Calculate the pairwise distances (rmsd) between a set of electrostatic maps, contained in Gaussian cube files, and report these distances in CVS and a Mega-compatible formats.
Given a set of electrostatic maps the pairwise distances (as rmsd) are calculated. These maps are obtained by a Poisson Boltzmann analysis of proteins as implemented in software such as Delphi or APBS (APBS writes the maps in other format, OpenDX scalar, that need to be converted to a Gaussian cube, with tools such as openbabel).
For the calculated distances to make sense the maps source proteins should be similar/related (homologs, mutants, chimeric variants, etc) and being structurally superimposed when the electrostatic potential maps are calculated.
When the sizes of a specific pair of maps are not equal, two distances are computed and averaged for the pair, resizing each map at a time by interpolation to match the size of the other map, as the distance can only be calculated for maps with exactly the same size.
cubedist [-o OUTPUT] [--version] [-h] map...
positional arguments:
map electrostatic potential maps
optional arguments:
-o, --output OUTPUT output files base name (default:
"map_distances_rmsd")
--version show version information and exit
-h, --help show this help message and exit
This is not a Julia package, just a standalone script. Just download it and put it in your PATH. You need a working Julia environment and to install the dependencies.
This script depends on the following Julia packages:
ArgParseDistancesImagesPrintf