G'day,
> Your code looks OK, but I am not sure why you need
> to add implicit hydrogen before removing the explicit
> hydrogens, though atom typing is expected to be more
> accurate this way. Is that the reason?
Thanks for looking - it was a while ago now but I think I found that I
got better results doing the add followed by removal.
I have made a couple of tweaks; using the atoms Iterable for the typing
loop and just catching CDKException.
// 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
{
for (final IAtom atom : result.atoms())
{
AtomTypeManipulator.configure(atom,
matcher.findMatchingAtomType(result, atom));
}
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);
Thanks,
Chris.
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