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);
}
/// <summary>
/// Creates a ligancy for chirality around a single chiral atom, where the involved
/// atoms are identified by there index in the <see cref="IAtomContainer"/>. For the four ligand
/// atoms, <see cref="Hydrogen"/> can be passed as index, which will indicate the presence of
/// an implicit hydrogen, not explicitly present in the chemical graph of the
/// given <paramref name="container"/>.
/// </summary>
/// <param name="container"><see cref="IAtomContainer"/> for which the returned <see cref="ILigand"/>s are defined</param>
/// <param name="chiralAtom">int pointing to the <see cref="IAtom"/> index of the chiral atom</param>
/// <param name="ligand1">int pointing to the <see cref="IAtom"/> index of the first <see cref="ILigand"/></param>
/// <param name="ligand2">int pointing to the <see cref="IAtom"/> index of the second <see cref="ILigand"/></param>
/// <param name="ligand3">int pointing to the <see cref="IAtom"/> index of the third <see cref="ILigand"/></param>
/// <param name="ligand4">int pointing to the <see cref="IAtom"/> index of the fourth <see cref="ILigand"/></param>
/// <param name="stereo"><see cref="TetrahedralStereo"/> for the chirality</param>
/// <returns>the created <see cref="LigancyFourChirality"/></returns>
public static LigancyFourChirality DefineLigancyFourChirality(IAtomContainer container, int chiralAtom, int ligand1, int ligand2, int ligand3, int ligand4, TetrahedralStereo stereo)
{
var atomIndices = new int[] { ligand1, ligand2, ligand3, ligand4 };
var visitedAtoms = new VisitedAtoms();
var ligands = new ILigand[4];
for (int i = 0; i < 4; i++)
{
ligands[i] = DefineLigand(container, visitedAtoms, chiralAtom, atomIndices[i]);
}
return(new LigancyFourChirality(container.Atoms[chiralAtom], ligands, stereo));
}
/// <summary>
/// Returns a CIP-expanded array of side chains of a ligand. If the ligand atom is only connected to
/// the chiral atom, the method will return an empty list. The expansion involves the CIP rules,
/// so that a double bonded oxygen will be represented twice in the list.
/// </summary>
/// <param name="ligand">the <see cref="ILigand"/> for which to return the ILigands</param>
/// <returns>a <see cref="ILigand"/> array with the side chains of the ligand atom</returns>
public static IReadOnlyList <ILigand> GetLigandLigands(ILigand ligand)
{
if (ligand is TerminalLigand)
{
return(Array.Empty <ILigand>());
}
var container = ligand.AtomContainer;
var ligandAtom = ligand.LigandAtom;
var centralAtom = ligand.CentralAtom;
var visitedAtoms = ligand.VisitedAtoms;
var bonds = container.GetConnectedBonds(ligandAtom);
// duplicate ligands according to bond order, following the CIP rules
var ligands = new List <ILigand>();
foreach (var bond in bonds)
{
if (bond.Contains(centralAtom))
{
if (BondOrder.Single == bond.Order)
{
continue;
}
int duplication = GetDuplication(bond.Order) - 1;
if (duplication > 0)
{
for (int i = 1; i <= duplication; i++)
{
ligands.Add(new TerminalLigand(container, visitedAtoms, ligandAtom, centralAtom));
}
}
}
else
{
var duplication = GetDuplication(bond.Order);
var connectedAtom = bond.GetOther(ligandAtom);
if (visitedAtoms.IsVisited(connectedAtom))
{
ligands.Add(new TerminalLigand(container, visitedAtoms, ligandAtom, connectedAtom));
}
else
{
ligands.Add(new Ligand(container, visitedAtoms, ligandAtom, connectedAtom));
}
for (int i = 2; i <= duplication; i++)
{
ligands.Add(new TerminalLigand(container, visitedAtoms, ligandAtom, connectedAtom));
}
}
}
return(ligands);
}
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 TestCheckIfAllLigandsAreDifferentFalse()
{
var sameLigands = new ILigand[] { ligands[0], ligands[0], ligands[1], ligands[2] };
Assert.IsFalse(CIPTool.CheckIfAllLigandsAreDifferent(sameLigands));
}
