peptide
Version:
89 lines • 2.97 kB
JavaScript
;
Object.defineProperty(exports, "__esModule", { value: true });
exports.generatePeptideFragments = generatePeptideFragments;
function generatePeptideFragments(mf, options) {
if (options === undefined) {
options = {
a: false,
b: true,
c: false,
x: false,
y: true,
z: false,
i: false,
ya: false,
yb: false,
yc: false,
zc: false,
};
}
options.maxInternal = options.maxInternal || Number.MAX_VALUE;
options.minInternal = options.minInternal || 0;
let mfs = [];
// need to allow 0-9 to deal with neutral loss
let mfparts = mf
.replaceAll(/([\d)a-z])([A-Z][a-z](?=[a-z]))/g, '$1 $2')
.split(/ /);
let nTerm = '';
let cTerm = '';
if (mfparts[0].startsWith('(')) {
nTerm += mfparts[0];
mfparts = mfparts.splice(1);
}
if (mfparts.at(-1).includes('(')) {
cTerm += mfparts.at(-1).replace(/^[^()]*/, '');
mfparts[mfparts.length - 1] = mfparts.at(-1).replace(/\(.*/, '');
}
for (let i = 1; i < mfparts.length; i++) {
nTerm += mfparts[i - 1];
cTerm = mfparts[mfparts.length - i] + cTerm;
addNTerm(mfs, nTerm, i, options);
addCTerm(mfs, cTerm, i, options);
if (options.i)
mfs.push(`${mfparts[i]}HC-1O-1(+1)$i:${mfparts[i]}`);
if (options.ya || options.yb || options.yc || options.zc) {
// we have double fragmentations
for (let j = i + 1; j < Math.min(mfparts.length, options.maxInternal + i + 1); j++) {
let iTerm = '';
if (j - i >= options.minInternal) {
for (let k = i; k < j; k++) {
iTerm += mfparts[k];
}
addITerm(mfs, iTerm, mfparts.length - i, j, options);
}
}
}
}
// todo does this make sense ??? I think we should remote those 3 lines
if (mfs.length === 0) {
mfs = mfs.concat([mf]);
}
return mfs;
}
function addNTerm(mfs, nTerm, i, options) {
if (options.a)
mfs.push(`${nTerm}C-1O-1(+1)$a${i}`);
if (options.b)
mfs.push(`${nTerm}(+1)$b${i}`);
if (options.c)
mfs.push(`${nTerm}NH3(+1)$c${i}`);
}
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}`);
if (options.yc)
mfs.push(`H${iTerm}NH3(+1)$c${j}y${i}`);
if (options.zc)
mfs.push(`N-1${iTerm}NH3(+1)$c${j}z${i}`);
}
function addCTerm(mfs, cTerm, i, options) {
if (options.x)
mfs.push(`CO(+1)${cTerm}$x${i}`);
if (options.y)
mfs.push(`H2(+1)${cTerm}$y${i}`);
if (options.z)
mfs.push(`N-1H-1(+1)${cTerm}$z${i}`);
}
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