#!/bin/csh
#
# Command file for OS version 7.5
#
# NOTE: You need to create "os.fil" according to docs!
#
######################################################
#
# NOTE: Set the path at your installation on next line
#
setenv OSDIR /Users/fleming/Desktop/os_76
setenv PWD $cwd
#
######################################################
#
# RUN THE OS MAIN PROGRAM
#
set path = ( $OSDIR/bin $path )

# Check to see if possibly user-modified radii is present
if (! -r $PWD/radii ) then
   cp -p $OSDIR/data/radii $PWD/radii
endif
main75 < os.fil
######################################################
#
# Uncomment below to activate specific
#    programs for analysis of OS
#
######################################################
# Prepare files for plotting and analyzing Packing Value
#  for each residue
#
# The summary output will be in the file, "prot.pak"
# The x,y list for plotting will be in "pak.plt"
# The list of PakVal values will be in "pak.dat"
#   for statistics analysis
#
# If not wanted comment the next four lines
#
 respak75
 sed '/Resnum/d' prot.pak > tmp.pak
 awk '{print $1,$5}' tmp.pak > pak.plt
 awk '{print $5}' tmp.pak > pak.dat
 rm -f tmp.pak
######################################################
# Run program to evaluate OS environments
#
# Output is in file, "prot.eval"
#
# If wanted uncomment next three lines
#
cp $OSDIR/data/tot_aa_hsg.lis $PWD
occsurf75 > prot.eval
rm -f tot_aa_hsg.lis
######################################################
# Prepare file of Normalized Residue Surface Ratio, 
#  Ri, for plotting
#
# The x,y list for plotting is in "ri.plt"
#
# If wanted uncomment next three lines
#
grep 'Ri:' prot.eval > ri.tmp
awk '{printf("%4s%9.2f\n",$4,$2)}' ri.tmp > ri.plt
rm -f ri.tmp
######################################################
# Prepare file of average Raylengths  
#  for each residue
#
# The x,y list for plotting is in "raylength.plt"
#
# If wanted uncomment next three lines
#
grep 'Ray' prot.srf > ray.tmp
awk '{printf("%4s%9.2f\n",$5,$3)}' ray.tmp > raylength.plt
rm -f ray.tmp 
######################################################
# Analyze interchain occluded surface
#
# Concatenate the chains into the 
#  same PDB input file and reunumber consecutively
# Then edit the xxxx and yyyy in the line below to be
#  the residue number of the first and last residue in
#  the chain to be calculated and uncomment the line.
#
#/usr/bin/echo 'xxxx\nyyyy\n' | intchos75
######################################################
#
# Clean up after run
#
rm -f *.ms
rm -f part*
rm -f file.srf