nmr-processing 19.0.0 → 19.0.3

package/dist/nmr-processing.d.ts

@@ -57,7 +57,7 @@ import type { JoinBroadPeaksOptions } from 'ml-gsd';
 import type { LevenbergMarquardtOptions } from 'ml-levenberg-marquardt';
 import type { LightLogger } from 'cheminfo-types';
 import type { Logger } from 'cheminfo-types';
-import { MatchingMultiplicity as MatchingMultiplicity_2 } from '../index.js';
+import { MatchingMultiplicity as MatchingMultiplicity_2 } from '../index.ts';
 import { Matrix } from 'ml-matrix';
 import type { MatrixOptions } from '@zakodium/nmr-types';
 import type { Molecule } from 'openchemlib';
@@ -68,7 +68,7 @@ import type { NmrData2DFt } from 'cheminfo-types';
 import type { NMRPeak1D } from '@zakodium/nmr-types';
 import { NMRRange } from '@zakodium/nmr-types';
 import type { NMRSignal1D } from '@zakodium/nmr-types';
-import { NMRZoneWithID as NMRZoneWithID_2 } from './xyzAutoZonesPicking.js';
+import { NMRZoneWithID as NMRZoneWithID_2 } from './xyzAutoZonesPicking.ts';
 import type { NumberArray } from 'cheminfo-types';
 import type { NUSDimension2Options } from '@zakodium/nmr-types';
 import type { OCLMolecule } from 'cheminfo-types';
@@ -87,7 +87,7 @@ import type { PhaseCorrection2DOptions } from '@zakodium/nmr-types';
 import type { PhaseCorrectionTwoDFilter } from '@zakodium/nmr-types';
 import type { PhaseCorrectionTwoDOptions } from '@zakodium/nmr-types';
 import { PointXY } from 'cheminfo-types';
-import type { Range as Range_2 } from '@zakodium/nmr-types';
+import type { Range } from '@zakodium/nmr-types';
 import type { Ranges } from '@zakodium/nmr-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
 import type { Shapes } from '@zakodium/nmr-types';
@@ -110,7 +110,7 @@ import type { ZeroFillingOptions } from '@zakodium/nmr-types';
 import type { Zone } from '@zakodium/nmr-types';
 import type { Zones } from '@zakodium/nmr-types';
 
-declare function addDefaultSignal(range: Range_2): void;
+declare function addDefaultSignal(range: Range): void;
 
 declare type Apodization1D = FilterFactory<Entry1D, Apodization1DOptions> & Pick<Apodization1DFilterOptions, 'name'>;
 
@@ -329,9 +329,9 @@ export declare function checkIntegralKind(integral: Integral): boolean;
 
 export declare function checkMultiplicity(multiplicity: string, rejected?: OneLetterMultiplet[]): boolean;
 
-declare function checkRangeKind(range: Range_2): boolean;
+declare function checkRangeKind(range: Range): boolean;
 
-declare function checkSignalKinds(range: Range_2, kinds: string[]): boolean;
+declare function checkSignalKinds(range: Range, kinds: string[]): boolean;
 
 declare interface CompilePatternOptions {
     observedFrequencies?: number[] | Float64Array;
@@ -888,7 +888,7 @@ export declare function getDatabase(url?: string, options?: {
     format?: 'tsv' | 'json';
 }): Promise<DatabaseNMREntry[]>;
 
-declare function getDiaIDs(range: Range_2): string[];
+declare function getDiaIDs(range: Range): string[];
 
 /**
  * calculate the frequency of a nucleus with respect to a reference nucleus
@@ -909,7 +909,7 @@ declare interface GetKernelOptions {
 
 declare function getLineShapes(l: LineShapeData[]): LineShapeResult[];
 
-declare function getNbAtoms(range: Range_2, signalIndex?: number): number;
+declare function getNbAtoms(range: Range, signalIndex?: number): number;
 
 export declare function getPeakDelta(peak: Peak1D | NMRPeak1D, shiftTarget: ShiftTarget, shift: number): {
     originalX: number;
@@ -994,7 +994,7 @@ export declare function isEmptyMolecule(molecule: Molecule): boolean;
 
 export declare function isMolfileNotEmpty(molFile?: string): molFile is string;
 
-export declare function isRangeExists(range: Pick<Range_2, 'from' | 'to'>, spectrum: Entry1D, error: number): true | undefined;
+export declare function isRangeExists(range: Pick<Range, 'from' | 'to'>, spectrum: Entry1D, error: number): boolean;
 
 export declare function isZoneExists(zone: Pick<Zone, 'x' | 'y'>, spectrum: Entry2D, error: Zone2DError): boolean;
 
@@ -1072,7 +1072,7 @@ declare interface MapOptions {
 
 export declare function mapPeaks(peaks: Peak1D[], spectrum: Entry1D, options?: MapOptions): Peak1D[];
 
-export declare function mapRanges(ranges: Range_2[] | NMRRange[], spectrum: Entry1D, options?: MapOptions): Range_2[];
+export declare function mapRanges(ranges: Range[] | NMRRange[], spectrum: Entry1D, options?: MapOptions): Range[];
 
 export declare function mapZones(zones: Zone[], datum: Entry2D, options?: MapOptions): {
     signals: {
@@ -1148,9 +1148,9 @@ export declare function matrixToBoxPlot(input: NumberArray[], options?: {
     colors?: string[];
 }): {
     color: (string | undefined)[];
-    median: Float64Array<ArrayBufferLike>;
     max: Float64Array<ArrayBufferLike>;
     min: Float64Array<ArrayBufferLike>;
+    median: Float64Array<ArrayBufferLike>;
     q1: Float64Array<ArrayBufferLike>;
     q3: Float64Array<ArrayBufferLike>;
 };
@@ -1286,7 +1286,7 @@ export declare function optimizeSignals(data: DataXY, signals: Signal[], options
     delta: number;
     js: Jcoupling[];
     shape: {
-        kind: "gaussian" | "lorentzian" | "pseudoVoigt" | "generalizedLorentzian";
+        kind: "gaussian" | "lorentzian" | "pseudoVoigt" | "lorentzianDispersive" | "generalizedLorentzian";
         fwhm: number;
     };
     intensity: number;
@@ -2020,7 +2020,7 @@ export declare function reimComplexBackwardLinearPrediction(data: DataReIm, opti
     im: Float64Array<ArrayBuffer>;
 };
 
-declare function resetDiaIDs(range: Range_2): void;
+declare function resetDiaIDs(range: Range): void;
 
 declare interface RestrictionByCS {
     chemicalShiftRestriction: boolean;
@@ -2040,7 +2040,7 @@ export declare interface ResurrectOptions {
     logger?: Logger;
 }
 
-declare function setNbAtoms(range: Range_2, signalIndex?: number): void;
+declare function setNbAtoms(range: Range, signalIndex?: number): void;
 
 declare type Shape1DWithFWHM = Omit<Shape1D, 'fwhm'> & {
     fwhm: number;
@@ -2324,6 +2324,11 @@ export declare interface Simulate1DOptions extends SimulateXYPeaksOptions {
      * Options to add noise to the spectrum
      */
     noise?: Extract<GenerateSpectrumOptions, 'noise'>;
+    /**
+     * assume the spin system is a 1/2 (proton), if it's doesn't exists
+     * it is defined by checking if all the levels are 2.
+     */
+    isProton?: boolean;
 }
 
 declare interface SimulateXYPeaksOptions {
@@ -2489,7 +2494,7 @@ declare interface TwoDOptions {
     nbPoints: PointXY;
 }
 
-declare function unlink(range: Range_2, options?: UnlinkOptions): Range_2;
+declare function unlink(range: Range, options?: UnlinkOptions): Range;
 
 /**
  *