nmr-processing 14.0.6 → 15.1.0

package/nmr-processing.d.ts

@@ -1,4 +1,6 @@
+import { AnalizeMultipletOptions } from 'multiplet-analysis';
 import { BaseRegression } from 'ml-regression-base';
+import { DataXReIm } from 'ml-spectra-processing';
 import { DataXY } from 'cheminfo-types';
 import { DoubleArray } from 'cheminfo-types';
 import { ExponentialRegression } from 'ml-regression-exponential';
@@ -396,6 +398,8 @@ export declare interface DataResurrect {
     parts: string[];
 }
 
+export declare type DataXReOptionalIm = Omit<DataXReIm, 'im'> & Partial<Pick<DataXReIm, 'im'>>;
+
 export declare const DatumKind: {
     signal: string;
     mixed: string;
@@ -478,7 +482,7 @@ declare interface Entry2D<T extends NmrData2D = NmrData2D> {
     id?: string;
     zones: Zones;
     info: Record<string, any>;
-    customInfo?: Record<string, any>;
+    meta?: Record<string, any>;
     originalInfo?: Record<string, any>;
     data: T;
     originalData?: T;
@@ -567,11 +571,11 @@ export declare type Filter1DEntry = Filter1DOptions & BaseFilterEntry;
 
 export declare type Filter1DOptions = BaselineCorrectionFilterOptions | FFT1DOptions | ZeroFillingFilterOptions | SignalProcessingFilter | ShiftXFilterOptions | PhaseCorrection1DFilterOptions | ForwardLP1DOptions | ExclusionZonesOptions | EquallySpacedOptions | DigitalFilterOption | Apodization1DFilterOptions | BackwardLinearPredictionFilterOptions;
 
-export declare type Filter2D = ApodizationDimension1 | ApodizationDimension2 | BaselineCorrection2D | BackwardLPDimension1 | BackwardLPDimension2 | FFTDimension1 | FFTDimension2 | FordwardLPDimension1 | FordwardLPDimension2 | DigitalFilter2D | PhaseCorrection2D | ZeroFillingDimension1 | ZeroFillingDimension2 | SymmetrizeCosyLike | Shift2DX | Shift2DY;
+export declare type Filter2D = ApodizationDimension1 | ApodizationDimension2 | BaselineCorrection2D | BackwardLPDimension1 | BackwardLPDimension2 | NUSDimension2 | FFTDimension1 | FFTDimension2 | FordwardLPDimension1 | FordwardLPDimension2 | DigitalFilter2D | PhaseCorrection2D | ZeroFillingDimension1 | ZeroFillingDimension2 | SymmetrizeCosyLike | Shift2DX | Shift2DY;
 
 export declare type Filter2DEntry = Filter2DOptions & BaseFilterEntry;
 
-export declare type Filter2DOptions = ApodizationDimension1Options | ApodizationDimension2Options | BaselineCorrection2DFilterOptions | BackwardLPDimension1Options | BackwardLPDimension2Options | DigitalFilter2DOptions | FFTDimension1Options | FFTDimension2Options | FordwardLPDimension1Options | FordwardLPDimension2Options | PhaseCorrection2DOptions | Shift2DXFilterOptions | Shift2DYFilterOptions | SymmetrizeCosyLikeOptions | ZeroFillingDimension1Options | ZeroFillingDimension2Options;
+export declare type Filter2DOptions = ApodizationDimension1Options | ApodizationDimension2Options | BaselineCorrection2DFilterOptions | BackwardLPDimension1Options | BackwardLPDimension2Options | DigitalFilter2DOptions | FFTDimension1Options | NUSDimension2Options | FFTDimension2Options | FordwardLPDimension1Options | FordwardLPDimension2Options | PhaseCorrection2DOptions | Shift2DXFilterOptions | Shift2DYFilterOptions | SymmetrizeCosyLikeOptions | ZeroFillingDimension1Options | ZeroFillingDimension2Options;
 
 export declare interface FilterDomainUpdateRules {
     updateYDomain: boolean;
@@ -1306,6 +1310,13 @@ declare interface NumberField extends Field<number> {
     type: 'number';
 }
 
+declare type NUSDimension2 = FilterFactory<Entry2D, IndirectDimensionOptions> & Pick<NUSDimension2Options, 'name'>;
+
+declare interface NUSDimension2Options extends BaseFilter {
+    name: 'nusDimension2';
+    value: IndirectDimensionOptions;
+}
+
 declare type ObjectKeys = 'id' | 'multiplicity' | 'js';
 
 export declare interface ObservedNucleusData {
@@ -1557,6 +1568,33 @@ export declare interface Peaks {
  */
 export declare function peaksFilterImpurities<T extends NMRPeak1D>(peakList: T[], options?: OptionsPeaksFilterImpurities): T[];
 
+/**
+ * Generates an NMR Free Induction Decay (FID) signal from a list of peaks.
+ *
+ * @param {Array<{ x: number, y: number }>} peaks - The list of peaks, where:
+ *   - `x` is the chemical shift in ppm.
+ *   - `y` is the intensity of the peak.
+ * @param {object} options - The options for FID generation.
+ * @param {number} [options.from=0] - The start of the spectral window in ppm.
+ * @param {number} [options.to=10] - The end of the spectral window in ppm.
+ * @param {number} [options.nbPoints=1024] - The number of data points in the FID.
+ * @param {number} [options.frequency=400] - The spectrometer frequency in MHz.
+ * @param {NumberArray} [options.t2Relaxation] - An array of T2 relaxation times in milliseconds for each peak.
+ *   If not provided, all peaks are assigned a default T2 relaxation time of 100 ms.
+ * @returns {{ re: Float64Array, im: Float64Array }} - The generated FID signal, where:
+ *   - `re` is the real part of the FID.
+ *   - `im` is the imaginary part of the FID.
+ **/
+export declare function peaksToFID(peaks: Array<{
+    x: number;
+    y: number;
+}>, options: SignalsToFIDOptions & {
+    t2Relaxation?: NumberArray;
+}): {
+    re: Float64Array;
+    im: Float64Array;
+};
+
 export declare function peaksToXY(peaks: NMRPeak1D[], options: PeaksToXYOptions): DataXY<Float64Array>;
 
 /**
@@ -1693,22 +1731,23 @@ export declare interface PredictCarbonOptions {
 declare interface PredictCOSYOptions {
     /**
      * maximum number of bonds to take into account.
-     * @default 3
      */
     maxLength?: number;
     /**
      * minimum number of bonds to take into account
-     * @default 2
      */
     minLength?: number;
+    /**
+     * minimum scalar coupling in Hz to draw the cross-peak
+     * @default 1.5
+     */
+    minCoupling?: number;
     /**
      * signals with euclidean distance in ppm less than this it will
      * joined into a zone.
-     * @default {H:0.05,C:0.5}
      */
     joinDistance?: {
         H: number;
-        C: number;
     };
     /**
      * mono dimensional signal to generate the bidimenionals cross peaks.
@@ -1763,7 +1802,6 @@ declare interface PredictHMBCOptions {
     /**
      * signals with euclidean distance in ppm less than this it will
      * joined into a zone.
-     * @default {H:0.05,C:0.5}
      */
     joinDistance?: {
         H: number;
@@ -1846,7 +1884,7 @@ export declare interface PredictionBase2D {
  * or an empty value (empty string, null, or undefined) if no cache entry is found.
  * When the function is called with two parameters, the second parameter is the value that should be put in the cache.
  */
-declare type PredictionCacheFn = (id: string, result?: PredictionBase1D) => CacheResult;
+declare type PredictionCacheFn = (topicMolecule: TopicMolecule, result?: PredictionBase1D) => CacheResult;
 
 export declare interface PredictionOptionsByExperiment {
     H?: Partial<PredictProtonOptions>;
@@ -2575,6 +2613,21 @@ declare function unlink(range: Range_2, options?: UnlinkOptions): Range_2;
      predicted: Float64Array;
  };
 
+ export declare interface XreimMultipletAnalysis {
+     analyzer?: AnalizeMultipletOptions;
+     autoPhase?: boolean;
+ }
+
+ /**
+  * Determination of J couplings by recursive deconvolution in the frequency domain,
+  * it use the method published by Damien Jeannerat and Geoffrey Bodenhausen @link{https://doi.org/10.1006/jmre.1999.1845}
+  */
+ export declare function xreimMultipletAnalysis(
+ /**
+  * Imaginary data is optional for auto phase correction of the region before the analysis.
+  */
+ data: DataXReOptionalIm, options?: XreimMultipletAnalysis): any;
+
  export declare function xyAutoPeaksPicking(data: DataXY<Float64Array>, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithShapeID[];
 
  /**