nmr-processing 8.0.0 → 8.3.0

package/lib-esm/utilities/resurrectRange.js

@@ -34,13 +34,10 @@ export function resurrectRange(part, options = {}) {
                 signal.multiplicity = multiplicity;
             }
         }
-        else {
-            // looks like a real multiplicity, s, d, dd, etc..
-            if (!isARange) {
-                // a complex signal
-                signal.delta = from;
-                signal.multiplicity = multiplicity;
-            }
+        else if (!isARange) {
+            // a complex signal
+            signal.delta = from;
+            signal.multiplicity = multiplicity;
         }
     }
     const jCouplings = insideParts

package/lib-esm/utilities/resurrectRange.js.map

@@ -1 +1 @@
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package/lib-esm/xyz/util/formatZone.js

@@ -0,0 +1,34 @@
+export function formatZones(signals) {
+    let zones = [];
+    for (const signal of signals) {
+        let minMax1 = [Number.MAX_VALUE, 0];
+        let minMax2 = [Number.MAX_VALUE, 0];
+        for (const peak of signal.peaks || []) {
+            if (peak.minX < minMax1[0]) {
+                minMax1[0] = peak.minX;
+            }
+            if (peak.maxX > minMax1[1]) {
+                minMax1[1] = peak.maxX;
+            }
+            if (peak.minY < minMax2[0]) {
+                minMax2[0] = peak.minY;
+            }
+            if (peak.maxY > minMax2[1]) {
+                minMax2[1] = peak.maxY;
+            }
+        }
+        zones.push({
+            x: {
+                from: minMax1[0],
+                to: minMax1[1],
+            },
+            y: {
+                from: minMax2[0],
+                to: minMax2[1],
+            },
+            signals: [signal],
+        });
+    }
+    return zones;
+}
+//# sourceMappingURL=formatZone.js.map

package/lib-esm/xyz/util/formatZone.js.map

@@ -0,0 +1 @@
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package/lib-esm/xyz/xyzAutoZonesPicking.js

@@ -5,6 +5,7 @@ import simpleClustering from 'ml-simple-clustering';
 import { determineRealTop } from '../peaks/util/determineRealTop';
 import { getKernel } from '../peaks/util/getKernel';
 import * as PeakOptimizer from '../peaks/util/peakOptimizer';
+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],
@@ -80,39 +81,6 @@ export function xyzAutoZonesPicking(spectraData, options) {
     }
     return formatZones(signals);
 }
-function formatZones(signals) {
-    let zones = [];
-    for (const signal of signals) {
-        let minMax1 = [Number.MAX_VALUE, 0];
-        let minMax2 = [Number.MAX_VALUE, 0];
-        for (const peak of signal.peaks || []) {
-            if (peak.minX < minMax1[0]) {
-                minMax1[0] = peak.minX;
-            }
-            if (peak.maxX > minMax1[1]) {
-                minMax1[1] = peak.maxX;
-            }
-            if (peak.minY < minMax2[0]) {
-                minMax2[0] = peak.minY;
-            }
-            if (peak.maxY > minMax2[1]) {
-                minMax2[1] = peak.maxY;
-            }
-        }
-        zones.push({
-            x: {
-                from: minMax1[0],
-                to: minMax1[1],
-            },
-            y: {
-                from: minMax2[0],
-                to: minMax2[1],
-            },
-            signals: [signal],
-        });
-    }
-    return zones;
-}
 const createSignals2D = (peaks, options) => {
     let { nCols, nRows, absoluteData, originalData, observedFrequencies, tolerances, nuclei, realTopDetection, minY, maxY, minX, maxX, } = options;
     let [nucleusX, nucleusY] = nuclei;

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

@@ -1 +1 @@
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package/lib-esm/xyz/xyzJResAnalyzer.js

@@ -1,24 +1,25 @@
 import simpleClustering from 'ml-simple-clustering';
 import jAnalyzer from '../peaks/util/jAnalyzer';
+import { formatZones } from './util/formatZone';
 export function xyzJResAnalyzer(signals, options = {}) {
-    let { reference = 0, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
+    let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {
         jAxisKey: { jAxis: 'y', intensity: 'z' },
     }, } = options;
-    let temporalSignals = compilePattern(signals, {
+    let temporalSignals = compilePattern([...signals], {
         observedFrequencies,
         tolerances,
         nuclei,
         jAnalyzer,
     });
     //check if the signal are symmetric around the reference
-    let result = [];
+    let signals2D = [];
     for (const tempSignal of temporalSignals) {
         let delta = tempSignal.y.delta;
         if (Math.abs(delta - reference) > referenceMaxShiftError)
             continue;
-        result.push(tempSignal);
+        signals2D.push(tempSignal);
     }
-    return result;
+    return getZones ? formatZones(signals2D) : signals2D;
 }
 function compilePattern(signals, options) {
     let { observedFrequencies, tolerances, nuclei, jAnalyzer: jAnalyzerOptions, } = options;
@@ -67,9 +68,9 @@ function compilePattern(signals, options) {
             }
             if (peaksO.length > 0) {
                 peaksO.reverse();
-                let ranges = createSignals2D(peaksO, signalOptions);
-                for (const range of ranges) {
-                    newSignals.push(range);
+                let signals2D = createSignals2D(peaksO, signalOptions);
+                for (const signal of signals2D) {
+                    newSignals.push(signal);
                 }
             }
         }

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

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "8.0.0",
+  "version": "8.3.0",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -38,44 +38,46 @@
   },
   "homepage": "https://github.com/cheminfo/nmr-processing#readme",
   "devDependencies": {
-    "@types/jest": "^27.5.0",
+    "@types/jest": "^28.1.4",
     "cheminfo-build": "^1.1.11",
-    "cheminfo-types": "^1.1.0",
-    "eslint": "^8.14.0",
-    "eslint-config-cheminfo-typescript": "^10.4.0",
-    "jest": "^28.0.3",
+    "cheminfo-types": "^1.2.0",
+    "eslint": "^8.19.0",
+    "eslint-config-cheminfo-typescript": "^11.0.1",
+    "jest": "^28.1.2",
     "jest-matcher-deep-close-to": "^3.0.2",
     "md5": "^2.3.0",
     "ml-array-median": "^1.1.6",
     "nmr-xy-testdata": "^0.5.1",
     "openchemlib": "^7.4.3",
-    "prettier": "^2.6.2",
+    "prettier": "^2.7.1",
     "rimraf": "^3.0.2",
-    "ts-jest": "^28.0.1",
-    "typescript": "^4.6.4"
+    "ts-jest": "^28.0.5",
+    "typescript": "^4.7.4"
   },
   "dependencies": {
     "binary-search": "^1.3.6",
     "cross-fetch": "^3.1.5",
     "form-data": "^4.0.0",
+    "gyromagnetic-ratio": "^1.0.0",
     "is-any-array": "^2.0.0",
+    "linear-sum-assignment": "^1.0.4",
     "ml-array-mean": "^1.1.6",
     "ml-array-rescale": "^1.3.7",
     "ml-array-sequential-fill": "^1.1.8",
     "ml-array-sum": "^1.1.6",
-    "ml-gsd": "^11.2.0",
+    "ml-gsd": "^11.2.1",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.1.0",
-    "ml-matrix": "^6.10.0",
+    "ml-matrix": "^6.10.2",
     "ml-matrix-convolution": "^1.0.0",
     "ml-matrix-peaks-finder": "^1.0.0",
     "ml-peak-shape-generator": "^4.1.1",
     "ml-simple-clustering": "^0.1.0",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^11.5.0",
+    "ml-spectra-processing": "^11.7.0",
     "ml-tree-set": "^0.1.1",
-    "nmr-correlation": "^2.2.5",
+    "nmr-correlation": "^2.3.2",
     "openchemlib-utils": "^1.11.0",
-    "spectrum-generator": "^8.0.1"
+    "spectrum-generator": "^8.0.2"
   }
 }

package/src/apodization/apodization.ts

@@ -0,0 +1,34 @@
+import { DoubleArray } from 'cheminfo-types';
+
+import { applyWindow } from './applyWindow';
+import { compose, ShapeOptions } from './compose';
+
+export interface DataReIm {
+  /** Array of re values */
+  re: DoubleArray;
+  /** Array of im values */
+  im: DoubleArray;
+}
+
+interface ApodizationOptions {
+  /**
+   * number of points at the end of the shape to apply the window function inverted
+   * @default 0
+   */
+  pointsToShift?: number;
+  compose: ShapeOptions;
+}
+export function apodization(data: DataReIm, options: ApodizationOptions) {
+  const { compose: composeOptions, pointsToShift } = options;
+  const windowData = compose(composeOptions);
+
+  const applyWindowOptions = {
+    windowData,
+    pointsToShift,
+  };
+
+  const re = applyWindow(data.re, applyWindowOptions);
+  const im = applyWindow(data.im, applyWindowOptions);
+
+  return { re, im, windowData };
+}

package/src/apodization/applyWindow.ts

@@ -0,0 +1,51 @@
+import { DoubleArray } from 'cheminfo-types';
+
+export interface ApplyWindowOptions {
+  /**
+   * data of a window function it should be scaled to max = 1 to ensure compatibility with new apodizations.
+   */
+  windowData: DoubleArray;
+  /**
+   * Start Location for Applying Apodize Window
+   */
+  start?: number;
+  /**
+   * length of the window function
+   */
+  length?: number;
+  /**
+   * number of points at the end of the shape to apply the window function inverted
+   * @default 0
+   */
+  pointsToShift?: number;
+  /**
+   * output array
+   */
+  output?: DoubleArray;
+}
+
+/**
+ * pure function that applies a window function to the input data.
+ */
+export function applyWindow(data: DoubleArray, options: ApplyWindowOptions) {
+  const dataLength = data.length;
+
+  const {
+    windowData,
+    start = 0,
+    length = dataLength,
+    pointsToShift = 0,
+    output = new Float64Array(data),
+  } = options;
+
+  const firstEndPoint = Math.min(start + length, dataLength - pointsToShift);
+  for (let i = start, j = 0; i < firstEndPoint; i++) {
+    output[i] *= windowData[j++];
+  }
+
+  for (let i = dataLength - 1, j = 0; i > dataLength - pointsToShift - 1; i--) {
+    output[i] *= windowData[j++];
+  }
+
+  return output;
+}

package/src/apodization/compose.ts

@@ -0,0 +1,47 @@
+import { applyWindow } from './applyWindow';
+import { getFunction } from './getFunction';
+import type { WindowFunctions } from './shapes/WindowFunctions';
+import { getData } from './utils/getData';
+
+interface ShapeToAdd {
+  /**
+   * Start Location for Applying Apodize Window
+   */
+  start?: number;
+  /**
+   * parameters of the shape plus the kind of shape to identify
+   */
+  shape: WindowFunctions;
+}
+
+export interface ShapeOptions {
+  /**
+   * length of the window shape
+   */
+  length: number;
+
+  /**
+   * parameters of the shape plus the kind of shape to identify
+   */
+  shapes?: ShapeToAdd[];
+}
+
+export function compose(shapeOptions: ShapeOptions) {
+  const { length: dataLength, shapes = [] } = shapeOptions;
+  let data = new Float64Array(dataLength).fill(1);
+  shapes.forEach((options) => {
+    const { shape, start = 0 } = options;
+    const { options: shapeOptions } = shape;
+    const length =
+      'length' in shapeOptions ? shapeOptions.length : dataLength - start;
+
+    const windowData = getData(getFunction(shape), length);
+    applyWindow(data, {
+      windowData,
+      length,
+      start,
+      output: data,
+    });
+  });
+  return data;
+}

package/src/apodization/getFunction.ts

@@ -0,0 +1,15 @@
+import type { WindowFunctions } from './shapes/WindowFunctions';
+import { exponential } from './shapes/exponential';
+import { lorentzToGauss } from './shapes/lorentzToGauss';
+
+export function getFunction(shape: WindowFunctions) {
+  const { kind, options } = shape;
+  switch (kind) {
+    case 'exponential':
+      return exponential(options);
+    case 'lorentzToGauss':
+      return lorentzToGauss(options);
+    default:
+      throw Error(`Unknown distribution ${kind as string}`);
+  }
+}

package/src/apodization/shapes/WindowFunctions.ts

@@ -0,0 +1,14 @@
+import type { ExponentialOptions } from './exponential';
+import type { LorentzToGaussOptions } from './lorentzToGauss';
+
+interface Exponential {
+  kind: 'exponential';
+  options: ExponentialOptions;
+}
+
+interface LorentToGauss {
+  kind: 'lorentzToGauss';
+  options: LorentzToGaussOptions;
+}
+
+export type WindowFunctions = Exponential | LorentToGauss;

package/src/apodization/shapes/exponential.ts

@@ -0,0 +1,16 @@
+export interface ExponentialOptions {
+  /**
+   * line broadening value in Hz, a negative value will invert the shape
+   */
+  lb: number;
+  /**
+   * increment value in time or the independent value
+   */
+  dw: number;
+}
+
+export function exponential(options: ExponentialOptions) {
+  const { lb, dw } = options;
+  const coefExp = -lb * Math.PI * dw;
+  return (i: number) => Math.exp(coefExp * i);
+}

package/src/apodization/shapes/lorentzToGauss.ts

@@ -0,0 +1,41 @@
+export interface LorentzToGaussOptions {
+  /**
+   * size of the shape function
+   */
+  length: number;
+  /**
+   * increment value in time or the independent value
+   */
+  dw: number;
+  /**
+   * Gaussian Broaden Width, Hz
+   * @default 0
+   */
+  gaussianHz?: number;
+  /**
+   * Inverse Exponential Width, Hz
+   * @default 0
+   */
+  exponentialHz?: number;
+  /**
+   * Location of Gauss Maximum, this value should be between 0 to 1
+   * @default 0
+   */
+  center?: number;
+}
+
+export function lorentzToGauss(options: LorentzToGaussOptions) {
+  const { dw, length, gaussianHz = 0, exponentialHz = 0, center = 0 } = options;
+
+  if (center > 1 || center < 0) {
+    throw new Error(
+      'The center of gaussian shape should be inside of the window function: 0 - 1',
+    );
+  }
+
+  const C5 = Math.pow(0.6 * Math.PI * gaussianHz * dw, 2);
+  const C2 = center * (length - 1);
+  const C6 = Math.PI * dw * exponentialHz;
+
+  return (i: number) => Math.exp(i * C6 - Math.pow(C2 - i, 2) * C5);
+}

package/src/apodization/utils/getData.ts

@@ -0,0 +1,15 @@
+/**
+ * generate and scale the data of a window function
+ */
+export function getData(func: (i: number) => number, length: number) {
+  const data = new Float64Array(length);
+  let max = Number.MIN_SAFE_INTEGER;
+  for (let i = 0; i < length; i++) {
+    const value = func(i);
+    data[i] = value;
+    if (value > max) max = value;
+  }
+
+  for (let i = 0; i < length; i++) data[i] /= max;
+  return data;
+}

package/src/assignment/utils/buildAssignments.ts

@@ -1,4 +1,4 @@
-import treeSet from 'ml-tree-set';
+import TreeSet from 'ml-tree-set';
 
 import { Targets, NMRSignal1DWithAtomsAndDiaIDs } from '../get1HAssignments';
 
@@ -38,7 +38,7 @@ export interface Predictions1Dassignments {
 }
 
 export interface StoreAssignments {
-  solutions: treeSet;
+  solutions: TreeSet;
   nSolutions: number;
 }
 
@@ -64,7 +64,7 @@ export async function buildAssignments(props: BuildAssignmentsProps) {
   let timeStart = date.getTime();
 
   let store: StoreAssignments = {
-    solutions: new treeSet(comparator),
+    solutions: new TreeSet(comparator),
     nSolutions: 0,
   };
 
@@ -97,7 +97,7 @@ export async function buildAssignments(props: BuildAssignmentsProps) {
   let partial = fillPartial(nSources);
 
   store = {
-    solutions: new treeSet(comparator),
+    solutions: new TreeSet(comparator),
     nSolutions: 0,
   };
 

package/src/assignment/utils/exploreTreeRec.ts

@@ -113,7 +113,7 @@ function addSolution(store: StoreAssignments, props: AddSolutionProps) {
   store.nSolutions++;
   let solution: SolutionAssignment = {
     assignment: JSON.parse(JSON.stringify(partial)),
-    score: score,
+    score,
   };
 
   if (store.nSolutions >= maxSolutions) {

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

@@ -1,4 +1,4 @@
-import treeSet from 'ml-tree-set';
+import TreeSet from 'ml-tree-set';
 import { Values } from 'nmr-correlation';
 import { Molecule } from 'openchemlib';
 import { getConnectivityMatrix } from 'openchemlib-utils';
@@ -135,7 +135,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
   let lowerBoundScore = minScore;
 
   let store: StoreAssignments = {
-    solutions: new treeSet(comparator),
+    solutions: new TreeSet(comparator),
     nSolutions: 0,
   };
 
@@ -204,7 +204,7 @@ export async function buildAssignments(props: BuildAssignmentInput) {
     );
 
     store = {
-      solutions: new treeSet(comparator),
+      solutions: new TreeSet(comparator),
       nSolutions: 0,
     };
 

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

@@ -42,7 +42,7 @@ export function hasIDs(
   }
 }
 
-export function addIDs(data: NMRRange[] | NMRZone[]) {
+export function addIDs<T extends NMRRange[] | NMRZone[]>(data: T) {
   for (const element of data) {
     if (!element.id) element.id = generateID();
     for (let signal of element.signals || []) {

package/src/databases/DatabaseNMREntry.ts

@@ -1,6 +1,9 @@
+import { OCLMolecule } from 'cheminfo-types';
+
 import { NMRRange } from '../xy/NMRRange';
 
 export interface DatabaseNMREntry {
+  ocl?: OCLMolecule;
   smiles?: string;
   solvent: string;
   nucleus: string;