#!/usr/bin/perl

#perl script to convert assignments from a four column (genxpk) format
#to the format for importing spin systems into Felix97

#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 atomnames, "+" is substituted for "1" and "-" is substituted for 2

#command line: make_pat .assignments [>output]

#Melanie Nelson
#2/23/99

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]");

#initialize residue number
$resnum = -99;

while (<ASSIGFILE>) {

#skip comments
	next if /^#/;

	chomp;
	@inline = split;

	if ($inline[0] != $resnum){
		$resnum = $inline[0];
		if ($inline[0] == 0){ $patnum = 999 }
		else { $patnum = $inline[0] }
		print "PATTERN pa$patnum\n";
	}

#fix atom names
	$atmname = $inline[2];
	if ($inline[1] eq "THR" || $inline[1] eq "CYS" || $inline[1] eq "SER"){
		if ($inline[2] =~ /HG/){
			$atmname = "HG1";
		}
	} elsif ($inline[1] eq "ILE"){
		if ( $inline[2] eq "MD1" ){
			$atmname = "HD11";
		}
		if ( $inline[2] eq "MG2" ){
			$atmname = "HG21";
		}
	} elsif ($inline[1] eq "LEU"){
		if ($inline[2] eq "MD+" || $inline[2] eq "MD1"){
			$atmname = "HD11";
		} elsif ($inline[2] eq "MD-" || $inline[2] eq "MD2"){
			$atmname = "HD21";
		}
	} elsif ($inline[1] eq "ALA"){
		if ($inline[2] eq "MB"){
			$atmname = "HB1";
		}
	} elsif ($inline[1] eq "VAL"){
		if ($inline[2] eq "MG+" || $inline[2] eq "MG1"){
			$atmname = "HG11";
		} elsif ($inline[2] eq "MG-" || $inline[2] eq "MG2"){
			$atmname = "HG21";
		}
	} 

	$atmname =~ s/\+/1/;
	$atmname =~ s/\-/2/;

	$atmtype = substr($inline[2],0,1);

	print "1:$inline[1]_$inline[0]:$atmname   $inline[3] $atmtype\n";

}

close (ASSIGFILE);