nucleotide/lib/src/addInternalTerm.js

Deal with nucleotides and molecular formula

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.addInternalTerm = addInternalTerm;
const furanThreeTerm_js_1 = require("./furanThreeTerm.js");
// https://books.google.ch/books?id=B57e37bJjqAC&pg=PA172&lpg=PA172&dq=oligonucleotide+b+fragmentation&source=bl&ots=mRr29Pexx2&sig=1NUQcWV-wuj6o9q81my86AVoRto&hl=fr&sa=X&ved=2ahUKEwjI5M3yn-7fAhUJMewKHQR6Bcs4ChDoATADegQIBhAB#v=onepage&q=oligonucleotide%20b%20fragmentation&f=false
function addInternalTerm(mfs, internal, ter3, ter5, options = {}) {
    if (options.aw) {
        // without base loss
        mfs.push(`HO${internal}O-1H-1$w${ter3}:a${ter5}`); // A W
    }
    if (options.bw) {
        // without base loss
        mfs.push(`HO${internal}H$w${ter3}:b${ter5}`); // B W
    }
    if (options.abw) {
        // with base loss
        let fragment = (0, furanThreeTerm_js_1.furanThreeTerm)(internal);
        mfs.push(`HO${fragment}$w${ter3}:a${ter5}-B`); // A minus base - W
    }
    if (options.aby) {
        // with base loss
        let fragment = (0, furanThreeTerm_js_1.furanThreeTerm)(internal);
        mfs.push(`O-2P-1${fragment}$y${ter3}:a${ter5}-B`); // A minus base - Y
    }
}
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