public void TestBug1748257()
{
MDMolecule mol = new MDMolecule();
mol.Atoms.Add(builder.NewAtom("C")); // 0
mol.Atoms.Add(builder.NewAtom("C")); // 1
mol.Atoms.Add(builder.NewAtom("H")); // 2
mol.Atoms.Add(builder.NewAtom("H")); // 3
mol.Atoms.Add(builder.NewAtom("H")); // 4
mol.Atoms.Add(builder.NewAtom("H")); // 5
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Double); // 1
mol.AddBond(mol.Atoms[2], mol.Atoms[0], BondOrder.Single); // 3
mol.AddBond(mol.Atoms[3], mol.Atoms[0], BondOrder.Single); // 4
mol.AddBond(mol.Atoms[4], mol.Atoms[1], BondOrder.Single); // 5
mol.AddBond(mol.Atoms[5], mol.Atoms[1], BondOrder.Single); // 6
Convertor convertor = new Convertor(false, "");
CMLAtom cmlatom = convertor.CDKAtomToCMLAtom(mol, mol.Atoms[2]);
Assert.AreEqual(cmlatom.HydrogenCount, 0);
}
public void SetParentMolecule(MDMolecule parentMolecule)
{
this.parentMolecule = parentMolecule;
}
/// <summary>
/// Constructor to create a Residue based on an AC, a number, and a MDMolecule.
/// </summary>
public Residue(IAtomContainer container, int number, MDMolecule parentMolecule)
: base(container)
{
this.number = number;
this.parentMolecule = parentMolecule;
}
/// <summary>
/// Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.
/// </summary>
/// <param name="container"></param>
/// <param name="number"></param>
/// <param name="parentMolecule"></param>
public ChargeGroup(IAtomContainer container, int number, MDMolecule parentMolecule)
: base(container)
{
this.number = number;
this.parentMolecule = parentMolecule;
}
public void TestMDMolecule()
{
MDMolecule mol = new MDMolecule();
mol.Atoms.Add(builder.NewAtom("C")); // 0
mol.Atoms.Add(builder.NewAtom("C")); // 1
mol.Atoms.Add(builder.NewAtom("C")); // 2
mol.Atoms.Add(builder.NewAtom("C")); // 3
mol.Atoms.Add(builder.NewAtom("C")); // 4
mol.Atoms.Add(builder.NewAtom("C")); // 5
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single); // 1
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Double); // 2
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single); // 3
mol.AddBond(mol.Atoms[3], mol.Atoms[4], BondOrder.Double); // 4
mol.AddBond(mol.Atoms[4], mol.Atoms[5], BondOrder.Single); // 5
mol.AddBond(mol.Atoms[5], mol.Atoms[0], BondOrder.Double); // 6
//Create 2 residues
var ac = builder.NewAtomContainer();
ac.Atoms.Add(mol.Atoms[0]);
ac.Atoms.Add(mol.Atoms[1]);
ac.Atoms.Add(mol.Atoms[2]);
Residue res1 = new Residue(ac, 0, mol);
res1.Name = "myResidue1";
mol.AddResidue(res1);
var ac2 = builder.NewAtomContainer();
ac2.Atoms.Add(mol.Atoms[3]);
ac2.Atoms.Add(mol.Atoms[4]);
ac2.Atoms.Add(mol.Atoms[5]);
Residue res2 = new Residue(ac2, 1, mol);
res2.Name = "myResidue2";
mol.AddResidue(res2);
//Test residue creation
Assert.AreEqual(res1.GetParentMolecule(), mol);
Assert.AreEqual(res2.GetParentMolecule(), mol);
Assert.AreEqual(res1.Atoms.Count, 3);
Assert.AreEqual(res2.Atoms.Count, 3);
Assert.AreEqual(res1.Name, "myResidue1");
Assert.AreEqual(res2.Name, "myResidue2");
Assert.IsNotNull(mol.GetResidues());
Assert.AreEqual(mol.GetResidues().Count, 2);
Assert.AreEqual(mol.GetResidues()[0], res1);
Assert.AreEqual(mol.GetResidues()[1], res2);
//Create 2 chargegroups
var ac3 = builder.NewAtomContainer();
ac3.Atoms.Add(mol.Atoms[0]);
ac3.Atoms.Add(mol.Atoms[1]);
ChargeGroup chg1 = new ChargeGroup(ac3, 0, mol);
mol.AddChargeGroup(chg1);
var ac4 = builder.NewAtomContainer();
ac4.Atoms.Add(mol.Atoms[2]);
ac4.Atoms.Add(mol.Atoms[3]);
ac4.Atoms.Add(mol.Atoms[4]);
ac4.Atoms.Add(mol.Atoms[5]);
ChargeGroup chg2 = new ChargeGroup(ac4, 1, mol);
mol.AddChargeGroup(chg2);
//Test chargegroup creation
Assert.AreEqual(chg1.GetParentMolecule(), mol);
Assert.AreEqual(chg2.GetParentMolecule(), mol);
Assert.AreEqual(chg1.Atoms.Count, 2);
Assert.AreEqual(chg2.Atoms.Count, 4);
Assert.IsNotNull(mol.GetChargeGroups());
Assert.AreEqual(mol.GetChargeGroups().Count, 2);
Assert.AreEqual(mol.GetChargeGroups()[0], chg1);
Assert.AreEqual(mol.GetChargeGroups()[1], chg2);
}
/// <summary>
/// Create a benzene molecule with 2 residues and 2 charge groups
/// </summary>
/// <returns></returns>
public MDMolecule MakeMDBenzene()
{
MDMolecule mol = new MDMolecule();
mol.Atoms.Add(builder.NewAtom("C")); // 0
mol.Atoms.Add(builder.NewAtom("C")); // 1
mol.Atoms.Add(builder.NewAtom("C")); // 2
mol.Atoms.Add(builder.NewAtom("C")); // 3
mol.Atoms.Add(builder.NewAtom("C")); // 4
mol.Atoms.Add(builder.NewAtom("C")); // 5
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single); // 1
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Double); // 2
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single); // 3
mol.AddBond(mol.Atoms[3], mol.Atoms[4], BondOrder.Double); // 4
mol.AddBond(mol.Atoms[4], mol.Atoms[5], BondOrder.Single); // 5
mol.AddBond(mol.Atoms[5], mol.Atoms[0], BondOrder.Double); // 6
//Create 2 residues
var ac = builder.NewAtomContainer();
ac.Atoms.Add(mol.Atoms[0]);
ac.Atoms.Add(mol.Atoms[1]);
ac.Atoms.Add(mol.Atoms[2]);
Residue res1 = new Residue(ac, 0, mol);
res1.Name = "myResidue1";
mol.AddResidue(res1);
var ac2 = builder.NewAtomContainer();
ac2.Atoms.Add(mol.Atoms[3]);
ac2.Atoms.Add(mol.Atoms[4]);
ac2.Atoms.Add(mol.Atoms[5]);
Residue res2 = new Residue(ac2, 1, mol);
res2.Name = "myResidue2";
mol.AddResidue(res2);
//Create 2 chargegroups
var ac3 = builder.NewAtomContainer();
ac3.Atoms.Add(mol.Atoms[0]);
ac3.Atoms.Add(mol.Atoms[1]);
ChargeGroup chg1 = new ChargeGroup(ac3, 2, mol);
chg1.SetSwitchingAtom(mol.Atoms[1]);
mol.AddChargeGroup(chg1);
var ac4 = builder.NewAtomContainer();
ac4.Atoms.Add(mol.Atoms[2]);
ac4.Atoms.Add(mol.Atoms[3]);
ac4.Atoms.Add(mol.Atoms[4]);
ac4.Atoms.Add(mol.Atoms[5]);
ChargeGroup chg2 = new ChargeGroup(ac4, 3, mol);
chg2.SetSwitchingAtom(mol.Atoms[4]);
mol.AddChargeGroup(chg2);
return(mol);
}
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);
}