#!/usr/bin/perl
# 
# Add Tropp correction to methyls.
#

while(<>)
{
   print if(/^#/);
   next if(/^#/);

#   2 ALA MB      7 GLN HN    6.0 # met_cnstr_vols.intra2:12

   chop;
   ($resNum1, $resName1, $atomName1,
    $resNum2, $resName2, $atomName2,
    $distance, $garb, $comment) = split(' ');

   if(($atomName1 =~ /^QD1/) or ($atomName1=~ /^QD2/)) 
   { $distance += 0.5; $comment .= " T-"; }
   if(($atomName1 =~ /^QG1/) or ($atomName1=~ /^QG2/))
   { $distance += 0.5; $comment .= " T-"; }
   if(($atomName2 =~ /^QG1/) or ($atomName2=~ /^QG2/))
   { $distance += 0.5; $comment .= " -T"; }
   if(($atomName2 =~ /^QD1/) or ($atomName2=~ /^QD2/))
   { $distance += 0.5; $comment .= " -T"; }
   if(($atomName1 =~ /^QQG/) or ($atomName1=~ /^QQD/))
   { $distance += 0.5; $comment .= " -T"; }
   if(($atomName2 =~ /^QQG/) or ($atomName2=~ /^QQD/))
   { $distance += 0.5; $comment .= " -T"; }
   if(($resName1 eq ALA) and ($atomName1 eq QB))
   { $distance += 0.5; $comment .= " T-"; }
   if(($resName2 eq ALA) and ($atomName2 eq QB))
   { $distance += 0.5; $comment .= " -T"; }
   if(($resName1 eq MET) and ($atomName1 eq QE))
   { $distance += 0.5; $comment .= " T-"; }
   if(($resName2 eq MET) and ($atomName2 eq QE))
   { $distance += 0.5; $comment .= " -T"; }

   printf("%3d %-5s%-5s%4d %-5s%-5s%7.2f \n",
      $resNum1, $resName1, $atomName1,
      $resNum2, $resName2, $atomName2,
      $distance);
}