nmr-processing 9.4.1 → 9.4.2-pre.1684301205

package/lib-esm/xyz/xyzAutoZonesPicking.js

@@ -1,193 +1,7 @@
-import { v4 as generateID } from '@lukeed/uuid';
-import { Matrix } from 'ml-matrix';
-import * as convolution from 'ml-matrix-convolution';
-import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
-import simpleClustering from 'ml-simple-clustering';
-import { addMissingIDs } from '../peaks/util/addMissingIDs';
-import { determineRealTop } from '../peaks/util/determineRealTop';
-import { getKernel } from '../peaks/util/getKernel';
-import * as PeakOptimizer from '../peaks/util/peakOptimizer';
+import { xyzAutoSignalsPicking } from '..';
 import { formatZones } from './util/formatZone';
-const smallFilter = [
-    [0, 0, 1, 2, 2, 2, 1, 0, 0],
-    [0, 1, 4, 7, 7, 7, 4, 1, 0],
-    [1, 4, 5, 3, 0, 3, 5, 4, 1],
-    [2, 7, 3, -12, -23, -12, 3, 7, 2],
-    [2, 7, 0, -23, -40, -23, 0, 7, 2],
-    [2, 7, 3, -12, -23, -12, 3, 7, 2],
-    [1, 4, 5, 3, 0, 3, 5, 4, 1],
-    [0, 1, 3, 7, 7, 7, 3, 1, 0],
-    [0, 0, 1, 2, 2, 2, 1, 0, 0],
-];
 export function xyzAutoZonesPicking(spectraData, options) {
-    let { sizeToPad = 14, realTopDetection = true, thresholdFactor = 0.5, nuclei = ['1H', '1H'], observedFrequencies, enhanceSymmetry = false, clean = true, maxPercentCutOff = 0.03, tolerances = [24, 24], convolutionByFFT = true, kernel: kernelOptions, } = options;
-    if (!Array.isArray(observedFrequencies) &&
-        !ArrayBuffer.isView(observedFrequencies)) {
-        throw new Error('observedFrequencies is mandatory');
-    }
-    thresholdFactor = thresholdFactor === 0 ? 1 : Math.abs(thresholdFactor);
-    let nbPoints = spectraData.z[0].length;
-    let nbSubSpectra = spectraData.z.length;
-    if (nbSubSpectra < sizeToPad) {
-        spectraData = padData(spectraData, { width: sizeToPad });
-        nbPoints = spectraData.z[0].length;
-        nbSubSpectra = spectraData.z.length;
-    }
-    let absoluteData = new Float64Array(nbPoints * nbSubSpectra);
-    let originalData = new Float64Array(nbPoints * nbSubSpectra);
-    for (let iSubSpectra = 0; iSubSpectra < nbSubSpectra; iSubSpectra++) {
-        let spectrum = spectraData.z[iSubSpectra];
-        for (let iCol = 0; iCol < nbPoints; iCol++) {
-            let index = iSubSpectra * nbPoints + iCol;
-            absoluteData[index] = Math.abs(spectrum[iCol]);
-            originalData[index] = spectrum[iCol]; //@todo pensar si se puede evitar originalData
-        }
-    }
-    const kernel = kernelOptions ? getKernel(kernelOptions) : smallFilter;
-    let convolutedSpectrum = convolutionByFFT
-        ? convolution.fft(absoluteData, kernel, {
-            rows: nbSubSpectra,
-            cols: nbPoints,
-        })
-        : convolution.direct(absoluteData, kernel, {
-            rows: nbSubSpectra,
-            cols: nbPoints,
-        });
-    let peaksMC1 = matrixPeakFinders.findPeaks2DRegion(absoluteData, {
-        originalData,
-        filteredData: convolutedSpectrum,
-        rows: nbSubSpectra,
-        cols: nbPoints,
-        nStdDev: thresholdFactor,
-    });
-    if (clean) {
-        // Remove peaks with less than x% of the intensity of the highest peak
-        peaksMC1 = PeakOptimizer.clean(peaksMC1, maxPercentCutOff);
-    }
-    let signals = createSignals2D(addMissingIDs(peaksMC1), {
-        nRows: nbSubSpectra,
-        nCols: nbPoints,
-        minX: spectraData.minX,
-        maxX: spectraData.maxX,
-        minY: spectraData.minY,
-        maxY: spectraData.maxY,
-        absoluteData,
-        originalData,
-        tolerances,
-        nuclei,
-        observedFrequencies,
-        realTopDetection,
-    });
-    if (enhanceSymmetry) {
-        signals = PeakOptimizer.enhanceSymmetry(signals);
-    }
+    const signals = xyzAutoSignalsPicking(spectraData, options);
     return formatZones(signals);
 }
-function createSignals2D(peaks, options) {
-    let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
-    let [nucleusX, nucleusY] = nuclei;
-    let [toleranceX, toleranceY] = tolerances;
-    let [observeFrequencyX, observeFrequencyY] = observedFrequencies;
-    let dy = (maxY - minY) / (nRows - 1);
-    let dx = (maxX - minX) / (nCols - 1);
-    if (realTopDetection) {
-        peaks = determineRealTop(peaks, {
-            nCols,
-            absoluteData,
-            originalData,
-            minX,
-            maxX,
-            minY,
-            maxY,
-        });
-    }
-    for (let i = peaks.length - 1; i >= 0; i--) {
-        let { x, y } = peaks[i];
-        peaks[i].x = minX + dx * x;
-        peaks[i].y = minY + dy * y;
-        peaks[i].minX = minX + dx * peaks[i].minX;
-        peaks[i].minY = minY + dy * peaks[i].minY;
-        peaks[i].maxX = minX + dx * peaks[i].maxX;
-        peaks[i].maxY = minY + dy * peaks[i].maxY;
-        // Still having problems to correctly detect peaks on those areas. So I'm removing everything there.
-    }
-    // The connectivity matrix is an square and symmetric matrix, so we'll only store the upper diagonal in an
-    // array like form
-    let connectivity = [];
-    for (let i = 0; i < peaks.length; i++) {
-        for (let j = i; j < peaks.length; j++) {
-            if (Math.abs(peaks[i].x - peaks[j].x) * observeFrequencyX < toleranceX &&
-                Math.abs(peaks[i].y - peaks[j].y) * observeFrequencyY < toleranceY) {
-                // 24*24Hz We cannot distinguish peaks with less than 20 Hz of separation
-                connectivity.push(1);
-            }
-            else {
-                connectivity.push(0);
-            }
-        }
-    }
-    let clusters = simpleClustering(connectivity);
-    let signals = [];
-    if (clusters) {
-        for (const cluster of clusters) {
-            let signal = {
-                id: generateID(),
-                x: {
-                    delta: 0,
-                    nucleus: nucleusX,
-                    resolution: dx,
-                },
-                y: {
-                    delta: 0,
-                    nucleus: nucleusY,
-                    resolution: dy,
-                },
-            };
-            let peaks2D = [];
-            let sumZ = 0;
-            for (let jPeak = 0; jPeak < cluster.length; jPeak++) {
-                if (cluster[jPeak] === 1) {
-                    peaks2D.push(peaks[jPeak]);
-                    signal.x.delta += peaks[jPeak].x * peaks[jPeak].z;
-                    signal.y.delta += peaks[jPeak].y * peaks[jPeak].z;
-                    sumZ += peaks[jPeak].z;
-                }
-            }
-            signal.x.delta /= sumZ;
-            signal.y.delta /= sumZ;
-            signal.peaks = peaks2D;
-            signals.push(signal);
-        }
-    }
-    return signals;
-}
-function padData(spectraData, options) {
-    let { minX, maxX, minY, maxY } = spectraData;
-    const width = options.width;
-    let nbPoints = spectraData.z[0].length;
-    let nbSubSpectra = spectraData.z.length;
-    let yInterval = (maxY - minY) / (nbSubSpectra - 1);
-    let xInterval = (maxX - minX) / (nbPoints - 1);
-    let yDiff = width - nbSubSpectra;
-    let xDiff = Math.max(width - nbPoints, 0);
-    if (xDiff % 2)
-        xDiff++;
-    if (yDiff % 2)
-        yDiff++;
-    let xOffset = xDiff / 2;
-    let yOffset = yDiff / 2;
-    let newMatrix = Matrix.zeros(nbSubSpectra + yDiff, nbPoints + xDiff);
-    for (let i = 0; i < nbSubSpectra; i++) {
-        for (let j = 0; j < nbPoints; j++) {
-            newMatrix.set(i + yOffset, j + xOffset, spectraData.z[i][j]);
-        }
-    }
-    return {
-        z: newMatrix.to2DArray(),
-        minX: minX - xOffset * xInterval,
-        maxX: maxX + xOffset * xInterval,
-        minY: minY - yOffset * yInterval,
-        maxY: maxY + yOffset * yInterval,
-    };
-}
 //# sourceMappingURL=xyzAutoZonesPicking.js.map

package/lib-esm/xyz/xyzAutoZonesPicking.js.map

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+{"version":3,"file":"xyzAutoZonesPicking.js","sourceRoot":"","sources":["../../src/xyz/xyzAutoZonesPicking.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,qBAAqB,EAAE,MAAM,IAAI,CAAC;AAK3C,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAmEhD,MAAM,UAAU,mBAAmB,CACjC,WAAmB,EACnB,OAAmC;IAEnC,MAAM,OAAO,GAAG,qBAAqB,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;IAC5D,OAAO,WAAW,CAAC,OAAO,CAAC,CAAC;AAC9B,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.4.1",
+  "version": "9.4.2-pre.1684301205",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",

package/src/constants/MultiplicityPatterns.ts

@@ -1,18 +1,20 @@
 export interface MultipletDefinition {
   label: string;
   value: string;
+  acs?: string;
   names: string[];
   multiplicity: number | null;
 }
 
 export const MultiplicityPatterns: MultipletDefinition[] = [
   { label: 'singlet', value: 's', multiplicity: 1, names: ['br s'] },
-  { label: 'doublet', value: 'd', multiplicity: 2, names: [] },
   { label: 'triplet', value: 't', multiplicity: 3, names: [] },
+  { label: 'doublet', value: 'd', multiplicity: 2, names: [] },
   { label: 'quartet', value: 'q', multiplicity: 4, names: [] },
   {
     label: 'quintet',
     value: 'i',
+    acs: 'quint',
     multiplicity: 5,
     names: ['quint', 'qui', 'qnt', 'pentet', 'pnt', 'pent'],
   },
@@ -25,6 +27,7 @@ export const MultiplicityPatterns: MultipletDefinition[] = [
   {
     label: 'septet',
     value: 'p',
+    acs: 'sept',
     multiplicity: 7,
     names: ['sept', 'spt', 'heptet', 'hpt', 'hept'],
   },

package/src/constants/couplingPatterns.ts

@@ -1,3 +1,12 @@
 import { MultiplicityPatterns } from './MultiplicityPatterns';
 
+MultiplicityPatterns.sort((a, b) =>
+  a.multiplicity !== null && b.multiplicity !== null
+    ? a.multiplicity - b.multiplicity
+    : Number.MAX_SAFE_INTEGER,
+);
 export const couplingPatterns = MultiplicityPatterns.map((m) => m.value);
+
+export const couplingACSPatterns = MultiplicityPatterns.map(
+  (m) => m.acs || m.value,
+);

package/src/index.ts

@@ -29,7 +29,6 @@ export * from './signals/signalsToFID';
 export * from './signal/signalJoinCouplings';
 
 export * from './utilities/resurrect';
-export * from './utilities/splitPatterns';
 export * from './utilities/rangeFromSignal';
 export * from './utilities/getFrequency';
 
@@ -38,6 +37,7 @@ export * from './xy/xyAutoRangesPicking';
 export * from './xy/xyPeaksOptimization';
 
 export * from './xyz/xyzAutoZonesPicking';
+export * from './xyz/xyzAutoSignalsPicking';
 export * from './xyz/xyzJResAnalyzer';
 
 export * from './databases/getDatabase';
@@ -51,6 +51,12 @@ export * from './apodization/apodization';
 
 export * from './constants/MultiplicityPatterns';
 
+export * from './multiplicity/findMultiplet';
+export * from './multiplicity/splitPatterns';
+export * from './multiplicity/checkMultiplet';
+export * from './multiplicity/checkMultiplicity';
+export * from './multiplicity/translateMultiplet';
+
 export type { NMRSignal1D } from './signals/NMRSignal1D';
 export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';

package/src/multiplicity/checkMultiplet.ts

@@ -0,0 +1,11 @@
+import { findMultiplet } from './findMultiplet';
+
+export function checkMultiplet(string: string, rejected: string[] = []) {
+  const multiplet = findMultiplet(string);
+  return (
+    multiplet &&
+    !rejected.includes(multiplet.label) &&
+    !rejected.includes(multiplet.value) &&
+    !multiplet.names.some((name) => rejected.includes(name))
+  );
+}

package/src/multiplicity/checkMultiplicity.ts

@@ -0,0 +1,21 @@
+import { splitPatterns } from '..';
+
+import { checkMultiplet } from './checkMultiplet';
+
+export function checkMultiplicity(
+  multiplicity: string,
+  rejected: string[] = [],
+) {
+  // options to determine whether a massive (m), for example, should be considered as rejected multiplicity
+  if (multiplicity === undefined || multiplicity.length === 0) {
+    return false;
+  }
+
+  const multiplets = splitPatterns(multiplicity);
+  const allIncluded = multiplets.join('').length === multiplicity.length;
+
+  return (
+    allIncluded &&
+    multiplets.every((_multiplet) => checkMultiplet(_multiplet, rejected))
+  );
+}

package/src/multiplicity/findMultiplet.ts

@@ -0,0 +1,8 @@
+import { MultiplicityPatterns } from '..';
+
+export function findMultiplet(name: string) {
+  return MultiplicityPatterns.find((multiplet) => {
+    const { label, value, names } = multiplet;
+    return [label, value, ...names].includes(name);
+  });
+}

package/src/{utilities → multiplicity}/joinPatterns.ts

@@ -1,7 +1,13 @@
-import { couplingPatterns } from '../constants/couplingPatterns';
+import {
+  couplingACSPatterns,
+  couplingPatterns,
+} from '../constants/couplingPatterns';
 import { couplingValues } from '../constants/couplingValues';
 
-export function joinPatterns(patterns: string[]) {
+export function joinPatterns(
+  patterns: string[],
+  options?: { acsFormat?: boolean },
+) {
   const sum = patterns.reduce((sum, pattern) => {
     if (isNaN(couplingValues[pattern])) {
       throw new Error(
@@ -15,5 +21,5 @@ export function joinPatterns(patterns: string[]) {
     throw new Error("The joined pattern doesn't exist");
   }
 
-  return couplingPatterns[sum];
+  return options?.acsFormat ? couplingACSPatterns[sum] : couplingPatterns[sum];
 }

package/src/multiplicity/translateMultiplet.ts

@@ -0,0 +1,11 @@
+import { findMultiplet } from './findMultiplet';
+
+export function translateMultiplet(name: string) {
+  const multiplet = findMultiplet(name);
+
+  if (!multiplet) {
+    throw new Error(`multiplet ${name} is not supported`);
+  }
+  const { value, label } = multiplet;
+  return name === label ? value : label;
+}

package/src/ranges/rangesToACS.ts

@@ -219,6 +219,7 @@ function pushmultiplicityFromSignal(
   let multiplicity = signal.multiplicity;
   if (!multiplicity) {
     let joinedCouplings = signalJoinCouplings(signal, {
+      acsFormat: true,
       tolerance: 0.05,
       ignoreDiaIDs: true,
     });

package/src/signal/signalJoinCouplings.ts

@@ -1,11 +1,16 @@
 import sum from 'ml-array-sum';
 
+import { joinPatterns } from '../multiplicity/joinPatterns';
 import type { Jcoupling } from '../signals/Jcoupling';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
-import { joinPatterns } from '../utilities/joinPatterns';
 
 export interface SignalJoinCouplingsOptions {
+  /**
+   * if it is true the coupling pattens will normalized to ACS suggested values
+   * @default false
+   */
+  acsFormat?: boolean;
   /**
    * tolerance to merge the couplings
    * @default 0.05
@@ -52,24 +57,25 @@ export function signalJoinCouplings(
   signal: NMRSignal1D,
   options: SignalJoinCouplingsOptions = {},
 ) {
-  const { tolerance = 0.05, ignoreDiaIDs = false } = options;
+  const { tolerance = 0.05, ignoreDiaIDs = false, acsFormat = false } = options;
 
   if (!signal.js || signal.js.length < 2) return signal;
 
   if (ignoreDiaIDs) {
     checkJs(signal);
-    return groupJCouplings(signal, areThanClose, tolerance);
+    return groupJCouplings(signal, areThanClose, { tolerance, acsFormat });
   } else {
     checkJsAndDiaID(signal);
-    return groupJCouplings(signal, takeCareDiaIDs, tolerance);
+    return groupJCouplings(signal, takeCareDiaIDs, { tolerance, acsFormat });
   }
 }
 
 function groupJCouplings(
   signal: Signal1DWidthJs,
   comparator: any,
-  tolerance: number,
+  options: { tolerance: number; acsFormat?: boolean },
 ) {
+  const { tolerance, acsFormat } = options;
   signal.js.sort((a, b) => b.coupling - a.coupling);
 
   let currentGroup = [signal.js[0]];
@@ -118,6 +124,7 @@ function groupJCouplings(
       group
         .filter((group) => group.multiplicity)
         .map((group) => group.multiplicity) as string[],
+      { acsFormat },
     );
 
     let newJ: Jcoupling = {

package/src/signal/signalMultiplicityPattern.ts

@@ -1,15 +1,22 @@
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import { selectACSPattern } from '../utilities/selectACSPattern';
 /**
  * Return
  * @param {*} signal
  */
 
-export function signalMultiplicityPattern(signal: NMRSignal1D) {
+export function signalMultiplicityPattern(
+  signal: NMRSignal1D,
+  options?: { acsFormat?: boolean },
+) {
   let js = signal.js;
   let pattern = '';
   if (js && js.length > 0) {
     for (let coupling of js) {
-      pattern += coupling.multiplicity;
+      const { multiplicity = '' } = coupling;
+      pattern += options?.acsFormat
+        ? selectACSPattern(multiplicity)
+        : multiplicity;
     }
   } else if (signal.delta) {
     pattern = '';

package/src/utilities/normalizeNucleus.ts

@@ -0,0 +1,24 @@
+import { Nuclei, gyromagneticRatio } from 'gyromagnetic-ratio';
+
+import { NucleusName, nucleusSymbolMap } from './nucleusMap';
+
+export function normilizeNucleus(name: string) {
+  if (gyromagneticRatio[name as Nuclei]) {
+    return name;
+  }
+
+  const massNumber = name.replace(/\D/g, '');
+  const atomName = name.replace(/\d*\W*/g, '').toLowerCase();
+
+  const nucleusName =
+    atomName.length > 1
+      ? nucleusSymbolMap[atomName as NucleusName]
+      : atomName.toUpperCase();
+
+  const symbol = `${massNumber}${nucleusName}`;
+  if (!gyromagneticRatio[symbol as Nuclei]) {
+    throw new Error(`nucleus ${name} is not supported`);
+  }
+
+  return symbol;
+}

package/src/utilities/nucleusMap.ts

@@ -0,0 +1,40 @@
+export type NucleusName =
+  | 'proton'
+  | 'hydrogen'
+  | 'helium'
+  | 'lithium'
+  | 'carbon'
+  | 'nitrogen'
+  | 'oxigen'
+  | 'fluorine'
+  | 'sodium'
+  | 'aluminum'
+  | 'silicon'
+  | 'phosphorus'
+  | 'iron'
+  | 'copper'
+  | 'zinc'
+  | 'xenon';
+
+export type NucleusSymbolMap = {
+  [key in NucleusName]: string;
+};
+
+export const nucleusSymbolMap: NucleusSymbolMap = {
+  proton: '1H',
+  hydrogen: 'H',
+  helium: 'He',
+  lithium: 'Li',
+  carbon: 'C',
+  nitrogen: 'N',
+  oxigen: 'O',
+  fluorine: 'F',
+  sodium: 'Na',
+  aluminum: 'Al',
+  silicon: 'Si',
+  phosphorus: 'P',
+  iron: 'Fe',
+  copper: 'Cu',
+  zinc: 'Zn',
+  xenon: 'Xe',
+};

package/src/utilities/resurrectRange.ts

@@ -1,9 +1,9 @@
+import { splitPatterns } from '../multiplicity/splitPatterns';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import type { NMRRange } from '../xy/NMRRange';
 
 import { rangeFromSignal } from './rangeFromSignal';
 import { splitParenthesis } from './splitParenthesis';
-import { splitPatterns } from './splitPatterns';
 
 export function resurrectRange(part: string, options: any = {}) {
   const { nucleus = '1h', frequency = 400 } = options;

package/src/utilities/selectACSPattern.ts

@@ -0,0 +1,10 @@
+import { couplingACSPatterns } from '..';
+import { couplingValues } from '../constants/couplingValues';
+
+export function selectACSPattern(pattern: string) {
+  const multiplicity = couplingValues[pattern];
+  if (!multiplicity) {
+    throw new Error(`multiplicity pattern ${pattern} is not supported`);
+  }
+  return couplingACSPatterns[multiplicity];
+}

package/src/xyz/Data2D.ts

@@ -0,0 +1,7 @@
+export interface Data2D {
+  z: number[][] | Float64Array[];
+  minX: number;
+  maxX: number;
+  minY: number;
+  maxY: number;
+}

package/src/xyz/util/formatZone.ts

@@ -1,6 +1,7 @@
 import { v4 as generateID } from '@lukeed/uuid';
 
-import { NMRSignal2DWithID, NMRZoneWithID } from '../xyzAutoZonesPicking';
+import { NMRSignal2DWithID } from '../xyzAutoSignalsPicking';
+import { NMRZoneWithID } from '../xyzAutoZonesPicking';
 
 export function formatZones(signals: NMRSignal2DWithID[]) {
   let zones: NMRZoneWithID[] = [];

package/src/xyz/util/padData.ts

@@ -0,0 +1,37 @@
+import Matrix from 'ml-matrix';
+
+import { Data2D } from '../Data2D';
+
+export function padData(spectraData: Data2D, options: { width: number }) {
+  let { minX, maxX, minY, maxY } = spectraData;
+
+  const width = options.width;
+
+  let nbPoints = spectraData.z[0].length;
+  let nbSubSpectra = spectraData.z.length;
+
+  let yInterval = (maxY - minY) / (nbSubSpectra - 1);
+  let xInterval = (maxX - minX) / (nbPoints - 1);
+
+  let yDiff = width - nbSubSpectra;
+  let xDiff = Math.max(width - nbPoints, 0);
+  if (xDiff % 2) xDiff++;
+  if (yDiff % 2) yDiff++;
+
+  let xOffset = xDiff / 2;
+  let yOffset = yDiff / 2;
+  let newMatrix = Matrix.zeros(nbSubSpectra + yDiff, nbPoints + xDiff);
+  for (let i = 0; i < nbSubSpectra; i++) {
+    for (let j = 0; j < nbPoints; j++) {
+      newMatrix.set(i + yOffset, j + xOffset, spectraData.z[i][j]);
+    }
+  }
+
+  return {
+    z: newMatrix.to2DArray(),
+    minX: minX - xOffset * xInterval,
+    maxX: maxX + xOffset * xInterval,
+    minY: minY - yOffset * yInterval,
+    maxY: maxY + yOffset * yInterval,
+  };
+}