Attendees

• Elaine, Greg, Eric, TomG, TomF, Scooter (via Zoom)

Agenda

• ChimeraX registration
• ChimeraX 0.6 performance
• Review milestone priorities
• Wildcard/regex/case matching in commands

Discussion

• ChimeraX registration code almost works, Conrad will look into it
• ChimeraX 0.6 performance
  • From last meeting
    • 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
          • loop is in Cython
        • Cython with no wrapping: 0.156s
          • loop is in Python
      • Chimera 1:
        • access bfactor via wrappy2: 0.062s
        • custom library with no wrapping: 0.181s
  • Collect data
    • Cython is really fast
  • New Results
    • Cythonize Atom into Python type? method: 0.098s; property: 0.119s
      • bfactor property
        • straight type 0.080s
        • class inheriting type 0.092s
        • __dict__ enabled 0.082s; doesn't inherit non-builtin class attrs
      • coord property
        • returning numpy 1.48s
        • returning tuple 0.103s
    • Cythonize Atom (2ajq; 14791 atoms; contacts: chain A against others)
      • addh 1.1x faster (22.21s -> 20.14s)
      • hbonds 1.04x faster (3.44s -> 3.30s)
      • contacts 1.3x faster (0.444s -> 0.333s)
    • Cythonize Atom + Element
      • addh 1.4x faster (22.21s -> 15.71s)
      • hbonds 1.2x faster (3.44s -> 2.81s)
      • contacts 1.8x faster (0.444s -> 0.253s)
    • Cythonize Atom + Element and use tinyarray
      • addh 1.8x faster (22.21s -> 12.63s) [C1: 8.68s]
      • hbonds 1.3x faster (3.44s -> 2.64s) [C1: 3.04s]
      • contacts 2.1x faster (0.444s -> 0.211s) [C1: 0.216s]
    • Cythonize Atom methods? function: 0.074s; method: 0.204s; prop: 0.135s
    • Cythonize hydrogen bond code? How hard is this?
  • Approach
    • Cythonize major objects (ctypes)
      • Atom/Atoms
      • Bond/Bonds
      • Residue/Residues
      • Maybe higher level objects
    • Profile code and change data structures/algorithms to improve performance
    • Cythonize as it makes sense

Action Items

• Eric will convert Atom to Cython
• 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