On 4 October 2011 16:29, Egon Willighagen <egon.willighagen@gmail.com> wrote:
On Tue, Oct 4, 2011 at 2:36 PM, Egon Willighagen
<egon.willighagen@gmail.com> wrote:
> Ah, a recent patch (well, about a year ago:
> ae21ee2e39c61ae6d1c6aaf7f8919c0fb40170b3) caused atom typing to be not
> perceived when aromaticity is not perceived. I puzzled why I was happy
> with that change... I'll cook up a patch to ensure that atom types are
> again perceived, even when aromaticity is taking literally from the
> SMILES string.

OK, this patch actually required the atom typing to be inside the if
statement, because the atom type perception and configuration caused
earlier aromaticity information to be lost, caused by line 92 in the
AtomTypeManipulator.configure() method:

atom.setFlag(CDKConstants.ISAROMATIC,
atomType.getFlag(CDKConstants.ISAROMATIC));

I have not made up my mind if this instruction is important... what
d'you think? CDK atom types at least do not associate aromaticity with
atom types... however, Sybyl atom types do. So, removing this call
would cause this method to fail for such atom type schemes...


Do you mean it should not set the atom aromaticity, or not use the flag from the atom type for this?  

Nina
 
Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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