FAUNUS: An object oriented framework for molecular simulation
(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:
https://lup.lub.lu.se/record/1278257
- author
- Lund, Mikael LU ; Trulsson, Martin LU and Persson, Björn LU
- organization
- publishing date
- 2008
- 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}}, }