capdb2rdc.sh

#!/bin/bash

file="$1"
name="${1%.pdb}"
Bfile="${name}-bb.pdb"
Mfile="m_$Bfile"
Mname="${Mfile%.pdb}"

bbq="java apps.BBQ"
scwrl="Scwrl4"
pales="pales"

#===========================
#          MAIN
#===========================
main() {

# BBQ
echo " ---> start BBQ"
echo "$bbq -bbq.fix_r12=T -ip=$file"
$bbq -bbq.fix_r12=T -ip=$file

# Scwrl
echo " ---> start Scwrl" 
echo "$scwrl -i $Bfile -o $Mfile"
$scwrl -i $Bfile -o $Mfile
dummy_input $Mfile $Mname.tbl

# PALES
echo " ---> start PALES"
echo "$pales -pdb $Mfile -inD $Mname.tbl -outD out_$Mname.tab"
$pales -pdb $Mfile -inD $Mname.tbl -outD out_$Mname.tab
}

# ==========================
# INUPT FILE MAKER FOR PALES
# ==========================

dummy_input(){
Wfile="$1"
cat > $2 << EOF
VARS RESID_I	RESNAME_I	ATOMNAME_I	RESID_J	RESNAME_J	ATOMNAME_J	D	DD	W
FORMAT %5d	%6s	%6s	%5d	%6s	%6s	%9.3f	%9.3f	%.2f
EOF
cat $Wfile| \
awk '{if($3=="H"){print $5,$4,"N",$5,$4,"H","0.005","1.000","1.00"}}' >> $2
}

# ==========================
#        MAIN CALL
# ==========================
main