public void TestGetCIPChiralityDoubleBondTogether()
{
var container = CDK.SmilesParser.ParseSmiles("CCC(C)=C(C)CC");
CIPTool.CIPChirality label = CIPTool.GetCIPChirality(
container,
new DoubleBondStereochemistry(container.GetBond(container.Atoms[2], container.Atoms[4]),
new IBond[] { container.GetBond(container.Atoms[2], container.Atoms[3]),
container.GetBond(container.Atoms[4], container.Atoms[5]) },
DoubleBondConformation.Together));
Assert.AreEqual(CIPTool.CIPChirality.Z, label);
}
public void TestGetCIPChiralityAntiILigancyFourChirality()
{
var antiLigands = new ILigand[] { ligands[0], ligands[1], ligands[3], ligands[2] };
var ligandAtoms = new List <IAtom>();
foreach (var ligand in antiLigands)
{
ligandAtoms.Add(ligand.LigandAtom);
}
var chirality = new TetrahedralChirality(molecule.Atoms[1], ligandAtoms, TetrahedralStereo.AntiClockwise);
CIPTool.CIPChirality rsChirality = CIPTool.GetCIPChirality(molecule, chirality);
Assert.AreEqual(CIPTool.CIPChirality.S, rsChirality);
}
public void TestOla28()
{
var filename = "NCDK.Data.CML.mol28.cml";
IChemFile file;
IAtomContainer mol;
using (var reader = new CMLReader(ResourceLoader.GetAsStream(filename)))
{
file = reader.Read(builder.NewChemFile());
mol = ChemFileManipulator.GetAllAtomContainers(file).First();
}
foreach (var atom in mol.Atoms)
{
var neighbors = mol.GetConnectedAtoms(atom).ToReadOnlyList();
if (neighbors.Count == 4)
{
var stereo = StereoTool.GetStereo(neighbors[0], neighbors[1], neighbors[2], neighbors[3]);
ITetrahedralChirality stereoCenter = new TetrahedralChirality(mol.Atoms[0], neighbors, stereo);
CIPTool.CIPChirality chirality = CIPTool.GetCIPChirality(mol, stereoCenter);
}
}
}
