Loos: A Tool for Making New Tools for Analyzing Molecular Simulations

Abstract

We have developed LOOS (Lightweight Object Oriented Structure-analysis) as a tool for making new tools for analyzing molecular simulations. LOOS is an object-oriented library written in C++ with a Python interface and was designed to facilitate the rapid development of new methods for structural analysis in either C++ or Python. In addition, LOOS includes over 130 pre-built tools for common structural analysis tasks including 3D histograms for visualization, hydrogen bonding patterns, and assessing simulation convergence. LOOS also includes a set of libraries and tools for performing elastic network model calculations. LOOS supports reading the native file formats of most common simulation packages, such as Amber (including NetCDF-formatted), CHARMM, Gromacs, NAMD, and Tinker. LOOS can also write NAMD formatted PDB and DCD files. A dynamic atom selection language, based on the C expression syntax, is included in the library and is easily accessible to the tool writer. Through modern C++ design, LOOS is both simple to use, requiring knowledge of only 4 core classes, and easy to extend. LOOS makes extensive use of Boost and the Standard Template Library for correctness and ease of use, and relies on ATLAS for high performance numerical routines.