/// <summary>
/// </summary>
/// <param name="mol"></param>
/// <param name="mcss"></param>
/// <param name="shouldMatchBonds"></param>
/// <returns>IMolecule Set</returns>
/// <exception cref="CDKException"></exception>
private static IChemObjectSet <IAtomContainer> GetUncommon(IAtomContainer mol, IAtomContainer mcss, bool shouldMatchBonds)
{
List <int> atomSerialsToDelete = new List <int>();
var matches = CDKMCS.GetSubgraphAtomsMaps(mol, mcss, shouldMatchBonds);
var mapList = matches[0];
foreach (var o in mapList)
{
CDKRMap rmap = (CDKRMap)o;
atomSerialsToDelete.Add(rmap.Id1);
}
// at this point we have the serial numbers of the bonds to delete
// we should get the actual bonds rather than delete by serial numbers
List <IAtom> atomsToDelete = new List <IAtom>();
foreach (var serial in atomSerialsToDelete)
{
atomsToDelete.Add(mol.Atoms[serial]);
}
// now lets get rid of the bonds themselves
foreach (var atom in atomsToDelete)
{
mol.RemoveAtomAndConnectedElectronContainers(atom);
}
// now we probably have a set of disconnected components
// so lets get a set of individual atom containers for
// corresponding to each component
return(ConnectivityChecker.PartitionIntoMolecules(mol));
}
public void TestGetSubgraphAtomsMaps_IAtomContainer()
{
int[] result1 = { 6, 5, 7, 8, 0 };
int[] result2 = { 3, 4, 2, 1, 0 };
var mol = TestMoleculeFactory.MakeIndole();
var frag1 = TestMoleculeFactory.MakePyrrole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(frag1);
var adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(mol);
adder = CDK.HydrogenAdder;
adder.AddImplicitHydrogens(frag1);
Aromaticity.CDKLegacy.Apply(mol);
Aromaticity.CDKLegacy.Apply(frag1);
var list = CDKMCS.GetSubgraphAtomsMaps(mol, frag1, true);
var first = list[0];
for (int i = 0; i < first.Count; i++)
{
CDKRMap rmap = first[i];
Assert.AreEqual(rmap.Id1, result1[i]);
Assert.AreEqual(rmap.Id2, result2[i]);
}
}