contacts_analysis.pl

### Subroutines and Modules ###
use Cwd;
use File::Copy;
sub uniq {
    my %seen;
    grep !$seen{$_}++, @_;
}

########## global variables ####################
$usage="\nUsage: \.\/kmeans_structural_analysis\.pl \[Project\#\] \[Inhibitor 3-Letter Code\] \n\nKey_file.txt and final_trial.txt should be in current directory \n";
$proj     = $ARGV[0] || die "$usage\n";
$code     = $ARGV[1] || die "$usage\n";
chomp $proj;
chomp $code;
$dir = getcwd;


#### Read in Inhibitor Key File ####
$keyfile = "noncholine_key_file.txt";
#chomp $keyfile;
open(KI,"<$keyfile")|| die "\n\tError reading from $keyfile\n\n";
while (<KI>){
    if (/Proj $proj/i) {
        $spool = 1;
        next;
    }
    elsif ($_ =~ /Proj\s\d/ && $_ !~ /Proj $proj/) {
        $spool = 0;
    }
    elsif ($spool) {
                undef @singroup;
                $groupline = $_;
                for($groupline) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
                @logline = split(/ /,$groupline);
                $group = "@logline[0]";
                chomp $group;
                $atoms = "@logline[1..$#logline]";
                @singroup = split(/ /,$atoms);
                if ($group eq "PheCOP"){
                        push (@PheCOP,@singroup);
                        undef @singroup;
                }
                elsif ($group eq "OCH1"){
                        push (@OCH1, @singroup);
                        undef @singroup;
                }
                elsif ($group eq "OCH2"){
                        push (@OCH2, @singroup);
                        undef @singroup;
                }
                elsif ($group eq "Phos"){
                        push (@Phos, @singroup);
                        undef @singroup;
                }
    }
}

### Find Cluster Size and Number ###
$log = "proj$proj"."/$proj"."_trial.txt";
chomp $log;
open(LOG,"<$log")|| die "\n\tError reading from $log\n\n";
while (<LOG>) {
    if (/#  group  pop	Centers/i) {
        $spool = 1;
        next;
    }
    elsif (/Clusters \/ Data points \/ P\/R\/C\/T/i) {
        $spool = 0;
	}
    elsif ($spool) {
		$var = $_;
		for($var) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
		@logline = split(/ /,$var);
		$energy{$logline[0]} = $logline[1];
    }
}


### Rename/Organize by Cluster Size ###
$k=0;
foreach my $clusternum (sort { $energy{$b} <=> $energy{$a} or $a cmp $b } keys %energy){
	$clusternew{$clusternum} = $k;
	printf"%-8s %s%s\n", $clusternew{$clusternum};
	$k++;
}


### Make cluster directories ###
mkdir "$dir"."/proj$proj"."/proj$proj"."_vectors"."/clusters";
#mkdir clusters;
$clusterfolder = "$dir"."/proj$proj"."/proj$proj"."_vectors"."/clusters";

for($j=0; $j<$k; $j++){
	mkdir "$clusterfolder"."/$j";
}


### Look for a pdb's associated cluster number and move ###
seek (LOG, 0, 0);
while (<LOG>) {
    if (/Clusters \/ Data points \/ P\/R\/C\/T/i) {
		$spool = 1;
		next;
	}
    elsif ($spool) {
		$var2 = $_;
		for($var2) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
		@logline2 = split(/ /,$var2);
		$frame = @logline2[21]/100;
		$clone = @logline2[20];
		$oldclusternum = @logline2[0];
		$curlocation = "$dir"."/proj$proj"."/00$clone"."/$clone"."frame$frame".".pdb";
		$newlocation = "$clusterfolder"."/$clusternew{$oldclusternum}";
		move($curlocation, $newlocation) or die "Error when moving clone:$clone frame$frame.pdb: $!";
    }
}
close(LOG);


### Move into cluster folders and find distances ###
for($m=0; $m<$k; $m++){
	chdir "$clusterfolder"."/$m";
	$cluster = $m;
	my @pdbfiles = `ls *pdb`;
	$count = scalar(@pdbfiles);
	$clustertotal = $count;
	
	### Find distances for each pdb ###
	foreach $pdb(@pdbfiles){
		chomp $pdb;
		$temp = `head -2 $pdb | tail -1`;
		chomp $temp;
		for($temp) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
		@templine = split(/ /,$temp);
		$currenttime = $templine[11];


		### Open/Read pdb line and save protein coordinates ###
		open(PDB,"<$pdb") || die "\n\tError reading from $pdb\n\n";
		$i = 0;
		while(defined($origline=<PDB>)) {
			$line = $origline;
			chomp $line;
			for($line) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
			@input = split(/ /,$line);

			###Save protein coordinates###
			if(@input[0] eq 'ATOM'){
				$atomnum    = @input[1];
				$atomname   = @input[2];
				$resname[$atomnum] = @input[3];
				$resnum[$atomnum]  = @input[5];
				$x[$atomnum]= @input[6];
				$y[$atomnum]= @input[7];
				$z[$atomnum]= @input[8];
				if((@input[0] eq 'ATOM')&&(@input[3] ne 'SOL')&&(@input[3] ne '$code')&&(@input[3] ne 'UNK')&&(@input[3] ne 'CL')&&(@input[2] ne 'NA')){ 
					$protx[$atomnum] = $x[$atomnum];
					$proty[$atomnum] = $y[$atomnum];
					$protz[$atomnum] = $z[$atomnum];
					$i++;
				}
			}
		}
		close(PDB);

		### Find the inhibitor group's atom distance from protein ###

		foreach $num (@PheCOP){
			for ( $i=1; $i<8310; $i++){
				$X = $protx[$i]-$x[$num];
				$Y = $proty[$i]-$y[$num];
				$Z = $protz[$i]-$z[$num];
				$D2 = $X**2 + $Y**2 + $Z**2;
				$D = sqrt($D2);
				if ($D < 5){
					$phe = "$resname[$i]$resnum[$i]";
					for($phe) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
					push @pheline, $phe;
					@pheorg = uniq(@pheline);
				}
			}
		}
		foreach $num (@Phos){
			#print $num;
			for ( $i=1; $i<8310; $i++){
				$X = $protx[$i]-$x[$num];
				$Y = $proty[$i]-$y[$num];
				$Z = $protz[$i]-$z[$num];
				$D2 = $X**2 + $Y**2 + $Z**2;
				$D = sqrt($D2);
				if ($D < 5){
					@phoorg=();
					$jj = $j - 1;
					$pho = "$resname[$i]$resnum[$i]";
					for($pho) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
					push @pholine, $pho;
					@phoorg = uniq(@pholine);
				}
			}
		}
	
		foreach $num (@OCH1){
			for ( $i=1; $i<8310; $i++){
				$X = $protx[$i]-$x[$num];
				$Y = $proty[$i]-$y[$num];
				$Z = $protz[$i]-$z[$num];
				$D2 = $X**2 + $Y**2 + $Z**2;
				$D = sqrt($D2);
				if ($D < 5){
					@oc1org=();
					$jj = $j - 1;
					$oc1 = "$resname[$i]$resnum[$i]";
					for($oc1) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
					push @oc1line, $oc1;
					@oc1org = uniq(@oc1line);
				}
			}
		}

		foreach $num (@OCH2){
			for ( $i=1; $i<8310; $i++){
				$X = $protx[$i]-$x[$num];
				$Y = $proty[$i]-$y[$num];
				$Z = $protz[$i]-$z[$num];
				$D2 = $X**2 + $Y**2 + $Z**2;
				$D = sqrt($D2);
				if ($D < 5){
					@oc2org=();
					$jj = $j - 1;
					$oc2 = "$resname[$i]$resnum[$i]";
					for($oc2) {  s/^\s+//; s/\s+$//; s/\s+/ /g; }
					push @oc2line, $oc2;
					@oc2org = uniq(@oc2line);
				}
			}
		}


		push(@phecluster,@pheorg);
		@pheorg=();

		push(@phocluster,@phoorg);
		@phoorg=();

		push(@oc1cluster,@oc1org);
		@oc1org=();

		push(@oc2cluster,@oc2org);
		@oc2org=();
	}

	####Finding total interaction time###
	print"CLUSTER GROUP: $cluster\n";
	print "----------------------------------\n";
	print "----------------------------------\n";
	print "Interactions with Phenyl Group:\n";

	$phecount{$_}++ foreach @phecluster;

	foreach my $name (sort { $phecount{$b} <=> $phecount{$a} or $a cmp $b } keys %phecount){
		printf"%-8s%d%s\n", $name, $phecount{$name}*100/$clustertotal,"%";
	}
	
	@phecluster = ();

	print "----------------------------------\n";

	print "Interactions with Phosphate Group:\n";
	my %phocount;
	$phocount{$_}++ foreach @phocluster;

	foreach my $name (sort { $phocount{$b} <=> $phocount{$a} or $a cmp $b } keys %phocount){
		printf"%-8s%d%s\n", $name, $phocount{$name}*100/$clustertotal,"%";
	}

	@phocluster =();

	print "----------------------------------\n";

	print "Interactions with Alkyl (Left) Group:\n";
	my %oc1count;
	$oc1count{$_}++ foreach @oc1cluster;

	foreach my $name (sort { $oc1count{$b} <=> $oc1count{$a} or $a cmp $b } keys %oc1count){
		printf"%-8s%d%s\n", $name, $oc1count{$name}*100/$clustertotal,"%";
	}

	@oc1cluster = ();

	print "----------------------------------\n";

	print "Interactions with Alkyl (Right) Group:\n";
	my %oc2count;
	$oc2count{$_}++ foreach @oc2cluster;

	foreach my $name (sort { $oc2count{$b} <=> $oc2count{$a} or $a cmp $b } keys %oc2count){
		printf"%-8s%d%s\n", $name, $oc2count{$name}*100/$clustertotal,"%";
	}

	@oc2cluster=();

	print "----------------------------------\n";
	print"\n";

	undef %phecount;
	undef @phecount;
	undef @pheline;
	undef %seen;
	undef @pheorg;
	#this is where you left off #
	undef @phecluster;
	#undef &uniq;
	undef *phecount;
}