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));
}
private void RemoveHydrogenConstraints(IndigoObject mol)
{
// all this typically < 0.1 msec
List <int> HList = new List <int>();
foreach (IndigoObject atom in mol.iterateAtoms())
{
atom.removeConstraints("hydrogens"); // critical !!
if (atom.atomicNumber() == 1)
{
HList.Add(atom.index());
}
}
mol.removeAtoms(HList); // e.g. to make -n[H]- substructure of -n[C]-
}
private double calculateRgrpMassShift(fragmentationRule rule, IndigoObject structure)
{
Console.Out.WriteLine(rule._MassShift1);
double mshift = 0.00;
foreach (IndigoObject atom in structure.iterateAtoms())
{
if (atom.symbol().Equals("R"))
{
try
{
double RgrpMassShift = double.Parse(rmasses[rmasses.IndexOf(rmasses.Find(x => x.index == atom.index()))].interfaceText.Text);
mshift += RgrpMassShift;
}
catch (FormatException e)
{
MessageBox.Show("All R-Groups must have masses... R Group #" + atom.index() + " does not!");
}
}
}
Console.Out.WriteLine("MASS SHIFT FINAL " + mshift);
return(mshift);
}
