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
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