Implementing efficient concerted rotations using Mathematica and C code
| Autoři | |
|---|---|
| Rok publikování | 2018 |
| Druh | Článek v odborném periodiku |
| Časopis / Zdroj | EUROPEAN PHYSICAL JOURNAL E |
| Fakulta / Pracoviště MU | |
| Citace | |
| Doi | http://dx.doi.org/10.1140/epje/i2018-11694-7 |
| Klíčová slova | INTRINSICALLY UNSTRUCTURED PROTEINS; MONTE-CARLO SIMULATIONS; COARSE-GRAINED MODELS; MOLECULAR-DYNAMICS; SYSTEMS; ALGORITHM |
| Přiložené soubory | |
| Popis | 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. |
| Související projekty: |