Faunus: An object oriented framework for molecular simulation.
BACKGROUND
We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that - subsequently - are collected to automatically build a web-based manual.


RESULTS
We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction.


CONCLUSIONS
C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained.
Lund
Mikael
M
Institute of Organic Chemistry and Biochemistry, The Academy of Sciences of the Czech Republic, Flemingovo nam,2, CZ-16610 Prague 6, Czech Republic. mlund@mac.com.
Trulsson
Martin
M
Persson
Björn
B