/// <summary>
/// Returns the R or S chirality according to the CIP rules, based on the given
/// chirality information.
/// </summary>
/// <param name="container"><see cref="IAtomContainer"/> to which the <paramref name="stereoCenter"/> belongs.</param>
/// <param name="stereoCenter">Chiral center for which the CIP chirality is to be determined as <see cref="ITetrahedralChirality"/> object.</param>
/// <returns>A <see cref="CIPChirality"/> value.</returns>
public static CIPChirality GetCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter)
{
// the LigancyFourChirality is kind of redundant but we keep for an
// easy way to get the ILigands array
var tmp = new LigancyFourChirality(container, stereoCenter).ligands;
var stereo = stereoCenter.Stereo;
int parity = PermParity(tmp);
if (parity == 0)
{
return(CIPChirality.None);
}
if (parity < 0)
{
stereo = stereo.Invert();
}
if (stereo == TetrahedralStereo.Clockwise)
{
return(CIPChirality.R);
}
if (stereo == TetrahedralStereo.AntiClockwise)
{
return(CIPChirality.S);
}
return(CIPChirality.None);
}
public void TestTwoVersusDoubleBondedOxygenR()
{
var molecule = smiles.ParseSmiles("OC(O)C([H])(C)C=O");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 3, 4, 5, 1, 6, TetrahedralStereo.Clockwise);
Assert.AreEqual(CIPTool.CIPChirality.R, CIPTool.GetCIPChirality(chirality));
}
public void Test()
{
var molecule = smiles.ParseSmiles("ClC(Br)(I)[H]");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 1, 4, 0, 2, 3, TetrahedralStereo.Clockwise);
Assert.AreEqual(CIPTool.CIPChirality.R, CIPTool.GetCIPChirality(chirality));
}
public void Test2methylbutanolR()
{
var molecule = smiles.ParseSmiles("OCC([H])(C)CC");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 2, 3, 1, 4, 5, TetrahedralStereo.Clockwise);
Assert.AreEqual(CIPTool.CIPChirality.R, CIPTool.GetCIPChirality(chirality));
}
public void TestGetCIPChirality()
{
var chirality = new LigancyFourChirality(molecule.Atoms[1], ligands, TetrahedralStereo.Clockwise);
var rsChirality = CIPTool.GetCIPChirality(chirality);
Assert.AreEqual(CIPTool.CIPChirality.S, rsChirality);
}
public void TestProject()
{
var chirality = new LigancyFourChirality(molecule.Atoms[1], ligands, TetrahedralStereo.Clockwise);
chirality.Project(ligands);
Assert.AreEqual(TetrahedralStereo.Clockwise, chirality.Stereo);
}
public void TestImplicitHydrogen()
{
var molecule = smiles.ParseSmiles("CCC(C)CCC");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 2, CIPTool.Hydrogen, 3, 1, 4,
TetrahedralStereo.AntiClockwise);
Assert.AreEqual(CIPTool.CIPChirality.S, CIPTool.GetCIPChirality(chirality));
}
public void TestTetraHalogenMethane()
{
var molecule = smiles.ParseSmiles("FC(Br)(Cl)I");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 1, 0, 4, 2, 3,
TetrahedralStereo.AntiClockwise);
Assert.AreEqual(CIPTool.CIPChirality.R, CIPTool.GetCIPChirality(chirality));
}
public void TestProjectTwoChanges()
{
var chirality = new LigancyFourChirality(molecule.Atoms[1], ligands, TetrahedralStereo.Clockwise);
var newLigands = new ILigand[] { ligands[1], ligands[0], ligands[3], ligands[2] };
chirality = chirality.Project(newLigands);
Assert.AreEqual(TetrahedralStereo.Clockwise, chirality.Stereo);
}
public void TestGetCIPChiralityAnti()
{
var antiLigands = new ILigand[] { ligands[0], ligands[1], ligands[3], ligands[2] };
var chirality = new LigancyFourChirality(molecule.Atoms[1], antiLigands, TetrahedralStereo.AntiClockwise);
var rsChirality = CIPTool.GetCIPChirality(chirality);
Assert.AreEqual(CIPTool.CIPChirality.S, rsChirality);
}
public void TestConstructor()
{
var chirality = new LigancyFourChirality(molecule.Atoms[1], ligands, TetrahedralStereo.Clockwise);
Assert.IsNotNull(chirality);
Assert.AreEqual(molecule.Atoms[1], chirality.ChiralAtom);
for (int i = 0; i < ligands.Length; i++)
{
Assert.AreEqual(ligands[i], chirality.Ligands[i]);
}
Assert.AreEqual(TetrahedralStereo.Clockwise, chirality.Stereo);
}
/// <summary>
/// Returns the R or S chirality according to the CIP rules, based on the given
/// chirality information.
/// </summary>
/// <param name="stereoCenter">Chiral center for which the CIP chirality is to be
/// determined as <see cref="LigancyFourChirality"/> object.</param>
/// <returns>A <see cref="CIPChirality"/> value.</returns>
public static CIPChirality GetCIPChirality(LigancyFourChirality stereoCenter)
{
var ligands = Order(stereoCenter.Ligands);
var rsChirality = stereoCenter.Project(ligands);
bool allAreDifferent = CheckIfAllLigandsAreDifferent(ligands);
if (!allAreDifferent)
{
return(CIPChirality.None);
}
if (rsChirality.Stereo == TetrahedralStereo.Clockwise)
{
return(CIPChirality.R);
}
return(CIPChirality.S);
}
public void TestConstructorILigancyFourChirality()
{
var ligandAtoms = new List <IAtom>();
foreach (var ligand in ligands)
{
ligandAtoms.Add(ligand.LigandAtom);
}
var cdkChiral = new TetrahedralChirality(molecule.Atoms[1],
ligandAtoms, TetrahedralStereo.Clockwise);
var chirality = new LigancyFourChirality(molecule, cdkChiral);
Assert.IsNotNull(chirality);
Assert.AreEqual(molecule.Atoms[1], chirality.ChiralAtom);
for (int i = 0; i < ligands.Length; i++)
{
Assert.AreEqual(ligands[i].LigandAtom, chirality.Ligands[i].LigandAtom);
Assert.AreEqual(ligands[i].CentralAtom, chirality.Ligands[i].CentralAtom);
Assert.AreEqual(ligands[i].AtomContainer, chirality.Ligands[i].AtomContainer);
}
Assert.AreEqual(TetrahedralStereo.Clockwise, chirality.Stereo);
}
