Dear OpenBabel community,
how do I enable a "complete protonation" of all atoms within PyBEL? A small
test of the OpenBabel Windows version revealed that COO- is converted COOH,
but R-NH2 is not converted to R-NH3+.
As data source, I work with MOL2 files, and this shall be the output as
well.
For
Hi,
I am having a problem installing pybel in Windows XP. I am using
Windows XP SP3, have Python 2.7.1 installed on C:\, OpenBabel-2.3.0
installed on C:\ and installed the bindings via
openbabel-python-1.6.py27.exe. The OpenBabel GUI works fine,
BABEL_DATADIR is set to C:\OpenBabel-2.3.0\dat
Could you copy and paste the entire transcript of the installation
tests
(http://openbabel.org/docs/dev/UseTheLibrary/PythonInstall.html#test-the-installation)
from the same command prompt?
- Noel
On 4 April 2011 21:41, Paul Brennan wrote:
> Hi,
> I am having a problem installing pybel in Windo
Dear Paul,
> how do I enable a "complete protonation" of all atoms within PyBEL?
Do you mean ionization?
> A small
> test of the OpenBabel Windows version revealed that COO- is converted COOH,
> but R-NH2 is not converted to R-NH3+.
> As data source, I work with MOL2 files, and this shall be th
I'm happy to announce the release of an updated version of the ChemSpotlight
tool for Mac OS X 10.5 or later.
ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X, which reads
common chemical file formats using the Open Babel chemistry library. Spotlight
can then index and search
Dear Geoffrey,
I appreciate your help very much ! Thank you for your time.
At first I thought it is a very simple problem, so I am confident
to find such a tool when a chemist friend asked me for help. But maybe you
are right, there is no such opensource tool exists.
I ha
Perhaps a link to ChemSpotLight could be added to the Install Page
(http://openbabel.org/wiki/Install) under the Mac section?
- Noel
On 5 April 2011 16:25, Geoffrey Hutchison wrote:
>
> I'm happy to announce the release of an updated version of the ChemSpotlight
> tool for Mac OS X 10.5 or late
6. CIR
what's wrong with CIR?
Igor
On Tue, 2011-04-05 at 11:36 -0400, qiancheng shen wrote:
> Dear Geoffrey,
> I appreciate your help very much ! Thank you for your time.
> At first I thought it is a very simple problem, so I am
> confident to find such a tool when a chemist
Hello, i'm unable to add a formula in a .sdf file with 2.3.0, is this
option broken with the new Open Babel release?
Thank you,
David
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smartphone on the
I don't know about --add-formula but according to the docs
(http://openbabel.org/docs/2.3.0/Command-line_tools/babel.html#options)
this can be done as follows:
obabel -:CC(=O)Cl -osdf --add FORMULA
See "obabel -L descriptors" for more info.
- Noel
On 5 April 2011 16:54, wrote:
> Hello, i'm un
On 05/04/2011 16:54, ariste...@cbm.uam.es wrote:
> Hello, i'm unable to add a formula in a .sdf file with 2.3.0, is this
> option broken with the new Open Babel release?
To add to the title, use
--append formula
To as a property, use
--add formula.
The parameter on --append and --add can be a sp
Thank you very much!
> On 05/04/2011 16:54, ariste...@cbm.uam.es wrote:
>> Hello, i'm unable to add a formula in a .sdf file with 2.3.0, is this
>> option broken with the new Open Babel release?
>
> To add to the title, use
> --append formula
>
> To as a property, use
> --add formula.
>
> The para
On Apr 5, 2011, at 11:44 AM, Igor Filippov [Contr] wrote:
> 6. CIR
> what's wrong with CIR?
Indeed. Noel even indicated open source tools which allow batch access to CIR.
Cheers,
-Geoff
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It's a maj
Hello!
I am interested in the translation of crystallographic coordinates into
Cartesian.
During the conversion of *CIF file to *PDB file crystallographic
coordinates are converted into Cartesian. However, when I have tried to
translate coordinates, according to the formula introduced in the
Inter
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