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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 example. Example of a Monte Carlo simulation program to calculate protein ionization states in an aqueous salt solution using explicit ions and the detailed three-dimensional protein structure.
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Figure 4: Source code example. Example of a Monte Carlo simulation program to calculate protein ionization states in an aqueous salt solution using explicit ions and the detailed three-dimensional protein structure.

Mentions: Figure 4 shows – in 50 lines of code – a complete MC program for simulating the protonation state of a protein in a salt solution at a given pH value. Experimentally this corresponds to a standard potentiometric titration experiment where the net-charge is measured as a function of pH [18]. We will not go through all the lines in the code as the comments should be more or less self-explanatory. The overall program structure is


Faunus: An object oriented framework for molecular simulation.

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

Source code example. Example of a Monte Carlo simulation program to calculate protein ionization states in an aqueous salt solution using explicit ions and the detailed three-dimensional protein structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Source code example. Example of a Monte Carlo simulation program to calculate protein ionization states in an aqueous salt solution using explicit ions and the detailed three-dimensional protein structure.
Mentions: Figure 4 shows – in 50 lines of code – a complete MC program for simulating the protonation state of a protein in a salt solution at a given pH value. Experimentally this corresponds to a standard potentiometric titration experiment where the net-charge is measured as a function of pH [18]. We will not go through all the lines in the code as the comments should be more or less self-explanatory. The overall program structure is

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.