> Is it possible to extract coordinates (xyz) from these O, N atoms which are
> attached to one/two Hs using babel (lets say from a mol2/sdf file)? Or I
> need to use rdkit or custom python scripts for such tasks?
While the babel command line offers a lot of features it obviously can't offer
e
e articles (under About link) might also
>> help with creating SMARTS queries:
>>
>>
>>
>> https://smartsview.zbh.uni-hamburg.de/
>>
>>
>>
>> Vin
>>
>>
>>
>> *From:* Vaibhav Dixit
>> *Sent:* Tuesday, September 10, 2019 8:
abel myfile.sdf -s"*~[#6][OH1]" sim-alcohol.smi
>
>
>
> This web resource and reference articles (under About link) might also
> help with creating SMARTS queries:
>
>
>
> https://smartsview.zbh.uni-hamburg.de/
>
>
>
> Vin
>
>
>
> *From:* V
source and reference articles (under About link) might also help
with creating SMARTS queries:
https://smartsview.zbh.uni-hamburg.de/
Vin
From: Vaibhav Dixit
Sent: Tuesday, September 10, 2019 8:06 AM
To: Noel O'Boyle
Cc: babel
Subject: Re: [Open Babel] substructure search fails
Dear No
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
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 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
