nmr-processing 10.0.7 → 11.1.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "10.0.7",
+  "version": "11.1.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -38,25 +38,26 @@
   },
   "homepage": "https://github.com/cheminfo/nmr-processing#readme",
   "devDependencies": {
-    "@types/jest": "^29.5.3",
+    "@types/jest": "^29.5.4",
+    "@types/numeral": "^2.0.2",
     "cheminfo-build": "^1.2.0",
     "cheminfo-types": "^1.7.2",
-    "eslint": "^8.46.0",
+    "eslint": "^8.49.0",
     "eslint-config-cheminfo-typescript": "^12.0.4",
     "fifo-logger": "^0.6.1",
-    "jest": "^29.6.2",
+    "jest": "^29.7.0",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "nmr-xy-testdata": "^0.5.1",
     "openchemlib": "^8.5.0",
-    "prettier": "^3.0.1",
+    "prettier": "^3.0.3",
     "rimraf": "^5.0.1",
     "ts-jest": "^29.1.1",
-    "typescript": "^5.1.6"
+    "typescript": "~5.2.2"
   },
   "dependencies": {
     "@lukeed/uuid": "^2.0.1",
-    "@types/lodash": "^4.14.196",
+    "@types/lodash": "^4.14.198",
     "binary-search": "^1.3.6",
     "cross-fetch": "^4.0.0",
     "form-data": "^4.0.0",
@@ -77,9 +78,10 @@
     "ml-signal-processing": "^1.0.3",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^12.5.0",
+    "ml-spectra-processing": "^12.5.1",
     "ml-tree-set": "^0.1.1",
     "nmr-correlation": "^2.3.3",
+    "numeral": "^2.0.6",
     "openchemlib-utils": "^5.2.0",
     "spectrum-generator": "^8.0.8"
   }

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

@@ -8,20 +8,20 @@ import { Entry1D } from '../Entry1D';
 import { getShiftX } from './getShiftX';
 
 function getRange(integral: Integral, shiftTarget: ShiftTarget, shift: number) {
-  const { originFrom, originTo, from, to } = integral;
+  const { originalFrom, originalTo, from, to } = integral;
   if (shiftTarget === 'origin') {
     return {
-      originFrom: from - shift,
-      originTo: to - shift,
+      originalFrom: from - shift,
+      originalTo: to - shift,
       from,
       to,
     };
   } else {
     return {
-      originFrom,
-      originTo,
-      from: originFrom + shift,
-      to: originTo + shift,
+      originalFrom,
+      originalTo,
+      from: originalFrom + shift,
+      to: originalTo + shift,
     };
   }
 }

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

@@ -6,6 +6,7 @@ import { Entry1D } from '../Entry1D';
 
 import { getShiftX } from './getShiftX';
 import { getSpectrumErrorValue } from './getSpectrumErrorValue';
+import { NMRPeak1D } from '../../..';
 
 function isExists(peak: Peak1D, spectrum: Entry1D, error: number) {
   // check if the Peak is already exists
@@ -17,7 +18,11 @@ function isExists(peak: Peak1D, spectrum: Entry1D, error: number) {
   return false;
 }
 
-function getPeakDelta(peak: Peak1D, shiftTarget: ShiftTarget, shift: number) {
+export function getPeakDelta(
+  peak: Peak1D | NMRPeak1D,
+  shiftTarget: ShiftTarget,
+  shift: number,
+) {
   const { originalX = 0, x } = peak;
   if (shiftTarget === 'origin') {
     return {

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

@@ -11,6 +11,7 @@ import { Entry1D } from '../Entry1D';
 
 import { getShiftX } from './getShiftX';
 import { getSpectrumErrorValue } from './getSpectrumErrorValue';
+import { getPeakDelta } from './mapPeaks';
 
 function checkRange(range: Range, spectrum: Entry1D, error: number) {
   // check if the range is already exists
@@ -29,20 +30,20 @@ function getRange(
   shiftTarget: 'origin' | 'current',
   shift: number,
 ) {
-  const { originFrom, originTo, from, to } = range;
+  const { originalFrom, originalTo, from, to } = range;
   if (shiftTarget === 'origin') {
     return {
-      originFrom: from - shift,
-      originTo: to - shift,
+      originalFrom: from - shift,
+      originalTo: to - shift,
       from,
       to,
     };
   } else {
     return {
-      originFrom,
-      originTo,
-      from: (originFrom || 0) + shift,
-      to: (originTo || 0) + shift,
+      originalFrom,
+      originalTo,
+      from: (originalFrom || 0) + shift,
+      to: (originalTo || 0) + shift,
     };
   }
 }
@@ -52,16 +53,16 @@ function getSignalDelta(
   shiftTarget: ShiftTarget,
   shift: number,
 ) {
-  const { delta, originDelta } = signal;
+  const { delta, originalDelta } = signal;
   if (shiftTarget === 'origin') {
     return {
-      originDelta: delta - shift,
+      originalDelta: delta - shift,
       delta,
     };
   } else {
     return {
-      originDelta,
-      delta: (originDelta || 0) + shift,
+      originalDelta,
+      delta: (originalDelta || 0) + shift,
     };
   }
 }
@@ -112,10 +113,20 @@ export function mapRanges(
       { from: rangeBoundary.from, to: rangeBoundary.to, reverse: true },
     );
     const signals = range.signals.map((signal) => {
-      const { kind = null, id, ...resSignal } = signal;
+      const { kind = null, id, peaks: inputPeaks = [], ...resSignal } = signal;
+
+      const peaks = inputPeaks.map((peak) => {
+        const peakDelta = getPeakDelta(peak, shiftTarget, shiftX);
+        return {
+          id: peak?.id || v4(),
+          ...peak,
+          ...peakDelta,
+        };
+      });
       return {
         kind: kind || 'signal',
         id: id || v4(),
+        peaks,
         ...resSignal,
         ...getSignalDelta(signal, shiftTarget, shiftX),
       };

package/src/datum/data2d/utils/mapZones.ts

@@ -9,6 +9,7 @@ import { Entry2D } from '../Entry2D';
 import { get2DSpectrumErrorValue } from './get2DSpectrumErrorValue';
 import { getShift, Shift2D } from './getShift';
 import { isZoneExists } from './isZoneExists';
+import { Peak2D } from '../../..';
 
 function getSignal(signal: Signal2D, shiftTarget: ShiftTarget, shift: Shift2D) {
   const { x, y } = signal;
@@ -18,11 +19,11 @@ function getSignal(signal: Signal2D, shiftTarget: ShiftTarget, shift: Shift2D) {
       ...signal,
       x: {
         ...x,
-        originDelta: x.delta - shift.x,
+        originalDelta: x.delta - shift.x,
       },
       y: {
         ...y,
-        originDelta: y.delta - shift.y,
+        originalDelta: y.delta - shift.y,
       },
     };
   } else {
@@ -30,16 +31,65 @@ function getSignal(signal: Signal2D, shiftTarget: ShiftTarget, shift: Shift2D) {
       ...signal,
       x: {
         ...x,
-        delta: x.originDelta + shift.x,
+        delta: x.originalDelta + shift.x,
       },
       y: {
         ...y,
-        delta: y.originDelta + shift.y,
+        delta: y.originalDelta + shift.y,
       },
     };
   }
 }
 
+function getZoneAxis(zone: Zone, shiftTarget: ShiftTarget, shift: Shift2D) {
+  const { x, y } = zone;
+
+  if (shiftTarget === 'origin') {
+    return {
+      x: {
+        ...x,
+        originalFrom: x.from - shift.x,
+        originalTo: x.to - shift.x,
+      },
+      y: {
+        ...y,
+        originalFrom: y.from - shift.y,
+        originalTo: y.to - shift.y,
+      },
+    };
+  } else {
+    return {
+      x: {
+        ...x,
+        from: (x?.originalFrom || 0) + shift.x,
+        to: (x?.originalTo || 0) + shift.x,
+      },
+      y: {
+        ...y,
+        from: (y?.originalFrom || 0) + shift.y,
+        to: (y?.originalTo || 0) + shift.y,
+      },
+    };
+  }
+}
+function getPeak(peak: Peak2D, shiftTarget: ShiftTarget, shift: Shift2D) {
+  const { x, y, originalX = 0, originalY = 0 } = peak;
+
+  if (shiftTarget === 'origin') {
+    return {
+      ...peak,
+      originalX: x - shift.x,
+      originalY: y - shift.y,
+    };
+  } else {
+    return {
+      ...peak,
+      x: originalX + shift.x,
+      y: originalY + shift.y,
+    };
+  }
+}
+
 export function mapZones(
   zones: Zone[],
   datum: Entry2D,
@@ -56,13 +106,25 @@ export function mapZones(
   }
 
   return _zones.map((zone: Zone) => {
-    const x = zone.x || { from: 0, to: 0 };
-    const y = zone.y || { from: 0, to: 0 };
+    zone.x = zone.x || { from: 0, to: 0 };
+    zone.y = zone.y || { from: 0, to: 0 };
 
     const signals = zone.signals.map((signal) => {
       const { id, kind } = signal;
+      let peaks;
+      if (signal?.peaks) {
+        peaks = (signal?.peaks || []).map((peak) => {
+          const peakDelta = getPeak(peak, shiftTarget, shift);
+          return {
+            ...peak,
+            ...peakDelta,
+            id: peak?.id || v4(),
+          };
+        });
+      }
       return {
         ...getSignal(signal, shiftTarget, shift),
+        peaks,
         id: id || v4(),
         kind: kind || 'signal',
       };
@@ -71,8 +133,7 @@ export function mapZones(
     return {
       ...zone,
       id: zone.id || v4(),
-      x: { from: x.from, to: x.to },
-      y: { from: y.from, to: y.to },
+      ...getZoneAxis(zone, shiftTarget, shift),
       signals,
       kind: zone.kind || DatumKind.signal,
     };

package/src/index.ts

@@ -65,6 +65,7 @@ export * from './datum/data1d/utils/getShiftX';
 export * from './datum/data1d/utils/getSpectrumErrorValue';
 export * from './datum/data1d/utils/mapPeaks';
 export * from './datum/data1d/utils/mapRanges';
+export * from './datum/data2d/utils/mapZones';
 export * from './datum/data1d/utils/mapIntegrals';
 export * from './datum/data1d/utils/updateRanges';
 export * from './datum/data1d/utils/checkIntegralKind';

package/src/peaks/NMRPeak1D.ts

@@ -5,4 +5,5 @@ export interface NMRPeak1D extends PeakXYWidth {
   id?: string;
   kind?: string;
   shape?: Shape1D;
+  originalX?: number;
 }

package/src/ranges/rangesToACS.ts

@@ -5,31 +5,33 @@ import { signalMultiplicityPattern } from '../signal/signalMultiplicityPattern';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import type { NMRRange } from '../xy/NMRRange';
 
+import numeral from 'numeral';
+
 const globalOptions: Record<
   string,
   {
     nucleus: string;
-    nbDecimalDelta: number;
-    nbDecimalJ: number;
+    nbDecimalDelta: string;
+    nbDecimalJ: string;
     observedFrequency: number;
   }
 > = {
   h: {
     nucleus: '1H',
-    nbDecimalDelta: 2,
-    nbDecimalJ: 1,
+    nbDecimalDelta: '0.00',
+    nbDecimalJ: '0.0',
     observedFrequency: 400,
   },
   c: {
     nucleus: '13C',
-    nbDecimalDelta: 1,
-    nbDecimalJ: 1,
+    nbDecimalDelta: '0.0',
+    nbDecimalJ: '0.0',
     observedFrequency: 100,
   },
   f: {
     nucleus: '19F',
-    nbDecimalDelta: 2,
-    nbDecimalJ: 1,
+    nbDecimalDelta: '0.00',
+    nbDecimalJ: '0.0',
     observedFrequency: 400,
   },
 };
@@ -46,12 +48,12 @@ export interface RangesToACSOptions {
    * default value depends of nucleus
    * @default 1|2
    */
-  nbDecimalDelta?: number;
+  nbDecimalDelta?: string;
   /**
    * Number of decimals to round the scalar coupling value
    * @default 1
    */
-  nbDecimalJ?: number;
+  nbDecimalJ?: string;
   /**
    * default value depends of nucleus
    * @default 400|100
@@ -118,7 +120,9 @@ function spectroInformation(options: any) {
     parenthesis.push(formatMF(options.solvent));
   }
   if (options.observedFrequency) {
-    parenthesis.push(`${(options.observedFrequency * 1).toFixed(0)} MHz`);
+    parenthesis.push(
+      `${numeral(options.observedFrequency * 1).format('0')} MHz`,
+    );
   }
   if (parenthesis.length > 0) {
     strings += ` (${parenthesis.join(', ')}): δ `;
@@ -147,9 +151,11 @@ function pushDelta(range: NMRRange, acsRanges: string[], options: any) {
           return a.delta - b.delta;
         });
       }
-      strings += `${Math.min(...fromTo).toFixed(
+      const to = numeral(Math.max(...fromTo));
+      const from = numeral(Math.min(...fromTo));
+      strings += `${from.format(options.nbDecimalDelta)}-${to.format(
         options.nbDecimalDelta,
-      )}-${Math.max(...fromTo).toFixed(options.nbDecimalDelta)}`;
+      )}`;
       strings += ` (${getIntegral(range, options)}`;
 
       if (
@@ -162,7 +168,7 @@ function pushDelta(range: NMRRange, acsRanges: string[], options: any) {
           parenthesis = [];
           if (signal.delta !== undefined) {
             strings = appendSeparator(strings);
-            strings += signal.delta.toFixed(options.nbDecimalDelta);
+            strings += numeral(signal.delta).format(options.nbDecimalDelta);
           }
           const range: NMRRange = {
             from: Number.MIN_SAFE_INTEGER,
@@ -176,21 +182,25 @@ function pushDelta(range: NMRRange, acsRanges: string[], options: any) {
     } else {
       parenthesis = [];
       if (signals[0].delta !== undefined) {
-        strings += signals[0].delta.toFixed(options.nbDecimalDelta);
+        strings += numeral(signals[0].delta).format(options.nbDecimalDelta);
         switchFormat(range, signals[0], parenthesis, options);
         if (parenthesis.length > 0) strings += ` (${parenthesis.join(', ')})`;
       } else {
-        strings += `${Math.min(...fromTo).toFixed(
+        const to = numeral(Math.max(...fromTo));
+        const from = numeral(Math.min(...fromTo));
+        strings += `${from.format(options.nbDecimalDelta)}-${to.format(
           options.nbDecimalDelta,
-        )}-${Math.max(...fromTo).toFixed(options.nbDecimalDelta)}`;
+        )}`;
         switchFormat(range, signals[0], parenthesis, options);
         if (parenthesis.length > 0) strings += ` (${parenthesis})`;
       }
     }
   } else {
-    strings += `${Math.min(...fromTo).toFixed(
+    const to = numeral(Math.max(...fromTo));
+    const from = numeral(Math.min(...fromTo));
+    strings += `${from.format(options.nbDecimalDelta)}-${to.format(
       options.nbDecimalDelta,
-    )}-${Math.max(...fromTo).toFixed(options.nbDecimalDelta)}`;
+    )}`;
     const signal: any = {};
     switchFormat(range, signal, parenthesis, options);
     if (parenthesis.length > 0) strings += ` (${parenthesis.join(', ')})`;
@@ -204,7 +214,8 @@ function getIntegral(range: NMRRange, options: { nucleus: string[] }) {
     integration = String(range.pubIntegral);
   } else if (range.integration) {
     const { nucleus } = options;
-    integration = range.integration.toFixed(0) + nucleus[nucleus.length - 1];
+    integration =
+      numeral(range.integration).format('0') + nucleus[nucleus.length - 1];
   }
   return integration;
 }
@@ -290,7 +301,7 @@ function pushCoupling(
     const values = [];
     for (const j of signal.js) {
       if (j.coupling !== undefined) {
-        values.push(j.coupling.toFixed(options.nbDecimalJ));
+        values.push(numeral(j.coupling).format(options.nbDecimalJ));
       }
     }
     if (values.length > 0) {

package/src/types/Integral.ts

@@ -1,7 +1,7 @@
 export interface Integral {
   id: string;
-  originFrom: number;
-  originTo: number;
+  originalFrom: number;
+  originalTo: number;
   from: number;
   to: number;
   absolute: number;

package/src/types/Peaks/Peak2D.ts

@@ -4,8 +4,8 @@ export interface Peak2D extends BasePeak {
   x: number;
   y: number;
   z: number;
-  originX?: number;
-  originY?: number;
-  originZ?: number;
+  originalX?: number;
+  originalY?: number;
+  originalZ?: number;
   width?: number | { x: number; y: number };
 }

package/src/types/Ranges/Ranges.ts

@@ -9,8 +9,8 @@ export interface Ranges {
 
 export interface Range extends Omit<NMRRange, 'signals' | 'id'> {
   id: string;
-  originFrom?: number;
-  originTo?: number;
+  originalFrom?: number;
+  originalTo?: number;
   absolute: number;
   signals: Signal1D[];
   integration: number;

package/src/types/Signals/Signal1D.ts

@@ -4,5 +4,5 @@ type ObjectKeys = 'id' | 'multiplicity' | 'js';
 export interface Signal1D
   extends Required<Pick<NMRSignal1D, ObjectKeys>>,
     Omit<NMRSignal1D, ObjectKeys> {
-  originDelta?: number;
+  originalDelta?: number;
 }

package/src/types/Signals/Signal2D.ts

@@ -8,7 +8,7 @@ interface SignalAxis {
   delta: number;
   nbAtoms?: number;
   diaIDs?: string[];
-  originDelta: number;
+  originalDelta: number;
 }
 
 export interface Signal2D extends Signal {

package/src/types/Zones/Zone.ts

@@ -5,6 +5,8 @@ import { Signal2D } from '../Signals/Signal2D';
 interface ZoneAxis extends FromTo {
   nbAtoms?: number;
   diaIDs?: string[];
+  originalFrom?: number;
+  originalTo?: number;
 }
 
 export interface Zone {

package/src/utilities/getSum.ts

@@ -15,7 +15,7 @@ export function getSum<Type extends object>(
   for (const current of values) {
     if (check?.(current)) {
       const value = current[key];
-      if (!value || isNaN(value)) continue;
+      if (!value || typeof value !== 'number') continue;
       sum += Math.abs(value);
     }
   }