Egon, All,

Egon Willighagen wrote:
On Mon, Apr 19, 2010 at 11:42 AM, Vincent Le Guilloux
<vince.leguilloux@gmail.com> wrote:
  
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.
    

That situation was recently discussed on this mailing list. 
Yes indeed.
The
molfile specification does not have a bonder order 4, just 1-3. Many
files write, however, molfile query structures, where 4 indicates an
aromatic atom, but it is not a bond order.
  
This is correct, and still - wouldn't it be a better approach (more user friendly) to interpret bond order 4 as aromatic - or at least have this as optional behaviour in  MolReader code ?
Now, the CDK current does not have a unknown bond order (we need a
patch for that), so upon reading it (incorrectly?) defaults to
SINGLE... causing the cyclohexane... now, please let us know what
software created the incorrect MDL molfile, and please file a bug
report against that project...

Otherwise, use the DeduceBondOrder (or so) class to assign proper bond orders...
  
Unfortunately no code will be able to guess benzene from cyclohexane ...

Best regards,
Nina
Egon