(please cc the list)
When I said the command prompt, I meant the Windows command prompt.
PYTHONPATH is an environment variable.
You really should contact the author of the plugin at this point - he
can easily tell you how to do it.
- Noel
On 14 July 2016 at 17:59, Thomas Ryckmans <thomas.ryckm...@gmail.com> wrote:
> Hi Noel,
>
> I ran the sys.path.append... when I type pymol in the command line I get
>
>>>> Pymol
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> NameError: name 'Pymol' is not defined
>
> Yet I have installed pymol (from a .msi: EduPyMOL-v1.7.4.5-Win64)
>
> If I run pymol (I use the "C:\Program Files\PyMOL\PyMOL\PymolWin.exe" -J), I
> can use the python command line...
>
> is there another installer that would give me a pymol.py file??
>
> many thanks
>
> Thomas
>
> On 14 July 2016 at 07:55, Noel O'Boyle <baoille...@gmail.com> wrote:
>>
>> Just try setting the PYTHONPATH at the command line before running Pymol
>> at the same command line.
>>
>> On 13 Jul 2016 9:54 p.m., "Thomas Ryckmans" <thomas.ryckm...@gmail.com>
>> wrote:
>>>
>>> Hi Noel,
>>>
>>> thank you so much for your comment - I am a newbie and very much stuck.
>>> I tried both
>>>
>>> import sys
>>>
>>> sys.path.append("C:\Users\Thomas\Anaconda2\Lib\site-packages\openbabel\data")
>>> print sys.path
>>>
>>> import sys
>>> sys.path.append("C:\Users\Thomas\Anaconda2\Lib\site-packages\openbabel")
>>> print sys.path
>>>
>>> but I still get an error message:
>>>
>>> Error: 1
>>> <type 'exceptions.NameError'> Exception in Tk callback
>>> Function: <function set_conf_search at 0x00000000031FA2E8> (type: <type
>>> 'function'>)
>>> Args: ()
>>> Traceback (innermost last):
>>> File "C:\Program
>>> Files\PyMOL\\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in
>>> __call__
>>> return apply(self.func, args)
>>> File "C:\Users\Thomas\AppData\Roaming\pymol\startup\optimize.py", line
>>> 52, in set_conf_search
>>> conf_search(selection, forcefield, conf_method, nsteps1, conformers,
>>> lowest_conf)
>>> File "C:\Users\Thomas\AppData\Roaming\pymol\startup\optimize.py", line
>>> 266, in conf_search
>>> obconversion = ob.OBConversion()
>>> <type 'exceptions.NameError'>: global name 'ob' is not defined
>>>
>>> any ideas of what I should do next??
>>>
>>> Thomas
>>>
>>> On 13 July 2016 at 21:28, Noel O'Boyle <baoille...@gmail.com> wrote:
>>>>
>>>> You should ask the Pymol devs. Have you tried setting PYTHONPATH before
>>>> running Pymol?
>>>>
>>>> On 13 Jul 2016 5:55 p.m., "Thomas Ryckmans" <thomas.ryckm...@gmail.com>
>>>> wrote:
>>>>>
>>>>> Dear all,
>>>>>
>>>>> I am trying to install openbabel to run the Optimize plugin in Pymol
>>>>> (http://www.pymolwiki.org/index.php/Optimize).
>>>>> I installed the OpenBabelGUI 2.3.2
>>>>> I am using python 2.7 (Anaconda) with a 64 bit computer, so I I
>>>>> installed openbabel-1.8.4-cp27-none-win_amd64.whl, and the python
>>>>> bindings.
>>>>>
>>>>> It seems to work: I can follow the command lines here:
>>>>> and it works - e.g. these
>>>>>
>>>>> >>> import pybel
>>>>> >>> mol = pybel.readstring("smi", "CC(=O)Br")
>>>>> >>> mol.make3D()
>>>>> >>> print(mol.write("sdf"))
>>>>>
>>>>> give the expected output.
>>>>>
>>>>>
>>>>> However when I run pymol and try to use Optimize, I get the following
>>>>> error message:
>>>>> ---------------------------------------------------------------
>>>>> Error: 1
>>>>> <type 'exceptions.NameError'> Exception in Tk callback
>>>>> Function: <function set_conf_search at 0x0000000009CB02E8> (type:
>>>>> <type 'function'>)
>>>>> Args: ()
>>>>> Traceback (innermost last):
>>>>> File "C:\Program
>>>>> Files\PyMOL\\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in
>>>>> __call__
>>>>> return apply(self.func, args)
>>>>> File "C:\Users\Thomas\AppData\Roaming\pymol\startup\optimize.py",
>>>>> line 52, in set_conf_search
>>>>> conf_search(selection, forcefield, conf_method, nsteps1,
>>>>> conformers, lowest_conf)
>>>>> File "C:\Users\Thomas\AppData\Roaming\pymol\startup\optimize.py",
>>>>> line 266, in conf_search
>>>>> obconversion = ob.OBConversion()
>>>>> <type 'exceptions.NameError'>: global name 'ob' is not defined
>>>>> ----------------------------------------------------------------
>>>>> I am assuming (...) that this is because pymol does not know where to
>>>>> find openbabel. How can I change that??
>>>>>
>>>>> In the openbabel directory, there is a file called babelconfig.h;
>>>>> containing these two lines:
>>>>> /* Where the data files are located */
>>>>> #define BABEL_DATADIR "C:/Program Files/openbabel/share/openbabel"
>>>>>
>>>>> while the data folder is actually elsewhere:
>>>>> C:\Users\Thomas\Anaconda2\Lib\site-packages\openbabel
>>>>>
>>>>> if I try to change the babelconfig.h file to
>>>>> /* Where the data files are located */
>>>>> #define BABEL_DATADIR
>>>>> "C:\Users\Thomas\Anaconda2\Lib\site-packages\openbabel"...
>>>>> nothing changes...
>>>>>
>>>>> many thanks for your help!
>>>>>
>>>>> Thomas
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>> J-Flow, sFlow and other flows. Make informed decisions using capacity
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>>>>> _______________________________________________
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>>>>> OpenBabel-discuss@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>>
>>>
>
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patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
reports.http://sdm.link/zohodev2dev
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