Hi Egon,

Thanks for your answer. To my knowledge no one answered to this.

Just to sum up several issues (quite important in my opinion) I've encountered using the CDK:

** SDF reader / writer - Group Abbreviation error **
When a Group Abbreviation is used for a molecule, well it seems the CDK set this abbreviation as atomic symbol when writing back the molecule to MDL format, eg:
      2.1012   -2.6351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
(...)
G 15 10
Ph

Becomes the following when using SDF writer:

2.1012 -2.6351 0.0000 Ph 0 0 0 0 0 0 0 0 0 0 0 0
** SDF Reader / writer - Bond stereo **

When the bon stereochemistry is set to 4 (either up or down), a CDK exception occures when writing back the molecule. The location of this bug is identified: as the UNDEFINED stereo CDK constant is set to NULL, using the molecule stereo in a switch statement raise the NPE, for example in the MDL writer:
 297                         switch(bond.getStereo()){
** SDF Reader - Aromatic bond flag **

When the CDK load a molecule having aromatic bond flag set to 4, the bond order is set to 1. For example, if I load benzene with aromatic flag set to 4, and I write the molecule back, I will get cyclohexane. I think this is quite important issue that should be fixed asap.

Possible solutions:
- Throw an error if aromatic flag is found
- Guess bond orders if aromatic flag is found (I would choose this one).


On Wed, Mar 24, 2010 at 1:34 PM, Vincent Le Guilloux
> - When a Group Abbreviation is used for a molecule, well it seems the
> CDK set this abbreviation as atomic symbol when writing back the
> molecule to MDL format, eg:

Did someone reply on this yet? Like the author of the group support?

CDK developers: who wrote the functionality? Can he or she please
comment on the bug report?

Egon

--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
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