Hello
Can you construct similar SMILES like
C12CCCC(C1)CCCCC2
N12CCC(C1)C2
C1(CCC2)CCC12
Are other smiles in your dataset bicyclic systems?
Does it work with the rewritten smiles
C1C2CC1C2?
Best
Peter
On Sat, Mar 22, 2014 at 7:42 pm, Gerebtzoff, Gregori
<[email protected]="mailto:[email protected]";>> wrote:
Hi Greg,
It's just that particular smiles, I don't have any problem reading thousands of
other smiles and loading them in the cartridge.
Which version of the cartridge do you use?
Gregori
On Saturday, March 22, 2014, Greg Landrum <[email protected]> wrote:
Hi Grégori,
It doesn't seem to be a problem with the cartridge itself:
chembl_16=# select mol_from_smiles('C12CC(C1)C2');
mol_from_smiles
-----------------
C1C2CC1C2
(1 row)
I can also use it from psycopg2 without problems.
Can you read other SMILES or is it just that one that's problematic?
-greg
On Fri, Mar 21, 2014 at 6:30 PM, Gerebtzoff, Gregori
<[email protected]> wrote:
Hi guys,
I've been having problem reading this particular smiles string with the
PostgreSQL cartridge: C12CC(C1)C2
I don't know if I'm running the latest version of the cartridge though...
Thanks for your help!
Grégori
>>> cursor.execute("select rdkit_version()")
>>> cursor.fetchone()
['0.70.0']
>>> cursor.execute("select mol_from_smiles('C12CC(C1)C2')")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/apps64/python/lib/python2.7/site-packages/psycopg2/extras.py", line
122, in execute
return _cursor.execute(self, query, vars)
>>> import rdkit
>>> from rdkit import Chem, rdBase
>>> rdBase.rdkitVersion
'2013.09.2'
>>> mol = Chem.MolFromSmiles('C12CC(C1)C2')
<rdkit.Chem.rdchem.Mol object at 0x1ebd7a60>
>>> Chem.MolToSmiles(mol)
'C1C2CC1C2'
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