pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling
pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling
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DOI：
10.1093/bioinformatics/btt402
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发表时间：
2013-09-15
期刊：
影响因子：
5.8
通讯作者：
Guallar, Victor
中科院分区：
文献类型：
--
作者：
Gil, Victor A.;Guallar, Victor
我们介绍pyRMSD，一个开源的独立Python包，旨在提供一个综合的和有效的方式执行均方根偏差（RMSD）相关的大型结构集的计算。它被专门调整为快速集体RMSD计算，作为成对RMSD矩阵，实现多达三个众所周知的叠加算法。pyRMSD提供了自己的对称距离矩阵类，除了可以用作常规矩阵之外，还有助于节省内存并提高内存访问速度。最后一个特性可以显著提高使用它的任何Python算法的整体性能。此外，它的可扩展性，测试套件和文档使其成为那些需要开发或测试新算法的工作台的人的好选择。
We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms.