[Cdk-devel] Unset atomicNumber breaks canonical SMILES generation

[Nina J. <ni...@ac...>]

Hi all,

There has been a thread few weeks ago about IAtom.getAtomicNumber() 
returning zero and thus breaking SMARTS making use of atomic numbers. I 
don't recall if some decision had been taken how to resolve the issue.

It seems also canonical SMILES generation is broken for the same reason, 
since canonical labeling (CanonicalLabeler.java) depends on 
getAtomicNumber() return value (among other things).

Best regards,
Nina