Below is a summary of the tools currently distributed with LOOS. To get a detailed summary of the command line arguments, run the program without arguments or using "-h". Nearly all tools also support the "--fullhelp" options, which will display more detailed help information, including examples of how to use the tool.
In the documentation, the term "system" or "model" refers to a file that describes the contents of a system, such as a PDB file or one of the inputs from the various simulation packages (PSF, parmtop, gro, etc). All of the tools are now package agnostic, in the sense that they will take any of the supported file formats as input. However, not all files provide all of the needed information; for example, the order_params tool requires connectivity information to function properly, so the user must run it with a system file type that has that information, such as a CHARMM/NAMD PSF file or a PDB with CONECT records.
At present, LOOS assumes that all periodic boxes are rectangular, and will produce incorrect answers if trajectories using different box shapes (eg truncated octahedron) are used in programs which make use of periodicity (eg rdf). We have no immediate plans to generalize the code to handle other periodicities, but are willing to reconsider if there is significant demand from users.
LOOS uses angstroms as the output unit of distance, even when the input coordinates are in other units (e.g. nanometers for GROMACS files). All output is in plain text format, and follows general unix/linux conventions. Every program's output starts with a series of comment lines, marked by beginning with a "#", echoing the command line used to invoke the program, the user, the date teh program was run, the working directory, and the version of LOOS used. Any additional information, such as the meanings of various columns of output, is also provide on lines marked with "#".
LOOS tools are designed to make it easy to plot the results generated. As a rule, files are formatted such that they can be cleanly plotted using the gnuplot plotting program, standard with most modern linux distributions. In addition, if matrices or vectors are written out (e.g. from the svd tool or one of the tools from the ENM package), the format is consistent with that used by Matlab and Octave.
Categories of Tools