#!/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 r
+eading: $!\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$resid
+uename3$out";
        
        ($phiangle, $psiangle) =  ExtractFromDssp($residuenumber1, $re
+siduenumber2, $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";
    }             
    
    
}
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