helixgen: create DYANA restraints for ideal helices

Usage:

helixgen protein.seq protein.sec

Description:

extrang takes a DYANA sequence (.seq) file and a secondary structure file (.sec, see below), and prints out the canonical restraints (in DYANA format) for the helical segments.

An entry for a helix in the .seq file has the form of:
helix first_res-last_res
The capitalization of "helix" is not important. Comments are started with a "#" and continue until the end of the line. Other secondary structure types, e.g. "strand", may be present, but are ignored.

Example:

cobalt% cat test.sec
# helix 1
helix 5-11
# helix 2
helix 20-29

cobalt helixgen junk.seq junk.sec

# Residue 5
# H-bonds
5  PHE  O    9  GLY  HN    1.8
5  PHE  O    9  GLY  N    2.7
# NOEs
5  PHE  HN    6  GLY  HN    2.9
5  PHE  HN    7  ALA  HN    5.0
5  PHE  HN    8  PHE  HN    5.0
5  PHE  HA    8  PHE  HN    5.0
5  PHE  HA    8  PHE  HB    3.3
5  PHE  HA    9  GLY  HN    5.0

# Residue 6
# H-bonds
.
.
.