#!/usr/bin/perl

# Randal R. Ketchem, Ph.D.                619.784.9879 (voice1)
# Department of Molecular Biology, MB-9   619.784.8754 (voice2)
# The Scripps Research Institute          619.784.9985 (FAX)
# 10550 N. Torrey Pines Road              ketchemr@scripps.edu (email)
# La Jolla, CA 92037-1027                 http://www.scripps.edu/~ketchemr

# Create 7 column file for DIANA using the volume and peak files generated
# from felix.

# Bin file
# 0.103E+09 3.4
# 0.763E+07 4.2
# 0.0       5.5

# Volume file
#    14     0.622E+08

# Peak file
#    14   140.254     1.399   101  1:ILE_13:HN         44.994     1.200    88  1:LEU_12:HN         41.015     1.611   102  1:ILE_13:N            0.00

require "ctime.pl";
require "getopt.pl";

if($#ARGV < 7)
{
   $prgName = `basename $0`;
   chop($prgName);
   die <<EOHELP;

This program will create a 7 column file for DIANA using 
peak files generated from felix. It reads a bin file to get the
volume/intensity cutoffs and the corresponding bin distances. It reads a
stereo file to get the stereospecific assignments.

Volume file:
    14     0.622E+08     0.753E+06     0.753E+06

Peak File:
    14   140.254     1.399   101  1:ILE_13:HN         44.994     1.200    88  1:LEU_12:HN         41.015     1.611   102  1:ILE_13:N            0.00

Bin file:
0.103E+09 3.4
0.763E+07 4.2
0.0       5.5

Stereo file:
29 LEU HD11 MD1
29 LEU HD12 MD2
54 VAL HG11 MG1
54 VAL HG12 MG2

Usage: $prgName -b [bin file] -c [volume column] -p [peak file] -s [stereo file] -v [volume file]
Volume column must be 1..[number of columns]. The peak number column is 0.
EOHELP
}

&Getopt('bcpsv');
$binFile = $opt_b;
$column = $opt_c;
$peakFile = $opt_p;
$commentPeakFile = $peakFile;
$commentPeakFile =~ s/.*\///;
$stereoFile = $opt_s;
$volumeFile = $opt_v;

# Store the bins and their distances in a hash.
open(BINFILE, $binFile) || die("Cannot open $binFile.\n");
while(<BINFILE>)
{
   next if(/^\s*#/);		#skip commented lines
   next if(/^\s*$/);		#skip blank lines
   chop;
   @words = split(' ');
   $binNum{$words[0]} = $words[1];
}
close(BINFILE);
die("No volume bins in bin file $binFile.\n") unless(%binNum);

# Store the stereos in a hash.
if($stereoFile)
{
   open(STEREOFILE, $stereoFile) || die("Cannot open $stereoFile.\n");
   while(<STEREOFILE>)
   {
      next if(/^\s*#/);		#skip commented lines
      next if(/^\s*$/);		#skip blank lines
      chop;
      ($resNum, $resName, $atomName, $stereoName) = split(' ');
      $stereo{"$resNum $resName $atomName"} = $stereoName;
   }
   close(STEREOFILE);
}

# Store all the peak numbers and their volumes in a hash.
open(VOLUMEFILE, $volumeFile) || die("Cannot open $volumeFile.\n");
while(<VOLUMEFILE>)
{
   next if(/^\s*#/);		#skip commented lines
   next if(/^\s*$/);		#skip blank lines
   next if(/^[a-z]|^[A-Z]/);
	next if(/^c\*\*/);
	next if(/^vol/);
   chop;
   @words = split(' ');
   $numCols = scalar(@words);
   die("The column number must be [1..$numCols]")
         if($column < 1 || $column > $numCols);
   $volumeNum{$words[0]} = $words[$column];
}
close(VOLUMEFILE);
die("No volumes in volume file $volumeFile.\n") unless(%volumeNum);

# Loop through all of the peaks.
#MODIFIED by MN: added next if matches null to skipp unassigned
#peaks
open(PEAKFILE, $peakFile) || die("Cannot open $peakFile.\n");
while(<PEAKFILE>)

{
   next if(/^\s*#/);		#skip commented lines
   next if(/^\s*$/);		#skip blank lines
	next if(/^c\*\*/);
	next if(/^xpk/);
	next if(/null/);
   chop;
   @words = split(' ');
   $peakNum = $words[0];
   $resInfo1 = $words[4];
   $resInfo2 = $words[8];



# 1:ILE_13:HN -> 1 ILE_13 HN
   @res = split(':', $resInfo1);
   $chainID1 = $res[0];
   $atomName = $res[2];
# ILE_13 -> ILE 13
   @splitRes = split('_', $res[1]);
# Grab first three characters of the residue name.
   $resName1 = substr($splitRes[0], 0, 3);
   $resNum1 = $splitRes[1];
   $atomName1 = &ConvertAtomName($resNum1, $resName1, $atomName);

   @res = split(':', $resInfo2);
   $chainID2 = $res[0];
   $atomName = $res[2];
   @splitRes = split('_', $res[1]);
   $resName2 = substr($splitRes[0], 0, 3);
   $resNum2 = $splitRes[1];
   $atomName2 = &ConvertAtomName($resNum2, $resName2, $atomName);

# Make sure the volume exists.
   if($volumeNum{$peakNum} == 0)
   {
      die <<EONOVOL;

Argh. I'm melting! I'm melting!
No volume for peak number $peakNum.
$resNum1 $resName1 $atomName1 $resNum2 $resName2 $atomName2


EONOVOL
   }

# Divide methyl volumes by 3, etc.
   if($atomName1 =~ /MB|MG|QQG|MD|QQD|ME/) { $volumeNum{$peakNum} /= 3.0; }
   if($atomName1 =~ /CG|CZ/) { $volumeNum{$peakNum} /= 2.0; }
   if($atomName2 =~ /MB|MG|QQG|MD|QQD|ME/) { $volumeNum{$peakNum} /= 3.0; }
   if($atomName2 =~ /CG|CZ/) { $volumeNum{$peakNum} /= 2.0; }
# Divide pseudoatom volumes by 2. 
# This section is specific for each user --- must be edited!!!!!!
   if(($atomName2 =~ /QB/) && ($resNum2 =~ /22/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName2 =~ /QG/) && ($resNum2 =~ /22/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /24/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD/) && ($resNum1 =~ /24/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /25/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /26/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /26/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /28/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /29/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /29/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD/) && ($resNum1 =~ /29/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QE/) && ($resNum1 =~ /29/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /30/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG1/) && ($resNum1 =~ /32/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD1/) && ($resNum1 =~ /32/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /32/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /35/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /37/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /38/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /41/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /46/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG1/) && ($resNum1 =~ /47/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD1/) && ($resNum1 =~ /47/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /47/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /49/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /50/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /50/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD/) && ($resNum1 =~ /50/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QE/) && ($resNum1 =~ /50/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /53/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD/) && ($resNum1 =~ /53/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QE/) && ($resNum1 =~ /53/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /55/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /57/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /57/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD/) && ($resNum1 =~ /57/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /58/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /64/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /66/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /66/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /67/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD1/) && ($resNum1 =~ /68/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /68/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /69/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /70/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD/) && ($resNum1 =~ /70/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QE/) && ($resNum1 =~ /70/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG1/) && ($resNum1 =~ /72/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD1/) && ($resNum1 =~ /72/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /72/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /73/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG1/) && ($resNum1 =~ /75/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QD1/) && ($resNum1 =~ /75/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /75/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /77/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /77/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QE/) && ($resNum1 =~ /77/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /82/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QD1/) && ($resNum1 =~ /83/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /83/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /86/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG/) && ($resNum1 =~ /86/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /88/)) { $volumeNum{$peakNum} /= 2.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /90/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QG2/) && ($resNum1 =~ /93/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QB/) && ($resNum1 =~ /94/)) { $volumeNum{$peakNum} /= 3.0; }
   if(($atomName1 =~ /QE/) && ($resNum1 =~ /95/)) { $volumeNum{$peakNum} /= 2.0; }

# Assign a distance to the volume.

   foreach $bin (sort bynumber keys(%binNum))
   { if($volumeNum{$peakNum} >= $bin) { $distance = $binNum{$bin}; } }

# Only use intra assignments.
   if($chainID1 eq $chainID2)
   {
# Build a 7col array for printing later. Save the peak number as a comment.
      $line = sprintf("%3d %-5s%-5s%4d %-5s%-5s%7.2f \n",
            $resNum1, $resName1, $atomName1, $resNum2, $resName2, $atomName2, $distance
            );
      push(@lines, $line);
   }
}
close(PEAKFILE);

# Print some header info.
$date = &ctime(time);
print "# Date: $date";
print "# Bin File: $binFile\n";
print "# Stereo File: $stereoFile\n" if($stereoFile);
print "# Peak File: $peakFile\n";
print "# Volume File: $volumeFile\n";
print "# resNum1 resName1 atomName1 ";
print "resNum2 resName2 atomName2 distance # peakFile:peakNum\n";
# Print the sorted peaks.
foreach $line (sort @lines) { print $line; }

# Subroutine to sort by number as opposed to character.
sub bynumber { $a <=> $b; }

# Subroutine to convert the atom names into names disgeo will understand.
sub ConvertAtomName
{
   local($resNum, $resName, $oldName) = @_;
# Convert to upper case.
   $oldName = "\U${oldName}\E";
# If no conversion is done, the atom will be surrounded by 'xxx'. Convert
# everything!
   local($newName) = "xxx${oldName}xxx";


   if($resName1 eq "ARG") { $resName1 = "ARG+" };
   if($resName1 eq "ASP") { $resName1 = "ASP-" };
   if($resName1 eq "GLU") { $resName1 = "GLU-" };
   if($resName1 eq "LYS") { $resName1 = "LYS+" };

   if($resName2 eq "ARG") { $resName2 = "ARG+" };
   if($resName2 eq "ASP") { $resName2 = "ASP-" };
   if($resName2 eq "GLU") { $resName2 = "GLU-" };
   if($resName2 eq "LYS") { $resName2 = "LYS+" };

   if($resName eq "ARG") { $resName = "ARG+" };
   if($resName eq "ASP") { $resName = "ASP-" };
   if($resName eq "GLU") { $resName = "GLU-" };
   if($resName eq "LYS") { $resName = "LYS+" };



   if($resName eq "ALA")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
   }
   if($resName eq "ARG+")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HG1") { $newName = "QG" };
      if($oldName eq "HG2") { $newName = "QG" };
      if($oldName eq "HG") { $newName = "QG" };
      if($oldName eq "HD1") { $newName = "QD" };
      if($oldName eq "HD2") { $newName = "QD" };
      if($oldName eq "HE") { $newName = "HE" };
# Missing all past delta
   }
   if($resName eq "ASN")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HD21") { $newName = "QD2" };
      if($oldName eq "HD22") { $newName = "QD2" };
   }
   if($resName eq "ASP-")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "QB") { $newName = "QB" };
   }
   if($resName eq "CYS")
   {
   }
   if($resName eq "GLN")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HG1") { $newName = "QG" };
      if($oldName eq "HG2") { $newName = "QG" };
      if($oldName eq "HG") { $newName = "QG" };
      if($oldName eq "HE21") { $newName = "QE2" };
      if($oldName eq "HE1") { $newName = "QE2" };
      if($oldName eq "HE22") { $newName = "QE2" };
      if($oldName eq "HE2") { $newName = "QE2" };
   }
   if($resName eq "GLU-")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HG1") { $newName = "QG" };
      if($oldName eq "HG2") { $newName = "QG" };
      if($oldName eq "HG") { $newName = "QG" };
   }
   if($resName eq "GLY")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA1") { $newName = "QA" };
      if($oldName eq "HA2") { $newName = "QA" };
      if($oldName eq "HA") { $newName = "QA" };
   }
   if($resName eq "HIS")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HD2") { $newName = "HD2" };
      if($oldName eq "HE1") { $newName = "HE1" };
# Missing all past delta
   }
   if($resName eq "ILE")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB") { $newName = "HB" };
      if($oldName eq "HG11") { $newName = "QG1" };
      if($oldName eq "HG12") { $newName = "QG1" };
      if($oldName eq "HG21") { $newName = "QG2" };
      if($oldName eq "HG22") { $newName = "QG2" };
      if($oldName eq "HG23") { $newName = "QG2" };
      if($oldName eq "HD11") { $newName = "QD1" };
      if($oldName eq "HD12") { $newName = "QD1" };
      if($oldName eq "HD13") { $newName = "QD1" };
      if($oldName eq "HD1*") { $newName = "QD1" };   
      if($oldName eq "QD1") { $newName = "QD1" };   
      if($oldName eq "HG2*") { $newName = "QG2" };
      if($oldName eq "QG2") { $newName = "QG2" };
   }
   if($resName eq "LEU")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "QB") { $newName = "QB" };
      if($oldName eq "HG") { $newName = "HG" };
      if($oldName eq "HD11") { $newName = "QQD" };
      if($oldName eq "HD12") { $newName = "QQD" };
      if($oldName eq "HD13") { $newName = "QQD" };
      if($oldName eq "HD21") { $newName = "QQD" };
      if($oldName eq "HD22") { $newName = "QQD" };
      if($oldName eq "HD23") { $newName = "QQD" };
      if($oldName eq "HD2*") { $newName = "QQD" };
      if($oldName eq "MD2") { $newName = "QQD" };
      if($oldName eq "MD1") { $newName = "QQD" };
      if($oldName eq "HD1*") { $newName = "QQD" };
      if($oldName eq "HD*") { $newName = "QQD" };
      if($oldName eq "QQD") { $newName = "QQD" };
   }
   if($resName eq "LYS+")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "QB") { $newName = "QB" };
      if($oldName eq "HG1") { $newName = "QG" };
      if($oldName eq "HG2") { $newName = "QG" };
      if($oldName eq "HG") { $newName = "QG" };
      if($oldName eq "HG*") { $newName = "QG" };
      if($oldName eq "QG") { $newName = "QG" };
      if($oldName eq "HD1") { $newName = "QD" };
      if($oldName eq "HD2") { $newName = "QD" };
      if($oldName eq "HD") { $newName = "QD" };
      if($oldName eq "QD") { $newName = "QD" };
      if($oldName eq "HE1") { $newName = "QE" };
      if($oldName eq "HE2") { $newName = "QE" };
      if($oldName eq "HE") { $newName = "QE" };
      if($oldName eq "QE") { $newName = "QE" };
# Missing NH3
   }
   if($resName eq "MET")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HG1") { $newName = "QG" };
      if($oldName eq "HG2") { $newName = "QG" };
      if($oldName eq "HG") { $newName = "QG" };
      if($oldName eq "HE1") { $newName = "QE" };
      if($oldName eq "HE2") { $newName = "QE" };
      if($oldName eq "HE3") { $newName = "QE" };
      if($oldName eq "HE*") { $newName = "QE" }; 
   }
   if($resName eq "PHE")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HD1") { $newName = "CG" };
      if($oldName eq "HD2") { $newName = "CG" };
      if($oldName eq "HE1") { $newName = "CZ" };
      if($oldName eq "HE2") { $newName = "CZ" };
      if($oldName eq "HZ") { $newName = "HZ" };
      if($oldName eq "HD*") { $newName = "CG" };
      if($oldName eq "HD") { $newName = "CG" };
      if($oldName eq "HE*") { $newName = "CZ" };   
      if($oldName eq "HE") { $newName = "CZ" };   
   }
   if($resName eq "PRO")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "QB") { $newName = "QB" };
      if($oldName eq "HG1") { $newName = "QG" };
      if($oldName eq "HG2") { $newName = "QG" };
      if($oldName eq "HG") { $newName = "QG" };
      if($oldName eq "QG") { $newName = "QG" };
      if($oldName eq "HD1") { $newName = "QD" };
      if($oldName eq "HD2") { $newName = "QD" };
      if($oldName eq "HD") { $newName = "QD" };
      if($oldName eq "QD") { $newName = "QD" };
   }
   if($resName eq "SER")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "QB") { $newName = "QB" };
# Missing HO
   }
   if($resName eq "THR")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB") { $newName = "HB" };
      if($oldName eq "HG1") { $newName = "HG1" };
      if($oldName eq "HG21") { $newName = "QG2" };
      if($oldName eq "HG22") { $newName = "QG2" };
      if($oldName eq "HG23") { $newName = "QG2" };
      if($oldName eq "HG2*") { $newName = "QG2" };
      if($oldName eq "MG2") { $newName = "QG2" };
      if($oldName eq "QG2") { $newName = "QG2" };
      if($oldName eq "MG") { $newName = "QG2" };
# Missing HO
   }
   if($resName eq "TRP")
   {
   }
   if($resName eq "TYR")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB3") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HD1") { $newName = "CG" };
      if($oldName eq "HD2") { $newName = "CG" };
      if($oldName eq "HE1") { $newName = "CZ" };
      if($oldName eq "HE2") { $newName = "CZ" };
      if($oldName eq "HD*") { $newName = "CG" };
      if($oldName eq "HD") { $newName = "CG" };
      if($oldName eq "HE*") { $newName = "CZ" };
      if($oldName eq "HE") { $newName = "CZ" };
      if($oldName eq "HH") { $newName = "HH" };
# Missing HO
   }
   if($resName eq "VAL")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB") { $newName = "HB" };
      if($oldName eq "HG11") { $newName = "QQG" };
      if($oldName eq "HG12") { $newName = "QQG" };
      if($oldName eq "HG13") { $newName = "QQG" };
      if($oldName eq "HG21") { $newName = "QQG" };
      if($oldName eq "HG22") { $newName = "QQG" };
      if($oldName eq "HG23") { $newName = "QQG" };
      if($oldName eq "HG1*") { $newName = "QQG" };
      if($oldName eq "MG1") { $newName = "QQG" };
      if($oldName eq "MG2") { $newName = "QQG" };
      if($oldName eq "HG2*") { $newName = "QQG" };
      if($oldName eq "QQG*") { $newName = "QQG" };
   }

# Stereo's
   if($stereo{"$resNum $resName $oldName"})
   { $newName = $stereo{"$resNum $resName $oldName"} };

# Return the new atom name.
   $newName;


}