private static List <object> GetMappedFragment(IAtomContainer molecule, IEnumerable <IAtom> atomsMCS)
{
IAtomContainer subgraphContainer = molecule.Builder.NewAtomContainer(molecule);
var list = new List <IAtom>();
foreach (var atom in atomsMCS)
{
int post = molecule.Atoms.IndexOf(atom);
list.Add(subgraphContainer.Atoms[post]);
}
List <IAtom> rlist = new List <IAtom>();
foreach (var atoms in subgraphContainer.Atoms)
{
if (!list.Contains(atoms))
{
rlist.Add(atoms);
}
}
foreach (var atoms in rlist)
{
subgraphContainer.RemoveAtomAndConnectedElectronContainers(atoms);
}
List <object> l = new List <object>
{
list,
subgraphContainer
};
return(l);
}
/// <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));
}
private int GetMappedMoleculeFragmentSize(IReadOnlyDictionary <IAtom, IAtom> mcsAtomSolution)
{
IAtomContainer educt = ChemObjectBuilder.Instance.NewAtomContainer(rMol);
IAtomContainer product = ChemObjectBuilder.Instance.NewAtomContainer(pMol);
if (mcsAtomSolution != null)
{
foreach (var map in mcsAtomSolution)
{
IAtom atomE = map.Key;
IAtom atomP = map.Value;
educt.RemoveAtomAndConnectedElectronContainers(atomE);
product.RemoveAtomAndConnectedElectronContainers(atomP);
}
}
return(GetFragmentCount(educt) + GetFragmentCount(product));
}