= 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 methods? function: '''0.074s'''; method: '''0.204s'''; prop: '''0.135s'''
   - Cythonize hydrogen bond code?  How hard is this?
   - 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]
   - Above plus trivial Cythonization of module
    - contacts '''2.7x faster''' (0.444s -> 0.164s)
  - 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