********> bugfix.7
Author: Bill Ross
Date:   4/16/95, amended 4/21/95

Programs: makeCHIR_RST (shell script using awk)

Severity: moderate

Problem:  typo in path name in script; also older awk versions do not work

Affects:  mainly machines with old awk

Note:     now it uses nawk or gawk if possible; other improvements 
	  have also been made

Fix:  Replace src/nmr_aux/prepare_input/makeCHIR_RST with the following:
-------------------------------------------------------------------------
#!/bin/sh
#
#  This script reads in a pdb file, and generates constraints
#    for the nmr module that force the proper chirality on 
#    tetrahedral carbons.  The pdb file must have the proper
#    AMBER atom order, e.g. have been written by the edit or anal
#    programs.
#
#  It also generates "trans" constraints for all peptide bonds.
#  NOTE!!!  You must edit the output of this program manually to
#     change "trans" peptide constraints to "cis" peptide constraints
#     if needed!
#
#  Usage:  makeCHIR_RST pdb_file output_constraint_file
#
if [ $# = 0 ] ; then
	echo "usage:  $0  pdb_file  output_constraint_file "
	exit 1
fi
#
#  choose an awk cmd - some machines still have the 'old'
#	awk (10 years outdated), so to be conservative,
#	see if the more recent nawk or gawk versions exist
#	and use them. 
#
AWKS="nawk gawk awk"
AWK="none"
P=`echo $PATH | sed 's/:/ /g'`
for j in $AWKS ; do
	for i in $P ; do
		if [ -x ${i}/${j} ]  ; then
			AWK=$i/$j
			break
		fi
	done
	if [ $AWK != "none" ] ; then
		break
	fi
done
if [ $AWK = "none" ] ; then
	echo "$0: no awk version found in path (tried: $AWKS)"
	echo PATH = $PATH
	exit 1
fi
echo "  (using $AWK)"
exit
cat <<eof > /tmp/chiral_defs.$$
#
# chiral definitions for PDB proton nonemclature
# the triple product for these tetrads should always be positive
#
ALA N C HA CB
#
ARG CA CG HB2 HB3
ARG CB CD HG2 HG3
ARG CG NE HD2 HD3
ARG N C HA CB
#
ASN CA CG HB2 HB3
ASN N C HA CB
#
ASP CA CG HB2 HB3
ASP N C HA CB
#
CYS CA SG HB2 HB3
CYS N C HA CB
#
CYX CA SG HB2 HB3
CYX N C HA CB
#
GLN CA CG HB2 HB3
GLN CB CD HG2 HG3
GLN N C HA CB
#
GLU CA CG HB2 HB3
GLU CB CD HG2 HG3
GLU N C HA CB
#
GLY N C HA2 HA3
#
HIP  CA CG HB2 HB3
HIP  N C HA CB
#
HID  CA CG HB2 HB3
HID  N C HA CB
#
HIE  CA CG HB2 HB3
HIE  N C HA CB
#
ILE CA CG2 CG1 HB
ILE CB CD1 HG12 HG13
ILE N C HA CB
#
LEU CA CG HB2 HB3
LEU CB CD1 CD2 HG
LEU N C HA CB
#
LYS CA CG HB2 HB3
LYS CB CD HG2 HG3
LYS CD NZ HE2 HE3
LYS CG CE HD2 HD3
LYS N C HA CB
#
MET CA CG HB2 HB3
MET CB SD HG2 HG3
MET N C HA CB
#
PHE CA CG HB2 HB3
PHE N C HA CB
#
PRO CA CG HB2 HB3
PRO CB CD HG2 HG3
PRO CG N  HD2 HD3
PRO N C HA CB
#
SER CA OG HB2 HB3
SER N C HA CB
#
THR CA CG2 OG1 HB
THR N C HA CB
#
TRP CA CG HB2 HB3
TRP N C HA CB
#
TYR CA CG HB2 HB3
TYR N C HA CB
#
VAL CA CG1 CG2 HB
VAL N C HA CB
eof
$AWK '
BEGIN {
	while ( getline < "/tmp/chiral_defs.$$" > 0 ) {
		if (substr($1,1,1) != "#") {
			icons++
			rescons[icons] = $1
			atcons1[icons] = $2
			atcons2[icons] = $3
			atcons3[icons] = $4
			atcons4[icons] = $5
		}
	}
	ncons = icons
}
$1=="ATOM" {
	ind = $3 "," $5
	atno[ind] = $2; restype[$5] = $4
	lastres = $5
}
END { OFS = ""
	for (ires=1; ires<=lastres; ires++ ) {
		for (icons=1; icons<=ncons; icons++) {
			if (rescons[icons]==restype[ires]) {
				ind1 = atcons1[icons] "," ires	
				ind2 = atcons2[icons] "," ires	
				ind3 = atcons3[icons] "," ires	
				ind4 = atcons4[icons] "," ires	
				if (ind1 in atno && ind2 in atno && \
					       ind3 in atno && ind4 in atno ) {
					print "#"
					print "#  chirality for residue ", \
						ires, " atoms:  ", \
						atcons1[icons], " ", \
						atcons2[icons], " ", \
						atcons3[icons], " ", \
						atcons4[icons]
					icount++
					if (icount==1) {
						print " &rst iat=", \
							atno[ind1], ",", \
							atno[ind2], ",", \
							atno[ind3], ",", \
							atno[ind4], ", "
						print "   r1=10., r2=60.,", \
							" r3=80., r4=130.,"\
							" rk2 = 10., rk3=10.,",\
							"  &end"
					} else {
						print " &rst iat=", \
							atno[ind1], ",", \
							atno[ind2], ",", \
							atno[ind3], ",", \
							atno[ind4], ", &end"
					}
				} else {
					print "bad constraint for residue ", \
						ires, " atoms:  ", \
						atcons1[icons], " ", \
						atcons2[icons], " ", \
						atcons3[icons], " ", \
						atcons4[icons] > "/dev/tty"
				}
			}
		}
	}
	icount = 0
	for (ires=1; ires<=lastres; ires++ ) {
		inda = "CA," ires
		indn = "N," ires; indc = "C," ires
		iresm1 = ires-1
		indcm = "C," iresm1; indam = "CA," iresm1
		if (indam in atno) {
			icount++
			print "#"
			print "#  trans-omega constraint for residue ",ires
			if (icount==1) {
				print " &rst iat=", atno[inda], ",", \
					atno[indn], ",", \
					atno[indcm], ",", \
					atno[indam], ", "
				print "   r1=150., r2=170., r3=190., r4=210.,"\
					" rk2 = 50., rk3=50.,  &end"
			} else {
				print " &rst iat=", atno[inda], ",", \
					atno[indn], ",", \
					atno[indcm], ",", \
					atno[indam], ", &end"
			}
		}
	}
}'  $1 > $2
#
#  tip user off about results & clean up tmp file
#
COUNT=`grep rst $2 | wc -l `
echo $COUNT chiral restraints generated in $2
/bin/rm -f /tmp/chiral_defs.$$
-------------------------------------------------------------------------

Temporary workarounds: avoid machines w/ old awk