public void TestPyrrole_Silent()
{
var smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
var sp = new SmilesParser(builder, false);
var molecule = sp.ParseSmiles(smiles);
AtomContainerManipulator.SetSingleOrDoubleFlags(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
molecule = dbst.FixAromaticBondOrders(molecule);
Assert.IsNotNull(molecule);
molecule = (IAtomContainer)AtomContainerManipulator.RemoveHydrogens(molecule);
int doubleBondCount = 0;
for (int i = 0; i < molecule.Bonds.Count; i++)
{
IBond bond = molecule.Bonds[i];
Assert.IsTrue(bond.IsAromatic);
if (bond.Order == BondOrder.Double)
{
doubleBondCount++;
}
}
Assert.AreEqual(6, doubleBondCount);
}
public void RadicalCanon()
{
var builder = CDK.Builder;
IAtomContainer mola = builder.NewAtomContainer();
mola.Atoms.Add(builder.NewAtom("CH3"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH2"));
mola.Atoms.Add(builder.NewAtom("CH1"));
mola.Atoms.Add(builder.NewAtom("CH3"));
mola.AddBond(mola.Atoms[1], mola.Atoms[2], BondOrder.Single);
mola.AddBond(mola.Atoms[2], mola.Atoms[3], BondOrder.Single);
mola.AddBond(mola.Atoms[3], mola.Atoms[4], BondOrder.Single);
mola.AddBond(mola.Atoms[4], mola.Atoms[5], BondOrder.Single);
mola.AddBond(mola.Atoms[5], mola.Atoms[6], BondOrder.Single);
mola.AddBond(mola.Atoms[0], mola.Atoms[5], BondOrder.Single);
mola.AddSingleElectronTo(mola.Atoms[1]);
SmilesParser smipar = new SmilesParser(builder);
var molb = smipar.ParseSmiles("CC(CCC[CH2])C |^1:5|");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.Canonical | SmiFlavors.CxRadical);
Assert.AreEqual(smigen.Create(molb), smigen.Create(mola));
}
public void NonCXSMILESLayer()
{
var mol = smipar.ParseSmiles("c1ccccc1 |<benzene>|");
Assert.IsNotNull(mol);
Assert.AreEqual("|<benzene>|", (string)mol.Title);
}