Paper Citing NAMD - Abstract
Romo, Tod D.; Grossfield, Alan
LOOS: An Extensible Platform for the Structural Analysis of Simulations
2009 ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-20, 2332-2335, 2009
We have developed LOOS ((L) under bar ightweight (O) under bar bject-(O) under bar riented (S) under bar tructure-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) (http://loos.sourceforge.net). LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.
