nmr-processing 3.3.0 → 3.3.4

package/src/ranges/rangesToACS.ts

@@ -1,7 +1,7 @@
 import { signalJoinCouplings } from '../signal/signalJoinCouplings';
 import { signalMultiplicityPattern } from '../signal/signalMultiplicityPattern';
 import type { NMRRange } from '../types/NMRRange';
-import { NMRSignal1D } from '../types/NMRSignal1D';
+import type { NMRSignal1D } from '../types/NMRSignal1D';
 
 const globalOptions = {
   h: {

package/src/ranges/rangesToXY.ts

@@ -1,7 +1,7 @@
 import { DoubleArray } from 'cheminfo-types';
 import arraySequentialFill from 'ml-array-sequential-fill';
 import { SpectrumGenerator } from 'spectrum-generator';
-import type { Shape1DOption } from 'spectrum-generator';
+import type { Shape1DOptions } from 'spectrum-generator';
 
 import { hackSignalsToXY } from '../signals/hackSignalsToXY';
 import type { MakeMandatory } from '../types/MakeMandatory';
@@ -41,7 +41,7 @@ export interface RangeToXYOptions {
    * options of signals.
    * @default { kind: 'gaussian' }
    */
-  shape: Shape1DOption;
+  shape: Shape1DOptions;
 }
 function checkForSignals(
   ranges: NMRRange[],

package/src/signal/signalJoinCouplings.ts

@@ -1,8 +1,8 @@
 import sum from 'ml-array-sum';
 
 import type { MakeMandatory } from '../types/MakeMandatory';
-import { NMRSignal1D } from '../types/NMRSignal1D';
-import { Jcoupling } from '../types/jcoupling';
+import type { NMRSignal1D } from '../types/NMRSignal1D';
+import type { Jcoupling } from '../types/jcoupling';
 import { joinPatterns } from '../utilities/joinPatterns';
 
 export interface SignalJoinCouplingsOptions {
@@ -89,10 +89,10 @@ function groupJCouplings(
   signal.js = [];
   for (let group of groups) {
     let coupling = sum(group.map((group) => group.coupling)) / group.length;
-    let atomIDs = distinctValues(
+    let atoms = distinctValues(
       group
-        .filter((group) => group.atomIDs)
-        .map((group) => group.atomIDs)
+        .filter((group) => group.atoms)
+        .map((group) => group.atoms)
         .flat() as number[],
     ) as number[];
 
@@ -128,7 +128,7 @@ function groupJCouplings(
     if (diaIDs.length === 1) newJ.diaIDs = diaIDs;
     if (distances.length === 1 && distances[0]) newJ.distance = distances[0];
     if (assignment.length > 0) newJ.assignment = assignment;
-    if (atomIDs.length > 0) newJ.atomIDs = atomIDs;
+    if (atoms.length > 0) newJ.atoms = atoms;
     signal.js.push(newJ);
   }
   return signal;

package/src/signals/hackSignalsToXY.ts

@@ -1,6 +1,6 @@
 import { couplingPatterns } from '../constants/couplingPatterns';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
-import { Jcoupling } from '../types/jcoupling';
+import type { Jcoupling } from '../types/jcoupling';
 
 import { OptionsSignalsToXY, signalsToXY } from './signalsToXY';
 
@@ -16,7 +16,7 @@ export function hackSignalsToXY(
   let newSignals = JSON.parse(JSON.stringify(signals));
 
   signals.forEach((signal, s) => {
-    const { js: jCouplings = [], atomIDs: signalAssignment = [s] } = signal;
+    const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
 
     let { newCouplings, tempSignals } = checkCouplings(
       jCouplings,
@@ -27,7 +27,7 @@ export function hackSignalsToXY(
     if (tempSignals.length > 0) newSignals.push(...tempSignals);
 
     newSignals[s].js = newCouplings;
-    newSignals[s].atomIDs = signalAssignment;
+    newSignals[s].atoms = signalAssignment;
   });
 
   return signalsToXY(newSignals, options);
@@ -42,8 +42,8 @@ function checkCouplings(
   let tempSignals: NMRSignal1D[] = [];
   const newCouplings = jCouplings.reduce<Jcoupling[]>(
     (newCouplings, jCoupling) => {
-      const { atomIDs = [], multiplicity, coupling } = jCoupling;
-      if (atomIDs.length === 0) {
+      const { atoms = [], multiplicity, coupling } = jCoupling;
+      if (atoms.length === 0) {
         if (coupling && multiplicity) {
           let tempCouplings: Jcoupling[] = [];
           const nbLinks = couplingPatterns.indexOf(multiplicity);
@@ -51,7 +51,7 @@ function checkCouplings(
             newSignalAssignment++;
             tempCouplings.push({
               coupling,
-              atomIDs: [newSignalAssignment],
+              atoms: [newSignalAssignment],
             });
             tempSignals.push(
               formatSignal(coupling, [newSignalAssignment], signalAssignment),
@@ -75,11 +75,11 @@ function formatSignal(
 ) {
   return {
     delta: 100000,
-    atomIDs: newSignalAssignment,
+    atoms: newSignalAssignment,
     js: [
       {
         coupling,
-        atomIDs: signalAssignment,
+        atoms: signalAssignment,
       },
     ],
   };

package/src/signals/signals2DToZ.ts

@@ -51,7 +51,6 @@ export function signals2DToZ(
   );
 
   width = ensureXYNumber(width);
-
   return generateSpectrum2D(peaks, {
     generator: {
       from: ensureXYNumber(from),

package/src/signals/signalsJoin.ts

@@ -95,7 +95,7 @@ export function signalsJoin(
       nbAtoms: sum(group.map((item) => item.nbAtoms || 0)),
       delta: mean(group.map((item) => item.delta)),
       diaIDs: group[0].diaIDs,
-      atomIDs: group.map((item) => item.atomIDs || []).flat(),
+      atoms: group.map((item) => item.atoms || []).flat(),
       js,
     };
 

package/src/signals/signalsToRanges.ts

@@ -1,4 +1,4 @@
-import { MakeMandatory } from '../types/MakeMandatory';
+import type { MakeMandatory } from '../types/MakeMandatory';
 import type { NMRRange } from '../types/NMRRange';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
 import { rangeFromSignal } from '../utilities/rangeFromSignal';

package/src/signals/signalsToXY.ts

@@ -1,10 +1,10 @@
 import rescale from 'ml-array-rescale';
 import arraySequentialFill from 'ml-array-sequential-fill';
-import type { Shape1DOption } from 'spectrum-generator';
+import type { Shape1DOptions } from 'spectrum-generator';
 
-import { MakeMandatory } from '../types/MakeMandatory';
+import type { MakeMandatory } from '../types/MakeMandatory';
 import type { NMRSignal1D } from '../types/NMRSignal1D';
-import { Jcoupling } from '../types/jcoupling';
+import type { Jcoupling } from '../types/jcoupling';
 
 import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
 import simulate1D from './simulation/simulate1D';
@@ -25,7 +25,7 @@ export interface OptionsSignalsToXY {
   /**
    * Shape options for ml-spectrum-generator
    */
-  shape?: Shape1DOption;
+  shape?: Shape1DOptions;
   /**
    * The linewidth of the output spectrum, expresed in Hz.
    * @default 1
@@ -49,7 +49,7 @@ export interface OptionsSignalsToXY {
 }
 
 type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'distance'>;
-type Signal1DWidthAtomsIDsAndDiaID = MakeMandatory<NMRSignal1D, 'atomIDs'>;
+type Signal1DWidthAtomsIDsAndDiaID = MakeMandatory<NMRSignal1D, 'atoms'>;
 type Signal1DWidthJsAndDiaID = Omit<Signal1DWidthAtomsIDsAndDiaID, 'js'> & {
   js: JcouplingFromPrediction[];
 };
@@ -60,10 +60,10 @@ function checkForMandatory(
   for (const signal of signals) {
     if (!signal.js) throw new Error('There is not js');
     // if (!signal.diaID) throw new Error('There is not diaID');
-    if (!signal.atomIDs) throw new Error('There is not atomIDs');
+    if (!signal.atoms) throw new Error('There is not atoms');
     for (const j of signal.js) {
       // if (!j.diaID) throw new Error('There is not diaID');
-      if (!j.atomIDs) throw new Error('There is not atomIDs');
+      if (!j.atoms) throw new Error('There is not atoms');
     }
   }
 }

package/src/signals/simulation/signalsToSpinSystem.ts

@@ -1,17 +1,17 @@
 import { Matrix } from 'ml-matrix';
 import simpleClustering from 'ml-simple-clustering';
 
-import { MakeMandatory } from '../../types/MakeMandatory';
+import type { MakeMandatory } from '../../types/MakeMandatory';
 import type { NMRSignal1D } from '../../types/NMRSignal1D';
-import { Jcoupling } from '../../types/jcoupling';
+import type { Jcoupling } from '../../types/jcoupling';
 import type { SpinSystem } from '../../types/spinSystem';
 
 interface Ids {
   [index: number]: number;
 }
 
-type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'atomIDs'>;
-type Signal1DWidthAtomIDs = MakeMandatory<NMRSignal1D, 'atomIDs'>;
+type JcouplingFromPrediction = MakeMandatory<Jcoupling, 'atoms'>;
+type Signal1DWidthAtomIDs = MakeMandatory<NMRSignal1D, 'atoms'>;
 type Signal1DFromPrediction = Omit<Signal1DWidthAtomIDs, 'js'> & {
   js: JcouplingFromPrediction[];
 };
@@ -21,9 +21,9 @@ function checkForMandatory(
 ): asserts signals is Signal1DFromPrediction[] {
   for (const signal of signals) {
     if (!signal.js) throw new Error('there is not js');
-    if (!signal.atomIDs) throw new Error('there is not atomIDs');
+    if (!signal.atoms) throw new Error('there is not atoms');
     for (const jcoupling of signal.js) {
-      if (!jcoupling.atomIDs) throw new Error('there is not atomIDs');
+      if (!jcoupling.atoms) throw new Error('there is not atoms');
     }
   }
 }
@@ -39,16 +39,16 @@ export function signalsToSpinSystem(signals: NMRSignal1D[]): SpinSystem {
   for (let i = 0; i < nSpins; i++) {
     multiplicity[i] = 2;
     chemicalShifts[i] = signals[i].delta;
-    const index = signals[i].atomIDs[0];
+    const index = signals[i].atoms[0];
     ids[index] = i;
   }
   //create the coupling matrix
   for (let i = 0; i < nSpins; i++) {
-    let { atomIDs: signalAssignment, js: jCoupling } = signals[i];
+    let { atoms: signalAssignment, js: jCoupling } = signals[i];
     const fromIndex = signalAssignment[0];
     for (const jcoupling of jCoupling) {
-      let { coupling, atomIDs } = jcoupling;
-      const toIndex = atomIDs[0];
+      let { coupling, atoms } = jcoupling;
+      const toIndex = atoms[0];
       couplingConstants.set(ids[fromIndex], ids[toIndex], coupling);
       couplingConstants.set(ids[toIndex], ids[fromIndex], coupling);
     }

package/src/signals/simulation/simulate1D.ts

@@ -3,9 +3,9 @@ import { Matrix, EVD } from 'ml-matrix';
 import type { Matrix as MatrixClassType } from 'ml-matrix';
 import { SparseMatrix } from 'ml-sparse-matrix';
 import { SpectrumGenerator } from 'spectrum-generator';
-import type { Shape1DOption } from 'spectrum-generator';
+import type { Shape1DOptions } from 'spectrum-generator';
 
-import { SpinSystem } from '../../types/spinSystem';
+import type { SpinSystem } from '../../types/spinSystem';
 
 import getPauliMatrix from './getPauliMatrix';
 
@@ -46,7 +46,7 @@ interface Simulate1DOptions {
    * Shape options
    * @default {kind:'gaussian'}
    */
-  shape?: Shape1DOption;
+  shape?: Shape1DOptions;
 }
 
 /**

package/src/types/{NMRSignal1D.d.ts → NMRSignal1D.ts}

@@ -1,17 +1,17 @@
+import type { NMRPeak1D } from './NMRPeak1D';
 import type { Jcoupling } from './jcoupling';
-import { GSDPeak } from './ml-gsd/index.d';
 
-interface NMRSignal1D {
+export interface NMRSignal1D {
   delta: number;
   js?: Jcoupling[];
-  atomIDs?: number[];
+  atoms?: number[];
   assignment?: string;
   kind?: string;
   multiplicity?: string;
   diaIDs?: string[];
   nbAtoms?: number;
   integration?: number;
-  peaks?: GSDPeak[];
+  peaks?: NMRPeak1D[];
   statistic?: {
     mean: number;
     sd: number;

package/src/types/{NMRSignal2D.d.ts → NMRSignal2D.ts}

@@ -4,7 +4,7 @@ export interface Signal2DAxisData {
   nucleus?: string;
   delta: number;
   resolution?: number;
-  atomIDs?: number[];
+  atoms?: number[];
   diaIDs?: string[];
   fromTo?: {
     from: number;
@@ -15,5 +15,6 @@ export interface NMRSignal2D {
   x: Signal2DAxisData;
   y: Signal2DAxisData;
   peaks?: MPFPeak[];
+  kind?: string;
   _highlight?: (number | string)[];
 }

package/src/types/{NMRZone.d.ts → NMRZone.ts}

@@ -1,4 +1,4 @@
-import { NMRSignal2D } from "./NMRSignal2D";
+import type { NMRSignal2D } from "./NMRSignal2D";
 
 interface fromTo { from: number, to: number }
 

package/src/types/{jcoupling.d.ts → jcoupling.ts}

@@ -1,6 +1,6 @@
 export interface Jcoupling {
   coupling: number;
-  atomIDs?: number[];
+  atoms?: number[];
   assignment?: string | string[];
   diaIDs?: string[];
   multiplicity?: string;

package/src/types/{nmrAssigment.d.ts → nmrAssigment.ts}

@@ -1,7 +1,7 @@
 import { Molecule } from 'openchemlib';
 
 import type { NMRRange } from './NMRRange';
-import { NMRZone } from './NMRZone';
+import type { NMRZone } from './NMRZone';
 
 export interface NMRAssignmentType {
   /**

package/src/xyz/xyzAutoPeaksPicking.ts

@@ -7,7 +7,7 @@ import { determineRealTop } from '../peaks/util/determineRealTop';
 import { getKernel } from '../peaks/util/getKernel';
 import type { GetKernelOptions } from '../peaks/util/getKernel';
 import * as PeakOptimizer from '../peaks/util/peakOptimizer';
-import { MPFPeak } from '../types/MPFPeak';
+import type { MPFPeak } from '../types/MPFPeak';
 import type { NMRSignal2D } from '../types/NMRSignal2D';
 
 const smallFilter = [

package/src/xyz/xyzJResAnalyzer.ts

@@ -2,8 +2,8 @@ import simpleClustering from 'ml-simple-clustering';
 
 import type { JAxisKeys } from '../peaks/util/jAnalyzer';
 import jAnalyzer from '../peaks/util/jAnalyzer';
-import { MPFPeak } from '../types/MPFPeak';
-import { MakeMandatory } from '../types/MakeMandatory';
+import type { MPFPeak } from '../types/MPFPeak';
+import type { MakeMandatory } from '../types/MakeMandatory';
 import type { NMRSignal2D } from '../types/NMRSignal2D';
 
 interface CompilePatternOptions {

package/src/types/jest.d.ts

@@ -1,15 +0,0 @@
-declare namespace jest {
-  type Iterable =
-    | number
-    | Iterable[]
-    | { [k: string]: Iterable }
-    | string
-    | null
-    | undefined
-    | boolean;
-
-  interface Matchers<R> {
-    toBeDeepCloseTo: (expected: Iterable, decimals?: number) => R;
-    toMatchCloseTo: (expected: Iterable, decimals?: number) => R;
-  }
-}