funky reads clean coordinate files and writes file of protein-heterogen contact data.
Here is a sample session with funky:
% funky
Location of protein coordinate files for input (EMBL-like format).
Extension of protein coordinate files (EMBL-like format).
Location of domain coordinate files for input (EMBL-like format).
Extension of domain coordinate files (EMBL-like format).
Heterogen groups dictionary name.
Name of scop file for input (EMBL-like format).
Name of data file with van der Waals radii.
Threshold contact distance.
Name of output file.
Name of log file.