title: HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales.
abstract: 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.
authors: †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.
authors: Demian
authors: D
authors: Riccardi
authors: §Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States.
authors: Jerry M
authors: JM
authors: Parks
authors: ∥Environmental Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States.
authors: Alexander
authors: A
authors: Johs
authors: ‡UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States.|⊥Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States.
authors: Jeremy C
authors: JC
authors: Smith
mesh_terms: D008958:Models, Molecular; D008968:Molecular Conformation; D066295:Open Access Publishing; D012984:Software