Egon Willighagen wrote:
On Mon, Apr 19, 2010 at 11:42 AM, Vincent Le Guilloux
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.
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 ?
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.
Unfortunately no code will be able to guess benzene from cyclohexane ...
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...