G'day,
> The atom type perception is best done by passing the full molecule,
> rather than atom by atom. I do not know the exact speed up, but there
> is some replication involved when calculating atom type perception one
> by one (such as ring detection). Use he other findMatchingAtomType
> method
Thanks - that's better. My atom typing code was based on the snippet provided
in the JavaDoc for CDKHydrogenAdder:
IMolecule methane = new Molecule();
IAtom carbon = new Atom("C");
methane.addAtom(carbon);
CDKAtomTypeMatcher matcher =
CDKAtomTypeMatcher.getInstance(methane.getNewBuilder());
for (IAtom atom : methane.atoms) {
IAtomType type = matcher.findMatchingAtomType(methane, atom);
AtomTypeManipulator.configure(atom, type);
}
CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(methane.getNewBuilder());
adder.addImplicitHydrogens(methane);
So using Egon's suggestion I now have:
// Explicit -> Implicit H: addImpH then removeH is better than removeH then
addImpH.
final IChemObjectBuilder builder =
NoNotificationChemObjectBuilder.getInstance();
final CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(builder);
final IAtomContainer result = new AtomContainer(mol);
try
{
// Type the atoms.
int t = 0;
final IAtomType[] types = matcher.findMatchingAtomType(result);
for (final IAtom atom : result.atoms())
{
final IAtomType type = types[t++];
if (type != null)
{
AtomTypeManipulator.configure(atom, type);
}
}
// Add implicit hydrogens.
CDKHydrogenAdder.getInstance(builder).addImplicitHydrogens(result);
}
catch (final CDKException e)
{
LOG.log(Level.WARNING, "Failed to add hydrogens", e);
}
//Explicit -> Implicit H.
return AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(result);
Many thanks,
Chris.
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