Hi Long time back I used PL python with RDKit cartridge inside postgres i have made a blog post here is the link might be of help
http://data2quest.blogspot.com/2014/07/converting-inchi-to-mol-using-plpython.html Abhik Seal Indiana University Bloomington School of Informatics and Computing Cheminformatics and Chemgenomics group <http://registratio54.wix.com/ccrg> [email protected] http://mypage.iu.edu/~abseal/index.htm On Fri, Sep 25, 2015 at 1:37 PM, Jan Holst Jensen <[email protected]> wrote: > Hi Tim, > > A simple getting-started example is: > > CREATE FUNCTION smiles2molfile(smiles text) RETURNS text > LANGUAGE plpythonu AS $$ > import rdkit > from rdkit import Chem > > mol = Chem.MolFromSmiles(smiles) > return Chem.MolToMolBlock(mol) > $$; > > > and you can then > > select smiles2molfile('CC'); > > and get back a molfile. > > For more advanced usage it is worth taking a look at the rdchord project > that TJ has sent links to. > > Cheers > -- Jan > > > On 2015-09-25 15:54, Tim Dudgeon 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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