#!/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

#Modified by Melanie Nelson to read 3D genxpk results-- 
#just changed the split line in the ReadGenxpk subroutine

# Make 7 column NOE files from felix and genxpk ambiguous peak files.

# felix file
# Peak # 1         Intensity = 0.9773519e+06
#  Dimension      Position (ppm)     Width (Hz)    Multiple Peak Assignment
#    D1             7.712077           83.3832  #1    1:ARG+_62:HN
#    D2             7.909034           62.85505  #1    1:ASN_63:HN
#    D3             126.0308           48.79808  #1    1:ARG+_62:N
#    D1                                          #2    1:ARG+_62:HN
#    D2                                          #2    1:ASP-_59:HN
#    D3                                          #2    1:ARG+_62:N
#  Dimension      Frequency Assignment       Distance(ppm)       Pattern id
#    D1              1:ASP-_6:HN             0.92268e-03            pa71
#    D1              1:HISD_17:HN             0.0319228            pa8
#    D1              1:GLY_21:HN             0.0319228            pa13

# genxpk file
## 0 NULL NULL         0 NULL NULL          0.000000   3      0.884457 9.71784 10.6234   17.1897    # 1
#  42 LEU MD-          43 THR HN            0.000000   3      0.8836 9.70758 0         0            0.0103
#  9 ILE MG2           43 THR HN            0.000000   3      0.88449 9.70758 0         0            0.0103
## 0 NULL NULL         0 NULL NULL          0.000000   4      1.23074 9.70571 11.5142   26.0144    # 1
#  43 THR MG           43 THR HN            0.000000   4      1.23006 9.70758 0         0            0.0020

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

if($#ARGV < 3 || $#ARGV > 5)
{
   $prgName = `basename $0`;
   chop($prgName);
   die <<EOHELP;

This program will create a 7 column NOE file from felix or genxpk ambiguity
files. It reads a stereo file to get the stereospecific assignments.

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

Usage: $prgName -f [felix|genxpk] -p [peak file] -s [stereo file]
EOHELP
}

&Getopt('fps');
$fileType = $opt_f;
die("Unrecognized file type: $fileType\n") if($fileType !~ /felix|genxpk/);
$peakFile = $opt_p;
$commentPeakFile = $peakFile;
$commentPeakFile =~ s/.*\///;
$stereoFile = $opt_s;
$commentStereoFile = $stereoFile;
$commentStereoFile =~ s/.*\///;

$date = &ctime(time);
print "# Date: $date";
print "# Peak File: $commentPeakFile\n";
print "# Stereo File: $commentStereoFile\n" if($stereoFile);
print "# File Type: $fileType\n";
print "#   ATOM 1        ATOM 2      distance # peak file:peak #\n";

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

open(PEAKFILE, $peakFile) || die("Cannot open $peakFile: $!\n");
while(<PEAKFILE>)
{
   next if(/^\s*#/);
   next if(/^\s*$/);
#speeds things up to skip assigned lines
   next if(/UNDEF/);
#prevents catastrophic error if a pound sign is missing....
   next if(/pat/);
   if($fileType eq "felix") { &ReadFelix; }
   else { &ReadGenxpk; }
}
close(PEAKFILE);

foreach (@lines) { print; }

sub ReadFelix
{
# Peak # 1         Intensity = 0.9773519e+06
#  Dimension      Position (ppm)     Width (Hz)    Multiple Peak Assignment
#    D1             7.712077           83.3832  #1    1:ARG+_62:HN
#    D2             7.909034           62.85505  #1    1:ASN_63:HN
#    D3             126.0308           48.79808  #1    1:ARG+_62:N
#    D1                                          #2    1:ARG+_62:HN
#    D2                                          #2    1:ASP-_59:HN
#    D3                                          #2    1:ARG+_62:N
   if(/Peak # /)
   {
      chop;
      @words = split(' ');
      $peakNum = $words[2];

      $count = 0;
      $line = <PEAKFILE>;
      $line = <PEAKFILE>;
      while(($line !~ /Dimension/) and ($line =~ /:/))
      {
         chop($line);
         @words = split(':', $line);
         $atomName[$count] = $words[2];
         @resSplit = split('_', $words[1]);
         $resName[$count] = substr($resSplit[0], 0, 3);
         $resNum[$count] = $resSplit[1];
         $atomNameOrig[$count] = $atomName[$count];
         $atomName[$count] = &ConvertFelixName($resNum[$count],
                                               $resName[$count],
                                               $atomName[$count]);
         if($count < 2) { ++$count; }
         else
         {
            $line = sprintf("%4d %-3s %-4s %4d %-3s %-4s       0.01 # %s:%d\n",
                  $resNum[0], $resName[0], $atomName[0],
                  $resNum[1], $resName[1], $atomName[1],
                  $commentPeakFile, $peakNum);
            push(@lines, $line);
            $count = 0;
         }

         $line = <PEAKFILE>;
      }
   }
}

#MN: changed the first split to allow correct parsing of 3D genxpk output

sub ReadGenxpk
{
#need to fix problem with long peak numbers!
   s/\.000000/\.000000 /g;
   ($resNum[0], $resName[0], $atomName[0],
    $resNum[1], $resName[1], $atomName[1],
    $resNum[2], $resName[2], $atomName[2],
    $nullField, $peakNum) = split(' ');
   $atomNameOrig[0] = $atomName[0];
   $atomName[0] = &ConvertGenxpkName($resNum[0], $resName[0], $atomName[0]);
   $atomNameOrig[1] = $atomName[1];
   $atomName[1] = &ConvertGenxpkName($resNum[1], $resName[1], $atomName[1]);
   $line = sprintf("%4d %-3s %-4s %4d %-3s %-4s       0.01 # %s:%d\n",
         $resNum[0], $resName[0], $atomName[0],
         $resNum[1], $resName[1], $atomName[1],
         $commentPeakFile, $peakNum);
   push(@lines, $line);
}

sub ConvertFelixName
{
   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($resName eq "ALA")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "MB" };
      if($oldName eq "HB2") { $newName = "MB" };
      if($oldName eq "HB3") { $newName = "MB" };
   }
   if($resName eq "ARG")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HG1") { $newName = "QPG" };
      if($oldName eq "HG2") { $newName = "QPG" };
      if($oldName eq "HD1") { $newName = "QPD" };
      if($oldName eq "HD2") { $newName = "QPD" };
# Missing all past delta
   }
   if($resName eq "ASN")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HD21") { $newName = "ND2" };
      if($oldName eq "HD22") { $newName = "ND2" };
   }
   if($resName eq "ASP")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
   }
   if($resName eq "CYS")
   {
   }
   if($resName eq "GLN")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HG1") { $newName = "QPG" };
      if($oldName eq "HG2") { $newName = "QPG" };
      if($oldName eq "HE21") { $newName = "NE2" };
      if($oldName eq "HE22") { $newName = "NE2" };
   }
   if($resName eq "GLU")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HG1") { $newName = "QPG" };
      if($oldName eq "HG2") { $newName = "QPG" };
   }
   if($resName eq "GLY")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA1") { $newName = "QPA" };
      if($oldName eq "HA2") { $newName = "QPA" };
   }
   if($resName eq "HIS")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HD2") { $newName = "HD" };
      if($oldName eq "HE1") { $newName = "HE" };
# Missing all past delta
   }
   if($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") { $newName = "QPG" };
      if($oldName eq "HG12") { $newName = "QPG" };
      if($oldName eq "HG21") { $newName = "MG" };
      if($oldName eq "HG22") { $newName = "MG" };
      if($oldName eq "HG23") { $newName = "MG" };
      if($oldName eq "HD11") { $newName = "MD" };
      if($oldName eq "HD12") { $newName = "MD" };
      if($oldName eq "HD13") { $newName = "MD" };
   }
   if($resName eq "LEU")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($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") { $newName = "QQD" };
   }
   if($resName eq "LYS")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HG1") { $newName = "QPG" };
      if($oldName eq "HG2") { $newName = "QPG" };
      if($oldName eq "HD1") { $newName = "QPD" };
      if($oldName eq "HD2") { $newName = "QPD" };
      if($oldName eq "HE1") { $newName = "QPE" };
      if($oldName eq "HE2") { $newName = "QPE" };
# Missing NH3
   }
   if($resName eq "MET")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HG1") { $newName = "QPG" };
      if($oldName eq "HG2") { $newName = "QPG" };
      if($oldName eq "HE1") { $newName = "ME" };
      if($oldName eq "HE2") { $newName = "ME" };
      if($oldName eq "HE3") { $newName = "ME" };
   }
   if($resName eq "PHE")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($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") { $newName = "HZ" };
   }
   if($resName eq "PRO")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HG1") { $newName = "QPG" };
      if($oldName eq "HG2") { $newName = "QPG" };
      if($oldName eq "HD1") { $newName = "QPD" };
      if($oldName eq "HD2") { $newName = "QPD" };
   }
   if($resName eq "SER")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
# Missing HO
   }
   if($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") { $newName = "MG" };
      if($oldName eq "HG2") { $newName = "MG" };
      if($oldName eq "HG3") { $newName = "MG" };
      if($oldName eq "HG11") { $newName = "MG" };
      if($oldName eq "HG21") { $newName = "MG" };
# Missing HO
   }
   if($resName eq "TRP")
   {
   }
   if($resName eq "TYR")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB1") { $newName = "QPB" };
      if($oldName eq "HB2") { $newName = "QPB" };
      if($oldName eq "HD1") { $newName = "CG" };
      if($oldName eq "HD2") { $newName = "CG" };
      if($oldName eq "HE1") { $newName = "CZ" };
      if($oldName eq "HE2") { $newName = "CZ" };
# Missing HO
   }
   if($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" };
   }

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

# Return the new atom name.
   $newName;
}

sub ConvertGenxpkName
{
   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($resName eq "ALA")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "MB") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
   }
   if($resName eq "ARG")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HG+") { $newName = "QG" };
      if($oldName eq "HG-") { $newName = "QG" };
      if($oldName eq "HG1") { $newName = "QG" };
      if($oldName eq "HG2") { $newName = "QG" };
      if($oldName eq "HD+") { $newName = "QD" };
      if($oldName eq "HD-") { $newName = "QD" };
      if($oldName eq "HD1") { $newName = "QD" };
      if($oldName eq "HD2") { $newName = "QD" };
# Missing all past delta
   }
   if($resName eq "ASN")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HD2+") { $newName = "QD2" };
      if($oldName eq "HD2-") { $newName = "QD2" };
      if($oldName eq "HD2") { $newName = "QD2" };
      if($oldName eq "HD1") { $newName = "QD2" };
      if($oldName eq "HD") { $newName = "QD2" };
   }
   if($resName eq "ASP")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
   }
   if($resName eq "CYS")
   {
   }
   if($resName eq "GLN")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HG+") { $newName = "QG" };
      if($oldName eq "HG-") { $newName = "QG" };
      if($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 "HE2+") { $newName = "QE2" };
      if($oldName eq "HE2-") { $newName = "QE2" };
      if($oldName eq "HE2") { $newName = "QE2" };
      if($oldName eq "HE1") { $newName = "QE2" };
      if($oldName eq "HE*") { $newName = "QE2" };
      if($oldName eq "HE") { $newName = "QE2" };
   }
   if($resName eq "GLU")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HG+") { $newName = "QG" };
      if($oldName eq "HG-") { $newName = "QG" };
      if($oldName eq "HG1") { $newName = "QG" };
      if($oldName eq "HG2") { $newName = "QG" };
      if($oldName eq "HG*") { $newName = "QG" };
      if($oldName eq "HG") { $newName = "QG" };
   }
   if($resName eq "GLY")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA+") { $newName = "QA" };
      if($oldName eq "HA-") { $newName = "QA" };
      if($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 "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HD+") { $newName = "HD" };
      if($oldName eq "HD-") { $newName = "HD" };
      if($oldName eq "HD1") { $newName = "HD" };
      if($oldName eq "HD2") { $newName = "HD" };
      if($oldName eq "HD*") { $newName = "HD" };
      if($oldName eq "HD") { $newName = "HD" };
      if($oldName eq "HE+") { $newName = "HE" };
      if($oldName eq "HE-") { $newName = "HE" };
      if($oldName eq "HE1") { $newName = "HE" };
      if($oldName eq "HE2") { $newName = "HE" };
# Missing all past delta
   }
   if($resName eq "ILE")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB") { $newName = "HB" };
      if($oldName eq "HG1+") { $newName = "QG1" };
      if($oldName eq "HG1-") { $newName = "QG1" };
      if($oldName eq "HG12") { $newName = "QG1" };
      if($oldName eq "HG11") { $newName = "QG1" };
      if($oldName eq "MG2") { $newName = "QG2" };
      if($oldName eq "HG21") { $newName = "QG2" };
      if($oldName eq "HG22") { $newName = "QG2" };
      if($oldName eq "MD1") { $newName = "QD1" };
      if($oldName eq "HD11") { $newName = "QD1" };
      if($oldName eq "HD21") { $newName = "QD1" };
   }
   if($resName eq "LEU")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HG") { $newName = "HG" };
      if($oldName eq "MD+") { $newName = "QQD" };
      if($oldName eq "MD-") { $newName = "QQD" };
      if($oldName eq "HD11") { $newName = "QQD" };
      if($oldName eq "HD21") { $newName = "QQD" };
      if($oldName eq "HD*") { $newName = "QQD" };
   }
   if($resName eq "LYS")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HG+") { $newName = "QG" };
      if($oldName eq "HG-") { $newName = "QG" };
      if($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 "HD+") { $newName = "QD" };
      if($oldName eq "HD-") { $newName = "QD" };
      if($oldName eq "HD1") { $newName = "QD" };
      if($oldName eq "HD2") { $newName = "QD" };
      if($oldName eq "HD*") { $newName = "QD" };
      if($oldName eq "HD") { $newName = "QD" };
      if($oldName eq "HE+") { $newName = "QE" };
      if($oldName eq "HE-") { $newName = "QE" };
      if($oldName eq "HE1") { $newName = "QE" };
      if($oldName eq "HE2") { $newName = "QE" };
      if($oldName eq "HE*") { $newName = "QE" };
      if($oldName eq "HE") { $newName = "QE" };
# Missing NH3
   }
   if($resName eq "MET")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HG+") { $newName = "QG" };
      if($oldName eq "HG-") { $newName = "QG" };
      if($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 "ME") { $newName = "ME" };
   }
   if($resName eq "PHE")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HD") { $newName = "CG" };
      if($oldName eq "HE") { $newName = "CZ" };
      if($oldName eq "HZ") { $newName = "HZ" };
   }
   if($resName eq "PRO")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HG+") { $newName = "QG" };
      if($oldName eq "HG-") { $newName = "QG" };
      if($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 "HD+") { $newName = "QD" };
      if($oldName eq "HD-") { $newName = "QD" };
      if($oldName eq "HD1") { $newName = "QD" };
      if($oldName eq "HD2") { $newName = "QD" };
      if($oldName eq "HD*") { $newName = "QD" };
      if($oldName eq "HD") { $newName = "QD" };
   }
   if($resName eq "SER")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
# Missing HO
   }
   if($resName eq "THR")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB") { $newName = "HB" };
      if($oldName eq "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 "HB+") { $newName = "QB" };
      if($oldName eq "HB-") { $newName = "QB" };
      if($oldName eq "HB1") { $newName = "QB" };
      if($oldName eq "HB2") { $newName = "QB" };
      if($oldName eq "HB*") { $newName = "QB" };
      if($oldName eq "HB") { $newName = "QB" };
      if($oldName eq "HD") { $newName = "CG" };
      if($oldName eq "HE") { $newName = "CZ" };
# Missing HO
   }
   if($resName eq "VAL")
   {
      if($oldName eq "HN") { $newName = "HN" };
      if($oldName eq "HA") { $newName = "HA" };
      if($oldName eq "HB") { $newName = "HB" };
      if($oldName eq "MG+") { $newName = "QQG" };
      if($oldName eq "MG-") { $newName = "QQG" };
      if($oldName eq "HG11") { $newName = "QQG" };
      if($oldName eq "HG21") { $newName = "QQG" };
      if($oldName eq "MG2") { $newName = "QQG" };
   }

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

# Return the new atom name.
   $newName;
}