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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