/**
* Create a benzene molecule with 2 residues and 2 charge groups
*
* @return
*/
public MDMolecule makeMDBenzene() {
MDMolecule mol = new MDMolecule();
mol.addAtom(new Atom("C")); // 0
mol.addAtom(new Atom("C")); // 1
mol.addAtom(new Atom("C")); // 2
mol.addAtom(new Atom("C")); // 3
mol.addAtom(new Atom("C")); // 4
mol.addAtom(new Atom("C")); // 5
mol.addBond(0, 1, IBond.Order.SINGLE); // 1
mol.addBond(1, 2, IBond.Order.DOUBLE); // 2
mol.addBond(2, 3, IBond.Order.SINGLE); // 3
mol.addBond(3, 4, IBond.Order.DOUBLE); // 4
mol.addBond(4, 5, IBond.Order.SINGLE); // 5
mol.addBond(5, 0, IBond.Order.DOUBLE); // 6
// Create 2 residues
AtomContainer ac = new AtomContainer();
ac.addAtom(mol.getAtom(0));
ac.addAtom(mol.getAtom(1));
ac.addAtom(mol.getAtom(2));
Residue res1 = new Residue(ac, 0, mol);
res1.setName("myResidue1");
mol.addResidue(res1);
AtomContainer ac2 = new AtomContainer();
ac2.addAtom(mol.getAtom(3));
ac2.addAtom(mol.getAtom(4));
ac2.addAtom(mol.getAtom(5));
Residue res2 = new Residue(ac2, 1, mol);
res2.setName("myResidue2");
mol.addResidue(res2);
// Create 2 chargegroups
AtomContainer ac3 = new AtomContainer();
ac3.addAtom(mol.getAtom(0));
ac3.addAtom(mol.getAtom(1));
ChargeGroup chg1 = new ChargeGroup(ac3, 2, mol);
chg1.setSwitchingAtom(mol.getAtom(1));
mol.addChargeGroup(chg1);
AtomContainer ac4 = new AtomContainer();
ac4.addAtom(mol.getAtom(2));
ac4.addAtom(mol.getAtom(3));
ac4.addAtom(mol.getAtom(4));
ac4.addAtom(mol.getAtom(5));
ChargeGroup chg2 = new ChargeGroup(ac4, 3, mol);
chg2.setSwitchingAtom(mol.getAtom(4));
mol.addChargeGroup(chg2);
return mol;
}
/** Test an MDMolecule with residues and charge groups */
@Test
public void testMDMolecule() {
MDMolecule mol = new MDMolecule();
mol.addAtom(new Atom("C")); // 0
mol.addAtom(new Atom("C")); // 1
mol.addAtom(new Atom("C")); // 2
mol.addAtom(new Atom("C")); // 3
mol.addAtom(new Atom("C")); // 4
mol.addAtom(new Atom("C")); // 5
mol.addBond(0, 1, IBond.Order.SINGLE); // 1
mol.addBond(1, 2, IBond.Order.DOUBLE); // 2
mol.addBond(2, 3, IBond.Order.SINGLE); // 3
mol.addBond(3, 4, IBond.Order.DOUBLE); // 4
mol.addBond(4, 5, IBond.Order.SINGLE); // 5
mol.addBond(5, 0, IBond.Order.DOUBLE); // 6
// Create 2 residues
AtomContainer ac = new AtomContainer();
ac.addAtom(mol.getAtom(0));
ac.addAtom(mol.getAtom(1));
ac.addAtom(mol.getAtom(2));
Residue res1 = new Residue(ac, 0, mol);
res1.setName("myResidue1");
mol.addResidue(res1);
AtomContainer ac2 = new AtomContainer();
ac2.addAtom(mol.getAtom(3));
ac2.addAtom(mol.getAtom(4));
ac2.addAtom(mol.getAtom(5));
Residue res2 = new Residue(ac2, 1, mol);
res2.setName("myResidue2");
mol.addResidue(res2);
// Test residue creation
Assert.assertEquals(res1.getParentMolecule(), mol);
Assert.assertEquals(res2.getParentMolecule(), mol);
Assert.assertEquals(res1.getAtomCount(), 3);
Assert.assertEquals(res2.getAtomCount(), 3);
Assert.assertEquals(res1.getName(), "myResidue1");
Assert.assertEquals(res2.getName(), "myResidue2");
Assert.assertNotNull(mol.getResidues());
Assert.assertEquals(mol.getResidues().size(), 2);
Assert.assertEquals(mol.getResidues().get(0), res1);
Assert.assertEquals(mol.getResidues().get(1), res2);
// Create 2 chargegroups
AtomContainer ac3 = new AtomContainer();
ac3.addAtom(mol.getAtom(0));
ac3.addAtom(mol.getAtom(1));
ChargeGroup chg1 = new ChargeGroup(ac3, 0, mol);
mol.addChargeGroup(chg1);
AtomContainer ac4 = new AtomContainer();
ac4.addAtom(mol.getAtom(2));
ac4.addAtom(mol.getAtom(3));
ac4.addAtom(mol.getAtom(4));
ac4.addAtom(mol.getAtom(5));
ChargeGroup chg2 = new ChargeGroup(ac4, 1, mol);
mol.addChargeGroup(chg2);
// Test chargegroup creation
Assert.assertEquals(chg1.getParentMolecule(), mol);
Assert.assertEquals(chg2.getParentMolecule(), mol);
Assert.assertEquals(chg1.getAtomCount(), 2);
Assert.assertEquals(chg2.getAtomCount(), 4);
Assert.assertNotNull(mol.getChargeGroups());
Assert.assertEquals(mol.getChargeGroups().size(), 2);
Assert.assertEquals(mol.getChargeGroups().get(0), chg1);
Assert.assertEquals(mol.getChargeGroups().get(1), chg2);
}
@Test
public void testMDMoleculeCustomizationRoundtripping() throws Exception {
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.registerCustomizer(new MDMoleculeCustomizer());
MDMolecule molecule = makeMDBenzene();
cmlWriter.write(molecule);
String serializedMol = writer.toString();
logger.debug("****************************** testMDMoleculeCustomizationRoundtripping()");
logger.debug(serializedMol);
logger.debug("******************************");
logger.debug("****************************** testMDMoleculeCustomization Write first");
logger.debug(serializedMol);
logger.debug("******************************");
CMLReader reader = new CMLReader(new ByteArrayInputStream(serializedMol.getBytes()));
reader.registerConvention("md:mdMolecule", new MDMoleculeConvention(new ChemFile()));
IChemFile file = (IChemFile) reader.read(new ChemFile());
List containers = ChemFileManipulator.getAllAtomContainers(file);
Assert.assertEquals(1, containers.size());
Object molecule2 = containers.get(0);
Assert.assertTrue(molecule2 instanceof MDMolecule);
MDMolecule mdMol = (MDMolecule) molecule2;
Assert.assertEquals(6, mdMol.getAtomCount());
Assert.assertEquals(6, mdMol.getBondCount());
List residues = mdMol.getResidues();
Assert.assertEquals(2, residues.size());
Assert.assertEquals(3, ((Residue) residues.get(0)).getAtomCount());
Assert.assertEquals(3, ((Residue) residues.get(1)).getAtomCount());
Assert.assertEquals("myResidue1", ((Residue) residues.get(0)).getName());
Assert.assertEquals("myResidue2", ((Residue) residues.get(1)).getName());
Assert.assertEquals(0, ((Residue) residues.get(0)).getNumber());
Assert.assertEquals(1, ((Residue) residues.get(1)).getNumber());
List chargeGroup = mdMol.getChargeGroups();
Assert.assertEquals(2, chargeGroup.size());
Assert.assertEquals(2, ((ChargeGroup) chargeGroup.get(0)).getAtomCount());
Assert.assertEquals(4, ((ChargeGroup) chargeGroup.get(1)).getAtomCount());
Assert.assertNotNull(((ChargeGroup) chargeGroup.get(0)).getSwitchingAtom());
Assert.assertEquals("a2", ((ChargeGroup) chargeGroup.get(0)).getSwitchingAtom().getID());
Assert.assertNotNull(((ChargeGroup) chargeGroup.get(1)).getSwitchingAtom());
Assert.assertEquals("a5", ((ChargeGroup) chargeGroup.get(1)).getSwitchingAtom().getID());
Assert.assertEquals(2, ((ChargeGroup) chargeGroup.get(0)).getNumber());
Assert.assertEquals(3, ((ChargeGroup) chargeGroup.get(1)).getNumber());
writer = new StringWriter();
cmlWriter = new CMLWriter(writer);
cmlWriter.registerCustomizer(new MDMoleculeCustomizer());
cmlWriter.write(mdMol);
String serializedMDMol = writer.toString();
logger.debug("****************************** testMDMoleculeCustomizationRoundtripping()");
logger.debug(serializedMol);
logger.debug("******************************");
logger.debug("****************************** testMDMoleculeCustomization Write second");
logger.debug(serializedMDMol);
logger.debug("******************************");
Assert.assertEquals(serializedMol, serializedMDMol);
}