Attendees

• Conrad, Elaine, Greg, Eric, TomF, TomG, Scooter

Agenda

• ChimeraX 0.6 release
  • Performance
  • APIs
• Review milestone priorities

Discussion

• ChimeraX 0.6 performance
  • Looking up bfactor (1 million times):
    • ChimeraX:
      • ctypes: 1.38s
      • custom library with property wrapping: 0.5s
      • custom library with no wrapping: 0.185s
      • random floating point attribute in Python: 0.072s
      • Cython with no wrapping: 0.021s
    • Chimera 1:
      • access bfactor via wrappy2: 0.062s
      • custom library with no wrapping: 0.181s
  • Options:
    • wrappy3 (does not understand numpy arrays)
    • Cython
  • Collect data
    • Port custom library code to Chimera 1 and get timing. Is it 3x slower due to argument parsing?
    • Write custom library in Cython and compare against ctypes timing.
• ChimeraX 0.6 APIs
  • Release APIs used in tutorials
    • Tutorials need to be edited for clarity
      • First cut (dumping minimal required information into file) for all but "fetch" tutorial is in
      • First editing pass has not been done yet
    • Need to make sure all the links work and have real content
    • Need to add "Supported API" string to doc strings of public classes, methods and functions (see 2017-09-21)
  • APIs used in tutorials (so far)
    • :py:class:`chimerax.core.atomic.Atom`
    • :py:class:`chimerax.core.atomic.AtomicStructure`
    • :py:class:`chimerax.core.atomic.Bond`
    • :py:class:`chimerax.core.atomic.Collection`
    • :py:class:`chimerax.core.atomic.Residue`
    • :py:class:`chimerax.core.commands`
    • :py:class:`chimerax.core.commands.cli.CmdDesc`
    • :py:class:`chimerax.core.commands.ModelsArg`
    • :py:class:`chimerax.core.commands.register`
    • :py:class:`chimerax.core.commands.register_selector`
    • :py:func:`chimerax.core.commands.cli.register`
    • :py:func:`chimerax.core.commands.run`
    • :py:class:`chimerax.core.logger.Logger`
    • :py:class:`chimerax.core.models.Model`
    • :py:class:`chimerax.core.objects.Objects`
    • :py:class:`chimerax.core.session.Session`
    • :py:class:`chimerax.core.toolshed.BundleAPI`
    • :py:class:`chimerax.core.toolshed.BundleInfo`
    • :py:class:`chimerax.core.toolshed.CommandInfo`
    • :py:class:`chimerax.core.toolshed.SelectorInfo`
    • :py:class:`chimerax.core.toolshed.ToolInfo`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.fetch_from_database`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.finish`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.get_class`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.initialize`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.open_file`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.register_command`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.register_selector`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.save_file`
    • :py:class:`~chimerax.core.toolshed.BundleAPI.start_tool`
    • :py:class:`chimerax.core.ui.HtmlToolInstance`
    • :py:class:`chimerax.core.ui.widgets.HtmlView.
    • :py:func:`chimerax.core.io.open_filename`

Action Items

• Conrad will enable registration code
• Eric will collect data on custom library (Chimera 1, Cython, etc)
• Conrad will write bundle code tutorial
• Conrad will continue working on ribbon tickets
• Conrad will create ticket to investigate implementing the "like" operator
  • e.g., to specify polymer in atomspec