. Author manuscript; available in PMC: 2015 Dec 15.

Published in final edited form as: J Comput Chem. 2014 Oct 18;35(32):2305–2318. doi: 10.1002/jcc.23753

Table 4.

Comparing common tasks in C++ and Python with LOOS. All times reported in seconds as average of five runs. The systems used were LfB in water (LfB), Opsin molecule in membrane with water (Opsin), and a cannabiniod receptor dimer bound to cognate G protein in a membrane with water (GPCR-complex). These timing runs were performed using LOOS v2.1.1 on a modern workstation (Intel i7-3770 CPU @ 3.40GHz, 32 GB memory).

		System
Task	Language	LfB	Opsin	GPCR-complex
Iteratively Align Structures	C++	3	58	276
Iteratively Align Structures	Python	20	80	394
All-to-all RMSD	C++	91	170	484
All-to-all RMSD	Python	148	233	534
Inter-atomic Distance	C++	0	6	37
Inter-atomic Distance	Python	0	6	38

Trajectory size (GB)		0.15	2.25	12.19
System size (atoms)		2,746	46,210	276,122
Number of Frames		4,285	4,058	3,678
Selection Size (atoms)		24	205	1,076