Quick and dirty workaround: Convert it to .xyz (removing the Hs if needed)
then compute the atom types from that file and see what happens...
On 22 May 2017 19:24, "Marcos Villarreal" wrote:
> Hello,
>
> For an application we are developing, we would like to get an atom typing
> independent of t
In addition to Fredrik advise, you may also want to take a look at:
http://openbabel.org/wiki/Obminimize
As for fingerprints, I have found Filter-It to be more efficient than OB:
http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/software.html
--
Edelmiro Moman, PhD
Department of
The descriptor "ROTATABLE_BONDS" is used as an example in the online
documentation but not actually implemented in the code.
The easiest solution would be this:
https://sourceforge.net/p/openbabel/mailman/message/30659149/
Add the following item to
/"OBABEL_INSTALLATION_DIRECTORY"/data/plugindef
Hi Stuart,
I have you tried removing the space between the "-p" flag and the value,
like "-p7.4"?
Best,
Miro
--
Edelmiro Moman, PhD
Department of Molecular Medicine
Royal College of Surgeons in Ireland
POSTAL ADDRESS:
L5.08
Trinity Biomedical Sciences Institute - TBSI
Trinity College Dublin
It is probably unrelated and not the case any more but in the past I have
had issues with line breaks format with certain files from the PDB. So I
needed to use dos2unix (in your case it would be unix2dos). Another similar
problems had to do with exotic (like old Windows) character encodings (I do
Hello,
I have several PDB files containing protein-ligand complexes. The
protein atoms are in the ATOM record and the ligand atoms in the HETATM
record. However, when I add hydrogens with Open Babel 2.3.1 all the
added hydrogens, including those belonging to the ligand, appear as
ATOM. The res
('_openbabel', fp, pathname, description)
>> ImportError: dynamic module does not define init function (init_openbabel)
>>
>> On 09/15/2011 12:16 PM, Noel O'Boyle wrote:
>>> One Python is 2.6, the other is 2.7. You need to decide which you want
>>> t
oes not define init function (init_openbabel)
>>
>> On 09/15/2011 12:16 PM, Noel O'Boyle wrote:
>>> One Python is 2.6, the other is 2.7. You need to decide which you want
>>> to use as you can't compile against 2.7 and then use the 2.6 one. Can
>>> you c
; they point to the version you want to use (and then "touch
> openbabel-python.i" and recompile)?
>
> - Noel
>
> On 15 September 2011 11:05, Miro Moman wrote:
>> Debian 6.0.2 64-bit.
>>
>> Yes, I have OpenBabel installed globally using apt-get because ther
helper()
File "/home/mirix/python/lib/python2.7/site-packages/openbabel.py",
line 166, in swig_import_helper
_mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError: dynamic module does not define init function (init_openbabel)
>>>
[
So, I do not understand what is wrong. Is this a bug?
On 09/14/2011 02:50 PM, Geoff Hutchison wrote:
>> How do I know if Swig is actually being used?
> The development version doesn't include any scripting modules, so if it's
> even attempting to compile/link, then it's using swig.
>
> -Geoff
-
ngs on your computer. I
> recommend you install both Open Babel and its bindings locally, set
> the appropriate environment variables (e.g. LD_LIBRARY_PATH,
> PYTHONPATH and so forth, and try again).
>
> - Noel
>
> On 13 September 2011 20:24, Miro Moman wrote:
>> I have c
t; PYTHONPATH and so forth, and try again).
>
> - Noel
>
> On 13 September 2011 20:24, Miro Moman wrote:
>> I have compiled the latest development version of OpenBabel with python
>> bindings (Swig 2.0.0 and Eigen2). However, when I try to run the python
>> scr
I have compiled the latest development version of OpenBabel with python
bindings (Swig 2.0.0 and Eigen2). However, when I try to run the python
script from https://gist.github.com/974477, I get the following error:
python dockedpose.py
Traceback (most recent call last):
File "dockedpose.py", lin
14 matches
Mail list logo
