@Override public IChemObject newTestObject() { return new AminoAcid(); } });
/** {@inheritDoc} */ @Override public void addAtom(IAtom atom) { logger.debug("Adding atom: ", atom); super.addAtom(atom); }
/** {@inheritDoc} */ @Override public void addBond(IBond bond) { logger.debug("Adding bond: ", bond); super.addBond(bond); }
/** * Clones this AminoAcid object. * * @return The cloned object */ @Override public IAminoAcid clone() throws CloneNotSupportedException { AminoAcid clone = (AminoAcid) super.clone(); // copying the new N-terminus and C-terminus pointers if (getNTerminus() != null) clone.setNTerminus(clone.getAtom(getAtomNumber(getNTerminus()))); if (getCTerminus() != null) clone.setCTerminus(clone.getAtom(getAtomNumber(getCTerminus()))); return clone; }
AminoAcid aminoAcid = new AminoAcid(); Iterator<IAtom> atoms = ac.atoms().iterator(); Iterator<Object> props = ac.getProperties().keySet().iterator(); aminoAcid.setProperty(RESIDUE_NAME, ac.getProperty(dictRef).toString().toUpperCase()); aminoAcid.setMonomerName(ac.getProperty(dictRef).toString()); } else if (dictRef.getType().equals("pdb:oneLetterCode")) { aminoAcid.setProperty(RESIDUE_NAME_SHORT, ac.getProperty(dictRef)); } else if (dictRef.getType().equals("pdb:id")) { aminoAcid.setProperty(ID, ac.getProperty(dictRef)); LOGGER.debug("Set AA ID to: ", ac.getProperty(dictRef)); } else { String dictRef = (String) atom.getProperty("org.openscience.cdk.dict"); if (dictRef != null && dictRef.equals("pdb:nTerminus")) { aminoAcid.addNTerminus(atom); } else if (dictRef != null && dictRef.equals("pdb:cTerminus")) { aminoAcid.addCTerminus(atom); } else { aminoAcid.addAtom(atom); while (bonds.hasNext()) { IBond bond = (IBond) bonds.next(); aminoAcid.addBond(bond); aminoAcid.setProperty(NO_ATOMS, "" + aminoAcid.getAtomCount()); aminoAcid.setProperty(NO_BONDS, "" + aminoAcid.getBondCount()); if (counter < aminoAcids.length) { aminoAcids[counter] = aminoAcid;
AminoAcid acid = aminoAcids[aa]; LOGGER.debug("#bonds for ", acid.getProperty(RESIDUE_NAME).toString(), " = " + acid.getBondCount()); total += acid.getBondCount(); LOGGER.debug("total #bonds: ", total); Iterator<IBond> bonds = acid.bonds().iterator(); while (bonds.hasNext()) { IBond bond = (IBond) bonds.next(); info[counter][0] = counter; info[counter][1] = acid.indexOf(bond.getBegin()); info[counter][2] = acid.indexOf(bond.getEnd()); info[counter][3] = bond.getOrder().numeric(); counter++;
/** {@inheritDoc} */ @Override public IAtom getCTerminus() { logger.debug("Getting C-terminus: ", super.getCTerminus()); return super.getCTerminus(); }
/** {@inheritDoc} */ @Override public Iterable<IBond> bonds() { logger.debug("Getting bonds iterator"); return super.bonds(); }
/** {@inheritDoc} */ @Override public int getAtomCount() { logger.debug("Getting atom count"); return super.getAtomCount(); }
/** {@inheritDoc} */ @Override public int getBondCount() { logger.debug("Getting bond count"); return super.getBondCount(); }
/** {@inheritDoc} */ @Override public void addNTerminus(IAtom atom) { logger.debug("Adding N-terminus: ", atom); super.addNTerminus(atom); }
/** {@inheritDoc} */ @Override public void addCTerminus(IAtom atom) { logger.debug("Adding C-terminus: ", atom); super.addCTerminus(atom); }
/** {@inheritDoc} */ @Override public IAtom getAtom(int idx) { logger.debug("Getting atom at: ", idx); return super.getAtom(idx); }
AminoAcid aminoAcid = new AminoAcid(); Iterator<IAtom> atoms = ac.atoms().iterator(); Iterator<Object> props = ac.getProperties().keySet().iterator(); aminoAcid.setProperty(RESIDUE_NAME, ac.getProperty(dictRef).toString().toUpperCase()); aminoAcid.setMonomerName(ac.getProperty(dictRef).toString()); } else if (dictRef.getType().equals("pdb:oneLetterCode")) { aminoAcid.setProperty(RESIDUE_NAME_SHORT, ac.getProperty(dictRef)); } else if (dictRef.getType().equals("pdb:id")) { aminoAcid.setProperty(ID, ac.getProperty(dictRef)); LOGGER.debug("Set AA ID to: ", ac.getProperty(dictRef)); } else { String dictRef = (String) atom.getProperty("org.openscience.cdk.dict"); if (dictRef != null && dictRef.equals("pdb:nTerminus")) { aminoAcid.addNTerminus(atom); } else if (dictRef != null && dictRef.equals("pdb:cTerminus")) { aminoAcid.addCTerminus(atom); } else { aminoAcid.addAtom(atom); while (bonds.hasNext()) { IBond bond = (IBond) bonds.next(); aminoAcid.addBond(bond); aminoAcid.setProperty(NO_ATOMS, "" + aminoAcid.getAtomCount()); aminoAcid.setProperty(NO_BONDS, "" + aminoAcid.getBondCount()); if (counter < aminoAcids.length) { aminoAcids[counter] = aminoAcid;
/** * Clones this AminoAcid object. * * @return The cloned object */ @Override public IAminoAcid clone() throws CloneNotSupportedException { AminoAcid clone = (AminoAcid) super.clone(); // copying the new N-terminus and C-terminus pointers if (getNTerminus() != null) clone.setNTerminus(clone.getAtom(getAtomNumber(getNTerminus()))); if (getCTerminus() != null) clone.setCTerminus(clone.getAtom(getAtomNumber(getCTerminus()))); return clone; }
AminoAcid acid = aminoAcids[aa]; LOGGER.debug("#bonds for ", acid.getProperty(RESIDUE_NAME).toString(), " = " + acid.getBondCount()); total += acid.getBondCount(); LOGGER.debug("total #bonds: ", total); Iterator<IBond> bonds = acid.bonds().iterator(); while (bonds.hasNext()) { IBond bond = (IBond) bonds.next(); info[counter][0] = counter; info[counter][1] = acid.indexOf(bond.getBegin()); info[counter][2] = acid.indexOf(bond.getEnd()); info[counter][3] = bond.getOrder().numeric(); counter++;
@Test public void testAminoAcid() { IAminoAcid oAminoAcid = new AminoAcid(); Assert.assertNotNull(oAminoAcid); }
/** {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); }
@BeforeClass public static void setUp() { setTestObjectBuilder(new ITestObjectBuilder() { @Override public IChemObject newTestObject() { return new AminoAcid(); } }); }
/** {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); }