#100 Import from SMILES

[Nils Kriege]

When importing molecules from SMILES this is problematic since we internally store molecules in MOL format. SMILES contain aromaticity information instead of bond orders, while the MOL format stores bond orders and no aromaticity. CDK currently is not able to convert this information by kekulisation. Therefore depiction of molecules imported from SMILES, calculation of additional properties etc. may be incorrect. This bug will be solved by upgrading to a new CDK version (not yet stable), cf. http://efficientbits.blogspot.nl/2013/12/new-smiles-behaviour-parsing-cdk-154.html

[Till Schäfer]

this bug depends on feature request 31 (Upgrade to CDK 1.6 as soon it is available)

[Till Schäfer]

@Nils: can you provide a test case?

[Nils Kriege]

This could be verified by importing the following SMILES: c1ccccc1

With the old version the imported molecule most likely contains 6 single bonds; the correct depiction should have 3 single and 3 double bonds. Please also check that the bug occurs with the old version of CDK, since there might be a work-around for simple cases implemented.

[Sven Schrinner]

Again, SF, somehow did not save my post ...

I tested the mentioned SMILES with both CDK versions. The old CDK creates a C-ring with only single bonds, while the new CDK adds three double bonds. Therefore, this bug will be resolved in the next major SH release.