Ropp Patrick, Friedman Aaron, Durrant Jacob D
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
J Cheminform. 2017 Sep 18;9(1):52. doi: 10.1186/s13321-017-0237-8.
Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/ . Graphical abstract .
第三方软件包已将Python编程语言转变为一个强大的计算生物学工具。对于有经验的用户来说，软件包安装很容易，但新手有时会在依赖项和编译器方面遇到困难。这形成了一个障碍，可能会阻碍新工具在其他方面的广泛采用。我们展示了Scoria，一个用于处理三维分子数据的Python软件包。与类似的软件包不同，Scoria不需要依赖项、编译或全系统安装。用户可以将Scoria源代码直接整合到自己的程序中。但Scoria并非旨在与其他类似软件包竞争。相反，它对它们起到补充作用。我们的软件包会利用其他软件包（如NumPy、SciPy）（如果存在的话）来加快并扩展自身功能。为展示其效用，我们使用Scoria分析分子动力学轨迹。我们的FootPrint脚本根据一条链上的原子与第二条链的接触频率为其着色。我们希望Scoria将成为计算生物学界的一个有用工具。可在http://durrantlab.com/scoria/免费下载一份（遵循Apache许可2.0）。图形摘要。
