G'day,
I'm migrating code from CDK 1.2 to 1.4. The code I wrote (several years
ago now) for implicitly representing hydrogens still compiles and runs
against CDK 1.4 but I'm wondering whether there are better techniques
available now.
The code I use is in a utility class (of static methods):
/**
* Implicitly represent the hydrogens in a structure.
*
* @param mol The structure to convert.
* @return The molecule(s) with implicit hydrogens.
*/
public static IAtomContainer makeHydrogensImplicit(final
IAtomContainer mol)
{
LOG.fine("Make H implicit");
// Explicit -> Implicit H: addExH then removeH is better than
// removeH then addImpH.
final CDKAtomTypeMatcher matcher =
CDKAtomTypeMatcher.getInstance(NoNotificationChemObjectBuilder.getInstance());
final IAtomContainer m2 = new AtomContainer(mol);
try
{
final int atom_cnt = m2.getAtomCount();
for (int i = 0;
i < atom_cnt;
i++)
{
final IAtom atom = m2.getAtom(i);
AtomTypeManipulator.configure(atom,
matcher.findMatchingAtomType(m2, atom));
}
CDKHydrogenAdder.getInstance(m2.getBuilder()).addImplicitHydrogens(m2);
}
catch (final Throwable e)
{
LOG.log(Level.WARNING, "Failed to add hydrogens", e);
}
// Explicit -> Implicit H.
return
AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(m2);
}
Thanks,
Chris.
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