Jan,
Thanks for posting about this. The idea of being able to use python and
call out to RDKit functionality from within Oracle is very entertaining. :-)
-greg
On Thu, Feb 27, 2014 at 10:56 PM, Jan Holst Jensen
<[email protected]>wrote:
> Hi RDKitters,
>
> I have dabbled with calling RDKit from Oracle and have succeeded. It is
> done via an Oracle cartridge that makes it possible to call Python scripts
> from Oracle. The cartridge is not nearly as sophisticated as Postgres'
> support for Python, but it gets the job done.
>
> The cartridge is open source, BSD-licensed, and can be downloaded from
> here:
> http://biochemfusion.com/downloads/pypl_2014-02-27.zip - Yes, it's only
> an 8.3 KB download.
>
> The cartridge was created on a Linux machine with CentOS 6.2 and Oracle
> 11g. It shouldn't be too hard to make it compile on Windows too, but I
> haven't had the need yet.
>
> With the cartridge we can create Oracle functions like below that operate
> on MDL molfiles, returning SMILES and LogP values:
>
> create function mol_to_smiles(molfile in clob) return varchar2
> is
> begin
> return pypl.run_script(
> 'from rdkit import Chem' || Chr(10) ||
> 'from rdkit.Chem import Descriptors' || Chr(10) ||
> 'molfile = """' || molfile || '"""' || Chr(10) ||
> 'result = Chem.MolToSmiles(Chem.MolFromMolBlock(molfile))', 'result');
> end;
> /
>
> create function mol_logp(molfile in clob) return number
> is
> begin
> return to_number(pypl.run_script(
> 'from rdkit import Chem' || Chr(10) ||
> 'from rdkit.Chem import Descriptors' || Chr(10) ||
> 'molfile = """' || molfile || '"""' || Chr(10) ||
> 'result = str(Descriptors.MolLogP(Chem.MolFromMolBlock(molfile)))',
> 'result'));
> end;
> /
>
> If we have a COMPOUNDS table where the STRUCTURE column has the molecule
> stored in Accelrys Direct format, we can then do the following select:
>
> select
> id,
> mol_to_smiles(molfile(structure)) as smiles,
> mol_logp(molfile(structure)) as logp
> from compounds
> where id <= 3;
>
> *ID* *SMILES* *LOGP* 1 O=C(O)c1ccccc1 1.3848 2 CCC(=O)OCCOc1ccccc1
> 2.0186 3 CC1=CC(=O)C=CC1=O 0.6407
> [The molfile() function is an Accelrys Direct function that produces a
> molfile CLOB from the STUCTURE BLOB column.]
>
> There you have it - RDKit functionality directly in an Oracle database.
> Hope that you will find this useful.
>
> Cheers
> -- Jan
>
>
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