Hi Hari,
You can use "mol_from_pkl()". Here's a quick demo:
In [20]: m = Chem.MolFromSmiles('c1cnccc1')
In [21]: pkl = buffer(m.ToBinary())
In [22]: curs.execute('select mol_from_pkl(%s)',(pkl,))
In [23]: curs.fetchone()
Out[23]: ('c1ccncc1',)
Is that enough to get you started?
-greg
On Tue, Feb 25, 2014 at 8:28 PM, hari jayaram <[email protected]> wrote:
> Hi ,
> I am a newbie to postgres and the rdkit postgres database cartridge.
>
> I have gotten the cartridge installed and can query sub-structure
> similarity and do other things as documented in the cartridge documentation
> page.
>
> To create a molecule from the cartridge the documentation
> <http://www.rdkit.org/docs/Cartridge.html>recommends something like:
>
>
> >>> curs.execute('select molregno,mol_send(m) from rdk.mols where m@
> >%s',('c1cccc2c1nncc2',))
> >>> row = curs.fetchone()
> >>> row
> (9830, <read-only buffer for 0x...>)
>
> Then the pickled output of mol_send will be used to create a new molecule
>
> >>> from rdkit import Chem
> >>> m = Chem.Mol(str(row[1]))
> >>> Chem.MolToSmiles(m,True)
> 'CC(C)Sc1ccc(CC2CCN(C3CCN(C(=O)c4cnnc5ccccc54)CC3)CC2)cc1'
>
>
> My question is : how about the other way .Is the only way to use the
> smiles and do an sql insert with the smiles and the mol_from_smiles
> function as in :
>
> insert into compounds (smiles,rdkit_mol,internal,external) VALUES
> ('CCCCC',mol_from_smiles('CCCCC);'ID-1111111','EI-2222222');
>
> Is there a way to insert the python rdkit mol object into the database
> rdkit "mol" column directly.
>
> This is in some ways connected to a question I just asked ( django
> related) on stack
> overflow.<http://stackoverflow.com/questions/22022163/how-to-handle-map-custom-postgresql-type-to-django-model>
>
> Thanks a tonne for your help in advance
> Hari
>
>
>
>
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
