/** {@inheritDoc} */ @Override public <T> T getProperty(Object description) { logger.debug("Getting property: ", description + "=" + super.getProperty(description)); return super.getProperty(description); }
/** * Returns the three letter code of an amino acid given a one letter code. * For example, it will return "Val" when "V" was passed. */ public static String convertOneLetterCodeToThreeLetterCode(String oneLetterCode) { AminoAcid[] monomers = createAAs(); for (int i = 0; i < monomers.length; i++) { if (monomers[i].getProperty(RESIDUE_NAME_SHORT).equals(oneLetterCode)) { return (String) monomers[i].getProperty(RESIDUE_NAME); } } return null; }
/** * Returns the one letter code of an amino acid given a three letter code. * For example, it will return "V" when "Val" was passed. */ public static String convertThreeLetterCodeToOneLetterCode(String threeLetterCode) { AminoAcid[] monomers = createAAs(); for (int i = 0; i < monomers.length; i++) { if (monomers[i].getProperty(RESIDUE_NAME).equals(threeLetterCode)) { return (String) monomers[i].getProperty(RESIDUE_NAME_SHORT); } } return null; }
/** * Returns the one letter code of an amino acid given a three letter code. * For example, it will return "V" when "Val" was passed. */ public static String convertThreeLetterCodeToOneLetterCode(String threeLetterCode) { AminoAcid[] monomers = createAAs(); for (int i = 0; i < monomers.length; i++) { if (monomers[i].getProperty(RESIDUE_NAME).equals(threeLetterCode)) { return (String) monomers[i].getProperty(RESIDUE_NAME_SHORT); } } return null; }
/** * Returns the three letter code of an amino acid given a one letter code. * For example, it will return "Val" when "V" was passed. */ public static String convertOneLetterCodeToThreeLetterCode(String oneLetterCode) { AminoAcid[] monomers = createAAs(); for (int i = 0; i < monomers.length; i++) { if (monomers[i].getProperty(RESIDUE_NAME_SHORT).equals(oneLetterCode)) { return (String) monomers[i].getProperty(RESIDUE_NAME); } } return null; }
/** * Returns a HashMap where the key is one of GLY, ALA, VAL, LEU, ILE, SER, * THR, CYS, MET, ASP, ASN, GLU, GLN, ARG, LYS, HIS, PHE, TYR, TRP AND PRO. */ public static Map<String, IAminoAcid> getHashMapByThreeLetterCode() { AminoAcid[] monomers = createAAs(); Map<String, IAminoAcid> map = new HashMap<String, IAminoAcid>(); for (int i = 0; i < monomers.length; i++) { map.put((String) monomers[i].getProperty(RESIDUE_NAME), monomers[i]); } return map; }
/** * Returns a HashMap where the key is one of GLY, ALA, VAL, LEU, ILE, SER, * THR, CYS, MET, ASP, ASN, GLU, GLN, ARG, LYS, HIS, PHE, TYR, TRP AND PRO. */ public static Map<String, IAminoAcid> getHashMapByThreeLetterCode() { AminoAcid[] monomers = createAAs(); Map<String, IAminoAcid> map = new HashMap<String, IAminoAcid>(); for (int i = 0; i < monomers.length; i++) { map.put((String) monomers[i].getProperty(RESIDUE_NAME), monomers[i]); } return map; }
AminoAcid acid = aminoAcids[aa]; LOGGER.debug("#bonds for ", acid.getProperty(RESIDUE_NAME).toString(), " = " + acid.getBondCount()); total += acid.getBondCount(); LOGGER.debug("total #bonds: ", total);
AminoAcid acid = aminoAcids[aa]; LOGGER.debug("#bonds for ", acid.getProperty(RESIDUE_NAME).toString(), " = " + acid.getBondCount()); total += acid.getBondCount(); LOGGER.debug("total #bonds: ", total);