Jan, thanks for that. I'll give it a try. Are there any examples of writing RDKit functions and procedures for postgres in python? I see this general postgres docs: http://www.postgresql.org/docs/9.4/static/plpython.html but wondered if there are any RDKit specific examples anywhere?
Tim On 25/09/2015 08:30, Jan Holst Jensen wrote: > On 2015-09-24 16:22, Tim Dudgeon wrote: >> I'm trying to get to grips with using the RDKit cartridge, and so far >> its going well. >> One thing I'm concerned about is molecule standardization, along the >> lines of the ChemAxon Standardizer that allows substructure searches to >> be done is a way that is largely independent of the quirks of structure >> representation. The classic example would be how nitro groups are >> represented, so that it didn't matter which nitro representation was in >> the query or target structures, because both were converted to a >> canonical form. >> >> My initial thoughts are that this would be done by: >> 1. loading the "raw" structures into a source column that would never be >> changed >> 2. defining a function that performed the necessary transform to >> generate the canonical form of a molecule. >> 3. generating a "canonical" structure column that was the result of >> passing the raw structures through that function >> 4. building the SSS index on that canonical column >> 5. executing queries using that function to canonicalize the query >> structure >> >> The problem I'm finding is that there do not seem to be postgres >> functions defined for doing molecular transforms (essentially a reaction >> transform) and doing things like removing explicit hydrogens. At least >> not in the functions listed on this page: >> http://rdkit.org/docs/Cartridge.html#functions >> >> Am I missing something here, or might I be barking up completely the >> wrong tree? >> >> Tim > > Hi Tim, > > We have about the same situation and we're adding standardization > (beyond what RDKit implicitly does when it sanitizes the molecule) > through Python stored procedures. You will need to build and maintain > a normal Python-enabled RDKit installation in parallel to the > cartridge. The Python stored procedures can access the normal RDKit > installation and then run whatever Python code is necessary to do > additional molecule cleanup. > > You will need to tweak your Postgres environment so the Python stored > procedures can load RDKit. This is what I have defined in an > environment file on CentOS: > > RDBASE=/opt/rdkit > LD_LIBRARY_PATH=/opt/rdkit/lib > PYTHONPATH=/opt/rdkit > > On Ubuntu this would go into /etc/postgresql/9.x/main/environment (in > a slightly different format where the values have to be single-quoted). > > Cheers > -- Jan, Biochemfusion ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
