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---
You would need to register the OID of the mol type in psycopg2, like
this for example:
def cast_cube(value, cursor):
"""
"""
if value:
return map(float, value[1:-1].split(','))
CUBE = psycopg2.extensions.new_type((CUBE_OID,), "CUBE", cast_cube)
psycopg2.extensions.register_type(CUBE)
Instead of cast_cube you would create an RDMol from the SMILES string.
On Tue, May 8, 2012 at 12:52 PM, Greg Landrum <[email protected]> wrote:
> Dear Jean-Paul,
>
> On Tue, May 8, 2012 at 11:59 AM, JP <[email protected]> wrote:
>>
>> I have an rdkit enabled database - with a table which contains a "mol"
>> column (called rdkitmol).
>>
>> I am using the python database driver psycopg2 to access this table from a
>> python program.
>>
>> My question is: Is there a way how to use the "mol" object in the DB as an
>> rdkit mol in python directly?
>>
>> I was thinking I could do something like:
>>
>>> cur.execute("SELECT rdkitmol FROM molecule LIMIT 5;")
>>> for t in cur:
>>> print t[0]
>>> print Descriptors.MolWt(t[0])
>>
>>
>> But this doesn't work as t[0] is not of the correct type (i.e.
>> rdkit.Chem.rdchem.Mol).
>>
>> Of course, I could use the rdkitmol smiles to create an
>> rdkit.Chem.rdchem.Mol instance in python (e.g. Chem.MolFromSmiles) but I was
>> wondering if there was a more efficient way to do this as presumably the
>> "mol" column stores an instance of the rdkit.Chem.rdchem.Mol already.
>
> There is. The solution is a bit ugly, but it should work. To prevent
> the automatic conversion to a string (which gives you a smiles), you
> need to do the following:
>
> In [5]: curs.execute("select molregno,m,mol_send(m) from rdk.mols limit 10")
>
> In [6]: r = curs.fetchone()
>
> In [7]: r
> Out[7]:
> (122,
> 'c1cc(CN2CCN(C[C@H]3NCCC3)CC2)ccn1',
> <read-only buffer for 0x100429a10, size 283, offset 0 at 0x1026b6c30>)
>
> In [10]: m = Chem.Mol(str(r[-1]))
>
> In [11]: Chem.MolToSmiles(m)
> Out[11]: 'c1cc(CN2CCN(CC3NCCC3)CC2)ccn1'
>
>> Hope you had a good holiday Greg!
>
> I did!
>
> -greg
>
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