Tim, I have a set of postgres python (PL/Python) functions using rdkit. It is available at https://github.com/tjod/rdchord and some docs at https://github.com/tjod/rdchord/wiki
TJ O'Donnell On Fri, Sep 25, 2015 at 6:54 AM, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > 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 >
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