Changes between Version 2 and Version 3 of 2018-01-25

Timestamp:

Jan 25, 2018, 2:31:09 PM (8 years ago)

Author:

Scooter Morris

Comment:

--

2018-01-25

@@ -12 +12 @@
 * ChimeraX registration code ''almost'' works, Conrad will look into it
 * 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'''
-       - 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'''
+ - 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
- - Paths forward
+ - New Results
    - Cythonize Atom into Python type? method: '''0.098s'''; property: '''0.119s'''
    - Cythonize Atom methods? function: '''0.074s'''; method: '''0.204s'''; prop: '''0.135'''
    - 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 =
-* ~~Conrad will enable registration code
-* Eric will investigate Cython for classes and methods
+* Eric will convert Atom to Cython
 * Conrad will write bundle code tutorial
 * Conrad will continue working on ribbon tickets