Re: [PyMOL] installing other libraries with pymol python
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 jwillis0...@gmail.com 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. -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical virtual servers, alerts via email sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] installing other libraries with pymol python
Wow that is so cool. Is there any drawbacks I can expect? On Jun 23, 2015, at 1:44 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: 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 jwillis0...@gmail.com 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. -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical virtual servers, alerts via email sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] installing other libraries with pymol python
Hi Jordan, I think there are no drawbacks, I'm using this version for several months now and it works great. Of course such a question is hard to answer a-priori, that's why we didn't simply replace the regular bundle but offer the syspython version in addition. Cheers, Thomas On 23 Jun 2015, at 18:04, Jordan Willis jwillis0...@gmail.com wrote: Wow that is so cool. Is there any drawbacks I can expect? On Jun 23, 2015, at 1:44 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: 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 jwillis0...@gmail.com 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. -- Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical virtual servers, alerts via email sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
