private static string F_ANGLE_FORMAT(double angle) => angle.ToString("F3", NumberFormatInfo.InvariantInfo).PadLeft(7); //"%3.3f";
public void WriteCrystal(ICrystal crystal)
{
try
{
WriteHeader();
Vector3 a = crystal.A;
Vector3 b = crystal.B;
Vector3 c = crystal.C;
double[] ucParams = CrystalGeometryTools.CartesianToNotional(a, b, c);
writer.Write("CRYST1 " + F_LENGTH_FORMAT(ucParams[0]));
writer.Write(F_LENGTH_FORMAT(ucParams[1]));
writer.Write(F_LENGTH_FORMAT(ucParams[2]));
writer.Write(F_ANGLE_FORMAT(ucParams[3]));
writer.Write(F_ANGLE_FORMAT(ucParams[4]));
writer.Write('\n');
// before saving the atoms, we need to create cartesian coordinates
foreach (var atom in crystal.Atoms)
{
// Debug.WriteLine($"PDBWriter: atom -> {atom}");
// if it got 3D coordinates, use that. If not, try fractional coordinates
if (atom.Point3D == null && atom.FractionalPoint3D != null)
{
Vector3 frac = atom.FractionalPoint3D.Value;
Vector3 cart = CrystalGeometryTools.FractionalToCartesian(a, b, c, frac);
atom.Point3D = cart;
}
}
WriteMolecule(crystal.Builder.NewAtomContainer(crystal));
}
catch (IOException exception)
{
throw new CDKException("Error while writing file: " + exception.Message, exception);
}
}
public void TestReading()
{
var filename = "NCDK.Data.ShelX.frame_1.res";
Trace.TraceInformation("Testing: " + filename);
var ins = ResourceLoader.GetAsStream(filename);
ShelXReader reader = new ShelXReader(ins);
Crystal crystal = (Crystal)reader.Read(new Crystal());
reader.Close();
Assert.IsNotNull(crystal);
Assert.AreEqual(42, crystal.Atoms.Count);
var notional = CrystalGeometryTools.CartesianToNotional(crystal.A, crystal.B, crystal.C);
Assert.AreEqual(7.97103, notional[0], 0.001);
Assert.AreEqual(18.77220, notional[1], 0.001);
Assert.AreEqual(10.26222, notional[2], 0.001);
Assert.AreEqual(90.0000, notional[3], 0.001);
Assert.AreEqual(90.0000, notional[4], 0.001);
Assert.AreEqual(90.0000, notional[5], 0.001);
}
private CMLMolecule CDKCrystalToCMLMolecule(ICrystal crystal, bool setIDs)
{
var molecule = CDKAtomContainerToCMLMolecule(crystal, false, false);
var cmlCrystal = new CMLCrystal();
if (useCMLIDs && setIDs)
{
IDCreator.CreateIDs(crystal);
}
if (!string.IsNullOrEmpty(crystal.Id))
{
cmlCrystal.Id = crystal.Id;
}
this.CheckPrefix(cmlCrystal);
cmlCrystal.Z = crystal.Z.Value;
var params_ = CrystalGeometryTools.CartesianToNotional(crystal.A, crystal.B, crystal.C);
Debug.WriteLine($"Number of cell params: {params_.Length}");
cmlCrystal.SetCellParameters(params_);
molecule.Add(cmlCrystal);
return(molecule);
}