Ebuild which allows you to install all plugins for pymol which are promoted in the pymolwiki right now. Perhaps they should be separated into several ebuilds but I just put them in one. Open for discussion about that. Depends on bug 209161
Created attachment 143410 [details] ebuild inclusive patches and digests
Please please please don't attach tarballs with ebuilds... http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=3#doc_chap2
Created attachment 143414 [details, diff] pymol-plugins-0.1.ebuild
Created attachment 143415 [details] dynmap-1.0.patch
Created attachment 143416 [details] rtools-0.7.2.patch
Created attachment 143417 [details] Manifest better to have the checksums of the code, because it is accessible to everyone.
Sorry about the tarball
Comment on attachment 143414 [details, diff] pymol-plugins-0.1.ebuild msms is now msms-bin
Created attachment 143420 [details] update msms is now msms-bin
works nearly ;-) on amd64: install: cannot stat `build/lib.linux-i686-2.4/ccealign.so': No such file or directory >>> Compiling source in /var/tmp/portage/sci-chemistry/pymol-plugins-0.1/work ... running build running build_ext building 'ccealign' extension creating build creating build/temp.linux-x86_64-2.4 creating build/temp.linux-x86_64-2.4/src x86_64-pc-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -march=nocona -O2 -pipe -fomit-frame-pointer -fPIC -I/usr/include/python2.4 -c src/ccealignmodule.c -o build/temp.linux-x86_64-2.4/src/ccealignmodule.o creating build/lib.linux-x86_64-2.4 x86_64-pc-linux-gnu-gcc -pthread -shared -march=nocona -O2 -pipe -fomit-frame-pointer build/temp.linux-x86_64-2.4/src/ccealignmodule.o -o build/lib.linux-x86_64-2.4/ccealign.so >>> Source compiled. >>> Test phase [not enabled]: sci-chemistry/pymol-plugins-0.1 >>> Install pymol-plugins-0.1 into /var/tmp/portage/sci-chemistry/pymol-plugins-0.1/image/ category sci-chemistry install: cannot stat `build/lib.linux-i686-2.4/ccealign.so': No such file or directory >>> Completed installing pymol-plugins-0.1 into /var/tmp/portage/sci-chemistry/pymol-plugins-0.1/image/ I'll take a look at this. regards Bjoern
okay, here's the problem: you have to check for x86 or x86_64 cause cealign uses different folders. x86 build/lib.linux-i686-2.4/ x86_64 build/lib.linux-x86_64-2.4/ regrads blubbi
Created attachment 146056 [details] pymol-plugins-0.1.ebuild | added amd64 ARCH check for cealign added amd64 ARCH check for cealign if use cealign; then cd cealign-0.8-RBS exeinto /usr/lib/python2.4/site-packages/ case ${ARCH} in x86) doexe build/lib.linux-x86-2.4/ccealign.so ;; amd64) doexe build/lib.linux-x86_64-2.4/ccealign.so ;; esac insinto /usr/lib/python2.4/site-packages/cealign doins qkabsch.py cealign.py dodoc PYMOLRC CHANGES doc/cealign.pdf cd .. regards Bjoern
Created attachment 146059 [details] pymol-plugins-0.1 arch and ${PYVER} aware removed static dirs for python 2.4 Actually I hope everything runs with 2.5 ;-) Please test..
Created attachment 146061 [details] pymol-plugins-0.1.ebuild | ARCH and ${PYVER} aware PROPER Sory, hade to patch some patches adn files.
Created attachment 146063 [details, diff] dynmap-1.0-python2.5.patch
Created attachment 146064 [details, diff] rtools-0.7.2-python2.5.patch
mmmh, lets extend pymol by one more plugin: DivScore: A Plugin for PyMOL http://shoichetlab.compbio.ucsf.edu/~raha/research/divscore.html Lets see what I can do...
Created attachment 146067 [details] pymol-plugins-0.2 Added useflag divscore DivScore: A Plugin for PyMOL by by Kaushik Raha http://shoichetlab.compbio.ucsf.edu/~raha/research/divscore.html regards Bjoern
Cool, someone is interested in that. They questions which is in my head for a long time is if we should divide this ebuild in one for each plugin? I think this would be more straight as introducing a bunch of new USE flags.
I seperated the first plugin into an extra ebuild. The is a new version, still beta, of the cealign plugin.
Created attachment 147634 [details] pymol-plugins-cealign-0.9_beta.ebuild
Created attachment 147809 [details] pymol-plugins-autodock-0.1.ebuild
Created attachment 147810 [details] pymol-plugins-cealign-0.8.ebuild
Created attachment 147811 [details] pymol-plugins-cealign-0.9_beta.ebuild
Created attachment 147812 [details] pymol-plugins-colorama-0.1.1.ebuild
Created attachment 147813 [details] pymol-plugins-dynmap-1.0.ebuild
Created attachment 147815 [details] pymol-plugins-emovie-1.0.4.ebuild
Created attachment 147817 [details] pymol-plugins-helicheck-1.0.ebuild
Created attachment 147819 [details] pymol-plugins-promol-3.2.ebuild
Created attachment 147821 [details] pymol-plugins-rendering-0.1.ebuild
Created attachment 147822 [details] pymol-plugins-resicolor-0.1.ebuild
Created attachment 147823 [details] pymol-plugins-rtools-0.7.2.ebuild
I split the meta ebuild in one ebuild per plugin. I think this is more practicable.
Created attachment 147827 [details] pymol-plugins-divscore-0.1.ebuild
Created attachment 147837 [details] pymol-plugins-cealign-0.8-r1.ebuild Use of "python setup.py install --prefix=" instead of the if phrase.
Nice, I am working on a AutoDockTools ebuild, I will post it today, late in the evening, if you are interested, you'r wellcome to test it. I would like to provide a amber ebuild, but the flags used there an the compiler need is way beyond my programming knowledge... So okay, lets test the new ebuild and I'll take a closer look at them when I am at home.
one quick fix: in pymol-plugins-rtools-0.7.2.ebuild change src_unpack(){ unpack rTools_0.7.2.zip edos2unix "${S}"/color_protscale.py to src_unpack(){ python_version unpack rTools_0.7.2.zip edos2unix "${S}"/color_protscale.py other fixes later ;-)
Another error on startup: Hit ESC anytime to toggle between text and graphics. Adapting to GeForce hardware. PyMOL>run /usr/lib/python2.5/site-packages/cealign/qkabsch.py PyMOL>run /usr/lib/python2.5/site-packages/cealign/cealign.py CmdLoad: "/otto/mdkt0/Desktop/test1.pdb" loaded as "test1". DivScore: A Plugin for PyMOL Copyright (C) 2003 Kaushik Raha Merz Research Group Penn State University Exception in plugin 'ProMOL_302' -- Traceback follows... Traceback (most recent call last): File "/usr/lib/python2.5/site-packages/pmg_tk/PMGApp.py", line 159, in initialize_plugins __builtin__.__import__(mod_name) File "/usr/lib/python2.5/site-packages/pmg_tk/startup/ProMOL_302.py", line 382, in <module> class PGUI: File "/usr/lib/python2.5/site-packages/pmg_tk/startup/ProMOL_302.py", line 432, in PGUI TACOBUENO = PhotoImage(file="/usr/lib/python2.5/site-packages/pmg_tk/startup/AminoPics/TACOBUENO.GIF") File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 3270, in __init__ Image.__init__(self, 'photo', name, cnf, master, **kw) File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 3226, in __init__ self.tk.call(('image', 'create', imgtype, name,) + options) TclError: couldn't open "/usr/lib/python2.5/site-packages/pmg_tk/startup/AminoPics/TACOBUENO.GIF": no such file or directory Error: unable to initialize plugin 'ProMOL_302'.
mmh, I guess this bug belongs to pymol... When aligning two molecules: Match-Error: unable to open matrix file '/usr/lib/python2.5/site-packages/pymol/data/pymol/matrices/BLOSUM62'. Same bug was filed here: https://bugs.launchpad.net/ubuntu/+source/pymol/+bug/71045 "When trying to align a molecule to another, Pymol reports this error: Match-Error: unable to open matrix file '/usr/lib/python2.4/site-packages/pymol//data/pymol/matrices/BLOSUM62'. But pymol-package installs the file in /usr/share/pymol/matrices/BLOSUM62 (A temporary workaround is simply adding a symlink). This is Debian bug #385550"
filed the above here http://bugs.gentoo.org/show_bug.cgi?id=215602 just symlink it to fix it for now: ln -s /usr/share/pymol/data /usr/lib/python2.5/site-packages/pymol/data
Created attachment 147863 [details] pymol-plugins-rtools-0.7.2.ebuild You are right, we need the python_version earlier.
Created attachment 147865 [details] pymol-plugins-rendering-0.1.ebuild Update!!
Created attachment 147867 [details] pymol-plugins-promol-3.2.ebuild Now it is working. The Plugin has an ugly effect, the whole documentation has to be inside the plugin dir because the help looks there for the html docs.
(In reply to comment #43) > Created an attachment (id=147867) [edit] > pymol-plugins-promol-3.2.ebuild > > Now it is working. The Plugin has an ugly effect, the whole documentation has > to be inside the plugin dir because the help looks there for the html docs. Try a symlink.
Created attachment 147889 [details] pymol-plugins-promol-3.2.ebuild
you could add pkg_postinst() { python_mod_optimize /path/to/files } if it makes any sense Bjoern
if this isn't going into mainline or overlay... wh should probably setup a cvs or something... it sucks to copy the ebuild from the bugtracker ;) I could make an svn or cvs repo regards Bjoern
(In reply to comment #47) > if this isn't going into mainline or overlay... wh should probably setup a cvs > or something... it sucks to copy the ebuild from the bugtracker ;) > > I could make an svn or cvs repo > > regards > Bjoern > Thats a good idea. I think there will be some chance to get it at least in the science overlay. If we want to do the optimization together a svn repo would be a good thing.
I did a mistake. I inherit the toolchain-funcs in all the ebuilds for no reason. I will not post all the ebuilds again but there is no need for the toolchain-funcs. Sorry for that.
I'll setup a svn repo today
Created attachment 147993 [details] pymol-plugins-pdbsearch-0.5.ebuild Just one new. It provides an interface for advanced search in the pdb.
@justin: I have setup an svn, but got problems running it correcty I'll send you a mail and we can than communicate via IRC or ICQ or JABBER By the way, here's another plugin I use: MOLE http://mole.chemi.muni.cz/index.php Program MOLE is an universal toolkit for rapid and fully automated location and characterization of channels and pores in molecular structures. The core of MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. MOLE is a powerful software for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories in which analysis of a large number of snapshots is required. Lets see if I find some time this week to write an ebuild for this
You can check out the latest pymol plugins and changes here: http://svn.olausson.de/molmod/trunk/sci-chemistry/ kind regards Bjoern
the plugins sci-chemistry/pymol-plugins-emovie-1.0.4 and sci-chemistry/pymol-plugins-dynmap-1.0 are not working. emovie installs to /usr/pyton/ instead of /usr/python${PYVER} dynmap does somthing other wrong... I'll fix that next week. regards Bjoern
Comment on attachment 147810 [details] pymol-plugins-cealign-0.8.ebuild InTree
Comment on attachment 147811 [details] pymol-plugins-cealign-0.9_beta.ebuild InTree
Comment on attachment 147837 [details] pymol-plugins-cealign-0.8-r1.ebuild InTree
Comment on attachment 147889 [details] pymol-plugins-promol-3.2.ebuild InTree
Comment on attachment 147815 [details] pymol-plugins-emovie-1.0.4.ebuild InTree
I will close this bug for now. Please open new bugs and request plugin additions there.
