#!/usr/bin/perl

$pdbprep = "/home/users/alison/pdb_folder/pdb";
$pdbext = ".ent";
$dssp = ".dssp";
$pdblist = $ARGV[0];
$combodir = $ARGV[1];
$out = ".out";

open(PDBLIST, "$pdblist") || die "ERROR: Unable to open $pdblist for reading: $!\n";

while(<PDBLIST>)
{
    
    my @fields = split;
    
    my $pdbcode = $fields[0];

    $pdbcode =~ tr/[A-Z]/[a-z]/;
    
    my $dsspfile = "$pdbcode$dssp";
    
    my $pdbstructure = "$pdbprep$pdbcode$pdbext";

    
    $residuecombofile = "$combodir$residue1$residue2$residue3$out";

    $outfile = "$pdbcode$out";

    if(open(PDB,"$pdbstructure"))
    {
	system("dsspcmbi $pdbstructure $dsspfile"); 
	CreateUniqueResidueFile($pdbstructure, $outfile);
	
    }
    else
    {
	$flag = 1;

    }

    if($flag == 0)
    {
	open(UNIQUE,"$outfile") || die "ERROR: Unable to open $outfile for reading: $!\n";

	@file = <UNIQUE>;

	$items = @file;
	    
	for($j = 0; $j <$items-2; $j++)
	{
	    $residuenumber1 = substr($file[$j], 1, 4);
	    
	    $residuename1 = substr($file[$j], 7, 3);
	    
	    $residuenumber2 = substr($file[$j+1], 1, 4);
	    
	    $residuename2 = substr($file[$j+1], 7, 3);
	    
	    $residuenumber3 = substr($file[$j+2], 1, 4);
	    
	    $residuename3 = substr($file[$j+2], 7, 3); 
	    
	    $residuecombofile = "$combodir$residuename1$residuename2$residuename3$out";
	    
	    ($phiangle, $psiangle) =  ExtractFromDssp($residuenumber1, $residuenumber2, $residuenumber3, $dsspfile);

	   	 
	    if($phiangle != 0)
	    {
		if($phiangle != 360)
		{
		    if($psiangle !=360)
		    {
				
			open(OUTFILE, ">>$residuecombofile") || die "ERROR: Unable to open $residuecomdofile for writing: $!\n";
			
			print OUTFILE "$phiangle\t$psiangle $pdbcode\n";
		    }
		}
	    }
	}
	
    
    system("rm $dsspfile");
    system("rm $outfile");		
	    	
    }
    else
    {
	print "No structure file. Moving to next structure in list\n";
    }  		   
	
    
}