nmr-processing 17.3.0 → 18.0.0

package/nmr-processing.d.ts

@@ -1,5 +1,7 @@
 import type { AnalizeMultipletOptions } from 'multiplet-analysis';
+import { AtomMapping } from './ctMolfileParser';
 import { BaseRegression } from 'ml-regression-base';
+import { CTSignal } from './ctCreateSignals';
 import type { DataReIm } from 'ml-spectra-processing';
 import type { DataXReIm } from 'ml-spectra-processing';
 import { DataXY } from 'cheminfo-types';
@@ -12,23 +14,30 @@ import type { GroupedDiaID } from 'openchemlib-utils';
 import type { GSDOptions } from 'ml-gsd';
 import { GSDPeakOptimized } from 'ml-gsd';
 import { GSDPeakOptimizedID } from 'ml-gsd';
+import { Jcoupling as Jcoupling_2 } from './Jcoupling';
 import type { JoinBroadPeaksOptions } from 'ml-gsd';
 import { LightLogger } from 'cheminfo-types';
 import type { Logger } from 'cheminfo-types';
+import { MatchingMultiplicity as MatchingMultiplicity_2 } from '..';
 import { Matrix } from 'ml-matrix';
-import type { Molecule } from 'openchemlib/full';
+import type { Molecule } from 'openchemlib';
 import type { NmrData1D } from 'cheminfo-types';
 import type { NmrData2D } from 'cheminfo-types';
 import type { NmrData2DContent } from 'cheminfo-types';
 import type { NmrData2DFt } from 'cheminfo-types';
+import { NMRRange as NMRRange_2 } from './NMRRange';
 import type { NumberArray } from 'cheminfo-types';
 import type { OCLMolecule } from 'cheminfo-types';
+import { OneLetterMultiplet as OneLetterMultiplet_2 } from './MultiplicityPatterns';
 import type { OptimizePeaksOptions } from 'ml-gsd';
 import type { OptionsSG1D } from 'spectrum-generator';
+import { ParsedCoupling } from './ctJSONParser';
+import { ParsedShift } from './ctJSONParser';
 import type { Peak2D as Peak2D_2 } from 'ml-matrix-peaks-finder';
 import type { PeakXYWidth } from 'cheminfo-types';
 import { PointXY } from 'cheminfo-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
+import { SpectraDataWithIds as SpectraDataWithIds_2 } from './nmrAssigment';
 import type { TopicMolecule } from 'openchemlib-utils';
 import type { XDistributionStats } from 'ml-spectra-processing';
 import type { XYEquallySpacedOptions } from 'ml-spectra-processing';
@@ -127,8 +136,6 @@ export declare interface ApplyWindowOptions {
     output?: DoubleArray;
 }
 
-declare type Atom = ReturnType<typeof getAtoms>[0];
-
 declare interface AtomInput {
     id: ID;
     pid: ID;
@@ -149,36 +156,6 @@ declare interface AtomInput {
     s: ID | null;
 }
 
-/**
- * Interface for atom mapping information
- */
-declare interface AtomMapping {
-    label: string;
-    atom: number;
-}
-
-declare interface AtomOutput {
-    id: ID;
-    parentID: ID;
-    name: string;
-    remarks: string;
-    nucleusType: NucleusType;
-    cipRank: {
-        canonical: number;
-        rd: number;
-        nmr: number;
-    };
-    ordinal: number;
-    stereochemistryFlags: number[];
-    spinSystemFlags: number[];
-    formalcharge: number;
-    partialCharge: number;
-    coordinates2D: [number, number, number];
-    coordinates3D: [number, number, number];
-    parent2D: string | null;
-    shift: ID | null;
-}
-
 declare type AtomTypes = 'H' | 'C';
 
 export declare interface AutoPhaseCorrection2D {
@@ -394,7 +371,7 @@ declare interface CouplingInput {
     s: [ID, ID];
 }
 
-export declare const couplingPatterns: OneLetterMultiplet[];
+export declare const couplingPatterns: OneLetterMultiplet_2[];
 
 export declare function createApodizationWindowData(options: {
     windowOptions: {
@@ -445,14 +422,6 @@ declare interface CTJSONInput {
     b: BondInput[];
 }
 
-declare interface CTSignal {
-    delta: number;
-    diaIDs: string[];
-    js: Jcoupling[];
-    nbAtoms: number;
-    atoms: number[];
-}
-
 export declare type DataBaseLevelEntry = number | [number] | [number, number, number, number | null, number] | undefined | XDistributionStats;
 
 export declare type DataBaseLevelStructure = Record<string, DataBaseLevelEntry>;
@@ -730,7 +699,7 @@ export declare namespace Filters2DManager {
  * Look for a multiplet based on the pattern name or abbreviation.
  * @param name - pattern name or abbreviation.
  */
-export declare function findMultiplet(name: string): MatchingMultiplicity | undefined;
+export declare function findMultiplet(name: string): MatchingMultiplicity_2 | undefined;
 
 /**
  * Finds a peak that can serve as a pivot point within specified boundaries.
@@ -871,7 +840,7 @@ export declare function get2DErrorFactor(spectrum: Entry2D): Zone2DError;
 
 export declare function getAssignments(input: GetAutoAssignmentInput, options?: GetAssignmentsOptions): Promise<{
     score: any;
-    assignment: SpectraDataWithIds[];
+    assignment: SpectraDataWithIds_2[];
 }[]>;
 
 export declare interface GetAssignmentsOptions {
@@ -919,8 +888,6 @@ export declare interface GetAssignmentsOptions {
     };
 }
 
-declare function getAtoms(a: AtomInput[]): AtomOutput[];
-
 export declare interface GetAutoAssignmentInput {
     spectra: SpectraData[];
     /**
@@ -1007,7 +974,7 @@ declare interface HOSEPrediction {
     /**
      * The HOSE code used to make the prediction.
      */
-    idCode: string;
+    hose: string;
 }
 
 declare type ID = string;
@@ -1417,11 +1384,6 @@ declare interface NMRZoneWithIds extends Omit<NMRZone, 'signals' | 'id'> {
  */
 export declare function normalizeNucleus(nucleus: string): string;
 
-declare interface NucleusType {
-    atomicNumber: number;
-    isotope: number;
-}
-
 declare interface NumberField extends Field<number> {
     type: 'number';
 }
@@ -1459,7 +1421,7 @@ export declare type OneLetterMultiplet = 's' | 'd' | 't' | 'q' | 'i' | 'h' | 'p'
 
 export declare function optimizeSignals(data: DataXY, signals: Signal[], options: OptimizeSignalsOptions): {
     delta: number;
-    js: Jcoupling[];
+    js: Jcoupling_2[];
     shape: {
         kind: "gaussian" | "lorentzian" | "pseudoVoigt" | "generalizedLorentzian";
         fwhm: number;
@@ -1652,23 +1614,6 @@ export declare function parseCT(json: CTJSONInput, molfile: string, options: {
     couplings: ParsedCoupling[];
 };
 
-/**
- * Interface for coupling data between atoms
- */
-declare interface ParsedCoupling {
-    from: Atom[];
-    to: Atom[];
-    value: number;
-}
-
-/**
- * Interface for chemical shift data
- */
-declare interface ParsedShift {
-    atoms: Atom[];
-    value: number;
-}
-
 export declare interface Peak1D extends Omit<NMRPeak1D, 'id'>, BasePeak {
     originalX?: number;
 }
@@ -2930,7 +2875,7 @@ declare function unlink(range: Range_2, options?: UnlinkOptions): Range_2;
   * @param data
   * @param options
   */
- export declare function xyAutoRangesPicking(data: DataXY<Float64Array>, options: OptionsXYAutoRangesPicking): NMRRange[];
+ export declare function xyAutoRangesPicking(data: DataXY<Float64Array>, options: OptionsXYAutoRangesPicking): NMRRange_2[];
 
  /**
   * Estimate the diffusion coefficient of an independent component by fitting of imput data with the Stejskal–Tanner equation.