Pyrrolysine.java

package com.compomics.util.experiment.biology.aminoacids;

import com.compomics.util.experiment.biology.AminoAcid;
import com.compomics.util.experiment.biology.Atom;
import com.compomics.util.experiment.biology.AtomChain;
import com.compomics.util.experiment.biology.AtomImpl;

/**
 * Pyrrolysine.
 *
 * @author Harald Barsnes
 */
public class Pyrrolysine extends AminoAcid {

    /**
     * Serial number for backward compatibility.
     */
    static final long serialVersionUID = 8680204019988094523L;

    /**
     * Constructor.
     */
    public Pyrrolysine() {
        singleLetterCode = "O";
        threeLetterCode = "Pyl";
        name = "Pyrrolysine";
        averageMass = 237.1477; //@TODO: what is the average mass in this case??
        monoisotopicMass = 237.1477;
        monoisotopicAtomChain = new AtomChain();
        monoisotopicAtomChain.append(new AtomImpl(Atom.C, 0), 12);
        monoisotopicAtomChain.append(new AtomImpl(Atom.H, 0), 19);
        monoisotopicAtomChain.append(new AtomImpl(Atom.N, 0), 3);
        monoisotopicAtomChain.append(new AtomImpl(Atom.O, 0), 2);
        subAminoAcidsWithoutCombination = new char[]{'O'};
        subAminoAcidsWithCombination = subAminoAcidsWithoutCombination;
        aminoAcidCombinations = new char[]{'X'};
        standardGeneticCode = new String[] {"TAG"};
    }

    @Override
    public boolean iscombination() {
        return false;
    }
}