internal static List <IReadOnlyList <int> > GetOverlaps(IAtomContainer ac1, IAtomContainer ac2, bool shouldMatchBonds)
{
Deque <IReadOnlyList <int> > maxCliqueSet = null;
var mappings = new List <IReadOnlyList <int> >();
try
{
GenerateCompatibilityGraph gcg = new GenerateCompatibilityGraph(ac1, ac2, shouldMatchBonds);
var compGraphNodes = gcg.GetCompGraphNodes();
var cEdges = gcg.GetCEgdes();
var dEdges = gcg.GetDEgdes();
BKKCKCF init = new BKKCKCF(compGraphNodes, cEdges, dEdges);
maxCliqueSet = init.GetMaxCliqueSet();
//clear all the compatibility graph content
gcg.Clear();
while (maxCliqueSet.Count != 0)
{
var cliqueList = maxCliqueSet.Peek();
int cliqueSize = cliqueList.Count;
if (cliqueSize < ac1.Atoms.Count && cliqueSize < ac2.Atoms.Count)
{
McGregor mgit = new McGregor(ac1, ac2, mappings, shouldMatchBonds);
mgit.StartMcGregorIteration(mgit.MCSSize, cliqueList, compGraphNodes);
mappings = mgit.mappings;
mgit = null;
}
else
{
mappings = ExactMapping.ExtractMapping(mappings, compGraphNodes, cliqueList);
}
maxCliqueSet.Pop();
if (IsTimeOut())
{
break;
}
}
}
catch (IOException ex)
{
Trace.TraceError(ex.Message);
}
return(mappings);
}
public void TestSomeMethod()
{
// TODO review the generated test code and remove the default call to fail.
Assert.IsNotNull(ExactMapping.ExtractMapping(new List <IReadOnlyList <int> >(), new List <int>(), new List <int>()));
}