title: LOOS: an extensible platform for the structural analysis of simulations.
abstract: We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.
authors: Department of Biochemistry & Biophysics, University of Rochester Medical School, Rochester, NY 14642, USA.
authors: Tod D
authors: TD
authors: Romo
authors: Alan
authors: A
authors: Grossfield
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D003201:Computers; D030562:Databases, Protein; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins