Titel
Implementing efficient concerted rotations using Mathematica and C code⋆
Autor*in
Miroslav Jurásek
Faculty of Science, Masaryk University
Autor*in
Ivan Coluzza
CIC biomaGUNE Parque Cientfico y Tecnolgico de Gipuzkoa
Abstract
In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second.
Stichwort
Advances in Computational Methods for Soft Matter Systems
Objekt-Typ
Sprache
Englisch [eng]
Persistent identifier
https://phaidra.univie.ac.at/o:937282
Erschienen in
Titel
The European Physical Journal E
Band
41
Ausgabe
7
Verlag
Springer Nature
Erscheinungsdatum
2018
Zugänglichkeit
Rechteangabe
© The Author(s) 2018

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