Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.
Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.
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DOI：
10.1186/1752-153x-2-5
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发表时间：
2008-03-09
影响因子：
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通讯作者：
Hutchison GR
中科院分区：
文献类型：
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作者：
O'Boyle NM;Morley C;Hutchison GR
像Python这样的脚本语言非常适合于化学信息学中的常见编程任务，如数据分析和从文件中解析信息。然而，出于效率的原因，诸如OpenBabel工具包之类的化学信息学工具包通常是用诸如C++之类的编译语言实现的。我们描述了Pybel，这是一个提供对OpenBabel工具包的访问的Python模块。Pybel包装了直接的工具包绑定，以简化读写分子文件和计算指纹等常见任务。广泛使用了Python迭代器来简化循环，例如对文件中所有分子的循环。可以很容易地将Pybel分子相互转化为OpenBabel OBMol，以访问未被Pybel包裹的那些方法或属性。Pybel允许化学信息学家快速开发处理化学信息的Python脚本。它是开放源码的，可跨平台使用，并为Python程序员提供了OpenBabel工具包的强大功能。
Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.