Re: [PyMOL] installing other libraries with pymol python

[Thomas H. <tho...@sc...>]

Hi Jordan,

if you want to use MacPyMOL with other libraries then I recommend to use the "syspython" version that we offer (installer named MacPyMOL-v1.7.x.x-syspython.dmg). It simply does not bundle a Python distribution, but uses /usr/bin/python2.7 to run MacPyMOL.

Related:
https://sourceforge.net/p/pymol/mailman/message/33531659/

Cheers,
  Thomas

On 21 Jun 2015, at 21:44, Jordan Willis <jwi...@gm...> wrote:

> Hi,
> 
> I’m trying to use the pandas library with MacPymol 1.7.05 but get the following with import pandas. 
> 
>   File "/Library/Python/2.7/site-packages/pandas/__init__.py", line 6, in <module>
>     from . import hashtable, tslib, lib
>   File "numpy.pxd", line 157, in init pandas.hashtable (pandas/hashtable.c:22315)
> ValueError: numpy.dtype has the wrong size, try recompiling
> 
> Obviously there is some conflict with PyMOLs python interpreter and the interpreter I installed pandas with. That’s fine, I’ll just compile pandas against PyMOLs python library, but I don’t know how to do it.
> 
> I used pip within pymol 
> 
> python
> import pip
> pip.main([‘install’,’pandas’,’—reinstall’])
> python end
> 
> 
> but got something wrong with the certificate in the pypy server
> 
> /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL run on Sun Jun 21 18:35:15 2015
> Getting page https://pypi.python.org/simple/pandas/
> Could not fetch URL https://pypi.python.org/simple/pandas/: connection error: [Errno 1] _ssl.c:504: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
> 
> . I thought before I dug too deep, I would check with the list to see if anyone has added the pandas library that is compatible with pymol. Or more generally, how would one install third party libraries for use with pymol. If you don’t use pandas, I highly recommend it. It’s incredibly useful for manipulating data and it would be very handy to have with pymol scrips.
> 
> Jordan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.