Dear Openbabel community,
I'm trying to extract all compounds from an sdf file which contain an OH
group (phenolic or aliphatic).
For this I have tried the following command in my anaconda prompt
installation of babel. But I'm not getting the expected result and no
molecule is retrieved.
I get resu
Can you provide a single example of a molecule that it misses? We can then
try to explain why or work out a solution.
Regards,
- Noel
On Tue, 10 Sep 2019 at 13:33, Vaibhav Dixit wrote:
> Dear Openbabel community,
> I'm trying to extract all compounds from an sdf file which contain an OH
> group
Dear Noel,
nabilone is one such example, but there are many phenol containing drugs in
the drugbank database, all of which are being missed.
I just tried to find alcohols with the following command and it gave me 334
structures.
Thus can't understand why it should fail with phenols.
babel Drugbank
Dear Vaibhav,
I think the pattern you specified (first one) is trying to match an oxygen
connected to aliphatic C (in 6 membered ring). I tried this more general SMARTS
pattern and it seems to match phenols:
*~[#6][OH1]
babel myfile.sdf -s"*~[#6][OH1]" sim-alcohol.smi
This web resource and re
