private byte[] RenderHighlightedObject(IndigoObject mol, IndigoObject query)
{
query.aromatize();
IndigoObject matcher = indigo.substructureMatcher(mol);
foreach (IndigoObject match in matcher.iterateMatches(query))
{
foreach (IndigoObject queryAtom in query.iterateAtoms())
{
IndigoObject atom = match.mapAtom(queryAtom);
atom.highlight();
foreach (IndigoObject nei in atom.iterateNeighbors())
{
if (!nei.isPseudoatom() && !nei.isRSite() && nei.atomicNumber() == 1)
{
nei.highlight();
nei.bond().highlight();
}
}
}
foreach (IndigoObject bond in query.iterateBonds())
{
match.mapBond(bond).highlight();
}
}
indigo.setOption("render-coloring", false);
mol.dearomatize();
mol.layout();
return(renderer.renderToBuffer(mol));
}
public void test1()
{
string strQmol = "[H]/N=C(C)/N1CCCCC1"; //shows problem!
//string strQmol = "[H]/N=C(C)/N"; // still shows problem
//string strQmol = "[H]/N=C(C)/C"; // no problem
//string strQmol = "[H]/N=C(C)/C(C)(C)"; // no problem again
// string strLmol = "[H]/N=C(C)/N1CCCCC1CCC";
string strLmol = "N(C(=N([H])[H])c1cccc(C=CCN(C(=O)CCC(=O)OCC)c2ccc(OC3CCN(C(=N[H])C)CC3)c(C(F)(F)F)c2)c1)([H])[H]";
IndigoObject qmol = indigo.loadQueryMolecule(strQmol);
IndigoObject mol = indigo.loadMolecule(strLmol);
System.Diagnostics.Debug.WriteLine("QueryMol 1: " + qmol.smiles());
//qmol.clearCisTrans();
//
string problem = mol.checkAmbiguousH();
problem = mol.checkBadValence();
System.Diagnostics.Debug.WriteLine("QueryMol 2: " + qmol.smiles());
System.Diagnostics.Debug.WriteLine("Largermol is : " + mol.smiles());
IndigoObject matcher = indigo.substructureMatcher(mol);
indigo.setOption("embedding-uniqueness", "atoms");
foreach (IndigoObject m in matcher.iterateMatches(qmol))
{
System.Diagnostics.Debug.WriteLine(m.highlightedTarget().smiles());
}
}