#!/usr/bin/perl -w

#perl script to fix nomenclature from PFJ's naming scheme in FELIX97
#to the format used for GENXPK.
#script works on the 4 column file which comes from the following conversions:
#Export "spin systems" from FELIX97 -- text file -- run pat_to_4col -- output
#is the .assignments file used when running GENXPK.  This is the file which
#needs to be fixed.

#genxpk format:
#1 LYS HA         4.538 
#1 LYS HB+        1.832
#1 LYS HB-        1.68
#1 LYS HD+        1.70

#the input file must have all assignments for a given residue in a
#contiguous group!

#in atmnames, "+" is substituted for "1" and "-" is substituted for 2

#command line: fix4colpfj .assignments [>output]

#Melanie Nelson
#2/23/99
#Patty Fagan Jones
#5/26/99

if ($#ARGV != 0) {
	$prg_name = $0;
	$prg_name = `basename $prg_name`;
	chomp ($prg_name);
	die<<EODIE;
This script converts the four column .assignments file used by
GENXPK to the format used by Felix97 for its spin systems. The
output file can be read into Felix97, allowing previously made
assignments to be used in a new Felix project.

4 column GENXPK format:
  1 LYS HA         4.538
  1 LYS HB1        1.832
  1 LYS HB2        1.68

Output Felix97 spin systems format:
PATTERN pa1
1:LYS_1:HA  4.538  4.538 4.538 4.538 4.538 4.538 4.538 4.538 4.538 H
1:LYS_1:HB1  1.832  1.832 1.832 1.832 1.832 1.832 1.832 1.832 1.832 H

Usage: $prg_name .assignments [>outputfile]
EODIE
}





open (ASSIGFILE, $ARGV[0]) ||
	die ("Could not open the assignments file, $ARGV[0]");

while (<ASSIGFILE>) {

#skip comments
	next if /^#/;

	chomp;
	@inline = split;

#print to see if the script is reading the proper atom name information
#print "$inline[1]\n";

#FIX RESIDUE NAMES (section added by PFJ)
	$resname = $inline[1];
#print to see if $resname is being defined correctly
#print "$resname\n";
	if ($resname eq "ASPN") { $resname = "ASP" };
	if ($resname eq "GLUN") { $resname = "GLU" };
        if ($resname eq "METN") { $resname = "MET" };
#print to see if $resname is being redefined correctly
#print "$resname\n";

#FIX ATOM NAMES (section added by PFJ)
   $atmname = $inline[2];
#print to see if $atmname is being defined correctly
#print "$atmname\n";
   if($resname eq "ALA")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "MB" };
      if($atmname eq "HB2") { $atmname = "MB" };
      if($atmname eq "HB3") { $atmname = "MB" };
      if($atmname eq "HB*") { $atmname = "MB" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "ARG")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HG1") { $atmname = "HG1" };
      if($atmname eq "HG2") { $atmname = "HG2" };
      if($atmname eq "HG*") { $atmname = "HG" };
      if($atmname eq "HD1") { $atmname = "HD1" };
      if($atmname eq "HD2") { $atmname = "HD2" };
      if($atmname eq "HD*") { $atmname = "HD" };
      if($atmname eq "HE") { $atmname = "HE" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "ASP")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "CYS")
   {
   }
   if($resname eq "GLN")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HG1") { $atmname = "HG1" };
      if($atmname eq "HG2") { $atmname = "HG2" };
      if($atmname eq "HG*") { $atmname = "HG" };
      if($atmname eq "HE21") { $atmname = "HE21" };
      if($atmname eq "HE22") { $atmname = "HE22" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "GLU")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HG1") { $atmname = "HG1" };
      if($atmname eq "HG2") { $atmname = "HG2" };
      if($atmname eq "HG*") { $atmname = "HG" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "GLY")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA1") { $atmname = "HA1" };
      if($atmname eq "HA2") { $atmname = "HA2" };
      if($atmname eq "HA*") { $atmname = "QA" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "ILE")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB") { $atmname = "HB" };
      if($atmname eq "HG11") { $atmname = "HG11" };
      if($atmname eq "HG12") { $atmname = "HG12" };
      if($atmname eq "HG1*") { $atmname = "HG1" };
      if($atmname eq "HG21") { $atmname = "MG2" };
      if($atmname eq "HG22") { $atmname = "MG2" };
      if($atmname eq "HG23") { $atmname = "MG2" };
      if($atmname eq "HD1") { $atmname = "MD1" };
      if($atmname eq "HD2") { $atmname = "MD1" };
      if($atmname eq "HD3") { $atmname = "MD1" };
      if($atmname eq "HD*") { $atmname = "MD1" };   
      if($atmname eq "HG2*") { $atmname = "MG2" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "LEU")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HG") { $atmname = "HG" };
      if($atmname eq "HD11") { $atmname = "MD1" };
      if($atmname eq "HD12") { $atmname = "MD1" };
      if($atmname eq "HD13") { $atmname = "MD1" };
      if($atmname eq "HD21") { $atmname = "MD2" };
      if($atmname eq "HD22") { $atmname = "MD2" };
      if($atmname eq "HD23") { $atmname = "MD2" };
      if($atmname eq "HD2*") { $atmname = "MD2" };
      if($atmname eq "HD1*") { $atmname = "MD1" };
      if($atmname eq "HD*") { $atmname = "QD" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "LYS")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HG1") { $atmname = "HG1" };
      if($atmname eq "HG2") { $atmname = "HG2" };
      if($atmname eq "HG*") { $atmname = "HG" };
      if($atmname eq "HD1") { $atmname = "HD1" };
      if($atmname eq "HD2") { $atmname = "HD2" };
      if($atmname eq "HD*") { $atmname = "HD" };
      if($atmname eq "HE1") { $atmname = "HE1" };
      if($atmname eq "HE2") { $atmname = "HE2" };
      if($atmname eq "HE*") { $atmname = "HE" };
      if($atmname eq "C") { $atmname = "CO" };
# Missing NH3
   }
   if($resname eq "MET")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HG1") { $atmname = "HG1" };
      if($atmname eq "HG2") { $atmname = "HG2" };
      if($atmname eq "HG*") { $atmname = "HG" };
      if($atmname eq "HE1") { $atmname = "ME" };
      if($atmname eq "HE2") { $atmname = "ME" };
      if($atmname eq "HE3") { $atmname = "ME" };
      if($atmname eq "HE*") { $atmname = "ME" }; 
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "PHE")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HD1") { $atmname = "HD" };
      if($atmname eq "HD2") { $atmname = "HD" };
      if($atmname eq "HE1") { $atmname = "HE" };
      if($atmname eq "HE2") { $atmname = "HE" };
      if($atmname eq "HZ") { $atmname = "HZ" };
      if($atmname eq "HD*") { $atmname = "HD" };
      if($atmname eq "HE*") { $atmname = "HE" }; 
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "PRO")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HG1") { $atmname = "HG1" };
      if($atmname eq "HG2") { $atmname = "HG2" };
      if($atmname eq "HG*") { $atmname = "HG" };
      if($atmname eq "HD1") { $atmname = "HD1" };
      if($atmname eq "HD2") { $atmname = "HD2" };
      if($atmname eq "HD*") { $atmname = "HD" };
      if($atmname eq "C") { $atmname = "CO" };
   }
   if($resname eq "SER")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "C") { $atmname = "CO" };
# Missing HO
   }
   if($resname eq "THR")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB") { $atmname = "HB" };
      if($atmname eq "HG1") { $atmname = "HG1" };
      if($atmname eq "HG21") { $atmname = "MG2" };
      if($atmname eq "HG22") { $atmname = "MG2" };
      if($atmname eq "HG23") { $atmname = "MG2" };
      if($atmname eq "HG2*") { $atmname = "MG2" };
      if($atmname eq "C") { $atmname = "CO" };
# Missing HO
   }
   if($resname eq "TRP")
   {
   }
   if($resname eq "TYR")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB1") { $atmname = "HB1" };
      if($atmname eq "HB2") { $atmname = "HB2" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HD1") { $atmname = "HD1" };
      if($atmname eq "HD2") { $atmname = "HD2" };
      if($atmname eq "HE1") { $atmname = "HE1" };
      if($atmname eq "HE2") { $atmname = "HE2" };
      if($atmname eq "HD*") { $atmname = "HD" };
      if($atmname eq "HE*") { $atmname = "HE" };
      if($atmname eq "HH") { $atmname = "HH" };
      if($atmname eq "C") { $atmname = "CO" };
# Missing HO
   }
   if($resname eq "VAL")
   {
      if($atmname eq "HN") { $atmname = "HN" };
      if($atmname eq "HA") { $atmname = "HA" };
      if($atmname eq "HB") { $atmname = "HB" };
      if($atmname eq "HB*") { $atmname = "HB" };
      if($atmname eq "HG11") { $atmname = "MG1" };
      if($atmname eq "HG12") { $atmname = "MG1" };
      if($atmname eq "HG13") { $atmname = "MG1" };
      if($atmname eq "HG21") { $atmname = "MG2" };
      if($atmname eq "HG22") { $atmname = "MG2" };
      if($atmname eq "HG23") { $atmname = "MG2" };
      if($atmname eq "HG1*") { $atmname = "MG1" };
      if($atmname eq "HG2*") { $atmname = "MG2" };
      if($atmname eq "HG*") { $atmname = "QG" };
      if($atmname eq "C") { $atmname = "CO" };
   }

	printf "%4d %3s %4s        %7.3f\n", $inline[0], $resname, $atmname, $inline[3];
}
close (ASSIGFILE);