public void TestFindHeavyAtomsInChain_IAtomContainer_IAtomContainer()
{
var filename = "NCDK.Data.MDL.allmol232.mol";
var ins = ResourceLoader.GetAsStream(filename);
// TODO: shk3-cleanuptests: best to use the STRICT IO mode here
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile);
var ac = new Silent.AtomContainer(containersList.First());
AddExplicitHydrogens(ac);
var chain = ac.Builder.NewAtomContainer();
for (int i = 16; i < 25; i++)
{
chain.Atoms.Add(ac.Atoms[i]);
}
chain.Atoms.Add(ac.Atoms[29]);
chain.Atoms.Add(ac.Atoms[30]);
int[] result = new AtomPlacer3D().FindHeavyAtomsInChain(ac, chain);
Assert.AreEqual(16, result[0]);
Assert.AreEqual(11, result[1]);
}
static IAtomContainer Mock(int n)
{
// builder.NewAtomContainer, ie, new AtomContainer2 does not work here with Moq.
var mock = new Silent.AtomContainer();
for (int i = 0; i < n; i++)
{
mock.Atoms.Add(new Moq.Mock <IAtom>().Object);
}
return(mock);
}
public void TestModelBuilder3D_bug_1241421()
{
var mb3d = ModelBuilder3D.GetInstance();
var filename = "NCDK.Data.MDL.bug1241421.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
IAtomContainer ac = new Silent.AtomContainer(containersList[0]);
ac = mb3d.Generate3DCoordinates(ac, false);
CheckAverageBondLength(ac);
}
public void TestModelBuilder3D_232()
{
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
var filename = "NCDK.Data.MDL.allmol232.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
var containersList = ChemFileManipulator.GetAllAtomContainers(chemFile).ToReadOnlyList();
IAtomContainer ac = new Silent.AtomContainer(containersList[0]);
AddExplicitHydrogens(ac);
ac = mb3d.Generate3DCoordinates(ac, false);
Assert.IsNotNull(ac.Atoms[0].Point3D);
CheckAverageBondLength(ac);
}
public void TestModelBuilder3D_keepChemObjectIDs()
{
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
IAtomContainer methanol = new Silent.AtomContainer();
IChemObjectBuilder builder = methanol.Builder;
IAtom carbon1 = builder.NewAtom("C");
carbon1.Id = "carbon1";
methanol.Atoms.Add(carbon1);
for (int i = 0; i < 3; i++)
{
IAtom hydrogen = builder.NewAtom("H");
methanol.Atoms.Add(hydrogen);
methanol.Bonds.Add(builder.NewBond(carbon1, hydrogen, BondOrder.Single));
}
IAtom oxygen1 = builder.NewAtom("O");
oxygen1.Id = "oxygen1";
methanol.Atoms.Add(oxygen1);
methanol.Bonds.Add(builder.NewBond(carbon1, oxygen1, BondOrder.Single));
{
IAtom hydrogen = builder.NewAtom("H");
methanol.Atoms.Add(hydrogen);
methanol.Bonds.Add(builder.NewBond(hydrogen, oxygen1, BondOrder.Single));
}
Assert.AreEqual(6, methanol.Atoms.Count);
Assert.AreEqual(5, methanol.Bonds.Count);
mb3d.Generate3DCoordinates(methanol, false);
CheckAverageBondLength(methanol);
Assert.AreEqual("carbon1", carbon1.Id);
Assert.AreEqual("oxygen1", oxygen1.Id);
}