peptide - npm Package Compare versions

Comparing version 2.2.0 to 2.2.1

package.json

 {
   "name": "peptide",
-  "version": "2.2.0",
+  "version": "2.2.1",
   "description": "Peptide",
@@ -20,3 +20,3 @@ "keywords": [
   "license": "MIT",
-  "main": "lib/index.js",
+  "main": "lib/src/index.js",
   "module": "src/index.js",
@@ -27,3 +27,3 @@ "files": [
   ],
-  "gitHead": "28dae91d3b42556a23097ee08acfe4061f276ed0"
+  "gitHead": "838f98a30846d4b1721b8ed7aa94a55e854d7521"
 }

src/allowNeutralLoss.js

@@ -18,6 +18,6 @@ /**
 function allowOneNeutralLoss(mf) {
-  mf = mf.replace(/(Ser|Thr|Asp|Glu)(?!\()/g, '$1(H-2O-1)0-1');
-  mf = mf.replace(/(Arg|Lys|Asn|Gln)(?!\()/g, '$1(N-1H-3)0-1');
+  mf = mf.replaceAll(/(Ser|Thr|Asp|Glu)(?!\()/g, '$1(H-2O-1)0-1');
+  mf = mf.replaceAll(/(Arg|Lys|Asn|Gln)(?!\()/g, '$1(N-1H-3)0-1');
 
   return mf;
 }

src/aminoAcids.js

@@ -24,3 +24,3 @@ // SOURCE: https://en.wikipedia.org/wiki/Amino_acid
     pKaC: 2.03,
-    pKaN: 9.0,
+    pKaN: 9,
   },
@@ -78,3 +78,3 @@ {
     pKaC: 2.18,
-    pKaN: 9.0,
+    pKaN: 9,
   },
@@ -81,0 +81,0 @@ {

src/chargePeptide.js

@@ -37,13 +37,13 @@ import { getAA } from './getAA';
   // basic AA
-  if (pH < getAA('Arg').sc.pKa) mf = mf.replace(/(Arg)(?!\()/g, '$1(H+)');
-  if (pH < getAA('His').sc.pKa) mf = mf.replace(/(His)(?!\()/g, '$1(H+)');
-  if (pH < getAA('Lys').sc.pKa) mf = mf.replace(/(Lys)(?!\()/g, '$1(H+)');
+  if (pH < getAA('Arg').sc.pKa) mf = mf.replaceAll(/(Arg)(?!\()/g, '$1(H+)');
+  if (pH < getAA('His').sc.pKa) mf = mf.replaceAll(/(His)(?!\()/g, '$1(H+)');
+  if (pH < getAA('Lys').sc.pKa) mf = mf.replaceAll(/(Lys)(?!\()/g, '$1(H+)');
 
   // acid AA
-  if (pH > getAA('Asp').sc.pKa) mf = mf.replace(/(Asp)(?!\()/g, '$1(H-1-)');
-  if (pH > getAA('Glu').sc.pKa) mf = mf.replace(/(Glu)(?!\()/g, '$1(H-1-)');
+  if (pH > getAA('Asp').sc.pKa) mf = mf.replaceAll(/(Asp)(?!\()/g, '$1(H-1-)');
+  if (pH > getAA('Glu').sc.pKa) mf = mf.replaceAll(/(Glu)(?!\()/g, '$1(H-1-)');
 
-  if (pH > getAA('Cys').sc.pKa) mf = mf.replace(/(Cys)(?!\()/g, '$1(H-1-)');
+  if (pH > getAA('Cys').sc.pKa) mf = mf.replaceAll(/(Cys)(?!\()/g, '$1(H-1-)');
 
   return mf;
 }

src/digestPeptide.js

@@ -18,6 +18,3 @@ /*
   let regexp = getRegexp(options.enzyme);
-  let fragments = sequence
-    .replace(regexp, '$1 ')
-    .split(/ /)
-    .filter((entry) => entry);
+  let fragments = sequence.replace(regexp, '$1 ').split(/ /).filter(Boolean);
 
@@ -28,5 +25,5 @@ {
       let nbResidue = fragments[i]
-        .replace(/([A-Z][a-z][a-z])/g, ' $1')
+        .replaceAll(/([A-Z][a-z]{2})/g, ' $1')
         .split(/ /)
-        .filter((entry) => entry).length;
+        .filter(Boolean).length;
       fragments[i] = {
@@ -72,3 +69,3 @@ sequence: fragments[i],
 function getRegexp(enzyme) {
-  switch (enzyme.toLowerCase().replace(/[^a-z0-9]/g, '')) {
+  switch (enzyme.toLowerCase().replaceAll(/[^\da-z]/g, '')) {
     case 'chymotrypsin':
@@ -89,3 +86,3 @@ return /(Phe|Tyr|Trp)(?!Pro)/g;
     case 'any':
-      return /()(?=[A-Z][a-z][a-z])/g;
+      return /()(?=[A-Z][a-z]{2})/g;
     default:
@@ -92,0 +89,0 @@ throw new Error(`Digestion enzyme: ${enzyme} is unknown`);

src/generatePeptideFragments.js

@@ -23,3 +23,3 @@ export function generatePeptideFragments(mf, options) {
   let mfparts = mf
-    .replace(/([a-z)0-9])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
+    .replaceAll(/([\d)a-z])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
     .split(/ /);
@@ -35,8 +35,5 @@
 
-  if (mfparts[mfparts.length - 1].includes('(')) {
-    cTerm += mfparts[mfparts.length - 1].replace(/^[^()]*/, '');
-    mfparts[mfparts.length - 1] = mfparts[mfparts.length - 1].replace(
-      /\(.*/,
-      '',
-    );
+  if (mfparts.at(-1).includes('(')) {
+    cTerm += mfparts.at(-1).replace(/^[^()]*/, '');
+    mfparts[mfparts.length - 1] = mfparts.at(-1).replace(/\(.*/, '');
   }
@@ -43,0 +40,0 @@

src/index.js

@@ -5,3 +5,3 @@ import { aminoAcids } from './aminoAcids';
 
-export * from './allowNeutralLoss';
+export * from './allowNeutralLoss.js';
 export * from './chargePeptide.js';
@@ -8,0 +8,0 @@ export * from './sequenceToMF.js';

src/isoElectricPoint.js

@@ -9,3 +9,3 @@ import { aminoAcids } from './aminoAcids';
 
-export function calculateCharge(aas, pH = 7.0) {
+export function calculateCharge(aas, pH = 7) {
   let combined = combine(aas);
@@ -82,4 +82,4 @@ if (!combined) return;
   }
-  if (aaObject[aas[aas.length - 1]]) {
-    combined.last = aaObject[aas[aas.length - 1]].pKaC;
+  if (aaObject[aas.at(-1)]) {
+    combined.last = aaObject[aas.at(-1)].pKaC;
   } else {
@@ -86,0 +86,0 @@ return;

src/sequenceToMF.js

@@ -14,6 +14,6 @@ import { aminoAcids } from './aminoAcids';
   // GLY VAL HIS PHE GLY HIS GLU ARG LYS ARG TRP ASN PRO
-  if (mf.search(/[A-Z]{3} [A-Z]{3} [A-Z]{3}/) > -1) {
+  if (mf.search(/(?:[A-Z]{3} ){2}[A-Z]{3}/) > -1) {
     // this is a PDB !
-    let tmpmf = mf.replace(/[\r\n]+/g, ' ');
-    tmpmf = tmpmf.replace(/(SEQRES|[0-9]+| [A-Z] | [0-9A-Z]{4-50})/g, '');
+    let tmpmf = mf.replaceAll(/[\n\r]+/g, ' ');
+    tmpmf = tmpmf.replaceAll(/(SEQRES|\d+| [A-Z] | [\dA-Z]{4-50})/g, '');
     // we need to correct the uppercase / lowercase
@@ -23,7 +23,7 @@ let parts = tmpmf.split(' ');
     for (let i = 0; i < parts.length; i++) {
-      newMF += parts[i].substr(0, 1) + parts[i].substr(1).toLowerCase();
+      newMF += parts[i].slice(0, 1) + parts[i].slice(1).toLowerCase();
     }
     newMF += 'OH';
   } else if (mf.includes('(') && isOneLetterCode(mf)) {
-    // we expect one letter code with modification
+    // we expect one-letter code with modification
     newMF = '';
@@ -56,3 +56,3 @@ let nTerminal = 'H';
     mf.search(/[A-Z]{3}/) > -1 &&
-    mf.search(/[a-zA-Z][a-z0-9]/) === -1
+    mf.search(/[A-Za-z][\da-z]/) === -1
   ) {
@@ -66,3 +66,3 @@ // UNIPROT
     // We remove all the number, all the spaces, etc
-    newMF = `H${convertAA1To3(newMF.replace(/[^A-Z]/g, ''))}OH`;
+    newMF = `H${convertAA1To3(newMF.replaceAll(/[^A-Z]/g, ''))}OH`;
   }
@@ -69,0 +69,0 @@

src/splitPeptide.js

 export function splitPeptide(sequence) {
-  let aas = sequence.replace(/([A-Z])/g, ' $1').split(/ /);
+  let aas = sequence.replaceAll(/([A-Z])/g, ' $1').split(/ /);
   let begin = 0;
@@ -4,0 +4,0 @@ while (aas[begin] === '' || aas[begin] === 'H') {

New alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

New author

Supply chain risk

A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

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Fixed alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

81069

increased by57.99%

Number of package files

34

increased by3.03%

Worsened metrics

Lines of code

1660

decreased by-0.54%

Number of medium supply chain risk alerts

2

increased by100%

No dependency changes