public void MethyleneCyclopropeneTest()
{
IAtomContainer mol = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(mol, 4);
AbstractSignatureTest.AddHydrogens(mol, 1, 2);
AbstractSignatureTest.AddHydrogens(mol, 2, 1);
AbstractSignatureTest.AddHydrogens(mol, 3, 1);
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Double);
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[3], BondOrder.Single);
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Double);
MoleculeSignature molSig = new MoleculeSignature(mol);
string sigFor2Height1 = molSig.SignatureStringForVertex(2, 1);
string sigFor3Height1 = molSig.SignatureStringForVertex(3, 1);
Assert.IsTrue(
sigFor2Height1.Equals(sigFor3Height1),
"Height 1 signatures for atoms 2 and 3" + " should be the same");
string sigFor2Height2 = molSig.SignatureStringForVertex(2, 1);
string sigFor3Height2 = molSig.SignatureStringForVertex(3, 1);
Assert.IsTrue(
sigFor2Height2.Equals(sigFor3Height2),
"Height 2 signatures for atoms 2 and 3" + " should be the same");
}
public void TestBenzeneWithDoubleBonds()
{
IAtomContainer benzene = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(benzene, 6);
for (int i = 0; i < 6; i++)
{
AbstractSignatureTest.AddHydrogens(benzene, i, 1);
}
benzene.AddBond(benzene.Atoms[0], benzene.Atoms[1], BondOrder.Single);
benzene.AddBond(benzene.Atoms[1], benzene.Atoms[2], BondOrder.Double);
benzene.AddBond(benzene.Atoms[2], benzene.Atoms[3], BondOrder.Single);
benzene.AddBond(benzene.Atoms[3], benzene.Atoms[4], BondOrder.Double);
benzene.AddBond(benzene.Atoms[4], benzene.Atoms[5], BondOrder.Single);
benzene.AddBond(benzene.Atoms[5], benzene.Atoms[0], BondOrder.Double);
MoleculeSignature signature = new MoleculeSignature(benzene);
string carbonSignature = signature.SignatureStringForVertex(0);
for (int i = 1; i < 6; i++)
{
string carbonSignatureI = signature.SignatureStringForVertex(i);
Assert.AreEqual(carbonSignature, carbonSignatureI);
}
}
public static IAtomContainer MakeSandwich(int ringSize, bool hasMethyl)
{
IAtomContainer mol = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(mol, (ringSize * 2));
mol.Atoms.Add(builder.NewAtom("Fe"));
int center = ringSize * 2;
// face A
for (int i = 0; i < ringSize - 1; i++)
{
mol.AddBond(mol.Atoms[i], mol.Atoms[i + 1], BondOrder.Single);
mol.AddBond(mol.Atoms[i], mol.Atoms[center], BondOrder.Single);
}
mol.AddBond(mol.Atoms[ringSize - 1], mol.Atoms[0], BondOrder.Single);
mol.AddBond(mol.Atoms[ringSize - 1], mol.Atoms[center], BondOrder.Single);
// // face B
for (int i = 0; i < ringSize - 1; i++)
{
mol.AddBond(mol.Atoms[ringSize + 1], mol.Atoms[i + ringSize + 1], BondOrder.Single);
mol.AddBond(mol.Atoms[ringSize + 1], mol.Atoms[center], BondOrder.Single);
}
mol.AddBond(mol.Atoms[(2 * ringSize) - 1], mol.Atoms[ringSize], BondOrder.Single);
mol.AddBond(mol.Atoms[(2 * ringSize) - 1], mol.Atoms[center], BondOrder.Single);
if (hasMethyl)
{
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[0], mol.Atoms.Last(), BondOrder.Single);
}
return(mol);
}
public void CyclobuteneTest()
{
string expectedA = "[C]([C]([C,0])=[C]([C,0]))";
string expectedB = "[C]([C]([C,0])[C](=[C,0]))";
IAtomContainer cyclobutene = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(cyclobutene, 4);
cyclobutene.AddBond(cyclobutene.Atoms[0], cyclobutene.Atoms[1], BondOrder.Single);
cyclobutene.AddBond(cyclobutene.Atoms[0], cyclobutene.Atoms[2], BondOrder.Single);
cyclobutene.AddBond(cyclobutene.Atoms[1], cyclobutene.Atoms[3], BondOrder.Double);
cyclobutene.AddBond(cyclobutene.Atoms[2], cyclobutene.Atoms[3], BondOrder.Single);
Assert.AreEqual(expectedA, CanonicalStringFromMolecule(cyclobutene));
string expectedFullString = "2" + expectedA + " + 2" + expectedB;
string actualFullString = FullStringFromMolecule(cyclobutene);
Assert.AreEqual(expectedFullString, actualFullString);
}
public void FusedSquareMultipleBondTest()
{
IAtomContainer mol = builder.NewAtomContainer();
string expected = "[C]([C]([C,1])[C]([C,0])[C](=[C,1])[C](=[C,0]))";
AbstractSignatureTest.AddCarbons(mol, 7);
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[3], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[4], BondOrder.Single);
mol.AddBond(mol.Atoms[1], mol.Atoms[5], BondOrder.Double);
mol.AddBond(mol.Atoms[2], mol.Atoms[5], BondOrder.Single);
mol.AddBond(mol.Atoms[3], mol.Atoms[6], BondOrder.Single);
mol.AddBond(mol.Atoms[4], mol.Atoms[6], BondOrder.Double);
MoleculeSignature molSig = new MoleculeSignature(mol);
string sigFor0 = molSig.SignatureStringForVertex(0);
Assert.AreEqual(expected, sigFor0);
}
public static IAtomContainer MakeC7H16C()
{
IAtomContainer mol = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(mol, 7);
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single);
mol.AddBond(mol.Atoms[3], mol.Atoms[4], BondOrder.Single);
mol.AddBond(mol.Atoms[4], mol.Atoms[5], BondOrder.Single);
mol.AddBond(mol.Atoms[5], mol.Atoms[6], BondOrder.Single);
AbstractSignatureTest.AddHydrogens(mol, 0, 3);
AbstractSignatureTest.AddHydrogens(mol, 1, 3);
AbstractSignatureTest.AddHydrogens(mol, 2, 1);
AbstractSignatureTest.AddHydrogens(mol, 3, 2);
AbstractSignatureTest.AddHydrogens(mol, 4, 2);
AbstractSignatureTest.AddHydrogens(mol, 5, 2);
AbstractSignatureTest.AddHydrogens(mol, 6, 3);
return(mol);
}