private string GetAsString(IAtomContainer mol)
{
StringWriter stringWriter = new StringWriter();
PDBWriter writer = new PDBWriter(stringWriter);
writer.WriteMolecule(mol);
writer.Close();
return(stringWriter.ToString());
}
public void WriteAsATOM()
{
IAtomContainer mol = SingleAtomMolecule();
StringWriter stringWriter = new StringWriter();
PDBWriter writer = new PDBWriter(stringWriter);
writer.IOSettings["WriteAsHET"].Setting = "false";
writer.WriteMolecule(mol);
writer.Close();
string asString = stringWriter.ToString();
Assert.IsTrue(asString.IndexOf("ATOM") != -1);
}
public void MolfactoryRoundtripTest()
{
IAtomContainer original = TestMoleculeFactory.MakePyrrole();
SetCoordinatesToZero(original);
StringWriter stringWriter = new StringWriter();
PDBWriter writer = new PDBWriter(stringWriter);
writer.WriteMolecule(original);
writer.Close();
string output = stringWriter.ToString();
PDBReader reader = new PDBReader(new StringReader(output));
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
IAtomContainer reconstructed = chemFile[0][0].MoleculeSet[0];
Assert.AreEqual(original.Atoms.Count, reconstructed.Atoms.Count);
Assert.AreEqual(original.Bonds.Count, reconstructed.Bonds.Count);
}
public void TestRoundTrip_fractionalCoordinates()
{
StringWriter sWriter = new StringWriter();
PDBWriter writer = new PDBWriter(sWriter);
Crystal crystal = new Crystal();
crystal.A = new Vector3(0, 1, 0);
crystal.B = new Vector3(1, 0, 0);
crystal.C = new Vector3(0, 0, 2);
IAtom atom = new Atom("C");
atom.FractionalPoint3D = 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 :(
}
