Hydra, desktop Chimera 2, progress

Tom Goddard
September 12, 2013

1. Added scenes. Uses same code as session save. Small fast.
2. Added cross-fade, used for switching scenes.
3. Tried motion blur. Not sure if its useful but was small variant of cross-fade code.
4. Put all OpenGL drawing code in one Python file, about 500 lines (buffers, shaders, textures, ...).
5. Added new show/hide atoms, ribbons, chains, molecules, atom specs like #0.B:213-422@CA or !#1.
6. Organized Python code with modules: draw (opengl), file_io, molecule, ui
7. Updated hydra user's guide (commands, shortcuts, toolbar icons)
8. Fixed lots of bugs.
9. Many small user interface improvements (e.g. file dialog starts in recent directory, show graphics toolbar icon, show/hide waters or ligands shortcuts, redirect print to log window, import Python scripts..., session thumbnails ordered by most recent use, session file suffix now .hy, fat and thin tube ribbons, purge missing sessions from thumbnails)
10. Put Qt bug list on wiki. Incomplete (have a few more to add from this week -- QGLFormat does not give correct buffer depths).
11. Mouse over gives status line atom spec.
12. Added HDF5 for reading large density maps. Required modules Cython, Numexpr, C++ hdf5, PyTables. Might consider h5py hdf5 wrapper instead to avoid cython, numexpr.
13. Added bond display, instanced cylinders, stick and ball and stick styles.