Dear Greg and rdkit-discuss list,Thank you very much for your detailed reply. Based on your reply I agree that RDKit seems to be just what I am looking for. The functionality of the cartridge described fits very well with my needs which include similarity searching by pharmacophore fingerprints, substructure searching by exact substructure (SMARTS are nice to have but not essential) and general fingerprint calculation for building predictive polypharmacology models. The limitations in terms of chirality of reactions and the missing canonical smiles are not relevant to my proposed use to that will certainly not be a problem. My main working experience have been with the Direct cartridge which only does similarity searching using MACCS keys and which does not have any additional features that RDKit cartridge does not seem to have so I agree that RDKit has an edge on the functionality side.
After spending a few hours I now have RDKit running on my laptop on Ubuntu 10.10. All but two of the ctests pass and I am sure I can get the last ones to pass soon too. In general the installation ran smoothly and the installation guide was easy to follow. Next steps are getting structures loaded into the database. I am already procrastinating other tasks to play with RDKit ;o).
Thanks once again for your reply and for making RDKit open source. Best regards, Sune
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