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Bug 125501 - add sidechain checking for pymol apbs plugin
Summary: add sidechain checking for pymol apbs plugin
Status: RESOLVED WONTFIX
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High enhancement (vote)
Assignee: Gentoo Science Related Packages
URL: http://www-personal.umich.edu/~mlerne...
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2006-03-08 10:18 UTC by Jeffrey Gardner (RETIRED)
Modified: 2008-08-17 04:11 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
ebuild to add sidechain_check (pymol-0.99_rc6-r1.ebuild,1.96 KB, text/plain)
2006-03-08 10:19 UTC, Jeffrey Gardner (RETIRED)
Details
patch to add "Sidechain Check" to the Wizard menu. (sidechain_check.patch,638 bytes, patch)
2006-03-08 10:20 UTC, Jeffrey Gardner (RETIRED)
Details | Diff
sidechain_check script (sidechain_check.py,13.09 KB, text/x-python)
2006-03-08 10:21 UTC, Jeffrey Gardner (RETIRED)
Details
new pymol ebuild to depend on >=apbs-0.4.0 (pymol-0.99_rc6-r1.ebuild,1.99 KB, text/plain)
2006-03-08 16:47 UTC, Jeffrey Gardner (RETIRED)
Details
ebuild to include sidechain_check plugin (pymol-0.99_rc6-r2.ebuild,2.09 KB, text/plain)
2006-03-21 15:49 UTC, Jeffrey Gardner (RETIRED)
Details
ebuild to add sidechain_check to pymol (sidechain_check-1.4.ebuild,1.91 KB, text/plain)
2006-06-19 05:12 UTC, Jeffrey Gardner (RETIRED)
Details

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Description Jeffrey Gardner (RETIRED) gentoo-dev 2006-03-08 10:18:14 UTC
here's an ebuild and patch for pymol-0.99_rc6 that includes the very useful sidechain_check wizard written by Michael Lernel
Comment 1 Jeffrey Gardner (RETIRED) gentoo-dev 2006-03-08 10:19:26 UTC
Created attachment 81704 [details]
ebuild to add sidechain_check
Comment 2 Jeffrey Gardner (RETIRED) gentoo-dev 2006-03-08 10:20:47 UTC
Created attachment 81705 [details, diff]
patch to add "Sidechain Check" to the Wizard menu.
Comment 3 Jeffrey Gardner (RETIRED) gentoo-dev 2006-03-08 10:21:29 UTC
Created attachment 81706 [details]
sidechain_check script
Comment 4 Donnie Berkholz (RETIRED) gentoo-dev 2006-03-08 11:09:23 UTC
How are we supposed to know when he updates his scripts? They're completely unversioned, and I can't even access a directory listing to find last modified date.
Comment 5 Jeffrey Gardner (RETIRED) gentoo-dev 2006-03-08 12:22:55 UTC
hmm....I'm not in contact with him, but I doubt it will need updating unless pymol changes drastically. If that happens I can look for an updated script, or disable it.
What do you suggest?

Comment 6 Jeffrey Gardner (RETIRED) gentoo-dev 2006-03-08 16:47:26 UTC
Created attachment 81735 [details]
new pymol ebuild to depend on >=apbs-0.4.0

I found out >=apbs-0.4.0 is required...modified ebuild.
Comment 7 Donnie Berkholz (RETIRED) gentoo-dev 2006-03-09 12:03:01 UTC
I suggest contacting him and asking if he can add version numbers to his script names so distributions are able to package them properly.
Comment 8 Michael G. Lerner 2006-03-09 13:10:09 UTC
(In reply to comment #7)
> I suggest contacting him and asking if he can add version numbers to his script
> names so distributions are able to package them properly.
> 

I added my CVS log to the top of the script.  Is that good enough?  I also added some contact information.  http://www.umich.edu/~mlerner/PyMOL/sidechain_check.py
Comment 9 Donnie Berkholz (RETIRED) gentoo-dev 2006-03-09 19:15:42 UTC
(In reply to comment #8)
> I added my CVS log to the top of the script.  Is that good enough?  I also
> added some contact information. 
> http://www.umich.edu/~mlerner/PyMOL/sidechain_check.py

Hi there, thanks for taking the time to reply. What we really need is a URL for a given file that will never change contents (e.g., the same URL is always the same md5sum). So something like http://www.umich.edu/~mlerner/PyMOL/sidechain_check-1.4.py (note the embedded version number).

(Also noticed you play ultimate, I did the same in my undergrad days.)
Comment 10 Michael G. Lerner 2006-03-10 12:37:00 UTC
(In reply to comment #9)
> (In reply to comment #8)
> > I added my CVS log to the top of the script.  Is that good enough?  I also
> > added some contact information. 
> > http://www.umich.edu/~mlerner/PyMOL/sidechain_check.py
> 
> Hi there, thanks for taking the time to reply. What we really need is a URL for
> a given file that will never change contents (e.g., the same URL is always the
> same md5sum). So something like
> http://www.umich.edu/~mlerner/PyMOL/sidechain_check-1.4.py (note the embedded
> version number).
> 
> (Also noticed you play ultimate, I did the same in my undergrad days.)
> 

Hmmn .. I'm a grad student, which means that I'll *eventually* leave www.umich.edu, but this should work as long as I'm here:

http://www.umich.edu/~mlerner/PyMOL/sidechain_check-1.4.py

(I'd *love* to have some eligibility left so I could keep playing college ultimate.  These days, I'm playing on a club team and in a league.  Ann Arbor has a ton of frisbee .. not as much as the northwest, but way better than the northeast where I went to college.)
Comment 11 Jeffrey Gardner (RETIRED) gentoo-dev 2006-03-21 15:49:18 UTC
Created attachment 82824 [details]
ebuild to include sidechain_check plugin

this works as expected on ~amd64
thanks!
Comment 12 Donnie Berkholz (RETIRED) gentoo-dev 2006-06-04 02:30:41 UTC
Hey there, this would actually work better as its own package. That way, if Lerner puts out a new plugin, people don't need to recompile all of pymol.

Could you attach an ebuild to do that? Should be pretty straightforward.
Comment 13 Jeffrey Gardner (RETIRED) gentoo-dev 2006-06-04 12:45:44 UTC
Aboslutely, give me a few days...got something important coming up. :D
Comment 14 Donnie Berkholz (RETIRED) gentoo-dev 2006-06-16 18:36:23 UTC
(In reply to comment #13)
> Aboslutely, give me a few days...got something important coming up. :D

ping
Comment 15 Jeffrey Gardner (RETIRED) gentoo-dev 2006-06-18 17:17:21 UTC
mmkay...working on it :D
Comment 16 Jeffrey Gardner (RETIRED) gentoo-dev 2006-06-19 05:12:45 UTC
Created attachment 89522 [details]
ebuild to add sidechain_check to pymol

Since sidechain_check modifies /usr/lib/python${PYVER}/site-packages/pmg_tk/skins/normal/__init__.py, I save a copy to restore in case the package is ever unmerged. If you can think of a better way to handle it (yeah, it's ugly) please let me know.
Thanks,
je_fro
Comment 17 Donnie Berkholz (RETIRED) gentoo-dev 2006-06-21 08:11:53 UTC
I'd actually suggest telling users to make the changes manually, or give a command to apply the patch in FILESDIR instead of doing that hacky stuff. Shouldn't need your own pymol tarball if you do this. I didn't realize that sidechain_check required apbs, that seems weird. Also you're missing multilib intelligence, replace all mentions of lib with $(get_libdir) and inherit multilib.eclass. Looks like you could add python_mod_optimize() in postinst and python_mod_cleanup in postrm().
Comment 18 Jeffrey Gardner (RETIRED) gentoo-dev 2006-06-21 09:33:31 UTC
Thanks for the input...I'll implement those tonight.
As for apbs, I suspect that most people who want this are going to use the apbs plugin next....
Comment 19 Donnie Berkholz (RETIRED) gentoo-dev 2006-06-21 10:25:39 UTC
(In reply to comment #18)
> As for apbs, I suspect that most people who want this are going to use the apbs
> plugin next....

I personally see no need to do so. Just because I'm fixing flips doesn't mean I want to look at an electrostatic surface.
Comment 20 Jeffrey Gardner (RETIRED) gentoo-dev 2006-06-21 11:19:46 UTC
How would you feel about a pymol "plugins" flag that will handle apbs _and_ sidechain_check?
Comment 21 Donnie Berkholz (RETIRED) gentoo-dev 2006-06-21 11:30:44 UTC
apbs plugin is already distributed with pymol, by upstream. That makes it totally different from this one.
Comment 22 Jeffrey Gardner (RETIRED) gentoo-dev 2006-06-21 11:38:04 UTC
Yes, but you still need to install apbs for the plugin to be of any value.