peptide - npm Package Compare versions

Comparing version 0.0.1 to 1.0.0

bower.json

 {
   "name": "peptide",
-  "version": "0.0.1",
+  "version": "1.0.0",
   "description": "Peptide",
@@ -29,2 +29,2 @@ "keywords": [
   ]
-}
+}

package.json

 {
   "name": "peptide",
-  "version": "0.0.1",
+  "version": "1.0.0",
   "description": "Peptide",
@@ -10,5 +10,2 @@ "keywords": [
   ],
-  "config": {
-    "name": "Peptide"
-  },
   "author": "Luc Patiny",
@@ -31,18 +28,10 @@ "contributors": [
     "test": "mocha --require should --reporter mocha-better-spec-reporter --recursive",
-    "build": "gulp build"
+    "build": "cheminfo build --root Peptide"
   },
   "devDependencies": {
-    "browserify": "^8.1.3",
-    "del": "^1.1.1",
-    "gulp": "^3.8.11",
-    "gulp-header": "^1.2.2",
-    "gulp-rename": "^1.2.0",
-    "gulp-sourcemaps": "^1.3.0",
-    "gulp-uglify": "^1.1.0",
-    "mocha": "latest",
-    "mocha-better-spec-reporter": "latest",
-    "should": "latest",
-    "vinyl-buffer": "^1.0.0",
-    "vinyl-source-stream": "^1.0.0"
+    "cheminfo-tools": "^1.0.2",
+    "mocha": "^2.2.5",
+    "mocha-better-spec-reporter": "^2.1.1",
+    "should": "^7.0.2"
   }
-}
+}

README.md

@@ -10,2 +10,83 @@ # peptide
 
+## Amino acids
+
+#### getInfo()
+
+Returns an array of information about amino acids
+
+
+## Amino acids sequence
+
+#### convertAASequence(sequence)
+
+Returns a peptidic sequence from a PDB or one letter code to the internal molecular formula format
+
+__Arguments__
+
+* `sequence` - string with the amino acids sequence
+
+#### chargePeptide(mf)
+
+Add a positive charge on Arg, His and Lys
+
+__Arguments__
+
+* `mf` - string with a molecular formula to charge
+
+#### generatePeptideFragments(mf, [options])
+
+Generate [peptide fragmentation](http://en.wikipedia.org/wiki/Peptide_sequence_tag).
+Returns an array of molecular formulas with the different fragments.
+
+__Arguments__
+
+* `mf` - string with the molecular formula
+* `options` - object with requested fragments. Default: `{a:false, b:true, c:false, x:false, y:true, z:false, i:false}`
+
+You can also specify internal fragments using the options 'ya' and 'yb'.
+
+## Isoelectric Point
+
+pKa of amino acids is based on https://en.wikipedia.org/wiki/Amino_acid.
+
+#### calculateCharge(sequence, ph)
+
+Calculate the charge for a specific amino acid sequence. The sequence should be entered in the form "HAlaGlyOH".
+Please take care about the N and C terminal end. You may use the methods "convertAASequence" to create such a sequence
+from other format.
+
+__Arguments__
+
+* `sequence` - string with the amino acids sequence
+* `ph` - ph for which to calculate the charge. Default: 7.0
+
+#### calculateIEP(sequence)
+
+Calculate the isoelectric point for a specific amino acid sequence. The sequence should be entered in the form "HAlaGlyOH".
+Please take care about the N and C terminal end. You may use the methods "convertAASequence" to create such a sequence
+from other format.
+
+__Arguments__
+
+* `sequence` - string with the amino acids sequence
+
+#### calculateIEPChart(sequence)
+
+Returns an object containing the y and yAbs array of the charge of the peptide for a pH that goes from 0 to 14.
+
+__Arguments__
+
+* `sequence` - string with the amino acids sequence
+
+#### getColorForIEP(iep)
+
+Returns a color based on the isoelectric point :
+
+* 0 -> 7 means that at pH 7 it is charged negatively (blue)
+* 7 -> 14 means that at pH7 it is charged positively (red)
+
+__Arguments__
+
+* `iep` - the value of the isoelectric point
+
 ## License
@@ -12,0 +93,0 @@

src/index.js

@@ -6,5 +6,3 @@ 'use strict';
 
-console.log(IEP);
 
-
 exports.getInfo = function () {
@@ -31,2 +29,12 @@ return aa;
 
+exports.getColorForIEP = function (iep) {
+    return IEP.getColor(iep);
+}
+
+exports.calculateCharge = function (sequence, ph) {
+    var aas=sequence.replace(/([A-Z])/g," $1").split(/ /);
+    aas=aas.slice(2,aas.length-2);
+    return IEP.calculateCharge(aas, ph);
+}
+
 exports.generatePeptideFragments = function generatePeptideFragments(mf, options) {
@@ -41,3 +49,5 @@ if (options === undefined) {
             z: false,
-            i: false
+            i: false,
+            yb: false,
+            ya: false
         };
@@ -57,4 +67,15 @@ }
         if (options.i) mfs.push(mfparts[i]+"HC-1O-1(+1)$i:"+mfparts[i]);
+
+        if (options.ya || options.yb) { // we have double fragmentations
+            for (var j=i+1; j<mfparts.length;j++) {
+                var iTerm='';
+                for (var k=i; k<j; k++) {
+                    iTerm+=mfparts[k];
+                }
+                addITerm(mfs, iTerm, i, j, options);
+            }
+        }
     }
 
+
     if (mfs.length === 0) {
@@ -140,2 +161,7 @@ mfs = mfs.concat([mf]);
 
+function addITerm(mfs, iTerm, i, j, options) {
+    if (options.ya) mfs.push("H"+iTerm+"C-1O-1(+1)$a"+j+"y"+i);
+    if (options.yb) mfs.push("H"+iTerm+"(+1)$b"+j+"y"+i);
+}
+
 function addCTerm(mfs, cTerm, i, options) {
@@ -142,0 +168,0 @@ if (options.x) mfs.push("CO(+1)"+cTerm+"$x"+i);

src/isoElectricPoint.js

@@ -14,5 +14,5 @@ 'use strict';
 
-function calculateCharge(aaSequence, pH) {
+function calculateCharge(aas, pH) {
     if (! pH) pH=7.0;
-    var combined=combine(aaSequence);
+    var combined=combine(aas);
     if (!combined) return;
@@ -79,11 +79,11 @@ var charge=calculateForPh(combined, pH);
 // we will combine the amino acids
-function combine(aaSequence) {
+function combine(aas) {
     var combined={};
-    if (aaObject[aaSequence[0]]) {
-        combined.first=aaObject[aaSequence[0]].pKaN;
+    if (aaObject[aas[0]]) {
+        combined.first=aaObject[aas[0]].pKaN;
     } else {
         return;
     }
-    if (aaObject[aaSequence[aaSequence.length-1]]) {
-        combined.last=aaObject[aaSequence[aaSequence.length-1]].pKaC;
+    if (aaObject[aas[aas.length-1]]) {
+        combined.last=aaObject[aas[aas.length-1]].pKaC;
     } else {
@@ -94,4 +94,4 @@ return;
     combined.acid={};
-    for (var i=0; i<aaSequence.length; i++) {
-        var aa=aaSequence[i];
+    for (var i=0; i<aas.length; i++) {
+        var aa=aas[i];
         if (! aaObject[aa]) return;
@@ -115,9 +115,26 @@ if (aaObject[aa].sc && aaObject[aa].sc.type) {
 
+/*
+ We can generate a color based on iep
+ 0 -> 7 means that at pH 7 it is charged negatively (blue)
+ 7 -> 14 means that at pH7 it is charged positively (red)
+ */
+function getColor(iep) {
+    if (iep<7) {
+        if (iep<3) iep=3;
+        var white=Math.round(255-(7-iep)*(200/4));
+        return "rgb("+white+","+white+",255)";
+    } else if (iep>7) {
+        if (iep>11) iep=11;
+        var white=Math.round(255-(iep-7)*(200/4));
+        return "rgb(255,"+white+","+white+")";
+    }
+    return "rgb(255,255,255)";
+}
 
-
 module.exports={
     calculateIEP: calculateIEP,
     calculateCharge: calculateCharge,
-    calculateChart: calculateChart
+    calculateChart: calculateChart,
+    getColor: getColor
 }
 

Fixed alerts

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

Total package byte prevSize

18416

increased by10.92%

Dev dependency count

4

decreased by-66.67%

Number of low quality alerts

0

decreased by-100%

Number of lines in readme file

103

increased by368.18%

Worsened metrics

Number of package files

12

decreased by-7.69%

Lines of code

540

decreased by-0.37%

No dependency changes