);
+__exportStar(require("./signals/optimizeSignals"), exports);
 __exportStar(require("./utilities/resurrect"), exports);
 __exportStar(require("./utilities/rangeFromSignal"), exports);
 __exportStar(require("./utilities/getFrequency"), 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,qDAAmC;AACnC,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAC9C,oDAAkC;AAClC,mDAAiC;AAEjC,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;AACvC,4DAA0C;AAE1C,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AACzC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C;AAE7C,6DAA2C;AAC3C,6DAA2C;AAE3C,4DAA0C"}

package/lib/prediction/{prediction1D.js → Prediction1D.js}

@@ -1,3 +1,3 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-//# sourceMappingURL=prediction1D.js.map
+//# sourceMappingURL=Prediction1D.js.map

package/lib/prediction/Prediction1D.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Prediction1D.js","sourceRoot":"","sources":["../../src/prediction/Prediction1D.ts"],"names":[],"mappings":""}

package/lib/prediction/predictAll.d.ts

@@ -1,7 +1,7 @@
 import type { Molecule } from 'openchemlib';
+import type { Prediction1D } from './Prediction1D';
 import { PredictCarbonOptions } from './predictCarbon';
 import { PredictProtonOptions } from './predictProton';
-import type { Prediction1D } from './prediction1D';
 import type { Predictor } from './utils/predict2D';
 export interface PredictAllOptions {
     /**

package/lib/prediction/predictAll.js.map

@@ -1 +1 @@
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package/lib/prediction/predictAllSpectra.js

@@ -14,8 +14,8 @@ async function predictAllSpectra(molecule, options = {}) {
         ...{
             proton: { from: 0, to: 14 },
             carbon: { from: 0, to: 200 },
-            nbPoints: 4098,
-            lineWidth: 0.03,
+            nbPoints: 65536,
+            lineWidth: 1,
         },
         ...(simulationOptions.oneD || {}),
     };

package/lib/prediction/predictAllSpectra.js.map

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

@@ -1,7 +1,7 @@
 /// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
 import { Molecule } from 'openchemlib';
+import type { Prediction1D } from './Prediction1D';
 import { PredictProtonOptions } from './predictProton';
-import type { Prediction1D } from './prediction1D';
 import { Predictor } from './utils/predict2D';
 export interface PredictCOSYOptions {
     /**

package/lib/prediction/predictCOSY.js.map

@@ -1 +1 @@
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+{"version":3,"file":"predictCOSY.js","sourceRoot":"","sources":["../../src/prediction/predictCOSY.ts"],"names":[],"mappings":";;;AAGA,mDAAsE;AACtE,iDAAyD;AA4CzD;;;GAGG;AAEI,KAAK,UAAU,WAAW,CAC/B,QAAkB,EAClB,UAA8B,EAAE;IAEhC,IAAI,EACF,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,CAAC,EACb,WAAW,EACX,SAAS,GAAG,EAAE,CAAC,EAAE,6BAAa,EAAE,EAChC,cAAc,EACd,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,eAAe,GAAG,IAAI,GACvB,GAAG,OAAO,CAAC;IAEZ,OAAO,IAAA,qBAAS,EAAC,QAAQ,EAAE;QACzB,IAAI,EAAE,GAAG;QACT,EAAE,EAAE,GAAG;QACP,SAAS;QACT,SAAS;QACT,SAAS;QACT,YAAY;QACZ,WAAW;QACX,eAAe;QACf,cAAc;KACf,CAAC,CAAC;AACL,CAAC;AAzBD,kCAyBC"}

package/lib/prediction/predictCarbon.d.ts

@@ -1,6 +1,6 @@
 import type { Molecule } from 'openchemlib';
+import type { Prediction1D } from './Prediction1D';
 import type { DataBaseStructure } from './dataStructure';
-import type { Prediction1D } from './prediction1D';
 export interface PredictCarbonOptions {
     /**
      * URL pointing to a database in json format

package/lib/prediction/predictHMBC.d.ts

@@ -1,8 +1,8 @@
 /// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
 import { Molecule } from 'openchemlib';
+import type { Prediction1D } from './Prediction1D';
 import type { PredictCarbonOptions } from './predictCarbon';
 import type { PredictProtonOptions } from './predictProton';
-import type { Prediction1D } from './prediction1D';
 import type { Predictor } from './utils/predict2D';
 /**
  * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms

package/lib/prediction/predictHMBC.js.map

@@ -1 +1 @@
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+{"version":3,"file":"predictHMBC.js","sourceRoot":"","sources":["../../src/prediction/predictHMBC.ts"],"names":[],"mappings":";;;AAGA,mDAAgD;AAEhD,mDAAgD;AAEhD,iDAA8C;AA+CvC,KAAK,UAAU,WAAW,CAC/B,QAAkB,EAClB,UAA8B,EAAE;IAEhC,IAAI,EACF,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,EAAE,CAAC,EAAE,6BAAa,EAAE,CAAC,EAAE,6BAAa,EAAE,EAClD,cAAc,EACd,WAAW,EACX,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,GACnC,GAAG,OAAO,CAAC;IAEZ,OAAO,IAAA,qBAAS,EAAC,QAAQ,EAAE;QACzB,IAAI,EAAE,GAAG;QACT,EAAE,EAAE,GAAG;QACP,SAAS;QACT,SAAS;QACT,SAAS;QACT,WAAW;QACX,cAAc;QACd,YAAY;KACb,CAAC,CAAC;AACL,CAAC;AAvBD,kCAuBC"}

package/lib/prediction/predictHSQC.d.ts

@@ -1,8 +1,8 @@
 /// <reference path="../../src/ml-matrix-peaks-finder.d.ts" />
 import { Molecule } from 'openchemlib';
+import type { Prediction1D } from './Prediction1D';
 import { PredictCarbonOptions } from './predictCarbon';
 import { PredictProtonOptions } from './predictProton';
-import type { Prediction1D } from './prediction1D';
 import { Predictor } from './utils/predict2D';
 export interface PredictHSQCOptions {
     /**

package/lib/prediction/predictHSQC.js.map

@@ -1 +1 @@
-{"version":3,"file":"predictHSQC.js","sourceRoot":"","sources":["../../src/prediction/predictHSQC.ts"],"names":[],"mappings":";;;AAEA,mDAAsE;AACtE,mDAAsE;AAEtE,iDAAyD;AAwCzD;;;GAGG;AAEI,KAAK,UAAU,WAAW,CAC/B,QAAkB,EAClB,UAA8B,EAAE;IAEhC,IAAI,EACF,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,EAAE,CAAC,EAAE,6BAAa,EAAE,CAAC,EAAE,6BAAa,EAAE,EAClD,WAAW,EACX,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,cAAc,GACf,GAAG,OAAO,CAAC;IAEZ,OAAO,IAAA,qBAAS,EAAC,QAAQ,EAAE;QACzB,IAAI,EAAE,GAAG;QACT,EAAE,EAAE,GAAG;QACP,SAAS;QACT,SAAS;QACT,SAAS;QACT,WAAW;QACX,cAAc;QACd,YAAY;KACb,CAAC,CAAC;AACL,CAAC;AAvBD,kCAuBC"}
+{"version":3,"file":"predictHSQC.js","sourceRoot":"","sources":["../../src/prediction/predictHSQC.ts"],"names":[],"mappings":";;;AAGA,mDAAsE;AACtE,mDAAsE;AACtE,iDAAyD;AAwCzD;;;GAGG;AAEI,KAAK,UAAU,WAAW,CAC/B,QAAkB,EAClB,UAA8B,EAAE;IAEhC,IAAI,EACF,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,CAAC,EACb,SAAS,GAAG,EAAE,CAAC,EAAE,6BAAa,EAAE,CAAC,EAAE,6BAAa,EAAE,EAClD,WAAW,EACX,YAAY,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,EAClC,cAAc,GACf,GAAG,OAAO,CAAC;IAEZ,OAAO,IAAA,qBAAS,EAAC,QAAQ,EAAE;QACzB,IAAI,EAAE,GAAG;QACT,EAAE,EAAE,GAAG;QACP,SAAS;QACT,SAAS;QACT,SAAS;QACT,WAAW;QACX,cAAc;QACd,YAAY;KACb,CAAC,CAAC;AACL,CAAC;AAvBD,kCAuBC"}

package/lib/prediction/predictProton.d.ts

@@ -1,5 +1,5 @@
 import type { Molecule } from 'openchemlib';
-import type { Prediction1D } from './prediction1D';
+import type { Prediction1D } from './Prediction1D';
 /**
  * Makes a prediction using proton.
  * @returns {Promise<object>} - object with molfile, diaIDs, signals, joined signals by diaIDs and ranges.

package/lib/prediction/utils/fetchPrediction.d.ts

@@ -1,5 +1,5 @@
 import { Molecule } from 'openchemlib';
-import type { Prediction1D } from '../prediction1D';
+import type { Prediction1D } from '../Prediction1D';
 interface FetchPredictionOptions {
     webserviceURL: string;
 }

package/lib/prediction/utils/getPredictions.d.ts

@@ -1,4 +1,4 @@
 import type { Molecule } from 'openchemlib';
-import type { Prediction1D } from '../prediction1D';
+import type { Prediction1D } from '../Prediction1D';
 import type { Predictions, PredictOptions, Predictors } from './predict2D';
 export declare function getPredictions(key: string, molecule: Molecule, predictOptions: PredictOptions, predictor?: Predictors, predictions?: Predictions): Promise<Prediction1D | undefined>;

package/lib/prediction/utils/predict2D.d.ts

@@ -1,9 +1,9 @@
 /// <reference path="../../../src/ml-matrix-peaks-finder.d.ts" />
 import { Molecule } from 'openchemlib';
 import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
+import type { Prediction1D } from '../Prediction1D';
 import type { PredictCarbon, PredictCarbonOptions } from '../predictCarbon';
 import type { PredictProton, PredictProtonOptions } from '../predictProton';
-import type { Prediction1D } from '../prediction1D';
 /**
  * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms
  * @returns {object} - object with molfile, diaIDs, 2D signals and zones.

package/lib/prediction/utils/predict2D.js

@@ -5,9 +5,9 @@ const uuid_1 = require("@lukeed/uuid");
 const ml_hclust_1 = require("ml-hclust");
 const ml_matrix_1 = require("ml-matrix");
 const openchemlib_utils_1 = require("openchemlib-utils");
+const setIDs_1 = require("../../peaks/util/setIDs");
 const getNuclei_1 = require("./getNuclei");
 const getPredictions_1 = require("./getPredictions");
-const setIDs_1 = require("../../peaks/util/setIDs");
 function checkFromTo(options) {
     if (!options.from || !options.to) {
         throw new Error('options from and to are mandatory');

package/lib/prediction/utils/predict2D.js.map

@@ -1 +1 @@
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package/lib/signals/{jcoupling.js → Jcoupling.js}

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

package/lib/signals/Jcoupling.js.map

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

package/lib/signals/NMRSignal1D.d.ts

@@ -1,5 +1,5 @@
 import type { NMRPeak1D } from '../peaks/NMRPeak1D';
-import type { Jcoupling } from './jcoupling';
+import type { Jcoupling } from './Jcoupling';
 export interface NMRSignal1D {
     delta: number;
     id?: string;

package/lib/signals/addDummySignals.js

@@ -4,9 +4,15 @@ exports.addDummySignals = void 0;
 const couplingPatterns_1 = require("../constants/couplingPatterns");
 function addDummySignals(signals) {
     let newSignals = JSON.parse(JSON.stringify(signals));
+    let nextAtomToAssign = signals.reduce((nextAtomToAssign, signal) => {
+        const { atoms = [] } = signal;
+        return Math.max(...atoms) > nextAtomToAssign
+            ? Math.max(...atoms)
+            : nextAtomToAssign;
+    }, 0) + 1;
     signals.forEach((signal, s) => {
-        const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
-        let { newCouplings, tempSignals } = checkCouplings(jCouplings, newSignals, signalAssignment);
+        const { js: jCouplings = [], atoms: signalAssignment = [nextAtomToAssign++], } = signal;
+        let { newCouplings, tempSignals } = checkCouplings(jCouplings, newSignals, signalAssignment, nextAtomToAssign + signals.length);
         if (tempSignals.length > 0)
             newSignals.push(...tempSignals);
         newSignals[s].js = newCouplings;
@@ -15,8 +21,7 @@ function addDummySignals(signals) {
     return newSignals.sort((a, b) => a.delta - b.delta);
 }
 exports.addDummySignals = addDummySignals;
-function checkCouplings(jCouplings, signals, signalAssignment) {
-    let newSignalAssignment = signals.length - 1;
+function checkCouplings(jCouplings, signals, signalAssignment, nextAtomToAssign) {
     let tempSignals = [];
     const newCouplings = jCouplings.reduce((newCouplings, jCoupling) => {
         const { atoms = [], multiplicity, coupling } = jCoupling;
@@ -25,12 +30,12 @@ function checkCouplings(jCouplings, signals, signalAssignment) {
                 let tempCouplings = [];
                 const nbLinks = couplingPatterns_1.couplingPatterns.indexOf(multiplicity);
                 for (let i = 0; i < nbLinks; i++) {
-                    newSignalAssignment++;
+                    nextAtomToAssign++;
                     tempCouplings.push({
                         coupling,
-                        atoms: [newSignalAssignment],
+                        atoms: [nextAtomToAssign],
                     });
-                    tempSignals.push(formatSignal(coupling, [newSignalAssignment], signalAssignment));
+                    tempSignals.push(formatSignal(coupling, [nextAtomToAssign], signalAssignment));
                 }
             }
             else {

package/lib/signals/addDummySignals.js.map

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package/lib/signals/optimization/defaultParameters.d.ts

@@ -0,0 +1 @@
+export declare const defaultParameters: Record<string, Record<string, (...args: any) => number>>;

package/lib/signals/optimization/defaultParameters.js

@@ -0,0 +1,36 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.defaultParameters = void 0;
+exports.defaultParameters = {
+    delta: {
+        init: (data) => data.signal.delta,
+        min: (data) => data.signal.delta - data.shape.fwhm * 2,
+        max: (data) => data.signal.delta + data.shape.fwhm * 2,
+        gradientDifference: () => 2e-3,
+    },
+    intensity: {
+        init: (data) => data.signal.intensity || 1,
+        min: () => 0,
+        max: () => 1.5,
+        gradientDifference: () => 1e-3,
+    },
+    fwhm: {
+        init: (data) => data.shape.fwhm,
+        min: (data) => data.shape.fwhm * 0.25,
+        max: (data) => data.shape.fwhm * 4,
+        gradientDifference: (data) => data.shape.fwhm * 2e-3,
+    },
+    mu: {
+        init: (data) => data.shape.mu || 0.5,
+        min: () => 0,
+        max: () => 1,
+        gradientDifference: () => 0.01,
+    },
+    coupling: {
+        init: (data) => data.jCoupling.coupling,
+        min: (data) => data.jCoupling.coupling * 0.8,
+        max: (data) => data.jCoupling.coupling * 1.2,
+        gradientDifference: () => 0.01,
+    },
+};
+//# sourceMappingURL=defaultParameters.js.map

package/lib/signals/optimization/defaultParameters.js.map

@@ -0,0 +1 @@
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package/lib/signals/optimization/directOptimization.d.ts

@@ -0,0 +1,20 @@
+import { DataXY } from 'cheminfo-types';
+import { SumOfShapes } from './getSumOfShapes';
+interface DirectOptions {
+    iterations?: number;
+    epsilon?: number;
+    tolerance?: number;
+    tolerance2?: number;
+    initialState?: any;
+}
+interface DirectOptimizationOptions extends DirectOptions {
+    directOptions?: DirectOptions;
+    minValues: number[];
+    maxValues: number[];
+}
+export declare function directOptimization(data: DataXY, sumOfShapes: SumOfShapes, options: DirectOptimizationOptions): {
+    error: number;
+    iterations: number;
+    parameterValues: number[];
+};
+export {};

package/lib/signals/optimization/directOptimization.js

@@ -0,0 +1,32 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.directOptimization = void 0;
+const ml_direct_1 = __importDefault(require("ml-direct"));
+function directOptimization(data, sumOfShapes, options) {
+    const { minValues, maxValues, directOptions = {} } = options;
+    const objectiveFunction = getObjectiveFunction(data, sumOfShapes);
+    const result = (0, ml_direct_1.default)(objectiveFunction, minValues, maxValues, directOptions);
+    const { optima } = result;
+    return {
+        error: result.minFunctionValue,
+        iterations: result.iterations,
+        parameterValues: optima[0],
+    };
+}
+exports.directOptimization = directOptimization;
+function getObjectiveFunction(data, sumOfShapes) {
+    const { x, y } = data;
+    const nbPoints = x.length;
+    return (parameters) => {
+        const fct = sumOfShapes(parameters);
+        let error = 0;
+        for (let i = 0; i < nbPoints; i++) {
+            error += Math.pow(y[i] - fct(x[i]), 2);
+        }
+        return error;
+    };
+}
+//# sourceMappingURL=directOptimization.js.map

package/lib/signals/optimization/directOptimization.js.map

@@ -0,0 +1 @@
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package/lib/signals/optimization/getInternalSignals.d.ts

@@ -0,0 +1,54 @@
+import { DataXY } from 'cheminfo-types';
+import { Shape1D, Shape1DInstance } from 'ml-peak-shape-generator';
+import { MakeMandatory } from '../../utilities/MakeMandatory';
+import { Jcoupling } from '../Jcoupling';
+import { Signal } from '../optimizeSignals';
+export interface InternalSignal {
+    shape: Shape1D;
+    shapeFct: Shape1DInstance;
+    signal: MakeMandatory<Signal, 'js' | 'intensity'>;
+    parameters: string[];
+    propertiesValues: Record<string, number[]>;
+    fromIndex: number;
+    toIndex: number;
+    fromIndexCoupling: number;
+    toIndexCoupling: number;
+}
+export declare type Parameter = 'delta' | 'intensity' | 'fwhm' | 'mu' | 'coupling';
+export declare type ParametersFromOptions = Record<Parameter, Record<string, number | ((options?: {
+    signal?: Signal;
+    shape?: Shape1D;
+    index?: number;
+    jCoupling?: Jcoupling;
+}) => number)>>;
+export interface GetInternalSignalsOptions {
+    /**
+     * Initial line width in Hz
+     * @default 1
+     */
+    lineWidth?: number;
+    /**
+     * frequency
+     */
+    frequency: number;
+    baseline?: number;
+    shape?: Shape1D;
+    parameters?: ParametersFromOptions;
+}
+export declare type Shape1DWithFWHM = Omit<Shape1D, 'fwhm'> & {
+    fwhm: number;
+};
+export declare function getInternalSignals(data: DataXY, signals: Signal[], minMaxY: Record<string, number>, options: GetInternalSignalsOptions): {
+    shape: Shape1DWithFWHM;
+    shapeFct: Shape1DInstance;
+    signal: Signal & {
+        js: Jcoupling[];
+        intensity: number;
+    };
+    parameters: Parameter[];
+    propertiesValues: Record<string, number[]>;
+    fromIndex: number;
+    toIndex: number;
+    fromIndexCoupling: number;
+    toIndexCoupling: number;
+}[];