nmr-processing - npm Package Compare versions

Comparing version 1.0.1 to 1.1.0

CHANGELOG.md

 # Changelog
 
+## [1.1.0](https://www.github.com/cheminfo/nmr-processing/compare/v1.0.1...v1.1.0) (2021-04-02)
+
+
+### Features
+
+* splitSystem as independent function ([#53](https://www.github.com/cheminfo/nmr-processing/issues/53)) ([1054423](https://www.github.com/cheminfo/nmr-processing/commit/10544234125147b57e4171458ae5882c0d60c021))
+
+
+### Bug Fixes
+
+* signalJoinCouplings assignment join ([2fce7cb](https://www.github.com/cheminfo/nmr-processing/commit/2fce7cb749d86dceccbddd355a66fcc2ac9b4a05))
+
 ### [1.0.1](https://www.github.com/cheminfo/nmr-processing/compare/v1.0.0...v1.0.1) (2021-03-24)
@@ -4,0 +16,0 @@

package.json

 {
   "name": "nmr-processing",
-  "version": "1.0.1",
+  "version": "1.1.0",
   "description": "",
@@ -63,3 +63,3 @@ "main": "lib/index.js",
     "ml-gsd": "^6.6.1",
-    "ml-hclust": "^3.0.0",
+    "ml-hclust": "^1.3.0",
     "ml-levenberg-marquardt": "^3.1.1",
@@ -72,3 +72,3 @@ "ml-matrix": "^6.7.0",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-spectra-processing": "^5.8.0",
+    "ml-spectra-processing": "^5.9.0",
     "node-fetch": "^2.6.1",
@@ -75,0 +75,0 @@ "openchemlib-utils": "^1.0.0",

README.md

@@ -0,0 +0,0 @@ # nmr-processing

src/constants/couplingPatterns.js

@@ -0,0 +0,0 @@ export const couplingPatterns = [

src/constants/gyromagneticRatio.js

@@ -0,0 +0,0 @@ // sources:

src/constants/impurities.js

@@ -0,0 +0,0 @@ /* eslint-disable camelcase */

src/index.js

@@ -0,0 +0,0 @@ /**

src/peaks/peaksFilterImpurities.js

@@ -0,0 +0,0 @@ import { impurities } from '../constants/impurities';

src/peaks/peaksToRanges.js

@@ -0,0 +0,0 @@ // import { Ranges } from 'spectra-data-ranges';

src/peaks/util/determineRealTop.js

@@ -0,0 +0,0 @@ import LM from 'ml-levenberg-marquardt';

src/peaks/util/getKernel.js

@@ -0,0 +0,0 @@ export function getKernel(options = {}) {

src/peaks/util/jAnalyzer.js

@@ -0,0 +0,0 @@ /*

src/peaks/util/joinRanges.js

@@ -0,0 +0,0 @@ export function joinRanges(ranges) {

src/peaks/util/peakOptimizer.js

@@ -0,0 +0,0 @@ let diagonalError = 0.05;

src/prediction/predictionProton.js

@@ -0,0 +0,0 @@ import FormData from 'form-data';

src/ranges/rangesToACS.js

@@ -0,0 +0,0 @@ import { signalJoinCouplings } from '../signal/signalJoinCouplings';

src/signal/signalJoinCouplings.js

 import { couplingPatterns } from '../constants/couplingPatterns';
 
+const getNbAssignments = (assignment) =>
+  Array.isArray(assignment) ? assignment.length : 1;
+
+const getArrayOfMembers = (assignment, key) =>
+  Array.isArray(assignment[key]) ? assignment[key] : [assignment[key]];
+
 /**
@@ -15,6 +21,6 @@ * Join couplings smaller than a define tolerance.
     signal = JSON.parse(JSON.stringify(signal));
-    let cont = couplings[0].assignment ? couplings[0].assignment.length : 1;
+    let cont = getNbAssignments(couplings[0].assignment);
     let newNmrJs = [];
     let diaIDs = [];
-    let atoms = [];
+    let assignment = [];
     couplings.sort(function (a, b) {
@@ -24,6 +30,6 @@ return b.coupling - a.coupling;
     if (couplings[0].diaID) {
-      diaIDs = [couplings[0].diaID];
+      diaIDs = getArrayOfMembers(couplings[0], 'diaID');
     }
     if (couplings[0].assignment) {
-      atoms = [couplings[0].assignment];
+      assignment = getArrayOfMembers(couplings[0], 'assignment');
     }
@@ -34,8 +40,8 @@ for (let i = 0; i < couplings.length - 1; i++) {
       ) {
-        cont += couplings[i + 1].assignment
-          ? couplings[i + 1].assignment.length
-          : 1;
-        if (couplings[i + 1].diaID) diaIDs.push(couplings[i + 1].diaID);
+        cont += getNbAssignments(couplings[i + 1].assignment);
+        if (couplings[i + 1].diaID) {
+          diaIDs.push(...getArrayOfMembers(couplings[i + 1], 'diaID'));
+        }
         if (couplings[i + 1].assignment) {
-          atoms.push(couplings[i + 1].assignment);
+          assignment.push(...getArrayOfMembers(couplings[i + 1], 'assignment'));
         }
@@ -50,4 +56,4 @@ } else {
         }
-        if (atoms.length > 0) {
-          jTemp.assignment = atoms;
+        if (assignment.length > 0) {
+          jTemp.assignment = assignment;
         }
@@ -58,12 +64,11 @@
         if (couplings[i + 1].diaID) {
-          diaIDs = [couplings[i + 1].diaID];
+          diaIDs = getArrayOfMembers(couplings[i + 1], 'diaID');
         }
         if (couplings[i + 1].assignment) {
-          atoms = [couplings[i + 1].assignment];
+          assignment = getArrayOfMembers(couplings[i + 1], 'assignment');
         }
-        cont = couplings[i + 1].assignment
-          ? couplings[i + 1].assignment.length
-          : 1;
+        cont = getNbAssignments(couplings[i + 1].assignment);
       }
     }
+
     let jTemp = {
@@ -76,4 +81,4 @@ coupling: Math.abs(couplings[couplings.length - 1].coupling),
     }
-    if (atoms.length > 0) {
-      jTemp.assignment = atoms;
+    if (assignment.length > 0) {
+      jTemp.assignment = assignment;
     }
@@ -84,3 +89,4 @@ newNmrJs.push(jTemp);
   }
+
   return signal;
 }

src/signal/signalMultiplicityPattern.js

@@ -0,0 +0,0 @@ /**

src/signals/signalsToRanges.js

@@ -0,0 +0,0 @@ export function signalsToRanges(signals, options = {}) {

src/signals/signalsToXY.js

@@ -5,2 +5,3 @@ import rescale from 'ml-array-rescale';
 import simulate1D from './simulation/simulate1D';
+import { splitSpinSystem } from './simulation/splitSpinSystem';
 
@@ -32,4 +33,9 @@ /**
 
-  let spinSystem = signalsToSpinSystem(signals, { frequency, maxClusterSize });
+  let spinSystem = signalsToSpinSystem(signals);
 
+  spinSystem.clusters = splitSpinSystem(spinSystem, {
+    frequency,
+    maxClusterSize,
+  });
+
   let spectrum = simulate1D(spinSystem, {
@@ -36,0 +42,0 @@ frequency,

src/signals/simulation/getPauliMatrix.js

@@ -0,0 +0,0 @@ import { SparseMatrix } from 'ml-sparse-matrix';

src/signals/simulation/signalsToSpinSystem.js

 import Matrix from 'ml-matrix';
 import simpleClustering from 'ml-simple-clustering';
 
-import { ensureClusterSize } from './ensureClusterSize';
-
-export function signalsToSpinSystem(signals, options = {}) {
-  let { frequency = 400, maxClusterSize = 8 } = options;
+export function signalsToSpinSystem(signals) {
   const nSpins = signals.length;
@@ -46,3 +43,3 @@ const chemicalShifts = new Array(nSpins);
 
-  let spinSystem = {
+  return {
     clusters,
@@ -54,9 +51,2 @@ couplingConstants,
   };
-
-  spinSystem.clusters = ensureClusterSize(spinSystem, {
-    frequency,
-    maxClusterSize,
-  });
-
-  return spinSystem;
 }

src/signals/simulation/simulate1D.js

@@ -42,2 +42,3 @@ import binarySearch from 'binary-search';
   let peakWidth = lineWidth / frequencyMHz;
+
   shapeOptions.peakWidthFct = () => peakWidth;
@@ -44,0 +45,0 @@ let spectrumGenerator = new SpectrumGenerator(shapeOptions);

src/xy/xyAutoPeaksPicking.js

@@ -0,0 +0,0 @@ import { gsd, joinBroadPeaks, optimizePeaks } from 'ml-gsd';

src/xy/xyAutoRangesPicking.js

@@ -0,0 +0,0 @@ import { peaksFilterImpurities } from '../peaks/peaksFilterImpurities';

src/xyz/xyzAutoPeaksPicking.js

@@ -0,0 +0,0 @@ import { Matrix } from 'ml-matrix';

src/xyz/xyzJResAnalyzer.js

@@ -0,0 +0,0 @@ import assignDeep from 'assign-deep';

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Improved metrics

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2

decreased by-33.33%

Worsened metrics

Total package byte prevSize

317691

decreased by-3.53%

Dependency changes

• + Addedml-distance-euclidean@1.0.0(transitive)

• + Addedml-distance-matrix@1.0.0(transitive)

• + Addedml-hclust@1.3.0(transitive)

• - Removedml-distance-euclidean@2.0.0(transitive)

• - Removedml-distance-matrix@2.0.1(transitive)

• - Removedml-hclust@3.1.0(transitive)

• Updatedml-hclust@^1.3.0

• Updatedml-spectra-processing@^5.9.0