sequaljs/dist/mass.js

JavaScript/TypeScript library for parsing and manipulating ProForma peptide sequence notation

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.calculateMass = calculateMass;
const resources_1 = require("./resources");
/**
 * Calculates the mass of a sequence.
 *
 * @param seq - The sequence of amino acids.
 * @param massDict - A dictionary of masses for the amino acids.
 * @param NTerminus - The mass of the N-terminus.
 * @param OTerminus - The mass of the O-terminus.
 * @param withWater - Whether to include the mass of water.
 * @returns The mass of the sequence.
 */
function calculateMass(seq, massDict, NTerminus = 0, OTerminus = 0, withWater = true) {
    let mass = 0;
    if (withWater) {
        mass += resources_1.H * 2 + resources_1.O;
    }
    for (const i of seq) {
        if (!i.mass) {
            if (massDict) {
                if (i.value in massDict) {
                    mass += massDict[i.value];
                }
                else {
                    throw new Error(`Block ${i.value} not found in massDict`);
                }
            }
            else {
                throw new Error(`Block ${i.value} mass is not available in mass attribute and no additional massDict was supplied`);
            }
        }
        else {
            mass += i.mass;
        }
        if (i.mods) {
            for (const m of i.mods) {
                if (m.mass !== 0 && !m.mass) {
                    if (massDict) {
                        if (m.value in massDict) {
                            mass += massDict[m.value];
                        }
                        else {
                            throw new Error(`Block ${m.value} not found in massDict`);
                        }
                    }
                    else {
                        throw new Error(`Block ${m.value} mass is not available in mass attribute and no additional massDict was supplied`);
                    }
                }
                else {
                    mass += m.mass;
                }
            }
        }
    }
    return mass + NTerminus + OTerminus;
}