[TestMethod(), Ignore()] // This is an example structure where this class fails
public void TestLargeBioclipseUseCase()
{
var smiles = "COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56";
var smilesParser = CDK.SmilesParser;
var molecule = smilesParser.ParseSmiles(smiles);
DeduceBondSystemTool dbst = new DeduceBondSystemTool(new AllRingsFinder());
molecule = dbst.FixAromaticBondOrders(molecule);
Assert.IsNotNull(molecule);
molecule = (IAtomContainer)AtomContainerManipulator.RemoveHydrogens(molecule);
Assert.AreEqual(40, molecule.Atoms.Count);
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.Bonds.Count; i++)
{
IBond bond = molecule.Bonds[i];
if (bond.Order == BondOrder.Double)
{
doubleBondCount++;
}
}
Assert.AreEqual(10, doubleBondCount);
}
public void TestPyrrole_CustomRingFinder()
{
var smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
var smilesParser = new SmilesParser(builder, false);
var molecule = smilesParser.ParseSmiles(smiles);
AtomContainerManipulator.SetSingleOrDoubleFlags(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
DeduceBondSystemTool dbst = new DeduceBondSystemTool(new AllRingsFinder());
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 TestLargeRingSystem()
{
var smiles = "O=C1Oc6ccccc6(C(O)C1C5c2ccccc2CC(c3ccc(cc3)c4ccccc4)C5)";
var smilesParser = CDK.SmilesParser;
var molecule = smilesParser.ParseSmiles(smiles);
DeduceBondSystemTool dbst = new DeduceBondSystemTool(new AllRingsFinder());
molecule = dbst.FixAromaticBondOrders(molecule);
Assert.IsNotNull(molecule);
molecule = (IAtomContainer)AtomContainerManipulator.RemoveHydrogens(molecule);
Assert.AreEqual(34, molecule.Atoms.Count);
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.Bonds.Count; i++)
{
IBond bond = molecule.Bonds[i];
if (bond.Order == BondOrder.Double)
{
doubleBondCount++;
}
}
Assert.AreEqual(13, doubleBondCount);
}