nmr-processing - npm Package Compare versions

Comparing version 0.11.1 to 0.12.0

CHANGELOG.md

 # Changelog
 
+## [0.12.0](https://www.github.com/cheminfo/nmr-processing/compare/v0.11.1...v0.12.0) (2021-03-05)
+
+
+### Features
+
+* add simulation of 1D nmr spectrum from signals ([247d523](https://www.github.com/cheminfo/nmr-processing/commit/247d523f80d2877713fa6d978027643b4fa78a3f))
+* use spectrum-generator in simulate1D ([9489d78](https://www.github.com/cheminfo/nmr-processing/commit/9489d78e1962c6cf834e14e24f46c876be6802e8))
+* use static function for spinSystem creation ([1db79c5](https://www.github.com/cheminfo/nmr-processing/commit/1db79c5c2e5901b366d48c88263116cbbb1d0972))
+
+
+### Bug Fixes
+
+* eslint ([69ac997](https://www.github.com/cheminfo/nmr-processing/commit/69ac9972cae991f27fe15648952593f92bcd91b9))
+* rename xyzJResAnalizer to xyzJResAnalyzer ([fbc80ee](https://www.github.com/cheminfo/nmr-processing/commit/fbc80ee9485f028f1c12f4a75571fa4eb6e6d031))
+
 ### [0.11.1](https://www.github.com/cheminfo/nmr-processing/compare/v0.11.0...v0.11.1) (2021-03-01)
@@ -4,0 +19,0 @@

package.json

 {
   "name": "nmr-processing",
-  "version": "0.11.1",
+  "version": "0.12.0",
   "description": "",
@@ -59,4 +59,8 @@ "main": "lib/index.js",
   "dependencies": {
+    "binary-search": "^1.3.6",
     "form-data": "^4.0.0",
+    "is-any-array": "^0.1.1",
+    "assign-deep": "^1.0.1",
     "ml-gsd": "^6.6.0",
+    "ml-hclust": "^1.3.0",
     "ml-levenberg-marquardt": "^3.1.0",
@@ -68,7 +72,9 @@ "ml-matrix": "^6.6.0",
     "ml-simple-clustering": "^0.1.0",
+    "ml-sparse-matrix": "^2.1.0",
     "ml-spectra-processing": "^5.5.3",
     "node-fetch": "^2.6.1",
     "openchemlib": "^7.3.0",
-    "openchemlib-utils": "^0.7.0"
+    "openchemlib-utils": "^0.7.0",
+    "spectrum-generator": "^4.7.0"
   }
 }

src/index.js

@@ -17,1 +17,2 @@ /**
 export * from './constants/couplingPatterns';
+export * from './xyz/xyzJResAnalyzer';

src/peaks/util/jAnalyzer.js

@@ -9,2 +9,3 @@ /*
 let maxErrorIter2 = 1; // Hz
+let jAxisKeys = { jAxis: 'x', intensity: 'intensity' };
 
@@ -18,3 +19,4 @@ export default {
    */
-  compilePattern: function (signal) {
+  compilePattern: function (signal, options = {}) {
+    let { jAxisKey = jAxisKeys } = options;
     signal.multiplicity = 'm';
@@ -24,3 +26,7 @@ // 1.1 symmetrize
     // the compilation process. The unit of those peaks will be in Hz
-    signal.symRank = symmetrizeChoiseBest(signal, maxErrorIter1, 1);
+    signal.symRank = symmetrizeChoiseBest(signal, {
+      maxError: maxErrorIter1,
+      iteration: 1,
+      jAxisKey,
+    });
     signal.asymmetric = true;
@@ -96,3 +102,2 @@ // Is the signal symmetric?
               for (let u = 2; u <= j; u++) {
-                // TODO improve those loops
                 let jSum = 0;
@@ -150,7 +155,5 @@ for (let i = 0; i < u; i++) {
     peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width;
-
   signal.integralData.from = peaks[0].x / signal.observe - peaks[0].width * 3;
   signal.integralData.to =
     peaks[nbPeaks - 1].x / signal.observe + peaks[nbPeaks - 1].width * 3;
-
   // Compile the pattern and format the constant couplings
@@ -160,6 +163,2 @@ signal.maskPattern = signal.mask2;
   signal.pattern = signal.multiplicity; // Our library depends on this parameter, but it is old
-  // console.log(signal);
-  /* if (DEBUG)        {
-        console.log('Final j-couplings: ' + JSON.stringify(Jc));
-    }*/
 }
@@ -338,4 +337,5 @@
  */
-function symmetrizeChoiseBest(signal, maxError, iteration) {
-  let symRank1 = symmetrize(signal, maxError, iteration);
+function symmetrizeChoiseBest(signal, options = {}) {
+  let { maxError, iteration, jAxisKey = jAxisKeys } = options;
+  let symRank1 = symmetrize(signal, maxError, iteration, jAxisKey);
   let tmpPeaks = signal.peaksComp;
@@ -346,3 +346,3 @@ let tmpMask = signal.mask;
     (signal.peaks[0].x + signal.peaks[signal.peaks.length - 1].x) / 2;
-  let symRank2 = symmetrize(signal, maxError, iteration);
+  let symRank2 = symmetrize(signal, maxError, iteration, jAxisKey);
   if (signal.peaksComp.length > tmpPeaks.length) {
@@ -367,3 +367,4 @@ return symRank2;
  */
-function symmetrize(signal, maxError, iteration) {
+function symmetrize(signal, maxError, iteration, key) {
+  let { jAxis, intensity } = key;
   // Before to symmetrize we need to keep only the peaks that possibly conforms the multiplete
@@ -375,4 +376,4 @@ let max, min, avg, ratio, avgWidth;
     peaks[i] = {
-      x: signal.peaks[i].x * signal.observe,
-      intensity: signal.peaks[i].intensity,
+      x: signal.peaks[i][jAxis] * signal.observe,
+      intensity: signal.peaks[i][intensity],
       width: signal.peaks[i].width,
@@ -408,3 +409,4 @@ };
     mask[i] = true;
-    heightSum += signal.peaks[i].intensity;
+    // heightSum += signal.peaks[i].intensity;
+    heightSum += peaks[i].intensity;
   }
@@ -510,3 +512,3 @@
   if (symFactor > 0.8 && symFactor < 0.97 && iteration < 2) {
-    return symmetrize(signal, maxErrorIter2, 2);
+    return symmetrize(signal, maxErrorIter2, 2, key);
   } else {
@@ -513,0 +515,0 @@ // Center the given pattern at cs and symmetrize x

src/prediction/predictionProton.js

@@ -74,3 +74,3 @@ import FormData from 'form-data';
         coupling: Number(couplings[i + 2]),
-        assignment: Number(couplings[i]),
+        assignment: Number(couplings[i] - 1),
       });
@@ -77,0 +77,0 @@ }

src/xyz/xyzAutoPeaksPicking.js

@@ -107,7 +107,2 @@ import { Matrix } from 'ml-matrix';
 
-// How noisy is the spectrum depending on the kind of experiment.
-//const getLoGnStdDevNMR = (isHomoNuclear) => {
-//  return isHomoNuclear ? 1.5 : 3;
-//};
-
 /**
@@ -161,2 +156,6 @@ * This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed
     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;
 
@@ -201,9 +200,6 @@ // Still having problems to correctly detect peaks on those areas. So I'm removing everything there.
       let sumZ = 0;
-      for (let jPeak = clusters[iCluster].length - 1; jPeak >= 0; jPeak--) {
+      // for (let jPeak = clusters[iCluster].length - 1; jPeak >= 0; jPeak--) {
+      for (let jPeak = 0; jPeak < clusters[iCluster].length; jPeak++) {
         if (clusters[iCluster][jPeak] === 1) {
-          peaks2D.push({
-            x: peaks[jPeak].x,
-            y: peaks[jPeak].y,
-            z: peaks[jPeak].z,
-          });
+          peaks2D.push(peaks[jPeak]);
           signal.shiftX += peaks[jPeak].x * peaks[jPeak].z;
@@ -228,4 +224,4 @@ signal.shiftY += peaks[jPeak].y * peaks[jPeak].z;
       signal.fromTo = [
-        { from: minX + dx * minMax1[0], to: minX + dx * minMax1[1] },
-        { from: minY + dy * minMax2[0], to: minY + dy * minMax2[1] },
+        { from: minMax1[0], to: minMax1[1] },
+        { from: minMax2[0], to: minMax2[1] },
       ];
@@ -232,0 +228,0 @@ signal.shiftX /= sumZ;

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Improved metrics

Total package byte prevSize

295911

increased by11.52%

Number of package files

32

increased by18.52%

Lines of code

11512

increased by8.19%

Worsened metrics

Dependency count

18

increased by50%

Dependency changes

• + Addedassign-deep@^1.0.1

• + Addedbinary-search@^1.3.6

• + Addedis-any-array@^0.1.1

• + Addedml-hclust@^1.3.0

• + Addedml-sparse-matrix@^2.1.0

• + Addedspectrum-generator@^4.7.0

• + Addedbinary-search@1.3.6(transitive)

• + Addedd3-random@2.2.2(transitive)

• + Addedheap@0.2.7(transitive)

• + Addedis-any-array@0.1.1(transitive)

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

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

• + Addedml-hash-table@1.0.0(transitive)

• + Addedml-hclust@1.3.0(transitive)

• + Addedml-sparse-matrix@2.1.0(transitive)

• + Addedml-xsadd@2.0.0(transitive)

• + Addednum-sort@2.1.0(transitive)

• + Addedspectrum-generator@4.8.1(transitive)