funky reads clean coordinate files and writes file of protein-heterogen contact data.

Here is a sample session with funky:

% funky

Mandatory qualifiers:

[-prot] (string)

Location of protein coordinate files for input (EMBL-like format).

[-protextn] (string)

Extension of protein coordinate files (EMBL-like format).

[-dom] (string)

Location of domain coordinate files for input (EMBL-like format).

[-domextn] (string)

Extension of domain coordinate files (EMBL-like format).

-dic (infile)

Heterogen groups dictionary name.

-scop (infile)

Name of scop file for input (EMBL-like format).

-vdwf (infile)

Name of data file with van der Waals radii.

-thresh (float)

Threshold contact distance.

Advanced qualifiers:

-outf (outfile)

Name of output file.

-logf (outfile)

Name of log file.