public void DichlorocyclopropaneTest()
{
Molecule mol = new Molecule();
mol.AddAtom("C");
mol.AddAtom("C");
mol.AddAtom("C");
mol.AddAtom("Cl");
mol.AddAtom("Cl");
mol.AddAtom("H");
mol.AddAtom("H");
mol.AddAtom("H");
mol.AddAtom("H");
mol.AddMultipleSingleBonds(0, 1, 2, 3, 5);
mol.AddMultipleSingleBonds(1, 2, 4, 6);
mol.AddMultipleSingleBonds(2, 7, 8);
// 5 symmetry classes - the non-chiral carbon, its hydrogens, the chiral
// carbons, their hydrogens, and the chlorines.
MoleculeSignature molSig = new MoleculeSignature(mol);
var symmetryClasses = molSig.GetSymmetryClasses();
// Console.Out.WriteLine(symmetryClasses);
Assert.AreEqual(5, symmetryClasses.Count);
// only two possible chiral centers
var tetraChiralCenters =
ChiralCenterFinder.FindTetrahedralChiralCenters(mol);
Assert.AreEqual(2, tetraChiralCenters.Count);
Assert.AreEqual(0, (int)tetraChiralCenters[0]);
Assert.AreEqual(1, (int)tetraChiralCenters[1]);
}
public void DihydroxyCyclohexane()
{
Molecule mol = new Molecule();
mol.AddMultipleAtoms(6, "C");
mol.AddMultipleAtoms(2, "O");
mol.AddMultipleAtoms(12, "H");
mol.AddMultipleSingleBonds(0, 1, 5, 6, 11);
mol.AddMultipleSingleBonds(1, 2, 12, 13);
mol.AddMultipleSingleBonds(2, 3, 14, 15);
mol.AddMultipleSingleBonds(3, 4, 7, 10);
mol.AddMultipleSingleBonds(4, 5, 16, 17);
mol.AddMultipleSingleBonds(5, 18, 19);
mol.AddMultipleSingleBonds(6, 8);
mol.AddMultipleSingleBonds(7, 9);
MoleculeSignature molSig = new MoleculeSignature(mol);
var symmetryClasses = molSig.GetSymmetryClasses();
Console.Out.WriteLine(symmetryClasses);
Assert.AreEqual(6, symmetryClasses.Count);
// this method cannot find the linked chiral centers
var tetraChiralCenters =
ChiralCenterFinder.FindTetrahedralChiralCenters(mol);
Assert.IsTrue(!tetraChiralCenters.Any());
}
public void SpiranTest()
{
Molecule mol = new Molecule();
mol.AddAtom("N");
mol.AddMultipleAtoms(12, "C");
mol.AddMultipleAtoms(24, "H");
mol.AddMultipleSingleBonds(0, 1, 4, 5, 8); // central N
mol.AddMultipleSingleBonds(1, 2, 33, 34); // ring 1 - CA
mol.AddMultipleSingleBonds(2, 3, 11, 15); // ring 1 - CB
mol.AddMultipleSingleBonds(3, 4, 12, 16); // ring 1 - CB
mol.AddMultipleSingleBonds(4, 35, 36); // ring 1 - CA
mol.AddMultipleSingleBonds(5, 6, 29, 30); // ring 2 - CA
mol.AddMultipleSingleBonds(6, 7, 9, 13); // ring 2 - CB
mol.AddMultipleSingleBonds(7, 8, 10, 14); // ring 2 - CB
mol.AddMultipleSingleBonds(8, 31, 32); // ring 2 - CA
mol.AddMultipleSingleBonds(9, 17, 18, 19); // CH3 A
mol.AddMultipleSingleBonds(10, 20, 21, 22); // CH3 B
mol.AddMultipleSingleBonds(11, 23, 24, 25); // CH3 C
mol.AddMultipleSingleBonds(12, 26, 27, 28); // CH3 D
// 7 symmetry classes - central N, CA, CB, CH3-C, HA, HB, CH3-H
MoleculeSignature molSig = new MoleculeSignature(mol);
var symmetryClasses = molSig.GetSymmetryClasses();
Assert.AreEqual(7, symmetryClasses.Count);
var tetraChiralCenters =
ChiralCenterFinder.FindTetrahedralChiralCenters(mol);
Assert.AreEqual(4, tetraChiralCenters.Count);
Assert.AreEqual(2, (int)tetraChiralCenters[0]);
Assert.AreEqual(3, (int)tetraChiralCenters[1]);
Assert.AreEqual(6, (int)tetraChiralCenters[2]);
Assert.AreEqual(7, (int)tetraChiralCenters[3]);
}