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FAUNUS: An object oriented framework for molecular simulation

Lund, Mikael LU ; Trulsson, Martin LU and Persson, Björn LU (2008) In Source Code for Biology and Medicine 3.
Abstract
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. CONCLUSION: C++ and the Standard... (More)
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. CONCLUSION: 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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
C++, proteins, monte carlo simulation
in
Source Code for Biology and Medicine
volume
3
publisher
BioMed Central
external identifiers
  • scopus:40749110634
ISSN
1751-0473
DOI
10.1186/1751-0473-3-1
language
English
LU publication?
yes
id
cf97eb56-7a06-4555-9335-24f1c395077a (old id 1278257)
date added to LUP
2009-01-29 14:28:44
date last changed
2017-07-30 04:21:39
@article{cf97eb56-7a06-4555-9335-24f1c395077a,
  abstract     = {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. CONCLUSION: 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.},
  articleno    = {1},
  author       = {Lund, Mikael and Trulsson, Martin and Persson, Björn},
  issn         = {1751-0473},
  keyword      = {C++,proteins,monte carlo simulation},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {Source Code for Biology and Medicine},
  title        = {FAUNUS: An object oriented framework for molecular simulation},
  url          = {http://dx.doi.org/10.1186/1751-0473-3-1},
  volume       = {3},
  year         = {2008},
}