Ideas

PyMOL Ideas Page for Google Summer of Code (GSoC 2008) and Beyond

On behalf of the PyMOL Project, DeLano Scientific LLC has applied for the 2008 Google Summer of Code. Even if we are not chosen, this page should be a helpful inspiration for ongoing PyMOL development efforts!

Where to Start

Always start with Python and only delve down into the C code when absolutely necessary. Although PyMOL is mostly a C-based application, much of the that code is opaque, fragile, and unforgiving. One C mistake could potentially to destabilize the entire platform, and although refactoring is an important project goal, such work may not be ideal for GSoC-type efforts.

Fortunately, the Python interpreter and the PyMOL command and selection languages make it possible to extend PyMOL safely and quickly. Even when code performance is critical, Python can still serve as the interface between external C, C++, and Java code and PyMOL's internal C data structures.

Choosing a Topic

The best open-source code is usually written by an end-users attempting to meet their own pressing needs. So if you have already have a specific interest or need which relates to PyMOL, then we strongly encourage you to follow that up first!

If you are looking for ideas or suggestions, then try to seek out enhancements and/or integrations that will impact the largest potential user base. For example, imagine what new things might be useful to virtually all medicinal chemists, all structural biologists, all movie-makers, all paper-writers, and so on?

The ideas below are organized by category. Right now, integration with other open-source projects seems like the approach most likely to yield significant benefit, so those ideas are listed first.

Integration Ideas (Linking Out to Useful Open-Source Tools)

In most cases, depending on the need, integration can be accomplished through standalone Python scripts, through new PyMOL commands, through simple Wizards, or via Tkinter plugins.

• APBS (electrostatics calculations): Improve the existing plugin. Michael Lerner is currently leading this effort. See APBS
• RDKit (cheminformatics, depiction, UFF cleanup, etc.): Lots of potential here, however C++ coding may be necessary.
• mengine (MMFF small molecule cleanup): work is in progress (Delsci).
• mpeg_encode (MPEG movie production on Linux, etc.): work is in progress (Delsci).
• GIMP (image manipulation): Streamline & document the process of exporting images from PyMOL into GIMP and preparing them for submission to scientific Journals.
• Blender (general-purpose 3D modeling & animation): Streamline & document the process of getting molecular geometry out of PyMOL and into Blender.
• Jmol (publishing visualizations inside of web pages): Liason between PyMOL & Jmol projects to develop a shared molecular visualization data model compatible with both applications.
• Firefox (plugin): Develop an PyMOL plugin compatible with Firefox.
• MMTK (molecular mechanics -- Python/flexible): Develop the ability to round-trip molecular systems from PyMOL, into MMTK, and back.
• GROMACS (molecular mechanics -- C/fast) - Maybe some ideas can be shared with this guy. Gromacs GUI
• OpenOffice (escape Microsoft hegemony): Develop an PyMOL plugin.
• IPython integration (interactive shell): a robust alternative to the PyMOL command line?
• R (statistics): PyMOL a 3D viewer environment for visualizating & manipulating large statistical data sets?

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

High-Level Enhancement Ideas (Mostly Python-oriented)

• Develop new plugins which automate routine tasks.
• Improve the Python API documentation.
• Flesh out the new "from pymol2 import PyMOL" instance-based PyMOL API.
• Develop alternate Tkinter "skins" (for custom OEM-like applications).
• Develop a Tkinter/TOGL widget which holds a PyMOL viewer instance.
• Develop a PyQt widget which holds a PyMOL viewer instance.
• Create 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.
• Add a plugin for a GUI window with the same functionality as the "Control Panel" window in SwissPDB Viewer.
• Extend and modify the PyMOL command language so as to be compatible with existing RasMol and/or Jmol scripts.
• Enhance the Mutagenesis Wizard in order to support Nucleic acids and/or Sugars.
• Streamline the process of creating movies out of Scenes.

Low-Level Enhancement Ideas (Mostly C-oriented)

• Provide a "split" view with multiple molecules each in their own pane (already partially implemented).
• Add a movie slider similar to that found in Maya, Cinema4D, 3DSMax.
• Enable editing of displayed sequence alignments.
• Add multi-line textual annotations
• Support additional annotation object including: arrow, lines, and blobs.
• Add display of secondary structure into the sequence viewer.
• Enable per-object Z clipping (especially in the ray tracer)
• Hilite H-bonds, salt bridges, Pi-stacking, Pi-cations, etc.
• Build in a simple forcefield and energy minimizer suitable for use with Mutagenesis.
• Improve the ability to animate objects independently when creating movies.
• Incorporate a suite of standard NMR visualizations (restraint violations, per-residue RMS, etc.)
• Enumeration and display of low-energy conformers.
• Automated structure grafting (poor-man's homology modeling).
• Import of alignment files.

Difficult C-level Code Refactoring Ideas

• Assemble a test suite which thoroughly exercises the existing code (a prerequisite to major refactoring).
• Catch & handle memory-allocation failures gracefully (instead of crashing).
• Replace PyMOL's memory management & custom containers with a simple runtime object model.
• Separate the View and the Controllers from the Model so that they can all run asynchronously (on multiple cores).
• Enable generalized undo of changes made to the Model.
• Clean up the internal matrix handling code.

Ideas Involving Proprietary APIs

Since these involve closed-source APIs and infrastructure, they aren't suitable for GSoC. However, such requests are noted here for the sake of complete coverage. These development projects may be available to independent contractors outside of GSoC.

• Build an ActiveX Control for PowerPoint and/or Internet Explorer (work is in progress - Delsci)
• Support direct export of Windows Media files (AVI movies).
• Create a Windows port with "native" look & feel.
• Integrate directly via Mathematica via MathLink.
• Further enhance JyMOL (Java-JNI/wrapped PyMOL)
• Integrate with Matlab.

More Ideas (Add your own!)

• Provide a 2D chemical depiction of the current 3D view.
• Spreadsheet view with additional information (e.g. IC50's).
• Create additional documentation, screen casts, & tutorials.
• Export 3D PDF images.