On 3/17/11 11:40 AM, andi wrote:
> Hey everyone, I am kind of new to openbabel, but I was wondering if there is
> a way to produce fragments given one or more molecules. And if not, anything
> close to what openbabel supports
>
> An example is like the one on the openbabel documention page at addre
Sorry - our emails crossed. You don't say what OS you're using, but
it's a simple matter to check to go to its website to check what
version of Open Babel the bindings are linked against. It sounds like
it's 2.2.3 but you can verify with "print
pybel.ob.OBReleaseVersion()".
I think you'll have to
Can you confirm that you are running OB 2.3.0?
On 18 March 2011 13:53, Bradley Calhoun wrote:
> I have to wonder then what the difference is. I ran the code again to make
> sure, and the program sat for 30 minutes without any progress.
> I added a few other molecules that cause the same response
I am using Open Babel 2.3.0 and the most recent apt-get version of
python-openbabel, which I believe is where the openbabel python module is.
I think this is version 2.2.3. My python is 2.6.6 (we have to keep this on
the same page as python's scipy package).
- Brad
On Fri, Mar 18, 2011 at 8:57
Maybe; you have a different version number than NoB than?
Details!Details!
On 18 March 2011 13:53, Bradley Calhoun wrote:
> I have to wonder then what the difference is. I ran the code again to make
> sure, and the program sat for 30 minutes without any progress.
>
> I added a few other molec
I have to wonder then what the difference is. I ran the code again to make
sure, and the program sat for 30 minutes without any progress.
I added a few other molecules that cause the same response. (seeming to
hang)
These are all real molecules. The Substance IDs 23587365, 34132506,
and 3413250
Hi Brad,
It works for me, but it takes 10 seconds. It also uncovers a bug - the
system is not detected as aromatic.
Is this a real molecule?
- Noel
On 17 March 2011 17:53, Bradley Calhoun wrote:
> Hello,
> I am currently struggling with a particular interaction in openbabel.
> When I run the f
Fragments could mean a lot of things, but see
http://openbabel.org/docs/dev/UseTheLibrary/PythonExamples.html for
examples of code (by others) for Murcko and RECAP fragmentation.
Also, see the "s" option of fingerprint FP2 as described at
http://openbabel.org/docs/dev/FileFormats/Fingerprint_forma
Hello,
I am currently struggling with a particular interaction in openbabel.
When I run the following python code, the obConversion object correctly
reads X, but it just stalls on Y.
***
import openbabel
import sys
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "
Hey everyone, I am kind of new to openbabel, but I was wondering if there is
a way to produce fragments given one or more molecules. And if not, anything
close to what openbabel supports
An example is like the one on the openbabel documention page at address:
http://openbabel.org/docs/2.3.0/Chemi
It's not quite the same but see
http://blueobelisk.shapado.com/questions/convert-sln-to-smarts and
links therein.
- Noel
On 18 March 2011 07:52, Hans De Winter wrote:
> Dear,
>
> I have a library of ~60,000 structures defined in SLN (sybyl line
> notation) and I need to convert these in smiles o
Dear,
I have a library of ~60,000 structures defined in SLN (sybyl line
notation) and I need to convert these in smiles or sdf format. I don't
believe that Open Babel can help me on that (unless I missed it), so
are there any other tools (preferably on Mac OS X) that can do this?
Thx in adv
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