public void TestMDMoleculeCustomizationRoundtripping()
{
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new MDMoleculeCustomizer());
MDMolecule molecule = MakeMDBenzene();
cmlWriter.Write(molecule);
cmlWriter.Close();
string serializedMol = writer.ToString();
Debug.WriteLine("****************************** TestMDMoleculeCustomizationRoundtripping()");
Debug.WriteLine(serializedMol);
Debug.WriteLine("******************************");
Debug.WriteLine("****************************** testMDMoleculeCustomization Write first");
Debug.WriteLine(serializedMol);
Debug.WriteLine("******************************");
CMLReader reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(serializedMol)));
reader.RegisterConvention("md:mdMolecule", new MDMoleculeConvention(builder.NewChemFile()));
IChemFile file = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
var containers = ChemFileManipulator.GetAllAtomContainers(file).ToReadOnlyList();
Assert.AreEqual(1, containers.Count);
var molecule2 = containers[0];
Assert.IsTrue(molecule2 is MDMolecule);
MDMolecule mdMol = (MDMolecule)molecule2;
Assert.AreEqual(6, mdMol.Atoms.Count);
Assert.AreEqual(6, mdMol.Bonds.Count);
var residues = mdMol.GetResidues();
Assert.AreEqual(2, residues.Count);
Assert.AreEqual(3, ((Residue)residues[0]).Atoms.Count);
Assert.AreEqual(3, ((Residue)residues[1]).Atoms.Count);
Assert.AreEqual("myResidue1", ((Residue)residues[0]).Name);
Assert.AreEqual("myResidue2", ((Residue)residues[1]).Name);
Assert.AreEqual(0, ((Residue)residues[0]).GetNumber());
Assert.AreEqual(1, ((Residue)residues[1]).GetNumber());
var chargeGroup = mdMol.GetChargeGroups();
Assert.AreEqual(2, chargeGroup.Count);
Assert.AreEqual(2, ((ChargeGroup)chargeGroup[0]).Atoms.Count);
Assert.AreEqual(4, ((ChargeGroup)chargeGroup[1]).Atoms.Count);
Assert.IsNotNull(((ChargeGroup)chargeGroup[0]).GetSwitchingAtom());
Assert.AreEqual("a2", ((ChargeGroup)chargeGroup[0]).GetSwitchingAtom().Id);
Assert.IsNotNull(((ChargeGroup)chargeGroup[1]).GetSwitchingAtom());
Assert.AreEqual("a5", ((ChargeGroup)chargeGroup[1]).GetSwitchingAtom().Id);
Assert.AreEqual(2, ((ChargeGroup)chargeGroup[0]).GetNumber());
Assert.AreEqual(3, ((ChargeGroup)chargeGroup[1]).GetNumber());
writer = new StringWriter();
cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new MDMoleculeCustomizer());
cmlWriter.Write(mdMol);
cmlWriter.Close();
string serializedMDMol = writer.ToString();
Debug.WriteLine("****************************** TestMDMoleculeCustomizationRoundtripping()");
Debug.WriteLine(serializedMol);
Debug.WriteLine("******************************");
Debug.WriteLine("****************************** testMDMoleculeCustomization Write second");
Debug.WriteLine(serializedMDMol);
Debug.WriteLine("******************************");
Assert.AreEqual(serializedMol, serializedMDMol);
}
