public void TestADoubleRingWithANitrogenAtom()
{
// Should have 4 double bonds and all three bonds to/from the nitrogen
// should be single
var smiles = "c1ccn2cccc2c1";
var mol = sp.ParseSmiles(smiles);
AtomContainerManipulator.PercieveAtomTypesAndConfigureUnsetProperties(mol);
IAtom nitrogen = mol.Atoms[3];
atasc.DecideBondOrder(mol, true);
int doubleBondCount = 0, singleBondCount = 0;
foreach (var bond in mol.Bonds)
{
if (bond.Order.Equals(BondOrder.Double))
{
doubleBondCount++;
}
if (bond.Contains(nitrogen))
{
if (bond.Order.Equals(BondOrder.Single))
{
singleBondCount++;
}
}
}
Assert.AreEqual(4, doubleBondCount);
Assert.AreEqual(3, singleBondCount);
}
public static IAtomContainer ParseSmiles(string smiles)
{
var molecule = CDK.SmilesParser.ParseSmiles(smiles);
AtomContainerManipulator.PercieveAtomTypesAndConfigureUnsetProperties(molecule);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(molecule);
Aromaticity.CDKLegacy.Apply(molecule);
return(molecule);
}
