nmr-processing 9.3.0 → 9.3.1-pre.1669649322

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.3.0",
+  "version": "9.3.1-pre.1669649322",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -38,20 +38,20 @@
   },
   "homepage": "https://github.com/cheminfo/nmr-processing#readme",
   "devDependencies": {
-    "@types/jest": "^29.2.2",
+    "@types/jest": "^29.2.3",
     "cheminfo-build": "^1.1.11",
     "cheminfo-types": "^1.4.0",
-    "eslint": "^8.27.0",
+    "eslint": "^8.28.0",
     "eslint-config-cheminfo-typescript": "^11.2.2",
     "jest": "^29.3.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "nmr-xy-testdata": "^0.5.1",
     "openchemlib": "^8.0.1",
-    "prettier": "^2.7.1",
+    "prettier": "^2.8.0",
     "rimraf": "^3.0.2",
     "ts-jest": "^29.0.3",
-    "typescript": "^4.8.4"
+    "typescript": "^4.9.3"
   },
   "dependencies": {
     "@lukeed/uuid": "^2.0.0",
@@ -77,7 +77,7 @@
     "ml-spectra-processing": "^11.14.0",
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.3.3",
-    "openchemlib-utils": "^2.0.0",
-    "spectrum-generator": "^8.0.4"
+    "openchemlib-utils": "2.1.1-pre.1669644163",
+    "spectrum-generator": "^8.0.6"
   }
 }

package/src/assignment/get13CAssignments.ts

@@ -1,5 +1,5 @@
 import { v4 as generateID } from '@lukeed/uuid';
-import { Molecule } from 'openchemlib';
+import { Molecule } from 'openchemlib/full';
 import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
 
 import { NMRRange, NMRRangeWithIntegration } from '..';

package/src/assignment/get1HAssignments.ts

@@ -1,5 +1,5 @@
 import { v4 as generateID } from '@lukeed/uuid';
-import { Molecule } from 'openchemlib';
+import { Molecule } from 'openchemlib/full';
 import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
 
 import { NMRRange } from '..';

package/src/assignment/getAssignments.ts

@@ -1,4 +1,4 @@
-import { Molecule } from 'openchemlib';
+import { Molecule } from 'openchemlib/full';
 import { addDiastereotopicMissingChirality } from 'openchemlib-utils';
 
 import { NMRSignal1D } from '..';

package/src/assignment/utils/getAssignment/buildAssignments.ts

@@ -1,6 +1,6 @@
 import TreeSet from 'ml-tree-set';
 import { Values } from 'nmr-correlation';
-import { Molecule } from 'openchemlib';
+import { Molecule } from 'openchemlib/full';
 import { getConnectivityMatrix } from 'openchemlib-utils';
 
 import {

package/src/openchemlib-utils.d.ts

@@ -1,5 +1,5 @@
 declare module 'openchemlib-utils' {
-  import { Molecule } from 'openchemlib';
+  import { Molecule } from 'openchemlib/full';
 
   export interface GroupDiastereotopicAtomIDs {
     counter: number;
@@ -7,10 +7,13 @@ declare module 'openchemlib-utils' {
     oclID: string;
     atomLabel: string;
   }
+
   export type GroupedDiastereotopicAtomIDs = GroupDiastereotopicAtomIDs[];
   function getGroupedDiastereotopicAtomIDs(
     molecule: Molecule,
+    options?: { atomLabel: string }
   ): GroupedDiastereotopicAtomIDs;
+
   interface GetHoseCodesForAtomOptions {
     minSphereSize?: number;
     maxSphereSize?: number;
@@ -155,4 +158,6 @@ declare module 'openchemlib-utils' {
   ): number[][] | Float64Array[];
 
   function getDiastereotopicAtomIDs(molecule: Molecule): string[];
+
+  function groupDiasterotopicAtomIDs(diaIDs: string[], molecule: Molecule, options?: { atomLabel: string }): GroupedDiastereotopicAtomIDs
 }

package/src/peaks/peaksToRanges.ts

@@ -206,17 +206,7 @@ export function peaksToRanges(
       }
     }
     // it was a updateIntegrals function.
-    let sumIntegral = 0;
-    let sumObserved = 0;
-    for (const signal of signals) {
-      sumObserved += Math.abs(Math.round(signal.integralData.value));
-    }
-    if (sumObserved !== integrationSum) {
-      sumIntegral = integrationSum / sumObserved;
-      for (const signal of signals) {
-        signal.integralData.value *= sumIntegral;
-      }
-    }
+    updateIntegration(signals, integrationSum);
   }
 
   signals.sort((a, b) => {
@@ -230,6 +220,7 @@ export function peaksToRanges(
       }
     }
   }
+
   let ranges: NMRRange[] = [];
   for (let i = 0; i < signals.length; i++) {
     let signal = signals[i];
@@ -243,7 +234,6 @@ export function peaksToRanges(
       delta: signal.delta,
       kind: signal.kind || 'signal',
       multiplicity: signal.multiplicity,
-      integration: signal.integralData.value,
     };
     if (keepPeaks) {
       signalResult.peaks = signal.peaks.map((peak) => {
@@ -299,7 +289,7 @@ export function detectSignals(
   let peaks;
   let signals = [];
   let prevPeak = { x: Number.MIN_SAFE_INTEGER };
-  let spectrumIntegral = 0;
+
   frequencyCluster /= frequency;
   for (const peak of peakList) {
     if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
@@ -349,15 +339,10 @@ export function detectSignals(
     } else {
       integration.value = integralPeaks;
     }
-    spectrumIntegral += integration.value;
   }
 
   if (integrationSum > 0) {
-    let integralFactor = integrationSum / spectrumIntegral;
-    for (let signal of signals) {
-      let integration = signal.integralData;
-      integration.value *= integralFactor;
-    }
+    updateIntegration(signals, integrationSum);
   }
 
   return signals;
@@ -370,3 +355,22 @@ export function detectSignals(
 function computeArea(peak: Peak1DIntern, frequency: number) {
   return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
 }
+
+/**
+ * update the integration Values
+ * @param signals
+ * @param integrationSum
+ */
+function updateIntegration(signals: SignalIntern[], integrationSum: number) {
+  let sumIntegral = 0;
+  let sumObserved = 0;
+  for (const signal of signals) {
+    sumObserved += Math.abs(Math.round(signal.integralData.value));
+  }
+  if (sumObserved !== integrationSum) {
+    sumIntegral = integrationSum / sumObserved;
+    for (const signal of signals) {
+      signal.integralData.value *= sumIntegral;
+    }
+  }
+}

package/src/prediction/Prediction1D.ts

@@ -1,4 +1,4 @@
-import type { Molecule } from 'openchemlib';
+import type { Molecule } from 'openchemlib/full';
 
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import type { NMRRange } from '../xy/NMRRange';

package/src/prediction/predictAll.ts

@@ -1,5 +1,5 @@
-import type { Molecule } from 'openchemlib';
-
+import type { Molecule } from 'openchemlib/full';
+import { getDiastereotopicAtomIDs, getGroupedDiastereotopicAtomIDs } from 'openchemlib-utils';
 import type { Prediction1D } from './Prediction1D';
 import { predictCOSY } from './predictCOSY';
 import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
@@ -75,6 +75,8 @@ export async function predictAll(
     predictOptions = {},
   } = options;
 
+  const diaIDs = getDiastereotopicAtomIDs(molecule);
+  console.log('entra correction')
   const xPrediction = await getPredictions(
     from,
     molecule,
@@ -100,7 +102,7 @@ export async function predictAll(
     C: yPrediction,
   };
 
-  const { molfile, diaIDs } = xPrediction;
+  const { molfile } = xPrediction;
 
   const spectra: any = {
     proton: predictions.H,

package/src/prediction/predictAllSpectra.ts

@@ -1,5 +1,5 @@
 import { FromTo, PointXY } from 'cheminfo-types';
-import type { Molecule } from 'openchemlib';
+import type { Molecule } from 'openchemlib/full';
 
 import { signals2DToZ } from '../signals/signals2DToZ';
 import { OptionsSignalsToXY, signalsToXY } from '../signals/signalsToXY';

package/src/prediction/predictCOSY.ts

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

package/src/prediction/predictCarbon.ts

@@ -1,6 +1,6 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import fetch from 'cross-fetch';
-import type { Molecule } from 'openchemlib';
+import type { Molecule } from 'openchemlib/full';
 
 import { setIDs } from '../peaks/util/setIDs';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
@@ -13,6 +13,7 @@ import { fetchPrediction } from './utils/fetchPrediction';
 import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
 import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';
 import { Prediction, queryByHose } from './utils/queryByHOSE';
+import { getDiastereotopicAtomIDs } from 'openchemlib-utils';
 
 const cache: { [key: string]: DataBaseStructure } = {};
 
@@ -48,6 +49,10 @@ export interface PredictCarbonOptions {
    * @default 'maximum level in the database'
    */
   maxSphereSize?: number;
+  /**
+   * diastereotopic atom ids.
+   */
+  diaIDs?: string[];
 }
 
 export type PredictCarbon = typeof predictCarbon;
@@ -72,7 +77,12 @@ export async function predictCarbon(
   molecule: Molecule,
   options: PredictCarbonOptions = {},
 ): Promise<Prediction1D> {
-  let { url, database, webserviceURL } = options;
+  let {
+    url,
+    database,
+    webserviceURL,
+    diaIDs = getDiastereotopicAtomIDs(molecule),
+  } = options;
 
   if (webserviceURL) {
     return fetchPrediction(molecule, { webserviceURL });
@@ -90,12 +100,10 @@ export async function predictCarbon(
 
   if (maxSphereSize > maxLevel) maxSphereSize = maxLevel;
 
-  const { groupedDiaIDs, carbonDiaIDs, molfile } = getFilteredIDiaIDs(
-    molecule,
-    {
-      maxSphereSize,
-    },
-  );
+  const { carbonDiaIDs, molfile } = getFilteredIDiaIDs(molecule, {
+    maxSphereSize,
+    diaIDs,
+  });
 
   let predictions = queryByHose(carbonDiaIDs, database, {
     maxSphereSize,
@@ -106,7 +114,7 @@ export async function predictCarbon(
   return {
     molfile,
     nucleus: '13C',
-    diaIDs: flatGroupedDiaIDs(groupedDiaIDs),
+    diaIDs,
     joinedSignals,
     signals,
     ranges: signalsToRanges(joinedSignals),

package/src/prediction/predictHMBC.ts

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

package/src/prediction/predictProton.ts

@@ -1,7 +1,7 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import fetch from 'cross-fetch';
 import FormData from 'form-data';
-import type { Molecule } from 'openchemlib';
+import type { Molecule } from 'openchemlib/full';
 import {
   addDiastereotopicMissingChirality,
   getConnectivityMatrix,
@@ -24,6 +24,10 @@ export interface PredictProtonOptions {
    * A callback receiving a molfile and the result
    */
   cache?: (molfile: string, result?: string) => void | string | undefined;
+  /**
+   * diastereotopic atom ids.
+   */
+  diaIDs?: string[];
 }
 
 export type PredictProton = typeof predictProton;
@@ -56,7 +60,7 @@ export async function predictProton(
     }
   }
 
-  const diaIDs = getDiastereotopicAtomIDs(molecule);
+  const { diaIDs = getDiastereotopicAtomIDs(molecule) } = options;
   const signals = protonParser(result, molecule, diaIDs);
   const joinedSignals = signalsJoin(signals);
   return {

package/src/prediction/utils/fetchPrediction.ts

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

package/src/prediction/utils/getFilteredIDiaIDs.ts

@@ -1,8 +1,9 @@
-import type { Molecule } from 'openchemlib';
+import type { Molecule } from 'openchemlib/full';
 import {
   getGroupedDiastereotopicAtomIDs,
   getHoseCodesFromDiastereotopicID,
   addDiastereotopicMissingChirality,
+  groupDiasterotopicAtomIDs,
 } from 'openchemlib-utils';
 import type { GroupDiastereotopicAtomIDs } from 'openchemlib-utils';
 
@@ -14,9 +15,9 @@ export type GroupedDiaIDsWithHose = GroupDiaIDsWithHose[];
 
 export function getFilteredIDiaIDs(
   molecule: Molecule,
-  options: { maxSphereSize: number },
+  options: { maxSphereSize: number; diaIDs: string[] },
 ) {
-  const { maxSphereSize } = options;
+  const { maxSphereSize, diaIDs } = options;
 
   molecule.addImplicitHydrogens();
   molecule.addMissingChirality();
@@ -24,16 +25,16 @@ export function getFilteredIDiaIDs(
 
   const molfile = molecule.toMolfile();
 
-  let groupedDiaIDs = getGroupedDiastereotopicAtomIDs(molecule);
+  let groupedDiaIDs = groupDiasterotopicAtomIDs(diaIDs, molecule, {
+    atomLabel: 'C',
+  });
 
-  let carbonDiaIDs = groupedDiaIDs
-    .filter((e) => e.atomLabel === 'C')
-    .sort((a, b) => {
-      if (a.atomLabel === b.atomLabel) {
-        return b.counter - a.counter;
-      }
-      return a.atomLabel < b.atomLabel ? 1 : -1;
-    }) as any;
+  let carbonDiaIDs = groupedDiaIDs.sort((a, b) => {
+    if (a.atomLabel === b.atomLabel) {
+      return b.counter - a.counter;
+    }
+    return a.atomLabel < b.atomLabel ? 1 : -1;
+  }) as any;
 
   const OCL = molecule.getOCL();
   for (const diaId of carbonDiaIDs) {
@@ -48,7 +49,6 @@ export function getFilteredIDiaIDs(
   let toReturn = {
     molfile,
     carbonDiaIDs: carbonDiaIDs as GroupedDiaIDsWithHose,
-    groupedDiaIDs,
   };
 
   return toReturn;

package/src/prediction/utils/getPredictions.ts

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

package/src/prediction/utils/predict2D.ts

@@ -1,10 +1,11 @@
 import { v4 as generateID } from '@lukeed/uuid';
 import { agnes, Cluster } from 'ml-hclust';
 import { Matrix } from 'ml-matrix';
-import { Molecule } from 'openchemlib';
+import { Molecule } from 'openchemlib/full';
 import {
   getGroupedDiastereotopicAtomIDs,
   getPathsInfo,
+  groupDiasterotopicAtomIDs,
 } from 'openchemlib-utils';
 import type {
   AtomInfo,
@@ -86,6 +87,10 @@ export interface Predict2DOptions {
    * @default false
    */
   includeDiagonal?: boolean;
+  /**
+   * diastereotopic atom ids of the molecule.
+   */
+  diaIDs?: string[];
 }
 
 export interface PredictOptions {
@@ -125,9 +130,12 @@ export async function predict2D(
 ) {
   checkFromTo(options);
 
+  molecule.addImplicitHydrogens();
+
   let {
     from,
     to,
+    diaIDs,
     minLength = 0,
     maxLength,
     predictOptions = {},
@@ -137,10 +145,6 @@ export async function predict2D(
     includeDiagonal = false,
   } = options;
 
-  molecule.addImplicitHydrogens();
-
-  let diaIDs = getGroupedDiastereotopicAtomIDs(molecule);
-
   const pathsInfo = getPathsInfo(molecule, {
     fromLabel: from,
     toLabel: to,
@@ -148,8 +152,10 @@ export async function predict2D(
     maxLength,
   });
 
+  const groupedDiaIDS = diaIDs ? groupDiasterotopicAtomIDs(diaIDs, molecule) : getGroupedDiastereotopicAtomIDs(molecule)
+
   let diaIDswithAtomInfo: GroupDiastereotopicAtomIDsWithAtomInfo[] = [];
-  for (let diaID of diaIDs) {
+  for (let diaID of groupedDiaIDS) {
     diaIDswithAtomInfo.push({
       ...diaID,
       pathInfo: JSON.parse(

package/src/utilities/hasProperty.ts

@@ -1,4 +1,4 @@
-export function hasProperty<T, K extends keyof T>(
+export function hasProperty<T extends object, K extends keyof T>(
   data: T,
   key: K,
 ): data is T & { [P in K]-?: T[P] } {

package/src/xy/xyAutoPeaksPicking.ts

@@ -106,7 +106,11 @@ export function xyAutoPeaksPicking(
     direction = 'positive',
   } = options;
 
-  const { windowSize = 9, polynomial = 3 } = sgOptions;
+  let pointsPerHz = 1 / frequency / (data.x[1] - data.x[0]);
+  // we can consider a peak with of 0.5 Hz for the windowSize
+  let ws = Math.max(Math.round(pointsPerHz / 2), 5);
+
+  const { windowSize = ws - (ws % 2) + 1, polynomial = 3 } = sgOptions;
 
   if (data.x.length < windowSize) return [];