public void TestNewCrystal_IAtomContainer()
{
IChemObjectBuilder builder = RootObject.Builder;
ICrystal crystal = builder.NewCrystal(builder.NewAtomContainer());
Assert.IsNotNull(crystal);
}
public void TestNewCrystal()
{
IChemObjectBuilder builder = RootObject.Builder;
ICrystal crystal = builder.NewCrystal();
Assert.IsNotNull(crystal);
}
public void TestIsEmpty_Crystal()
{
var model = (IChemModel)NewChemObject();
IChemObjectBuilder builder = model.Builder;
ICrystal crystal = builder.NewCrystal();
model.Crystal = crystal;
Assert.IsTrue(model.IsEmpty());
crystal.Atoms.Add(builder.NewAtom("C"));
Assert.IsFalse(model.IsEmpty());
model.Crystal = null;
Assert.IsTrue(model.IsEmpty());
}
public void TestRoundTrip()
{
StringWriter sWriter = new StringWriter();
PDBWriter writer = new PDBWriter(sWriter);
ICrystal crystal = builder.NewCrystal();
crystal.A = new Vector3(0, 1, 0);
crystal.B = new Vector3(1, 0, 0);
crystal.C = new Vector3(0, 0, 2);
IAtom atom = builder.NewAtom("C");
atom.Point3D = new Vector3(0.1, 0.1, 0.3);
crystal.Atoms.Add(atom);
writer.Write(crystal);
writer.Close();
string output = sWriter.ToString();
Assert.IsNotNull(output);
Assert.IsTrue(output.Length > 0);
PDBReader reader = new PDBReader(new StringReader(""));
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
IChemSequence sequence = chemFile[0];
Assert.AreEqual(1, sequence.Count);
IChemModel chemModel = sequence[0];
Assert.IsNotNull(chemModel);
// can't do further testing as the PDBReader does not read
// Crystal structures :(
}
public void TestCMLCrystal()
{
var writer = new StringWriter();
var crystal = builder.NewCrystal();
var silicon = builder.NewAtom("Si");
silicon.FractionalPoint3D = new Vector3(0, 0, 0);
crystal.Atoms.Add(silicon);
crystal.A = (new Vector3(1.5, 0.0, 0.0));
crystal.B = (new Vector3(0.0, 2.0, 0.0));
crystal.C = (new Vector3(0.0, 0.0, 1.5));
using (var cmlWriter = new CMLWriter(writer))
{
cmlWriter.Write(crystal);
}
var cmlContent = writer.ToString();
Debug.WriteLine("****************************** TestCMLCrystal()");
Debug.WriteLine(cmlContent);
Debug.WriteLine("******************************");
Assert.IsTrue(cmlContent.IndexOf("</crystal>") != -1); // the cystal info has to be present
Assert.IsTrue(cmlContent.IndexOf("<atom") != -1); // an Atom has to be present
}