nmr-simulation - npm Package Compare versions

Comparing version 0.2.0 to 0.2.1

package.json

 {
   "name": "nmr-simulation",
-  "version": "0.2.0",
+  "version": "0.2.1",
   "description": "Simulate NMR spectra from spin systems",
@@ -53,3 +53,3 @@ "main": "src/index.js",
     "babili": "0.0.8",
-    "cheminfo-tools": "^1.3.4",
+    "cheminfo-tools": "^1.11.0",
     "eslint": "^3.9.1",
@@ -61,4 +61,4 @@ "eslint-config-cheminfo": "^1.5.2",
     "should": "^11.1.1",
-    "nmr-predictor": "0.2.3"
+    "nmr-predictor": "0.5.2"
   }
 }

src/__tests__/simulate1D.js

@@ -33,3 +33,3 @@ 'use strict';
         const predictor = new NmrPredictor('spinus');
-        predictor.predict(molfile, {group: false}).then(prediction => {
+        predictor.spinus(molfile, {group: true}).then(prediction => {
 
@@ -36,0 +36,0 @@ const spinSystem = nmr.SpinSystem.fromPrediction(prediction);

src/simulate1D.js

@@ -55,3 +55,3 @@ 'use strict';
         const intensities = [];
-        if (cluster.length>maxClusterSize) {
+        if (cluster.length > maxClusterSize) {
             //This is a single spin, but the cluster exceeds the maxClusterSize criteria
@@ -67,3 +67,3 @@ //we use the simple multiplicity algorithm
                 if (cluster[i] < 0) {
-                    jc = spinSystem.couplingConstants[index][clusterFake[i]];
+                    jc = spinSystem.couplingConstants[index][clusterFake[i]] / 2;
                     currentSize = frequencies.length;
@@ -280,3 +280,3 @@ for ( j=0 ; j < currentSize; j++) {
 
-                clusterHam.add(kron1.mul(couplingConstants[n][k]));
+                clusterHam.add(kron1.mul(couplingConstants[n][k] / 2));
             }
@@ -283,0 +283,0 @@ }

src/SpinSystem.js

@@ -38,3 +38,3 @@ 'use strict';
                 var idx = ids[withID];
-                jc[i][idx] = +tokens[6 + 3 * j]/2;
+                jc[i][idx] = +tokens[6 + 3 * j];
             }
@@ -51,4 +51,5 @@ }
 
-    static fromPrediction(result) {
-        const nSpins = result.length;
+    static fromPrediction(input) {
+        let predictions = SpinSystem._ungroupAtoms(input);
+        const nSpins = predictions.length;
         const cs = new Array(nSpins);
@@ -60,14 +61,14 @@ const jc = Matrix.zeros(nSpins, nSpins);
         for(i=0;i<nSpins;i++) {
-            cs[i] = result[i].delta;
-            ids[result[i].atomIDs[0]] = i;
+            cs[i] = predictions[i].delta;
+            ids[predictions[i].atomIDs[0]] = i;
         }
         for( i = 0; i < nSpins; i++) {
-            cs[i] = result[i].delta;
-            j = result[i].j;
+            cs[i] = predictions[i].delta;
+            j = predictions[i].j;
             for( k = 0; k < j.length; k++) {
                 //console.log(ids[result[i].atomIDs[0]],ids[j[k].assignment]);
-                jc[ids[result[i].atomIDs[0]]][ids[j[k].assignment]] = j[k].coupling;
-                jc[ids[j[k].assignment]][ids[result[i].atomIDs[0]]] = j[k].coupling;
+                jc[ids[predictions[i].atomIDs[0]]][ids[j[k].assignment]] = j[k].coupling;
+                jc[ids[j[k].assignment]][ids[predictions[i].atomIDs[0]]] = j[k].coupling;
             }
-            multiplicity[i] = result[i].integral+1;
+            multiplicity[i] = predictions[i].integral+1;
         }
@@ -78,2 +79,19 @@
 
+
+    static _ungroupAtoms(prediction) {
+        let result = [];
+        prediction.forEach(pred => {
+            let atomIDs = pred['atomIDs'];
+            for(let i = 0; i < atomIDs.length; i++) {
+                let tempPred = JSON.parse(JSON.stringify(pred));
+                tempPred.atomIDs = [atomIDs[i]];
+                tempPred.integral = 1;
+                result.push(tempPred);
+            }
+        });
+
+        return result;
+    }
+
+
     _initClusters() {
@@ -80,0 +98,0 @@ this.clusters = simpleClustering(this.connectivity, {out:"indexes"});

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Improved metrics

Total package byte prevSize

26514

increased by2.35%

Number of package files

9

increased by12.5%

Lines of code

597

increased by2.58%

No dependency changes