Egon Willighagen wrote:
On Tue, Apr 20, 2010 at 12:56 PM, Nina Jeliazkova <nina@acad.bg> wrote:
  
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 ?
    

If not mistaken, the RELAXED mode is doing this... but would need to check...
  
Ah, good to know!

Nina
  
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 ...
    

True... but the data model in the file is not really cyclohexane...
the lack of explicit hydrogens ensures this to work...

Egon