It depends what your work flow looks like, code hosted anywhere?
Essentially from well-formed Molfiles and SMILES the hydrogen count on each
atom will be set. You therefore should not need to call CDK atom typing at
all. Atom typing is only needed when information is missing, e.g. PDB,
CML, XYZ files, badly-formed Molfiles.
It sounds like you have bad Molfiles with aromatic bond orders. You should
check whether this is the case (not all files will have this) and do your
bond order fudging as needed. I was/am planning to write a utility to fix
these bad molfiles correctly but haven't got around to it yet.
If you want to make the hydrogens explicit for SMARTS you should just need
to call
> 'AtomContainerManipulator.convertImplicitToExplictHydrogens'.
For aromaticity, use the following, it does not need atom types:
> Aromaticity arom = new Aromaticity(ElectronDontation.daylight(),
> Cycles.or(Cycles.all(), Cycles.all(6)));
John
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