nmr-processing 6.0.0 → 6.0.1

package/lib/assignment/get1HAssignments.d.ts

@@ -1,8 +1,8 @@
 import { Molecule } from 'openchemlib';
 import { NMRRange } from '..';
 import { PredictProtonOptions } from '../prediction/predictProton';
-import { MakeMandatory } from '../types/MakeMandatory';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import { MakeMandatory } from '../utilities/MakeMandatory';
 import { RestrictionByCS } from './utils/buildAssignments';
 export declare type NMRSignal1DWithAtomsAndDiaIDs = MakeMandatory<NMRSignal1D, 'atoms' | 'diaIDs' | 'nbAtoms'>;
 export declare type NMRRangeWithIntegration = MakeMandatory<NMRRange, 'integration'>;

package/lib/{types → assignment}/nmrAssigment.d.ts

@@ -1,6 +1,6 @@
 import { Molecule } from 'openchemlib';
-import type { NMRRange } from './NMRRange';
-import type { NMRZone } from './NMRZone';
+import type { NMRRange } from '../xy/NMRRange';
+import type { NMRZone } from '../xyz/NMRZone';
 export interface NMRAssignmentType {
     /**
      * It has the number of each atoms in the chemical structure. e.g. { C: 6, H: 6 }

package/lib/assignment/nmrAssigment.js.map

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

package/lib/assignment/utils/createMapPossibleAssignments.d.ts

@@ -1,4 +1,4 @@
-import { MakeMandatory } from '../../types/MakeMandatory';
+import { MakeMandatory } from '../../utilities/MakeMandatory';
 import type { Targets } from '../get1HAssignments';
 import type { RestrictionByCS, Predictions1Dassignments } from './buildAssignments';
 declare type RestrictionByCSMandatory = MakeMandatory<RestrictionByCS, 'chemicalShiftRestriction' | 'tolerance' | 'useChemicalShiftScore'>;

package/lib/databases/DatabaseNMREntry.d.ts

@@ -1,4 +1,4 @@
-import { NMRRange } from '../types/NMRRange';
+import { NMRRange } from '../xy/NMRRange';
 export interface DatabaseNMREntry {
     smiles?: string;
     solvent: string;

package/lib/index.d.ts

@@ -24,12 +24,11 @@ export * from './xyz/xyzJResAnalyzer';
 export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
-export type { NMRSignal1D } from './types/NMRSignal1D';
-export type { NMRSignal2D } from './types/NMRSignal2D';
-export type { NMRRange } from './types/NMRRange';
-export type { NMRZone } from './types/NMRZone';
-export type { XYNumberArray } from './types/XYNumberArray';
-export type { NMRPeak1D } from './types/NMRPeak1D';
-export type { Prediction1D } from './types/prediction1D';
-export type { Jcoupling } from './types/jcoupling';
-export type { DataBaseLevelStructure, DataBaseStructure, } from './types/dataStructure';
+export type { NMRSignal1D } from './signals/NMRSignal1D';
+export type { NMRSignal2D } 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 { DataBaseLevelStructure, DataBaseStructure, } from './prediction/dataStructure';

package/lib/ml-matrix-convolution.d.ts

@@ -0,0 +1,8 @@
+declare module 'ml-matrix-convolution' {
+    interface ConvolutionOptions {
+        rows: number;
+        cols: number;
+    }
+    function fft(absoluteData: number[] | Float64Array, kernel: number[][] | Float64Array[], options: ConvolutionOptions): number[] | Float64Array;
+    function direct(absoluteData: number[] | Float64Array, kernel: number[][] | Float64Array[], options: ConvolutionOptions): number[] | Float64Array;
+}

package/lib/ml-matrix-convolution.js

@@ -0,0 +1,2 @@
+"use strict";
+//# sourceMappingURL=ml-matrix-convolution.js.map

package/lib/ml-matrix-convolution.js.map

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

package/lib/ml-simple-clustering.d.ts

@@ -0,0 +1,8 @@
+declare module 'ml-simple-clustering' {
+    export = simpleClustering;
+    function simpleClustering(dataMatrix: number[] | number[][], options?: OptionsSimpleClustering): number[][];
+}
+interface OptionsSimpleClustering {
+    threshold?: number;
+    out?: 'assignment' | 'indexes' | 'values';
+}

package/lib/ml-simple-clustering.js

@@ -0,0 +1,2 @@
+"use strict";
+//# sourceMappingURL=ml-simple-clustering.js.map

package/lib/ml-simple-clustering.js.map

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

package/{lib-esm/types → lib/peaks}/NMRPeak1D.js.map

@@ -1 +1 @@
-{"version":3,"file":"NMRPeak1D.js","sourceRoot":"","sources":["../../src/types/NMRPeak1D.ts"],"names":[],"mappings":""}
+{"version":3,"file":"NMRPeak1D.js","sourceRoot":"","sources":["../../src/peaks/NMRPeak1D.ts"],"names":[],"mappings":""}

package/lib/peaks/peaksFilterImpurities.d.ts

@@ -1,5 +1,5 @@
 import { impurities } from '../constants/impurities';
-import type { NMRPeak1D } from '../types/NMRPeak1D';
+import type { NMRPeak1D } from './NMRPeak1D';
 declare type Solvent = keyof typeof impurities;
 export interface OptionsPeaksFilterImpurities {
     /**

package/lib/peaks/peaksFilterImpurities.js.map

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

@@ -1,6 +1,6 @@
 import type { DataXY } from 'cheminfo-types';
-import type { NMRPeak1D } from '../types/NMRPeak1D';
-import type { NMRRange } from '../types/NMRRange';
+import type { NMRRange } from '../xy/NMRRange';
+import type { NMRPeak1D } from './NMRPeak1D';
 export interface OptionsPeaksToRanges {
     /**
      * Number of hydrogens or some number to normalize the integration data. If it's zero return the absolute integration value

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

@@ -1,5 +1,5 @@
-import type { MakeMandatory } from '../../types/MakeMandatory';
-import type { NMRPeak1D } from '../../types/NMRPeak1D';
+import type { MakeMandatory } from '../../utilities/MakeMandatory';
+import type { NMRPeak1D } from '../NMRPeak1D';
 export interface JAxisKeys {
     [key: string]: string;
     jAxis: string;

package/lib/peaks/util/joinRanges.d.ts

@@ -1,2 +1,2 @@
-import type { NMRRange } from '../../types/NMRRange';
+import type { NMRRange } from '../../xy/NMRRange';
 export declare function joinRanges(ranges: NMRRange[]): NMRRange[];

package/lib/peaks/util/peakOptimizer.d.ts

@@ -1,4 +1,4 @@
 import type { Peak2D } from 'ml-matrix-peaks-finder';
-import type { NMRSignal2D } from '../../types/NMRSignal2D';
+import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
 export declare function clean(peaks: Peak2D[], threshold: number): Peak2D[];
 export declare function enhanceSymmetry(signals: NMRSignal2D[]): any[];

package/lib/prediction/dataStructure.js.map

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

package/lib/prediction/predictAll.d.ts

@@ -1,7 +1,7 @@
 import type { Molecule } from 'openchemlib';
-import type { Prediction1D } from '../types/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/predictCOSY.d.ts

@@ -1,6 +1,6 @@
 import { Molecule } from 'openchemlib';
-import type { Prediction1D } from '../types/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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package/lib/prediction/predictCarbon.d.ts

@@ -1,6 +1,6 @@
 import type { Molecule } from 'openchemlib';
-import type { DataBaseStructure } from '../types/dataStructure';
-import type { Prediction1D } from '../types/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/predictCarbon.js.map

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

@@ -1,7 +1,7 @@
 import { Molecule } from 'openchemlib';
-import type { Prediction1D } from '../types/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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package/lib/prediction/predictHSQC.d.ts

@@ -1,7 +1,7 @@
 import { Molecule } from 'openchemlib';
-import type { Prediction1D } from '../types/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 @@
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package/lib/prediction/predictProton.d.ts

@@ -1,5 +1,5 @@
 import type { Molecule } from 'openchemlib';
-import type { Prediction1D } from '../types/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/predictProton.js.map

@@ -1 +1 @@
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package/lib/{types → prediction}/prediction1D.d.ts

@@ -1,6 +1,6 @@
 import type { Molecule } from 'openchemlib';
-import type { NMRRange } from './NMRRange';
-import type { NMRSignal1D } from './NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import type { NMRRange } from '../xy/NMRRange';
 export interface Prediction1D {
     molfile: string;
     diaIDs: string[];

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/utils/fetchPrediction.d.ts

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

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

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

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

@@ -1,4 +1,4 @@
 import type { Molecule } from 'openchemlib';
-import type { Prediction1D } from '../../types/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

@@ -1,8 +1,8 @@
 import { Molecule } from 'openchemlib';
-import type { NMRSignal2D } from '../../types/NMRSignal2D';
-import type { Prediction1D } from '../../types/prediction1D';
+import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
 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/queryByHOSE.d.ts

@@ -1,4 +1,4 @@
-import type { DataBaseStructure } from '../../types/dataStructure';
+import type { DataBaseStructure } from '../dataStructure';
 import type { GroupedDiaIDsWithHose } from './getFilteredIDiaIDs';
 export interface Prediction {
     diaIDs: string[];

package/lib/ranges/rangesToACS.d.ts

@@ -1,4 +1,4 @@
-import type { NMRRange } from '../types/NMRRange';
+import type { NMRRange } from '../xy/NMRRange';
 export interface RangesToACSOptions {
     /**
      * nucleus

package/lib/ranges/rangesToXY.d.ts

@@ -1,5 +1,5 @@
 import type { Shape1D } from 'ml-peak-shape-generator';
-import type { NMRRange } from '../types/NMRRange';
+import type { NMRRange } from '../xy/NMRRange';
 export interface RangeToXYOptions {
     /**
      * frequency observed

package/lib/ranges/rangesToXY.js.map

@@ -1 +1 @@
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package/lib/signal/signalJoinCouplings.d.ts

@@ -1,4 +1,4 @@
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
 export interface SignalJoinCouplingsOptions {
     /**
      * tolerance to merge the couplings

package/lib/signal/signalMultiplicityPattern.d.ts

@@ -1,4 +1,4 @@
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
 /**
  * Return
  * @param {*} signal

package/lib/{types → signals}/NMRSignal1D.d.ts

@@ -1,4 +1,4 @@
-import type { NMRPeak1D } from './NMRPeak1D';
+import type { NMRPeak1D } from '../peaks/NMRPeak1D';
 import type { Jcoupling } from './jcoupling';
 export interface NMRSignal1D {
     delta: number;

package/lib/{types → signals}/NMRSignal1D.js.map

@@ -1 +1 @@
-{"version":3,"file":"NMRSignal1D.js","sourceRoot":"","sources":["../../src/types/NMRSignal1D.ts"],"names":[],"mappings":""}
+{"version":3,"file":"NMRSignal1D.js","sourceRoot":"","sources":["../../src/signals/NMRSignal1D.ts"],"names":[],"mappings":""}

package/lib/signals/hackSignalsToXY.d.ts

@@ -1,4 +1,4 @@
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from './NMRSignal1D';
 import { OptionsSignalsToXY } from './signalsToXY';
 /**
  * Create the xy object from an array of 1D signals.

package/lib/{types → signals}/jcoupling.js.map

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

package/lib/signals/signals2DToZ.d.ts

@@ -1,5 +1,5 @@
 import type { XYNumber } from 'spectrum-generator';
-import type { NMRSignal2D } from '../types/NMRSignal2D';
+import type { NMRSignal2D } from '../xyz/NMRSignal2D';
 interface Signals2DToZOptions {
     /**
      * lower limit in the spectrum, if it is a number the value will be defined for both axes

package/lib/signals/signalsJoin.d.ts

@@ -1,7 +1,7 @@
 import type { SignalJoinCouplingsOptions } from '../signal/signalJoinCouplings';
-import type { MakeMandatory } from '../types/MakeMandatory';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
-import type { Jcoupling } from '../types/jcoupling';
+import type { MakeMandatory } from '../utilities/MakeMandatory';
+import type { NMRSignal1D } from './NMRSignal1D';
+import type { Jcoupling } from './jcoupling';
 export interface SignalsJoinOptions {
     /**
      * options for signalJoinCouplings

package/lib/signals/signalsJoin.js.map

@@ -1 +1 @@
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package/lib/signals/signalsToRanges.d.ts

@@ -1,5 +1,5 @@
-import type { NMRRange } from '../types/NMRRange';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRRange } from '../xy/NMRRange';
+import type { NMRSignal1D } from './NMRSignal1D';
 interface SignalsToRangesOptions {
     /**
      * minimal artificial width of a signal in ppm

package/lib/signals/signalsToRanges.js.map

@@ -1 +1 @@
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package/lib/signals/signalsToXY.d.ts

@@ -1,5 +1,5 @@
 import type { Shape1D } from 'ml-peak-shape-generator';
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from './NMRSignal1D';
 export interface OptionsSignalsToXY {
     frequency?: number;
     /**

package/lib/signals/simulation/signalsToSpinSystem.d.ts

@@ -1,3 +1,3 @@
-import type { NMRSignal1D } from '../../types/NMRSignal1D';
-import type { SpinSystem } from '../../types/spinSystem';
+import type { NMRSignal1D } from '../NMRSignal1D';
+import type { SpinSystem } from '../spinSystem';
 export declare function signalsToSpinSystem(signals: NMRSignal1D[]): SpinSystem;

package/lib/signals/simulation/simulate1D.d.ts

@@ -1,6 +1,6 @@
 import { DataXY } from 'cheminfo-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
-import type { SpinSystem } from '../../types/spinSystem';
+import type { SpinSystem } from '../spinSystem';
 interface Simulate1DOptions {
     /**
      * The linewidth of the output spectrum, expresed in Hz.

package/lib/signals/simulation/splitSpinSystem.d.ts

@@ -1,4 +1,4 @@
-import type { SpinSystem } from '../../types/spinSystem';
+import type { SpinSystem } from '../spinSystem';
 export interface SplitSpinSystemOptions {
     /**
      * @default 400

package/lib/{types → signals}/spinSystem.js.map

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

package/lib/utilities/MakeMandatory.js.map

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

package/lib/utilities/rangeFromSignal.d.ts

@@ -1,4 +1,4 @@
-import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
 export interface RangeFromSignalOptions {
     /**
      * nucleus

package/lib/utilities/resurrect.d.ts

@@ -1,4 +1,4 @@
-import type { NMRRange } from '../types/NMRRange';
+import type { NMRRange } from '../xy/NMRRange';
 export interface DataResurrect {
     experiment: {
         solvent?: string;

package/lib/utilities/resurrectRange.d.ts

@@ -1,2 +1,2 @@
-import type { NMRRange } from '../types/NMRRange';
+import type { NMRRange } from '../xy/NMRRange';
 export declare function resurrectRange(part: string, options?: any): NMRRange | undefined;

package/lib/{types → xy}/NMRRange.d.ts

@@ -1,4 +1,4 @@
-import type { NMRSignal1D } from './NMRSignal1D';
+import type { NMRSignal1D } from '../signals/NMRSignal1D';
 export interface NMRRange {
     from: number;
     to: number;

package/lib/{types → xy}/NMRRange.js.map

@@ -1 +1 @@
-{"version":3,"file":"NMRRange.js","sourceRoot":"","sources":["../../src/types/NMRRange.ts"],"names":[],"mappings":""}
+{"version":3,"file":"NMRRange.js","sourceRoot":"","sources":["../../src/xy/NMRRange.ts"],"names":[],"mappings":""}