[Joelib-help] Aromaticity typer bug

[Joerg K. W. <we...@in...>]

Hi all,
Hi Geoff,
Hi Hou,

i've found a serious bug in the SMARTS matcher.
This is caused when picking bridging closure ring atoms (root atoms) by 
the aromatic typer.
This will cause the false negative detection of aromatic atoms in this 
special ring.

E.g. when treating: Oc1c(O)c2cccc3ccc4cccc1c4c23, Pyrene-4,5-diol
Atoms 2,3 should be aromatic also !

I've implemented a bug fix, i would recommend to add these things to 
OpenBabel, also.
For JOELib users it's recommended to get the latest version from the CVS 
or download only the changed JOEAromaticTyper.java
under (with one day delay, because of SF server strategy, sorry !)
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/joelib/joelib/src/joelib/data/

Regards, Joerg
JOELib Administrator

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
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