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Faunus: An object oriented framework for molecular simulation.

Lund M, Trulsson M, Persson B - Source Code Biol Med (2008)

Bottom Line: We further discuss performance issues related to high level coding abstraction.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 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.

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.

No MeSH data available.


Source code manual. Code documentation through code comments. All code is commented with special keywords that are eventually collected into a web based manual.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 2: Source code manual. Code documentation through code comments. All code is commented with special keywords that are eventually collected into a web based manual.

Mentions: We provide a class library and as such need to describe both what the classes do as well as how to use them. This can be conveniently achieved using a code documentation system – here we have chosen Doxygen[13] since (i) the documentation appears as normal code comments and (ii) the output is highly configurable, allowing LaTeX equations to be inserted etc. In Figure 2 we show how commented code is used to construct a web based manual of the available classes and functions in the code library. Another very useful feature of Doxygen is the ability to generate a graphical view of the class hierarchy. This enables the end programmer to visually see how a class is constructed as shown in Figure 1.


Faunus: An object oriented framework for molecular simulation.

Lund M, Trulsson M, Persson B - Source Code Biol Med (2008)

Source code manual. Code documentation through code comments. All code is commented with special keywords that are eventually collected into a web based manual.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2266748&req=5

Figure 2: Source code manual. Code documentation through code comments. All code is commented with special keywords that are eventually collected into a web based manual.
Mentions: We provide a class library and as such need to describe both what the classes do as well as how to use them. This can be conveniently achieved using a code documentation system – here we have chosen Doxygen[13] since (i) the documentation appears as normal code comments and (ii) the output is highly configurable, allowing LaTeX equations to be inserted etc. In Figure 2 we show how commented code is used to construct a web based manual of the available classes and functions in the code library. Another very useful feature of Doxygen is the ability to generate a graphical view of the class hierarchy. This enables the end programmer to visually see how a class is constructed as shown in Figure 1.

Bottom Line: We further discuss performance issues related to high level coding abstraction.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: 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.

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.

No MeSH data available.