Fingerprint problem

Hi,





I have a few smiles (see attachment) , I have trouble to generate finger print for structure searching. The smiles can be drawn in Marvin. Maybe there are too many loops to analyze. Would you please check them?








Thanks





Bin

Hi,





I have edited the file to be a legal smiles file by removing the numbers from the beginning of each line (attached fro convenience).





These structures appear to be chessboard-like complex "ring systems".





This causes a combinatorial explosion during ring detection, which can lead


to very long calculation times in older JChem versions.





The latest JChem version seems to be importing them fine, and one can search the database with the same structures.





Which JChem version do you use ?





Best regards,





Szilard





PS: Please always state the JChem version in use when posting a problem.

Hi, Szilard,





Thank you for your reply.








I am using MolHandler in jchem.jar. I can find these two version information, MARVIN_VERSION = "4.0.6" and JCHEM_VERSION = "3.1.7".





I have no problem to open your smi with my MarvinView 4.1.3. I have trouble to generate finger print using MolHandler.





Thanks.





Bin

Hi,





I have checked, our code can deal with these structures since JChem 3.2.


I suggest you to upgrade to the latest version, it contains a lot of other improvements and fixes as well.





Best regards,





Szilard