se.lth.immun.chem.PeptideFragment Maven / Gradle / Ivy

Show more of this group Show more artifacts with this name
Show all versions of Proteins Show documentation

Library for general purpose in silico chemistry, mainly intended for mass spectrometry proteomics computations.

There is a newer version: 1.3.3

package se.lth.immun.chem;

public class PeptideFragment implements IMolecule {

	public EPeptideFragment		fragmentType;
	public int					ordinal;
	public double				mass;
	public Peptide 				peptide;
	
	public PeptideFragment(EPeptideFragment fragmentType, int ordinal, double mass, Peptide peptide) {
		this.fragmentType = fragmentType;
		this.ordinal = ordinal;
		this.mass = mass;
		this.peptide = peptide;
	}

	public ElementComposition getComposition() {
		return null;
	}
	public double monoisotopicMass() { return mass; }
	
	public boolean same(PeptideFragment pf) {
		return ordinal == pf.ordinal && fragmentType == pf.fragmentType;
	}
	
	public String toString() {
		return "PF("+fragmentType.type + ordinal+", m="+mass+")";
	}

	private IsotopeDistribution _dist = null;
	public IsotopeDistribution getIsotopeDistribution() {
		if (_dist == null) {
			_dist = new IsotopeDistribution();
			if (fragmentType == EPeptideFragment.b) {
				for (int i = 0; i < ordinal; i++)
					_dist.add(peptide.aminoAcids[i].getIsotopeDistribution());
			} else if (fragmentType == EPeptideFragment.y) {
				for (int i = 0; i < ordinal; i++)
					_dist.add(peptide.aminoAcids[peptide.aminoAcids.length - i - 1].getIsotopeDistribution());
			}
		}
		return _dist;
	}
}