Bug 817463

Summary: Users must be able to use PyMol as default molecular viewer application
Product: [Fedora] Fedora Reporter: Gökçen Eraslan <gokcen.eraslan>
Component: pymolAssignee: Tim Fenn <tim.fenn>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: 17CC: tim.fenn
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Last Closed: 2012-06-03 23:28:15 UTC Type: Bug
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Description Flags
Patch fixing the issue
none
Another patch fixing argument handling none

Description Gökçen Eraslan 2012-04-30 06:55:17 UTC 
Description of problem:

PyMol application is able to display/parse a lot of file formats[1] including PDB[2], Fasta[3], xyz[4], SDF[5], MOL[6], MOL2[7] etc. It would be great to define those mimetypes in pymol.desktop file and use pymol as the default molecular viewer application.

This line defines according mimetypes:

MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;

Some notes:

1- Also, it would be great to be able to open .pse pymol session files by double clicking but I don't know if they have any standard mimetypes defined.

2- Currently none of those mimetypes are defined in shared-mime-info[8] but in this bug report[9], it's still being discussed.


[1] http://www.pymolwiki.org/index.php/Load
[2] http://reference.wolfram.com/mathematica/ref/format/PDB.html
[3] http://reference.wolfram.com/mathematica/ref/format/FASTA.html
[4] http://reference.wolfram.com/mathematica/ref/format/XYZ.html
[5] http://reference.wolfram.com/mathematica/ref/format/SDF.html
[6] http://reference.wolfram.com/mathematica/ref/format/MOL.html
[7] http://reference.wolfram.com/mathematica/ref/format/MOL2.html
[8] http://cgit.freedesktop.org/xdg/shared-mime-info/tree/freedesktop.org.xml.in
[9] https://bugs.freedesktop.org/show_bug.cgi?id=335

Version-Release number of selected component (if applicable):
pymol-1.5.0.2-1.20120218svn3982.fc17.x86_64
Comment 1 Tim Fenn 2012-04-30 07:01:11 UTC 
Sure thing - I'll look into this, but patches are certainly welcome!
Comment 2 Gökçen Eraslan 2012-05-01 09:57:26 UTC 
Created attachment 581340 [details]
Patch fixing the issue

Validate, correct desktop file and add mimetypes. Also chemical-mime-data is needed to define chemical/* mimetypes.
Comment 3 Gökçen Eraslan 2012-05-01 10:33:34 UTC 
By the way, source tarball has .svn directories. Why? Any reason to not using "svn export" command?
Comment 4 Gökçen Eraslan 2012-05-01 11:10:01 UTC 
Created attachment 581353 [details]
Another patch fixing argument handling

I have discovered another bug while playing with this patch. Following command does not work:

pymol "some dir with space/1KJF.pdb" 

since pymol wrapper is written as:

/usr/bin/python /usr/lib64/python2.7/site-packages/pymol/__init__.py $*

This expands to:

/usr/bin/python /usr/lib64/python2.7/site-packages/pymol/__init__.py some dir with space/1KJF.pdb

which is wrong. pymol 4 parameters in this case, instead of 1.

Correct wrapper must be:

/usr/bin/python /usr/lib64/python2.7/site-packages/pymol/__init__.py "$@"

to hand arguments including spaces correctly[1]. Patch is attached.

[1] http://www.thegeekstuff.com/2010/05/bash-shell-special-parameters/
Comment 5 Fedora Update System 2012-05-09 02:50:34 UTC 
pymol-1.5.0.2-2.20120218svn3982.fc16 has been submitted as an update for Fedora 16.
https://admin.fedoraproject.org/updates/pymol-1.5.0.2-2.20120218svn3982.fc16
Comment 6 Fedora Update System 2012-05-09 02:50:43 UTC 
pymol-1.5.0.2-2.20120218svn3982.fc17 has been submitted as an update for Fedora 17.
https://admin.fedoraproject.org/updates/pymol-1.5.0.2-2.20120218svn3982.fc17
Comment 7 Tim Fenn 2012-05-09 02:52:23 UTC 
(In reply to comment #3)
> By the way, source tarball has .svn directories. Why? Any reason to not using
> "svn export" command?

Oops, I'll fix this the next time a do a pull.  Sorry!
Comment 8 Fedora Update System 2012-05-09 16:10:47 UTC 
Package pymol-1.5.0.2-2.20120218svn3982.fc17:
* should fix your issue,
* was pushed to the Fedora 17 testing repository,
* should be available at your local mirror within two days.
Update it with:
# su -c 'yum update --enablerepo=updates-testing pymol-1.5.0.2-2.20120218svn3982.fc17'
as soon as you are able to.
Please go to the following url:
https://admin.fedoraproject.org/updates/FEDORA-2012-7519/pymol-1.5.0.2-2.20120218svn3982.fc17
then log in and leave karma (feedback).
Comment 9 Fedora Update System 2012-06-03 23:28:15 UTC 
pymol-1.5.0.2-2.20120218svn3982.fc16 has been pushed to the Fedora 16 stable repository.  If problems still persist, please make note of it in this bug report.
Comment 10 Fedora Update System 2012-06-03 23:34:51 UTC 
pymol-1.5.0.2-2.20120218svn3982.fc17 has been pushed to the Fedora 17 stable repository.  If problems still persist, please make note of it in this bug report.