nmr-processing 22.22.2 → 22.23.1

package/dist/nmr-processing.d.ts

@@ -95,10 +95,14 @@ import type { Shift2DXFilterOptions } from '@zakodium/nmr-types';
 import type { Shift2DYFilterOptions } from '@zakodium/nmr-types';
 import type { ShiftXFilterOptions } from '@zakodium/nmr-types';
 import type { ShiftXOptions } from '@zakodium/nmr-types';
+import type { Signal1D } from '@zakodium/nmr-types';
 import type { Signal2D } from '@zakodium/nmr-types';
 import type { SignalKind } from '@zakodium/nmr-types';
 import type { SignalProcessingFilter } from '@zakodium/nmr-types';
 import type { SineBellOptions } from '@zakodium/nmr-types';
+import type { Spectra } from '@zakodium/nmr-types';
+import type { Spectrum } from '@zakodium/nmrium-core';
+import type { Spectrum2D } from '@zakodium/nmr-types';
 import type { SymmetrizeCosyLikeOptions } from '@zakodium/nmr-types';
 import type { TopicMolecule } from 'openchemlib-utils';
 import type { TrafOptions } from '@zakodium/nmr-types';
@@ -113,6 +117,14 @@ import type { ZeroFillingOptions } from '@zakodium/nmr-types';
 import type { Zone } from '@zakodium/nmr-types';
 import type { Zones } from '@zakodium/nmr-types';
 
+/**
+ * Adds a link to a correlation.
+ *
+ * @param correlation
+ * @param link
+ */
+declare function addLink(correlation: Correlation, link: CorrelationLink): Correlation;
+
 declare type Apodization1D = FilterFactory<Entry1D, Apodization1DOptions> & Pick<Apodization1DFilterOptions, 'name'>;
 
 declare type ApodizationDimension1 = FilterFactory<Entry2D, Apodization2D1Options> & Pick<ApodizationDimension1Options, 'name'>;
@@ -299,6 +311,43 @@ declare interface BondOutput {
     atoms: [ID, ID];
 }
 
+/**
+ * Builds a correlation object with some existing default values.
+ *
+ * @param {CorrelationOptions} options
+ */
+declare function buildCorrelation(options: CorrelationOptions): Correlation;
+
+/**
+ * Builds the correlation data from spectra data and some options.
+ *
+ * @param spectra
+ * @param options
+ */
+declare function buildCorrelationData(spectra: Spectrum[], options: CorrelationBuildOptions): CorrelationData;
+
+/**
+ * Builds a link object with some existing default values.
+ *
+ * @param options
+ */
+declare function buildLink(options: LinkOptions): CorrelationLink;
+
+/**
+ * Builds a state from current values and an optional molecular formula.
+ *
+ * @param {CorrelationValues} values
+ * @param {string} mf
+ */
+declare function buildState(values: CorrelationValues, mf: string): CorrelationState;
+
+/**
+ * Builds the correlation data values from given input spectra and options.
+ * @param spectra
+ * @param options
+ */
+declare function buildValues(spectra: Spectra, options: CorrelationBuildOptions): CorrelationValues;
+
 declare type CacheResult = EmptyValue | PredictionBase1D | Promise<EmptyValue | PredictionBase1D>;
 
 export declare interface CalculateDiffussionCoefficientOptions {
@@ -353,10 +402,114 @@ export declare const carbonImpurities: DatabaseNMREntry[];
  */
 export declare function checkIntegralKind(integral: Integral): boolean;
 
+/**
+ * Checks for a numeric match within a certain tolerance.
+ *
+ * @param {number} value1
+ * @param {number} value2
+ * @param {number} tolerance
+ */
+declare function checkMatch(value1: number, value2: number, tolerance: number): boolean;
+
 export declare function checkMultiplicity(multiplicity: string, rejected?: OneLetterMultiplet[]): boolean;
 
 declare function checkSignalKinds(range: Range_2, kinds: ReadonlySet<SignalKind>): boolean;
 
+export declare interface Correlation extends CorrelationAndLinkFields {
+    atomType: string;
+    label: Record<string, string>;
+    link: CorrelationLink[];
+    equivalence: number;
+    attachment: Record<string, number[]>;
+    protonsCount: number[];
+    hybridization: number[];
+}
+
+declare interface CorrelationAndLinkFields {
+    id: string;
+    pseudo: boolean;
+    edited: Record<string, boolean>;
+}
+
+declare interface CorrelationAndLinkOptions {
+    id?: string;
+    pseudo?: boolean;
+    edited?: Record<string, boolean>;
+}
+
+export declare namespace correlationApi {
+    export {
+        Correlation,
+        CorrelationBuildOptions,
+        CorrelationData,
+        CorrelationLink,
+        CorrelationState,
+        CorrelationTolerance,
+        CorrelationValues,
+        buildCorrelationData,
+        buildValues,
+        buildState,
+        addLink,
+        buildCorrelation,
+        buildLink,
+        removeLink,
+        setCorrelation,
+        checkMatch,
+        findLinkedCorrelationsBySignalID,
+        findLinksBySignalID,
+        getAtomCounts,
+        getAtomTypeFromNucleus,
+        getCorrelationDelta,
+        getCorrelationIndex,
+        getCorrelationsByAtomType,
+        getLabel,
+        getLabels,
+        getLinkDelta,
+        getLinkDim,
+        isEditedHSQC,
+        setPathLength
+    }
+}
+
+export declare interface CorrelationBuildOptions {
+    tolerance?: CorrelationTolerance;
+    mf?: string;
+    values?: CorrelationValues;
+    skipDataUpdate?: boolean;
+}
+
+export declare interface CorrelationData {
+    values: CorrelationValues;
+    options: CorrelationBuildOptions;
+    state: CorrelationState;
+}
+
+export declare interface CorrelationLink extends CorrelationAndLinkFields {
+    atomType: string[];
+    signal: Signal1D | Signal2D;
+    axis: string | undefined;
+    match: number[];
+    experimentLabel: string;
+    experimentType: string;
+    experimentID: string;
+}
+
+declare interface CorrelationOptions extends CorrelationAndLinkOptions {
+    atomType?: string;
+    label?: Record<string, string>;
+    link?: CorrelationLink[];
+    equivalence?: number;
+    attachment?: Record<string, number[]>;
+    protonsCount?: number[];
+    hybridization?: number[];
+}
+
+declare type CorrelationState = Record<string, StateAtomType>;
+
+export declare type CorrelationTolerance = Record<string, number>;
+
+export declare type CorrelationValues = Correlation[];
+
 export declare const couplingACSPatterns: string[];
 
 declare interface CouplingGroupInput {
@@ -685,6 +838,10 @@ export declare namespace Filters2DManager {
 
 declare type FilterSymbols = (typeof Filters)[keyof typeof Filters];
 
+declare function findLinkedCorrelationsBySignalID(correlations: CorrelationValues, signalID: string): Correlation[];
+
+declare function findLinksBySignalID(correlations: CorrelationValues, signalID: string): CorrelationLink[];
+
 /**
  * Look for a multiplet based on the pattern name or abbreviation.
  * @param name - pattern name or abbreviation.
@@ -880,8 +1037,21 @@ export declare interface GetAssignmentsOptions {
     };
 }
 
+/**
+ * Returns the number of atoms per atom type for a given molecular formula.
+ *
+ * @param {string} mf
+ */
+declare function getAtomCounts(mf: string): Record<string, number>;
+
 declare function getAtoms(a: AtomInput[]): AtomOutput[];
 
+/**
+ * Returns the atom type from nucleus.
+ * @param {string} nucleus
+ */
+declare function getAtomTypeFromNucleus(nucleus: string): string;
+
 export declare interface GetAutoAssignmentInput {
     spectra: SpectraData[];
     /**
@@ -917,6 +1087,24 @@ export declare function getBaselineZonesByDietrich(data: NmrData1D, options?: Ba
 
 declare function getBonds(b: BondInput[]): BondOutput[];
 
+declare function getCorrelationDelta(correlation: Correlation): number | undefined;
+
+/**
+ * Returns the array index of a correlation.
+ *
+ * @param correlations
+ * @param correlation
+ */
+declare function getCorrelationIndex(correlations: CorrelationValues, correlation: Correlation): number;
+
+/**
+ * Returns all correlations of a certain atom type.
+ *
+ * @param correlations
+ * @param atomType
+ */
+declare function getCorrelationsByAtomType(correlations: CorrelationValues, atomType: string): CorrelationValues;
+
 declare function getCouplingGroups(cg: CouplingGroupInput[]): {
     id: string;
     parentID: string;
@@ -961,8 +1149,16 @@ declare interface GetKernelOptions {
     yLength?: number;
 }
 
+declare function getLabel(correlations: CorrelationValues, correlation: Correlation): string;
+
+declare function getLabels(correlations: CorrelationValues, correlation: Correlation, experimentType: string): string[];
+
 declare function getLineShapes(l: LineShapeData[]): LineShapeResult[];
 
+declare function getLinkDelta(link: CorrelationLink): number | undefined;
+
+declare function getLinkDim(link: CorrelationLink): number;
+
 export declare function getPeakDelta(peak: Peak1D | NMRPeak1D, shiftTarget: ShiftTarget, shift: number): {
     originalX: number;
     x: number;
@@ -1047,6 +1243,8 @@ declare interface HOSEPrediction {
 
 declare type ID = string;
 
+declare function isEditedHSQC(experiment: Pick<Spectrum2D, 'info'>): boolean;
+
 export declare function isEmptyMolecule(molecule: Molecule): boolean;
 
 export declare function isMolfileNotEmpty(molFile?: string): molFile is string;
@@ -1105,6 +1303,16 @@ declare interface LineShapeResult {
     };
 }
 
+declare interface LinkOptions extends CorrelationAndLinkOptions {
+    atomType?: string[];
+    experimentType?: string;
+    experimentID?: string;
+    signal?: Signal1D | Signal2D;
+    axis?: string;
+    match?: number[];
+    experimentLabel?: string;
+}
+
 declare type MakeMandatory<T, K extends keyof T> = T & {
     [P in K]-?: T[P];
 };
@@ -2075,6 +2283,14 @@ export declare function reimComplexBackwardLinearPrediction(data: DataReIm, opti
     im: Float64Array<ArrayBuffer>;
 };
 
+/**
+ * Removes a link by id search.
+ *
+ * @param {Correlation} correlation
+ * @param {string} id
+ */
+declare function removeLink(correlation: Correlation, id: string): Correlation;
+
 declare interface RestrictionByCS {
     chemicalShiftRestriction: boolean;
     tolerance: Record<string, number>;
@@ -2111,6 +2327,17 @@ declare interface SelectAnchorOptions {
     windowSize?: number;
 }
 
+/**
+ * Searches for a correlation index by id in correlation data and replaces it with a given correlation.
+ *
+ * @param {CorrelationData} data
+ * @param {string} id
+ * @param {Correlation} correlation
+ */
+declare function setCorrelation(data: CorrelationData, id: string, correlation: Correlation): CorrelationData;
+
+declare function setPathLength(correlations: CorrelationValues, signalID: string, pathLength: number | FromTo | undefined): CorrelationValues;
+
 declare type Shift2DX = FilterFactory<Entry2D, Shift2DXOptions> & Pick<Shift2DXFilterOptions, 'name'>;
 
 declare type Shift2DXOptions = Shift2DXFilterOptions['value'];
@@ -2542,6 +2769,15 @@ export declare interface SplitSpinSystemOptions {
     maxClusterSize?: number;
 }
 
+declare interface StateAtomType {
+    current: number;
+    total?: number;
+    complete?: boolean;
+    error?: StateAtomTypeError;
+}
+
+declare type StateAtomTypeError = Record<string, boolean | number[]>;
+
 declare type SymmetrizeCosyLike = FilterFactory<Entry2D, Record<string, never>> & Pick<SymmetrizeCosyLikeOptions, 'name'>;
 
 declare class T1Regression extends BaseRegression {