Hello all,
I was trying to install the python bindings. I have installed the gui and
when testing the installation every thing was going as expected in the
windows command line, but once I opened python and tried to import pybel it
could not find the module pybel. I installed the pybel for python 3.3 and I
am using python 3.4 which I installed with anaconda so this may be the
problem, however if you know a way to fix this I would greatly appreciate
any help. I have pasted the command line text bellow.
Thanks,
Michael
Microsoft Windows [Version 6.3.9600]
(c) 2013 Microsoft Corporation. All rights reserved.
C:\Users\Michael>obabel -V
Open Babel 2.3.2 -- Oct 5 2012 -- 10:00:48
C:\Users\Michael>obabel -Hsdf
sdf MDL MOL format
Reads and writes V2000 and V3000 versions
Open Babel supports an extension to the MOL file standard
that allows cis/trans and tetrahedral stereochemistry to be
stored in 0D MOL files. The tetrahedral stereochemistry is
stored as the atom parity, while the cis/trans stereochemistry
is stored using Up and Down bonds similar to how it is
represented in a SMILES string. Use the ``S`` option
when reading or writing if you want to avoid storing
or interpreting stereochemistry in 0D MOL files.
Read Options, e.g. -as
s determine chirality from atom parity flags
The default setting for 2D and 3D is to ignore atom parity and
work out the chirality based on the bond
stereochemistry (2D) or coordinates (3D).
For 0D the default is already to determine the chirality
from the atom parity.
S do not read stereochemistry from 0D MOL files
Open Babel supports reading and writing cis/trans
and tetrahedral stereochemistry to 0D MOL files.
This is an extension to the standard which you can
turn off using this option.
T read title only
P read title and properties only
When filtering an sdf file on title or properties
only, avoid lengthy chemical interpretation by
using the ``T`` or ``P`` option together with the
:ref:`copy format <Copy_raw_text>`.
Write Options, e.g. -x3
3 output V3000 not V2000 (used for >999 atoms/bonds)
m write no properties
w use wedge and hash bonds from input (2D only)
S do not store cis/trans stereochemistry in 0D MOL files
A output in Alias form, e.g. Ph, if present
Specification at: http://www.mdl.com/downloads/public/ctfile/ctfile.jsp
C:\Users\Michael>dir "%BABEL_DATADIR%"\mr.txt
Volume in drive C is Windows8_OS
Volume Serial Number is 60ED-D981
Directory of C:\Users\Michael\AppData\Roaming\OpenBabel-2.3.2\data
10/03/2012 02:50 AM 4,295 mr.txt
1 File(s) 4,295 bytes
0 Dir(s) 329,470,558,208 bytes free
C:\Users\Michael>python
Python 3.4.1 |Anaconda 2.1.0 (64-bit)| (default, Sep 24 2014, 18:32:42)
[MSC v.1
600 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named 'pybel'
>>>
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