Topoly: Python package to analyze topology of polymers.
Topoly: Python package to analyze topology of polymers.
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DOI：
10.1093/bib/bbaa196
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发表时间：
2021-05-20
影响因子：
9.5
通讯作者：
Sulkowska JI
中科院分区：
文献类型：
--
作者：
Dabrowski-Tumanski P;Rubach P;Niemyska W;Gren BA;Sulkowska JI
拓扑结构在物质的（生物）物理性质中的作用越来越大，需要一种检测（生物）聚合物的拓扑结构的有效方法。然而，现有的工具只允许对最简单的结进行分类，不能用于自动化样品分析。为了满足这一需求，我们创建了Topoly Python包。该软件包能够通过计算不同的拓扑多项式不变量来区分结、滑结、链接和空间图形。它还使人们能够在给定的环上创建最小的跨越表面，例如检测套索基序或生成随机闭合聚合物。它能够阅读各种文件格式，包括PDB。丰富的文档沿着测试用例和Python编程语言的简单性使其成为一个非常简单易用但功能强大的工具，甚至适合没有经验的用户。Topoly可从https://topoly.cent.uw.edu.pl获得。
The increasing role of topology in (bio)physical properties of matter creates a need for an efficient method of detecting the topology of a (bio)polymer. However, the existing tools allow one to classify only the simplest knots and cannot be used in automated sample analysis. To answer this need, we created the Topoly Python package. This package enables the distinguishing of knots, slipknots, links and spatial graphs through the calculation of different topological polynomial invariants. It also enables one to create the minimal spanning surface on a given loop, e.g. to detect a lasso motif or to generate random closed polymers. It is capable of reading various file formats, including PDB. The extensive documentation along with test cases and the simplicity of the Python programming language make it a very simple to use yet powerful tool, suitable even for inexperienced users. Topoly can be obtained from https://topoly.cent.uw.edu.pl.
影响因子：
14.9
作者：
Lai YL;Yen SC;Yu SH;Hwang JK
通讯作者：
Hwang JK