Thanks for pointing out this gap in the docs.
I just added a section to the cartridge documentation about using it from
Python that includes the mol_send() tip:
http://rdkit.readthedocs.org/en/latest/Cartridge.html#using-the-cartridge-from-python
At some point it's probably worth going back to revisit that using
psycopg2's extension mechanism (as used at the bottom of the notebook post
George mentions).
-greg
On Wed, Oct 23, 2013 at 10:21 PM, George Papadatos <gpapada...@gmail.com>wrote:
> Yes it does; many thanks!
> I've just found the notebook I mentioned:
> http://nbviewer.ipython.org/4316426/
> (Scroll to bottom)
> I prefer Greg's first solution though, as it avoids the conversion from
> smiles completely.
>
> Best,
>
> George
>
> Sent from my gPad
>
> On 23 Oct 2013, at 20:39, JP <jeanpaul.ebe...@inhibox.com> wrote:
>
> Does the following help you george?
> http://comments.gmane.org/gmane.science.chemistry.rdkit.user/860
>
>
>
> On 23 October 2013 17:11, George Papadatos <gpapada...@gmail.com> wrote:
>
>> Hi RDKitters,
>> I must have seen this in an ipython notebook but can't find it right now:
>> If I have a table of rdkit mols generated by the cartridge, is there a
>> way to retrieve them using a psycopg2 connection within python - ideally
>> inside a pandas dataframe?
>>
>> I've got this snippet:
>> import pandas as pd
>> import psycopg2
>> conn = psycopg2.connect("port=5432 user=chembl dbname=chembl_17")
>> data = pd.read_sql(sql, conn)
>>
>> ...but I'm missing the step where I retrieve rdkit mol objects somehow
>> instead of smiles.
>>
>> Many thanks in advance,
>> George
>>
>>
>>
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