@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);
}
