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Faunus: An object oriented framework for molecular simulation.

Mikael Lund1, Martin Trulsson, Björn Persson

  • 1Institute 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.

Source Code for Biology and Medicine
|February 5, 2008
PubMed
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This study introduces a C++ library for Monte Carlo simulations of molecular systems, offering a modular design for easy feature expansion. It demonstrates object-oriented programming

Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Biophysics

Background:

  • Presents a C++ class library for Monte Carlo simulation of molecular systems, including proteins.
  • Highlights a generic and modular design for easy implementation of additional features.
  • Emphasizes statistical mechanical methods documented via code comments for automatic manual generation.

Purpose of the Study:

  • To demonstrate the utility of object-oriented design in molecular simulation.
  • To provide a framework for calculating protein protonation states.
  • To discuss performance considerations in high-level coding abstractions.

Main Methods:

  • Developed a C++ class library utilizing object-oriented principles.
  • Implemented a minimalistic C++ program for protein protonation state calculations.

Related Experiment Videos

  • Leveraged inline code comments for automatic documentation generation.

    • Main Results:

    • An object-oriented design creates an intuitive coding framework for molecular simulation.
    • A C++ program successfully calculates protein protonation states.
    • Performance issues related to high-level coding abstraction are discussed.

    Conclusions:

    • C++ and the Standard Template Library (STL) offer a high-performance platform for molecular modeling.
    • Automatic documentation generation from inline comments eliminates the need for a separate manual.
    • The library facilitates generic molecular modeling and efficient documentation.