Optimize within_distance
jlorieau opened this issue · comments
- Use multiprocessing
- See if a stack 2d Matrix works better for cKDtree
- Investigate the performance of an octree
http://www.gamedev.net/page/resources/_/technical/game-programming/introduction-to-octrees-r3529
- Optimize "nosetests-2.7 -a'bench' mollib/core/tests/test_geometry.py:TestGeometry.test_speed_within_distance"
- Optimize "mollib hbonds -i 5CJP --hydrogenate"
- Add tests for the Box algorithm
- optimize Molecule with add_atoms method so that the cache isn't cleared after adding every atom