#!/bin/sh -f
#
#
echo '                                                                      '
echo '----------------------------------------------------------------------'
echo '                                                                      '
echo '                 TOP  -- Internet version                             '
echo '           for searching homologous structures in database            '
echo '                                                                      '
echo '----------------------------------------------------------------------'
echo '                                                                      '
# first check if you have SEARCH.PARM in your directory
if test ! -e SEARCH.PARM ; then  
   cp $CLIBD'/SEARCH.PARM' . 
   echo copy $CLIBD'/SEARCH.PARM' here
   echo ' '
fi
#  if no arguments given, ask where is the probe protein
if test $# -lt 1 ;  then
  echo ' '
  echo "File name or PDB code for the probe structure: "
  echo -n "(examples: xxx.pdb or 2cnd@pdb) "
  mol1=$<
else
  mol1=$1
fi

while test `echo $mol1 | grep "/" | wc -l` -gt 0 ; do
mol1l=`echo $mol1 | cut -f 2- -d '/'`
mol1=$mol1l
done
mol1l=$mol1
mol1n=`echo $mol1l | cut -f 1 -d '.'`

echo PDB file name: $mol1
echo Molecule ID:   $mol1n
echo ' '
#
# Now you can run TOP
sitecmd=`grep -i SITE SEARCH.PARM `
sitename=`echo $sitecmd | cut -f 2- -d ' ' `
echo $sitecmd > topsearch.inp
echo Web site of the database: $sitename
#
echo mol1 $mol1 >> topsearch.inp
tail +2 SEARCH.PARM >> topsearch.inp
topp < topsearch.inp > topsearch_$mol1n.log
grep Str topsearch_$mol1n.log | sort +3 -4 > strdiv_$mol1n.lis
echo " The list of structure diversity is:" strdiv_$mol1n.lis
grep Top topsearch_$mol1n.log | sort +3 -4 > topdiv_$mol1n.lis
echo " The list of topology diversity is:" topdiv_$mol1n.lis