LOOS aims to provide a free and open source C++ library for the analysis of molecular dynamics simulations. This includes parsing a number of PDB format variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber.
LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing it rather than writing multiple formats.
While a number of useful tools are also included in LOOS, the goal of LOOS is to facillitate tools that you write, not duplicate the functionality of CHARMM, ptraj, or GROMACS
- This release addresses a number of bugs and includes a few improvements and new tools.
- The bugs include ones in gmxdump2pdb.pl where hybrid-36 encoding was used where it shouldn't have been, and problems handling cases with more topology segments than molecular segments (as can happen with bilayer systems).
- A bug in serial-selection was addressed that caused the output to be interleaved by molecule rather than contiguous.
- We have seen some cases where DCD trajectories could have 0 frames listed in the DCD header, yet the trajectory has many frames. Instantiating the DCD (or pTraj) for these trajectories would cause LOOS to throw an exception.
- This behavior has been fixed. However, these trajectories will not be read correctly, i.e. LOOS will think they have no frames in them.
- We have included a special fixdcd tool that will update the header (in-place) with the correct number of frames found by manually scanning the trajectory.
- Finally, a bug in the setup.csh script causing the ...