Ideas

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Ideas for projects.

The initial text is taken from the mail: Re: PyMOL Will Pymol participate in Google Summer of Code 2008?

Yes, we do have a long list of suggestions for PyMOL improvements, but many of them require a detailed understanding of PyMOL's fragile C-language internals, the study and modification of which is too much for Summer of Code. Also, in addition to the ActiveX effort just announced, some of the PyMOL-specific ideas have already been contracted and/or implemented.

My view is that the obvious low-hanging fruit for Open-Source PyMOL is integration with other open-source code. Since that mostly involves work at the Python level, such projects are well within the reach of students, especially if they have experience with both packages.

So from where I sit, the obvious open-source candidates are:

• APBS (electrostatics -- improve the current plugin)
• RDKit (cheminformatics, depiction, UFF cleanup, etc.)
• mengine (MMFF small molecule cleanup)
• mpeg_encode (MPEG movie production on Linux, etc.)
• GIMP (image manipulation)
• Blender (general-purpose 3D modeling & animation)
• Jmol (publishing visualizations inside of web pages)
• Firefox (ditto)
• MMTK (molecular mechanics -- Python/flexible)
• GROMACS (molecular mechanics -- C/fast)
• OpenOffice (escape from the microsoft hegemony)

(NOTE: work is already underway for mpeg_encode and mengine...)

Are there other key open-source packages we might specifically target for integration with PyMOL, either through SOC or beyond?

Although there are many niche tools, from a prioritization standpoint, efforts should focus on integrations that will impact the largest potential user base. So what hypothetical integrations would be useful to virtually all medicinal chemists, all structural biologists, all movie-makers, all paper-writers, and so on?

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More ideas

• A plugin-manager GUI in the style of Firefox, Rythmbox, Gedit, Eclipse. A GUI where it is easy to turn off/on plugins, configure them and see help-contents for them. Maybe also some way to paste a url to install a new Plugin.

• A plugin for a GUI window with the same functionality as the "Control Panel" window in SwissPDB Viewer.