nmr-simulation - npm Package Compare versions

Comparing version 0.2.2 to 1.0.0

package.json

 {
   "name": "nmr-simulation",
-  "version": "0.2.2",
+  "version": "1.0.0",
   "description": "Simulate NMR spectra from spin systems",
@@ -9,7 +9,5 @@ "main": "src/index.js",
     "eslint-fix": "npm run eslint -- --fix",
-    "test": "npm run test-mocha",
-    "test-mocha": "mocha --compilers js:babel-register --require should --reporter mocha-better-spec-reporter --recursive src/**/__tests__/**/*.js",
-    "test-cov": "istanbul cover _mocha -- --compilers js:babel-register --require should --reporter dot --recursive src/**/__tests__/**/*.js",
-    "test-travis": "istanbul cover _mocha --report lcovonly -- --compilers js:babel-register --require should --reporter mocha-better-spec-reporter --recursive src/**/__tests__/**/*.js && npm run eslint",
-    "build": "cheminfo build --no-uglify"
+    "test": "npm run test-mocha && npm run eslint",
+    "test-mocha": "mocha --require should --reporter mocha-better-spec-reporter --recursive",
+    "build": "cheminfo build"
   },
@@ -39,4 +37,4 @@ "files": [
     "binary-search": "^1.3.2",
-    "ml-hclust": "1.1.0",
-    "ml-matrix": "^1.1.2",
+    "ml-hclust": "^1.3.0",
+    "ml-matrix": "^2.3.0",
     "ml-simple-clustering": "0.1.0",
@@ -48,9 +46,2 @@ "ml-sparse-matrix": "^0.2.1",
   "devDependencies": {
-    "babel-cli": "^6.2.0",
-    "babel-core": "^6.2.1",
-    "babel-plugin-transform-es2015-block-scoping": "^6.1.18",
-    "babel-preset-es2015-node4": "^2.0.1",
-    "babel-register": "^6.2.0",
-    "babelify": "^7.2.0",
-    "babili": "0.0.8",
     "cheminfo-tools": "^1.11.0",
@@ -62,5 +53,5 @@ "eslint": "^3.9.1",
     "mocha-better-spec-reporter": "^3.0.1",
-    "should": "^11.1.1",
-    "nmr-predictor": "0.5.2"
+    "nmr-predictor": "^1.0.0",
+    "should": "^11.1.1"
   }
 }

src/simulate1D.js

@@ -21,3 +21,3 @@ 'use strict';
     const maxClusterSize = options.maxClusterSize || 10;
-    const output = options.output || "y";
+    const output = options.output || 'y';
 
@@ -48,3 +48,3 @@ const chemicalShifts = spinSystem.chemicalShifts.slice();
         for (i = 0; i < cluster.length; i++) {
-            clusterFake[i] = cluster[i]<0?-cluster[i]-1:cluster[i];
+            clusterFake[i] = cluster[i] < 0 ? -cluster[i] - 1 : cluster[i];
         }
@@ -60,12 +60,12 @@
             //Add the central peak. It will be split with every single J coupling.
-            var index  = 0;
-            while (cluster[index++]<0);
-            index = cluster[index-1];
+            var index = 0;
+            while (cluster[index++] < 0);
+            index = cluster[index - 1];
             var currentSize, jc;
             frequencies.push(-chemicalShifts[index]);
-            for (i = 0;i < cluster.length; i++) {
+            for (i = 0; i < cluster.length; i++) {
                 if (cluster[i] < 0) {
                     jc = spinSystem.couplingConstants[index][clusterFake[i]] / 2;
                     currentSize = frequencies.length;
-                    for ( j=0 ; j < currentSize; j++) {
+                    for (j = 0; j < currentSize; j++) {
                         frequencies.push(frequencies[j] + jc);
@@ -78,6 +78,6 @@ frequencies[j] -= jc;
             frequencies.sort(sortAsc);
-            sumI=frequencies.length;
-            weight=1;
+            sumI = frequencies.length;
+            weight = 1;
 
-            for (i=0;i<sumI;i++){
+            for (i = 0; i < sumI; i++) {
                 intensities.push(1);
@@ -176,3 +176,2 @@ }
         const numFreq = frequencies.length;
-        //console.log("New Spin");
         if (numFreq > 0) {
@@ -199,11 +198,13 @@ weight = weight / sumI;
     }
-    if(output==="xy")
-        return {x:_getX(options.from, options.to, nbPoints),y:result};
-    if(output == "y")
+    if (output === 'xy') {
+        return {x: _getX(options.from, options.to, nbPoints), y: result};
+    }
+    if (output === 'y') {
         return result;
+    }
+    throw new RangeError('wrong output option');
 }
 
 function addPeak(result, freq, height, from, to, nbPoints, gaussian) {
-    //console.log(freq, height)
-    const center = (nbPoints * (-freq-from) / (to - from)) | 0;
+    const center = (nbPoints * (-freq - from) / (to - from)) | 0;
     const lnPoints = gaussian.length;
@@ -289,7 +290,7 @@ var index = 0;
 
-function _getX(from, to, nbPoints){
+function _getX(from, to, nbPoints) {
     const x = new Array(nbPoints);
-    const dx = (to-from)/(nbPoints-1);
-    for (var i = 0 ; i < nbPoints; i++) {
-        x[i]=from+i*dx;
+    const dx = (to - from) / (nbPoints - 1);
+    for (var i = 0; i < nbPoints; i++) {
+        x[i] = from + i * dx;
     }
@@ -296,0 +297,0 @@ return x;

src/simulate2D.js

@@ -5,6 +5,6 @@ 'use strict';
 
-let defOptions = {'H': {frequency: 400, lineWidth: 10}, 'C': {frequency: 100, lineWidth: 10}}
+let defOptions = {'H': {frequency: 400, lineWidth: 10}, 'C': {frequency: 100, lineWidth: 10}};
 
 function simule2DNmrSpectrum(table, options) {
-    var i, j;
+    var i;
     const fromLabel = table[0].fromAtomLabel;
@@ -14,4 +14,4 @@ const toLabel = table[0].toLabel;
     const frequencyY = options.frequencyY || defOptions[toLabel].frequency;
-    var lineWidthX = options.lineWidthX  || defOptions[fromLabel].lineWidth;
-    var lineWidthY = options.lineWidthY  || defOptions[toLabel].lineWidth;
+    var lineWidthX = options.lineWidthX || defOptions[fromLabel].lineWidth;
+    var lineWidthY = options.lineWidthY || defOptions[toLabel].lineWidth;
 
@@ -26,3 +26,3 @@ var sigmaX = lineWidthX / frequencyX;
     i = 1;
-    while(i < table.length) {
+    while (i < table.length) {
         minX = Math.min(minX, table[i].fromChemicalShift);
@@ -35,10 +35,14 @@ maxX = Math.max(maxX, table[i].fromChemicalShift);
 
-    if(options.firstX !== null && !isNaN(options.firstX))
+    if (options.firstX !== null && !isNaN(options.firstX)) {
         minX = options.firstX;
-    if(options.firstY !== null && !isNaN(options.firstY))
+    }
+    if (options.firstY !== null && !isNaN(options.firstY)) {
         minY = options.firstY;
-    if(options.lastX !== null && !isNaN(options.lastX))
-        maxX = options.lastX
-    if(options.lastY !== null && !isNaN(options.lastY))
+    }
+    if (options.lastX !== null && !isNaN(options.lastX)) {
+        maxX = options.lastX;
+    }
+    if (options.lastY !== null && !isNaN(options.lastY)) {
         maxY = options.lastY;
+    }
 
@@ -50,3 +54,3 @@ var nbPointsX = options.nbPointsX || 512;
     i = 0;
-    while(i < table.length) {
+    while (i < table.length) {
         //parameters.couplingConstant = table[i].j;
@@ -59,4 +63,4 @@ //parameters.pathLength = table[i].pathLength;
             widthX: unitsToArrayPoints(sigmaX + minX, minX, maxX, nbPointsX),
-            widthY: unitsToArrayPoints(sigmaY+ minY, minY, maxY, nbPointsY)
-        }
+            widthY: unitsToArrayPoints(sigmaY + minY, minY, maxY, nbPointsY)
+        };
         addPeak(spectraMatrix, peak);
@@ -76,3 +80,3 @@ i++;
     var toX = Math.min(matrix[0].length - 1, Math.round(peak.x + peak.widthX * nSigma));
-    var fromY =  Math.max(0, Math.round(peak.y - peak.widthY * nSigma));
+    var fromY = Math.max(0, Math.round(peak.y - peak.widthY * nSigma));
     var toY = Math.min(matrix.length - 1, Math.round(peak.y + peak.widthY * nSigma));
@@ -86,3 +90,3 @@
                 Math.pow(peak.y - j, 2) / squareSigmaY;
-            var result = 10000 * peak.z * Math.exp( - exponent);
+            var result = 10000 * peak.z * Math.exp(-exponent);
             matrix[j][i] += result;
@@ -94,2 +98,2 @@ }
 
-module.exports = simule2DNmrSpectrum;
+module.exports = simule2DNmrSpectrum;

src/SpinSystem.js

@@ -6,4 +6,3 @@ 'use strict';
 const simpleClustering = require('ml-simple-clustering');
-const hlClust = require("ml-hclust");
-const DEBUG = false;
+const hlClust = require('ml-hclust');
 
@@ -52,3 +51,3 @@ class SpinSystem {
     static fromPrediction(input) {
-        let predictions = SpinSystem._ungroupAtoms(input);
+        let predictions = SpinSystem.ungroupAtoms(input);
         const nSpins = predictions.length;
@@ -59,11 +58,11 @@ const cs = new Array(nSpins);
         const ids = {};
-        var i,k,j;
-        for(i=0;i<nSpins;i++) {
+        var i, k, j;
+        for (i = 0; i < nSpins; i++) {
             cs[i] = predictions[i].delta;
             ids[predictions[i].atomIDs[0]] = i;
         }
-        for( i = 0; i < nSpins; i++) {
+        for (i = 0; i < nSpins; i++) {
             cs[i] = predictions[i].delta;
             j = predictions[i].j;
-            for( k = 0; k < j.length; k++) {
+            for (k = 0; k < j.length; k++) {
                 //console.log(ids[result[i].atomIDs[0]],ids[j[k].assignment]);
@@ -73,3 +72,3 @@ jc[ids[predictions[i].atomIDs[0]]][ids[j[k].assignment]] = j[k].coupling;
             }
-            multiplicity[i] = predictions[i].integral+1;
+            multiplicity[i] = predictions[i].integral + 1;
         }
@@ -81,7 +80,7 @@
 
-    static _ungroupAtoms(prediction) {
+    static ungroupAtoms(prediction) {
         let result = [];
         prediction.forEach(pred => {
-            let atomIDs = pred['atomIDs'];
-            for(let i = 0; i < atomIDs.length; i++) {
+            let atomIDs = pred.atomIDs;
+            for (let i = 0; i < atomIDs.length; i++) {
                 let tempPred = JSON.parse(JSON.stringify(pred));
@@ -99,3 +98,3 @@ tempPred.atomIDs = [atomIDs[i]];
     _initClusters() {
-        this.clusters = simpleClustering(this.connectivity, {out:"indexes"});
+        this.clusters = simpleClustering(this.connectivity, {out: 'indexes'});
     }
@@ -118,16 +117,15 @@
 
-    _calculateBetas(J, frequency){
+    _calculateBetas(J, frequency) {
         var betas = Matrix.zeros(J.length, J.length);
         //Before clustering, we must add hidden J, we could use molecular information if available
-        var i,j;
-        for( i=0;i<J.rows;i++){
-            for( j=i;j<J.columns;j++){
-                if((this.chemicalShifts[i]-this.chemicalShifts[j])!=0){
-                    betas[i][j] = 1 - Math.abs(J[i][j]/((this.chemicalShifts[i]-this.chemicalShifts[j])*frequency));
+        var i, j;
+        for (i = 0; i < J.rows; i++) {
+            for (j = i; j < J.columns; j++) {
+                if ((this.chemicalShifts[i] - this.chemicalShifts[j]) !== 0) {
+                    betas[i][j] = 1 - Math.abs(J[i][j] / ((this.chemicalShifts[i] - this.chemicalShifts[j]) * frequency));
                     betas[j][i] = betas[i][j];
+                } else if (!(i === j || J[i][j] !== 0)) {
+                    betas[i][j] = 1;
+                    betas[j][i] = 1;
                 }
-                else if( !(i == j || J[i][j] !== 0) ){
-                        betas[i][j] = 1;
-                        betas[j][i] = 1;
-                    }
             }
@@ -138,28 +136,24 @@ }
 
-    ensureClusterSize(options){
-        var betas = this._calculateBetas(this.couplingConstants, options.frequency||400);
-        var cluster = hlClust.agnes(betas, {isDistanceMatrix:true});
+    ensureClusterSize(options) {
+        var betas = this._calculateBetas(this.couplingConstants, options.frequency || 400);
+        var cluster = hlClust.agnes(betas, {isDistanceMatrix: true});
         var list = [];
-        this._splitCluster(cluster, list, options.maxClusterSize||8, false);
+        this._splitCluster(cluster, list, options.maxClusterSize || 8, false);
         var clusters = this._mergeClusters(list);
         this.nClusters = clusters.length;
         //console.log(clusters);
-        this.clusters  = new Array(clusters.length);
+        this.clusters = new Array(clusters.length);
         //System.out.println(this.conmatrix);
-        for(var j=0;j<this.nClusters;j++) {
+        for (var j = 0; j < this.nClusters; j++) {
             this.clusters[j] = [];
-            for(var i = 0; i < this.nSpins; i++) {
-                if(clusters[j][i] !== 0) {
-                    if (clusters[j][i] < 0)
+            for (var i = 0; i < this.nSpins; i++) {
+                if (clusters[j][i] !== 0) {
+                    if (clusters[j][i] < 0) {
                         this.clusters[j].push(-(i + 1));
-                    else
+                    } else {
                         this.clusters[j].push(i);
+                    }
                 }
             }
         }
-        if(DEBUG){
-            console.log("Cluster list");
-            console.log(this.clusters);
-
-        }
     }
@@ -173,7 +167,6 @@
     _splitCluster(cluster, clusterList, maxClusterSize, force) {
-        if(!force && cluster.index.length <= maxClusterSize) {
+        if (!force && cluster.index.length <= maxClusterSize) {
             clusterList.push(this._getMembers(cluster));
-        }
-        else{
-            for(var child of cluster.children){
+        } else {
+            for (var child of cluster.children) {
                 if (!isNaN(child.index) || child.index.length <= maxClusterSize) {
@@ -184,6 +177,6 @@ var members = this._getMembers(child);
                     for (var i = 0; i < this.nSpins; i++) {
-                        if (members[i] == 1) {
+                        if (members[i] === 1) {
                             count++;
                             for (var j = 0; j < this.nSpins; j++) {
-                                if (this.connectivity[i][j] == 1 && members[j] == 0) {
+                                if (this.connectivity[i][j] === 1 && members[j] === 0) {
                                     members[j] = -1;
@@ -196,8 +189,8 @@ count++;
 
-                    if (count <= maxClusterSize)
+                    if (count <= maxClusterSize) {
                         clusterList.push(members);
-                    else {
-                        if (isNaN(child.index))
+                    } else {
+                        if (isNaN(child.index)) {
                             this._splitCluster(child, clusterList, maxClusterSize, true);
-                        else {
+                        } else {
                             //We have to threat this spin alone and use the resurrection algorithm instead of the simulation
@@ -208,4 +201,3 @@ members[child.index] = 2;
                     }
-                }
-                else{
+                } else {
                     this._splitCluster(child, clusterList, maxClusterSize, false);
@@ -224,11 +216,10 @@ }
         var members = new Array(this.nSpins);
-        for(var i = 0; i < this.nSpins; i++) {
-            members[i]=0;
+        for (var i = 0; i < this.nSpins; i++) {
+            members[i] = 0;
         }
-        if(!isNaN(cluster.index)) {
-            members[cluster.index*1] = 1;
-        }
-        else{
-            for(var index of cluster.index) {
-                members[index.index*1] = 1;
+        if (!isNaN(cluster.index)) {
+            members[cluster.index * 1] = 1;
+        } else {
+            for (var index of cluster.index) {
+                members[index.index * 1] = 1;
             }
@@ -242,12 +233,12 @@ }
         var clusterA, clusterB, i, j, index, common, count;
-        for(i = list.length-1; i >=0 ; i--) {
+        for (i = list.length - 1; i >= 0; i--) {
             clusterA = list[i];
             nElements = clusterA.length;
-            index=0;
+            index = 0;
 
             //Is it a candidate to be merged?
-            while(index < nElements && clusterA[index++] != -1);
+            while (index < nElements && clusterA[index++] !== -1);
 
-            if(index < nElements) {
-                for(j = list.length-1; j>= i+1; j--) {
+            if (index < nElements) {
+                for (j = list.length - 1; j >= i + 1; j--) {
                     clusterB = list[j];
@@ -258,7 +249,7 @@ //Do they have common elements?
                     count = 0;
-                    while(index < nElements) {
-                        if(clusterA[index]*clusterB[index] === -1) {
+                    while (index < nElements) {
+                        if (clusterA[index] * clusterB[index] === -1) {
                             common++;
                         }
-                        if(clusterA[index] !==0 || clusterB[index] !== 0) {
+                        if (clusterA[index] !== 0 || clusterB[index] !== 0) {
                             count++;
@@ -269,12 +260,11 @@ }
 
-                    if(common > 0 && count <= this.maxClusterSize) {
+                    if (common > 0 && count <= this.maxClusterSize) {
                         //Then we can merge those 2 clusters
                         index = 0;
-                        while(index<nElements) {
-                            if(clusterB[index] === 1) {
-                                clusterA[index]=1;
-                            }
-                            else{
-                                if(clusterB[index] === -1 && clusterA[index] !== 1) {
-                                    clusterA[index]=-1;
+                        while (index < nElements) {
+                            if (clusterB[index] === 1) {
+                                clusterA[index] = 1;
+                            } else {
+                                if (clusterB[index] === -1 && clusterA[index] !== 1) {
+                                    clusterA[index] = -1;
                                 }
@@ -285,3 +275,3 @@ }
                         //list.remove(clusterB);
-                        list.splice(j,1);
+                        list.splice(j, 1);
                         j++;
@@ -288,0 +278,0 @@ }

New alerts

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Found 1 instance in 1 package

Fixed alerts

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License

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Found 1 instance in 1 package

Dynamic require

Supply chain risk

Dynamic require can indicate the package is performing dangerous or unsafe dynamic code execution.

Found 1 instance in 1 package

No v1

Quality

Package is not semver >=1. This means it is not stable and does not support ^ ranges.

Found 1 instance in 1 package

Improved metrics

Dev dependency count

8

decreased by-46.67%

Number of low quality alerts

0

decreased by-100%

Number of low supply chain risk alerts

0

decreased by-100%

Worsened metrics

Total package byte prevSize

27081

decreased by-8.78%

Number of package files

8

decreased by-11.11%

Lines of code

616

decreased by-7.65%

Dependency changes

• + Addedheap@0.2.7(transitive)

• + Addedml-array-utils@0.3.0(transitive)

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

• + Addedml-hclust@1.3.0(transitive)

• + Addedml-matrix@2.3.0(transitive)

• - Removedml-array-utils@0.2.4(transitive)

• - Removedml-binary-search@1.1.2(transitive)

• - Removedml-hclust@1.1.0(transitive)

• - Removedml-matrix@1.4.0(transitive)

• Updatedml-hclust@^1.3.0

• Updatedml-matrix@^2.3.0