nmr-processing 9.8.1 → 9.9.0

package/src/datum/Filters.ts

@@ -9,10 +9,10 @@ import * as phaseCorrection from './data1d/filter1d/phaseCorrection';
 import * as shiftX from './data1d/filter1d/shiftX';
 import * as signalProcessing from './data1d/filter1d/signalProcessing';
 import * as zeroFilling from './data1d/filter1d/zeroFilling';
-import * as shift2DX from './data2d/filter2d/shiftX';
-import * as shift2DY from './data2d/filter2d/shiftY';
 import * as fftDimension1 from './data2d/filter2d/fftDimension1';
 import * as fftDimension2 from './data2d/filter2d/fftDimension2';
+import * as shift2DX from './data2d/filter2d/shiftX';
+import * as shift2DY from './data2d/filter2d/shiftY';
 
 export type { ApodizationOptions } from './data1d/filter1d/apodization/apodization';
 export type {

package/src/datum/data1d/utils/getShiftX.ts

@@ -2,9 +2,9 @@ import { Filters } from '../../Filters';
 import { Entry1D } from '../Entry1D';
 
 export function getShiftX(spectrum: Entry1D): number {
-  const filter =
-    spectrum?.filters &&
-    spectrum?.filters.find((filter) => filter.name === Filters.shiftX.id);
+  const filter = spectrum?.filters?.find(
+    (filter) => filter.name === Filters.shiftX.id,
+  );
 
   return filter?.flag ? filter.value.shift : 0;
 }

package/src/datum/data2d/filter2d/fftDimension1.ts

@@ -1,17 +1,18 @@
 import { DoubleArray, NmrData2DFid } from 'cheminfo-types';
-import { FilterDomainUpdateRules } from '../../FiltersManager';
-import { Entry2D } from '../Entry2D';
-import {
-  DirectDimensionOptions,
-  fftDirectDimension,
-} from '../../../xyz/util/fft2d/fftDirectDimension';
 import {
   xAdd,
   xEnsureFloat64,
   xMultiply,
   xSubtract,
 } from 'ml-spectra-processing';
+
 import { Data2DFidComplete } from '../../../utilities/checkData2DFid';
+import {
+  DirectDimensionOptions,
+  fftDirectDimension,
+} from '../../../xyz/util/fft2d/fftDirectDimension';
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry2D } from '../Entry2D';
 
 export const id = 'fftDimension1';
 export const name = 'FFT Dimension 1';
@@ -26,7 +27,6 @@ export function apply(datum2D: Entry2D, options: DirectDimensionOptions) {
     throw new Error('fft dimension 1 not applicable on this data');
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-unused-vars
   const { data, info } = datum2D;
   const { digitalFilter: digitalFilterValue = 0 } = info;
 

package/src/datum/data2d/filter2d/fftDimension2.ts

@@ -1,13 +1,14 @@
 import { NmrData2DFid, NmrData2DFt } from 'cheminfo-types';
-import { FilterDomainUpdateRules } from '../../FiltersManager';
-import { Entry2D } from '../Entry2D';
+import Matrix from 'ml-matrix';
+import { xEnsureFloat64 } from 'ml-spectra-processing';
+
 import {
   IndirectDimensionOptions,
   fftIndirectDimension,
 } from '../../../xyz/util/fft2d/fftIndirectDimension';
-import { xEnsureFloat64 } from 'ml-spectra-processing';
 import { getMinMaxXY } from '../../../xyz/util/getMinMaxXY';
-import Matrix from 'ml-matrix';
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry2D } from '../Entry2D';
 
 export const id = 'fftDimension2';
 export const name = 'FFT Dimension 2';

package/src/datum/data2d/filter2d/shiftX.ts

@@ -11,17 +11,15 @@ export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
   updateYDomain: false,
 };
 
-/**
- *
- * @param {Object} datum2d
- * @param {number} [shiftValue=0]
- */
-
-export function apply(datum2D: Entry2D, shiftValue = 0) {
+interface Shift2DXOptions {
+  shift: number;
+}
+export function apply(datum2D: Entry2D, options: Shift2DXOptions) {
+  const { shift } = options;
   const data: Record<string, NmrData2DContent> = { ...datum2D.data };
   for (const key in data) {
-    data[key].minX += shiftValue;
-    data[key].maxX += shiftValue;
+    data[key].minX += shift;
+    data[key].maxX += shift;
   }
 }
 
@@ -29,9 +27,12 @@ export function isApplicable() {
   return true;
 }
 
-export function reduce(previousValue: number, newValue: number) {
+export function reduce(previous: Shift2DXOptions, next: Shift2DXOptions) {
+  const { shift: previousValue = 0 } = previous;
+  const { shift: nextShift } = next;
+
   return {
     once: true,
-    reduce: previousValue + newValue,
+    reduce: previousValue + nextShift,
   };
 }

package/src/datum/data2d/filter2d/shiftY.ts

@@ -11,16 +11,16 @@ export const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules> = {
   updateYDomain: true,
 };
 
-/**
- *
- * @param {Object} datum2d
- * @param {number} [shiftValue=0]
- */
-export function apply(datum2D: Entry2D, shiftValue = 0) {
+interface Shift2DYOptions {
+  shift: number;
+}
+
+export function apply(datum2D: Entry2D, options: Shift2DYOptions) {
+  const { shift } = options;
   const data: Record<string, NmrData2DContent> = { ...datum2D.data };
   for (const key in data) {
-    data[key].minY += shiftValue;
-    data[key].maxY += shiftValue;
+    data[key].minY += shift;
+    data[key].maxY += shift;
   }
 }
 
@@ -28,9 +28,11 @@ export function isApplicable() {
   return true;
 }
 
-export function reduce(previousValue: number, newValue: number) {
+export function reduce(previous: Shift2DYOptions, next: Shift2DYOptions) {
+  const { shift: previousValue = 0 } = previous;
+  const { shift: nextShift } = next;
   return {
     once: true,
-    reduce: previousValue + newValue,
+    reduce: previousValue + nextShift,
   };
 }

package/src/openchemlib-utils.d.ts

@@ -1,5 +1,5 @@
 declare module 'openchemlib-utils' {
-  import { Molecule } from 'openchemlib/full';
+  import type { Molecule } from 'openchemlib/full';
 
   export interface GroupDiastereotopicAtomIDs {
     counter: number;
@@ -38,7 +38,7 @@ declare module 'openchemlib-utils' {
     options: GetHoseCodesForAtomOptions,
   ): string[];
 
-  function addDiastereotopicMissingChirality(molecule: Molecule): Molecule;
+  function ensureHeterotopicChiralBonds(molecule: Molecule): Molecule;
 
   export interface GetPathsInfoOptions {
     fromLabel?: string;

package/src/prediction/Prediction2D.ts

@@ -1,4 +1,4 @@
-import { Molecule } from 'openchemlib/full';
+import type { Molecule } from 'openchemlib/full';
 
 import { NMRSignal2D } from '../xyz/NMRSignal2D';
 import { NMRZone } from '../xyz/NMRZone';

package/src/prediction/predictAll.ts

@@ -72,10 +72,9 @@ export async function predictAll(
   } = options;
 
   const diaIDs = getDiastereotopicAtomIDs(molecule);
-
   let { predictions } = options;
 
-  const xPrediction = await getPredictions(
+  const protonPrediction = await getPredictions(
     'H',
     molecule,
     predictOptions,
@@ -83,7 +82,7 @@ export async function predictAll(
     predictions,
   );
 
-  const yPrediction = await getPredictions(
+  const carbonPrediction = await getPredictions(
     'C',
     molecule,
     predictOptions,
@@ -91,23 +90,23 @@ export async function predictAll(
     predictions,
   );
 
-  if (!xPrediction || !yPrediction) {
+  if (!protonPrediction || !carbonPrediction) {
     throw new Error('predictions are not availaible');
   }
 
   const spectra: any = {};
-  if (check1DPrediction(xPrediction)) {
-    spectra.proton = xPrediction;
+  if (check1DPrediction(protonPrediction)) {
+    spectra.proton = protonPrediction;
   }
-  if (check1DPrediction(yPrediction)) {
-    spectra.carbon = yPrediction;
+  if (check1DPrediction(carbonPrediction)) {
+    spectra.carbon = carbonPrediction;
   }
 
-  const { molfile } = xPrediction;
+  const { molfile } = protonPrediction;
 
   predictions = {
-    H: xPrediction,
-    C: yPrediction,
+    H: protonPrediction,
+    C: carbonPrediction,
   };
 
   if (spectra.proton) {

package/src/prediction/predictCOSY.ts

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

package/src/prediction/predictHMBC.ts

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

package/src/prediction/predictHSQC.ts

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

package/src/prediction/predictProton.ts

@@ -3,7 +3,7 @@ import fetch from 'cross-fetch';
 import FormData from 'form-data';
 import type { Molecule } from 'openchemlib/full';
 import {
-  addDiastereotopicMissingChirality,
+  ensureHeterotopicChiralBonds,
   getConnectivityMatrix,
   getDiastereotopicAtomIDs,
 } from 'openchemlib-utils';
@@ -51,7 +51,7 @@ export async function predictProton(
   const { cache } = options;
   molecule = molecule.getCompactCopy();
   molecule.addImplicitHydrogens();
-  addDiastereotopicMissingChirality(molecule);
+  ensureHeterotopicChiralBonds(molecule);
   const molfile = molecule.toMolfile();
 
   let result;

package/src/prediction/utils/fetchPrediction.ts

@@ -1,5 +1,5 @@
 import { fetch } from 'cross-fetch';
-import { Molecule } from 'openchemlib/full';
+import type { Molecule } from 'openchemlib/full';
 
 import type { Prediction1D } from '../Prediction1D';
 

package/src/prediction/utils/getFilteredIDiaIDs.ts

@@ -1,7 +1,7 @@
 import type { Molecule } from 'openchemlib/full';
 import {
   getHoseCodesFromDiastereotopicID,
-  addDiastereotopicMissingChirality,
+  ensureHeterotopicChiralBonds,
   groupDiastereotopicAtomIDs,
 } from 'openchemlib-utils';
 import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
@@ -20,7 +20,7 @@ export function getFilteredIDiaIDs(
 
   molecule.addImplicitHydrogens();
   molecule.addMissingChirality();
-  addDiastereotopicMissingChirality(molecule);
+  ensureHeterotopicChiralBonds(molecule);
 
   const molfile = molecule.toMolfile();
 

package/src/prediction/utils/isEmptyMolecule.ts

@@ -1,4 +1,4 @@
-import { Molecule } from 'openchemlib/full';
+import type { Molecule } from 'openchemlib/full';
 
 export function isEmptyMolecule(molecule: Molecule) {
   return molecule.getAllAtoms() < 1;

package/src/prediction/utils/predict2D.ts

@@ -1,7 +1,7 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import { agnes, Cluster } from 'ml-hclust';
 import { Matrix } from 'ml-matrix';
-import { Molecule } from 'openchemlib/full';
+import type { Molecule } from 'openchemlib/full';
 import {
   getGroupedDiastereotopicAtomIDs,
   getPathsInfo,

package/src/utilities/resurrectRange.ts

@@ -14,7 +14,7 @@ export function resurrectRange(part: string, options: any = {}) {
     split.before,
   );
 
-  if (!beforeMatch || !beforeMatch.groups) return;
+  if (!beforeMatch?.groups) return;
 
   const isARange = beforeMatch.groups.to !== '';
 

package/src/xyz/util/phaseCorrection/applyOverImag.ts

@@ -1,8 +1,10 @@
 import { NmrData2DFt } from 'cheminfo-types';
-import { PhaseCorrectionOptions } from '../../xyzPhaseCorrectionDirectDimension';
-import { getZMinMax } from './getZMinMax';
 import Matrix from 'ml-matrix';
+
+import { PhaseCorrectionOptions } from '../../xyzPhaseCorrectionDirectDimension';
+
 import { checkNmrData2DFourQuad } from './checkNmrData2DFourQuad';
+import { getZMinMax } from './getZMinMax';
 
 export function applyOverImag<T extends NmrData2DFt>(
   data: T,

package/src/xyz/util/phaseCorrection/applyOverReal.ts

@@ -1,9 +1,11 @@
 import { NmrData2DFt } from 'cheminfo-types';
-import { checkNmrData2DTwoQuad } from './checkNmrData2DTwoQuad';
 import Matrix from 'ml-matrix';
-import { getZMinMax } from './getZMinMax';
+
 import { PhaseCorrectionOptions } from '../../xyzPhaseCorrectionDirectDimension';
 
+import { checkNmrData2DTwoQuad } from './checkNmrData2DTwoQuad';
+import { getZMinMax } from './getZMinMax';
+
 export function applyOverReal<T extends NmrData2DFt>(
   data: T,
   options: PhaseCorrectionOptions,

package/src/xyz/xyzPhaseCorrectionDirectDimension.ts

@@ -1,7 +1,9 @@
 import { NmrData2DFt } from 'cheminfo-types';
-import { degreeToRadians } from '../constants/degreeToRadians';
 import Matrix from 'ml-matrix';
 import { reimPhaseCorrection } from 'ml-spectra-processing';
+
+import { degreeToRadians } from '../constants/degreeToRadians';
+
 import { applyOverImag } from './util/phaseCorrection/applyOverImag';
 import { applyOverReal } from './util/phaseCorrection/applyOverReal';
 

package/src/xyz/xyzPhaseCorrectionIndirectDimension.ts

@@ -1,10 +1,12 @@
 import { NmrData2DFt } from 'cheminfo-types';
-import { degreeToRadians } from '../constants/degreeToRadians';
 import Matrix from 'ml-matrix';
 import { reimPhaseCorrection } from 'ml-spectra-processing';
+
+import { degreeToRadians } from '../constants/degreeToRadians';
+
 import { applyOverImag } from './util/phaseCorrection/applyOverImag';
-import { PhaseCorrectionOptions } from './xyzPhaseCorrectionDirectDimension';
 import { applyOverReal } from './util/phaseCorrection/applyOverReal';
+import { PhaseCorrectionOptions } from './xyzPhaseCorrectionDirectDimension';
 
 export type PhaseCorrectionIndirectDimensionOptions = PhaseCorrectionOptions & {
   quad: 'imag' | 'real';