Riccardi Demian, Parks Jerry M, Johs Alexander, Smith Jeremy C
†Department of Chemistry, Earlham College, 801 National Road West, Richmond, Indiana 47374-4095, United States.
‡UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States.
J Chem Inf Model. 2015 Apr 27;55(4):721-6. doi: 10.1021/ci500359e. Epub 2015 Apr 2.
HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. The core is well-tested, well-documented, and easy to install across computational platforms. The goal of the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.
HackaMol是一个用现代Perl编写的开源、面向对象的工具包，它对分子中的原子进行组织，并提供具有化学直观性的属性和方法。该库由两个组件组成：HackaMol，即包含用于存储和操纵分子信息的类的核心组件，以及HackaMol::X，即使用该核心组件的扩展组件。核心组件经过了充分测试、有详细文档记录，并且易于在各种计算平台上安装。扩展组件的目标是为研究人员提供一个更灵活的空间来开发和共享新方法。在本应用笔记中，我们描述了核心类以及两个扩展组件：HackaMol::X::Calculator，一个抽象计算器，它使用代码引用对与外部程序的接口进行泛化；以及HackaMol::X::Vina，一个结构化类，它提供了与AutoDock Vina对接程序的接口。
