Incorrect Molecule Conversion

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Create a molecule from a SMILES with an aromatic ring in it
2. Convert the molecule to a Pybel molecule 
3. Write the molecule to a SMILES string

What is the expected output? What do you see instead?
The resulting SMILES will have lost its aromoaticity. For example a 
benzene will go from c1ccccc1 to C1CCCCC1.

What version of the product are you using? On what operating system?
v0.81 Windows Vista

Please provide any additional information below.
I believe this is because with CDK the SmilesGenerator needs to be told to 
output as aromatic (setUseAromaticityFlag), or you could convert the 
molecule to the Kekule form to turn the aromatic bonds to single/double 
bonds.

Original issue reported on code.google.com by tom.shel...@gmail.com on 25 Aug 2009 at 1:39

[GoogleCodeExporter]

Sorry - I wasn't notified of this bug. I will sort this out. Thanks.

Original comment by baoille...@gmail.com on 17 Dec 2009 at 8:38

• Changed state: Accepted
• Added labels: Priority-High
• Removed labels: Priority-Medium

[GoogleCodeExporter]

Fixed in r177.

Original comment by baoille...@gmail.com on 20 Dec 2009 at 9:27

• Changed state: Fixed