#!/bin/sh

# doambig
# this is a wrapper script which connects the ambiguity output from GENXPK
# with the pairwise distances between potential NOE proton pairs
# using the pdb output files from an AMBER run.  Then one can look through
# the possible assignments to see if some can be thrown out due to unreasonable
# distances in the pdbs.

if [ "$#" -ne 2 ]
then
   prgName=`basename $0`
   echo "Usage: $prgName YYMMDD [monomer|dimer]"
   exit 1
fi

date=$1
type=$2

if [ -d $date ]
then
   if [ -d $date.old ]
   then
      echo "$date.old exists"
      echo "Please fix this and try again."
      exit
   fi
   mv $date $date.old
fi
mkdir $date
cp family.all $date/.

# First do the felix files.
#stereo="/home/fagan/stereo.felix"
#files="\
#/home/lenam/felix/text/cc4d3.mul \
#"
#for file in $files
#do
#   name=`basename $file`
#   echo
#   echo "ambig2ncol on $name"
#   case "$type"
#   in
#      "monomer")
#         ambig2ncol -f felix -p $file -s $stereo > $date/7col.$name;;
#      "dimer")
#         ambig2ncol -f felix -p $file -s $stereo \
#               | ncol2dimer -r 90 > $date/7col.$name;;
#      *)
#         echo "must designate either monomer or dimer"
#         exit 1;;
#   esac
#
#   echo "noevio on $date/7col.$name"
#   noevio -fam family \
#          -pam /home/lenam/bin/ambi/ambi.pseudomap \
#          -sub "^[A-Z]" \
#          -noe $date/7col.$name \
#          -fun 2 \
#          -blo 0 \
#          > $date/7col.$name.noevio
#
#   echo "filter $date/7col.$name"
#   dofilter $type $date/7col.$name.noevio
#
#   /bin/rm $date/7col.$name
#done

# Second do the genxpk files.
stereo="crcn.ssa"
files="cnoe_asgresults \
"

for file in $files
do
   name=`basename $file`
   echo
   echo "ambig2ncol on $name"
   case "$type"
   in
      "monomer")
         ambig2ncol.3d -f genxpk -p $file -s $stereo > $date/7col.$name;;
      "dimer")
         ambig2ncol -f genxpk -p $file -s $stereo \
               | ncol2dimer -r 90 > $date/7col.$name;;
      *)
         echo "must designate either monomer or dimer"
         exit 1;;
   esac

   echo "noevio on $date/7col.$name"
   noevio -fam family.all \
          -pam /home/fagan/bin/ambi/ambi.pseudomap \
          -sub "^[A-Z]" \
          -noe $date/7col.$name \
          -fun 2 \
          -blo 0 \
          > $date/7col.$name.noevio

   echo "filter $date/7col.$name"
   dofilter $type $date/7col.$name.noevio

#   /bin/rm $date/7col.$name
done

# Third do 7col files. These need no ambig2ncol since they are already 7col.
#files="\
#/home/lenam/felix/text/7col.inter.c13noe.970714 \
#/home/lenam/felix/text/7col.intra.c13noe.970714 \
#"
#for file in $files
#do
#   name=`basename $file`
#   echo
#  54 VAL MG2    51 ALA MB    6.0 # 13cnoe.970714:736  
#   grep "^#" $file > $date/$name
#   case "$type"
#   in
#      "monomer")
#         grep -v "^#" $file \
#         | awk '{printf"%4d %3s %-4s %4d %3s %-4s       0.01 # %s\n", \
#               $1,$2,$3,$4,$5,$6,$9}' >> $date/$name;;
#      "dimer")
#         grep -v "^#" $file \
#         | awk '{printf"%4d %3s %-4s %4d %3s %-4s       0.01 # %s\n", \
#               $1,$2,$3,$4,$5,$6,$9}' | ncol2dimer -r 90 >> $date/$name;;
#      *)
#         echo "must designate either monomer or dimer"
#         exit 1;;
#   esac
#
#   echo "noevio on $name"
#   noevio -fam family \
#          -pam /home/ketchemr/bin/ambi/ambi.pseudomap \
#          -sub "^[A-Z]" \
#          -noe $date/$name \
#          -fun 2 \
#          -blo 0 \
#          > $date/$name.noevio
#
#   echo "filter $date/$name"
#   dofilter $type $date/$name.noevio
#
#   /bin/rm $date/$name
#done

echo