Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

FAUNUS: An object oriented framework for molecular simulation

Lund, Mikael LU orcid ; Trulsson, Martin LU orcid 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)
Please use this url to cite or link to this publication:
author
; and
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
article number
1
publisher
BioMed Central (BMC)
external identifiers
  • scopus:40749110634
  • pmid:18241331
ISSN
1751-0473
DOI
10.1186/1751-0473-3-1
language
English
LU publication?
yes
additional info
Open Access The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
id
cf97eb56-7a06-4555-9335-24f1c395077a (old id 1278257)
date added to LUP
2016-04-01 14:50:10
date last changed
2023-01-04 06:58:16
@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.}},
  author       = {{Lund, Mikael and Trulsson, Martin and Persson, Björn}},
  issn         = {{1751-0473}},
  keywords     = {{C++; proteins; monte carlo simulation}},
  language     = {{eng}},
  publisher    = {{BioMed Central (BMC)}},
  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}},
  doi          = {{10.1186/1751-0473-3-1}},
  volume       = {{3}},
  year         = {{2008}},
}