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Scripts/DoDC.pl

@@ -0,0 +1,60 @@
+#!/usr/bin/perl
+
+use FindBin;
+use lib $FindBin::Bin;
+use strict ; 
+
+#print @ARGV ;
+
+my $rdc="nhn.tab"; 
+
+my $total ;
+my $i ;
+my $outD ; 
+my $pdbf ; 
+
+my $pdb = $ARGV[0] ; 
+my $total = $ARGV[1] ; 
+$pdb =~ s/\.pdb// ; 
+
+open(S,">$pdb.script") ; 
+print(S "load pdb $pdb.pdb\n"); 
+print(S "to xplor\n");
+print(S "split $pdb\n");
+print(S "quit\n");
+close(S);
+system("/opt/software/bin/pdbstat -s < $pdb.script > $pdb.script.out"); 
+system("rm *Axis*");
+my $id ;
+
+my $Da_HN ; 
+my $Q ; 
+my $Rhomb ; 
+my $RMS ; 
+my $t1 ; 
+my $t2 ; 
+
+open(OU,">DC_Summary"); 
+print(OU "  Da_HN   Rhomb    Q     RMS  \n"); 
+print(OU " ======= ======  ====== ===== \n"); 
+for ($i = 1; $i <= $total; $i++ ) { 
+	if ( $i < 10 ) {
+        	$id = "0$i" ; 
+	} else {
+        	$id = "$i" ; 
+	}
+	$pdbf = $pdb . "_" . $i . ".pdb" ; 
+	$outD = $pdb . "_" . $id . "_" . $rdc . "_out" ; 
+	system("/Users/tejerr/bin/DC -pdb $pdbf -inD $rdc -outD $outD") ; 
+	open(F,"<$outD"); 
+	while ( <F> ) {
+		next if $_ !~ /DATA Q_FAC|DATA Da_HN|DATA Rhomb|DATA RMS/ ; 
+		($t1,$t2,$RMS)   = split(' ',$_)  if ( $_ =~ /RMS/ ); 
+		($t1,$t2,$Q)     = split(' ',$_)  if ( $_ =~ /Q_FACT/ ); 
+		($t1,$t2,$Da_HN) = split(' ',$_)  if ( $_ =~ /Da_HN/ ); 
+		($t1,$t2,$Rhomb) = split(' ',$_)  if ( $_ =~ /Rhomb/ ); 
+	}
+	print(OU " $Da_HN  $Rhomb  $Q  $RMS \n") ; 
+	close($outD); 
+}
+exit ; 

Scripts/Do_Avgs_DaR.pl

@@ -0,0 +1,29 @@
+#!/usr/bin/perl
+
+use FindBin;
+use lib $FindBin::Bin;
+use strict ; 
+
+my $inD = $ARGV[0] ; 
+my @family = (); 
+
+open(F,"<$inD") ;
+while ( <F> ) {
+	next if ($_ =~ /^\s*$/);
+	next if ($_ =~ /Media/) ; 
+	s/\[|\]//g ; 
+	my @spl = split(' ', $_);
+        push(@family, [$spl[12],$spl[6], $spl[7]]); 
+}
+close(F); 
+my $i = 0; 
+foreach my $l (@family) {
+	$i++ ; 
+	print(" @$l " );
+	#foreach (@$l) {
+	#	print(" $_") ;  
+	#}
+	print("\n"); 
+}
+
+exit ; 

Scripts/GetDaR_DC.pl

@@ -0,0 +1,29 @@
+#!/usr/bin/perl
+
+use FindBin;
+use lib $FindBin::Bin;
+use strict ; 
+
+my $outD = $ARGV[0] ; 
+
+my $Da_HN ; 
+my $Q ; 
+my $Rhomb ; 
+my $RMS ; 
+my $t1 ; 
+my $t2 ; 
+
+open(OU,">DC_Summary"); 
+print(OU "  Da_HN   Rhomb    Q     RMS  \n"); 
+print(OU " ======= ======  ====== ===== \n"); 
+open(F,"<$outD"); 
+while ( <F> ) {
+	next if $_ !~ /DATA Q_FAC|DATA Da_HN|DATA Rhomb|DATA RMS/ ; 
+	($t1,$t2,$RMS)   = split(' ',$_)  if ( $_ =~ /RMS/ ); 
+	($t1,$t2,$Q)     = split(' ',$_)  if ( $_ =~ /Q_FACT/ ); 
+	($t1,$t2,$Da_HN) = split(' ',$_)  if ( $_ =~ /Da_HN/ ); 
+	($t1,$t2,$Rhomb) = split(' ',$_)  if ( $_ =~ /Rhomb/ ); 
+}
+print(OU " $Da_HN  $Rhomb  $Q  $RMS \n") ; 
+close($outD); 
+exit ; 

Scripts/GetRPF_Scores.pl

@@ -0,0 +1,48 @@
+#!/usr/bin/perl
+
+use strict; 
+
+my $rpf = $ARGV[0] ;
+my @recall_s ; 
+my @precision_s ;
+my @fmeasure_s ; 
+my @dp_s ; 
+my $i = 0 ;
+
+my $recsum = 0 ; 
+my $precsum = 0 ;
+my $fmsum = 0 ; 
+my $dpsum = 0 ; 
+
+# extract and write out RPF scores
+if (open(SF, "<$rpf")) {
+	my ($recall_n, $precision_n, $f_measure_n, $dp_score_n) = (0, 0, 0, 0);
+	while (my $line_s = <SF>) {
+		next if $line_s !~ (/input query structures:/ || /DP-Score:/); 
+		if ($line_s =~ /Final Recall-score for input query structures:\s*(\S+)/) {
+			$recall_n = sprintf "%.3f", $1;
+			push(@recall_s, $recall_n); 
+		} elsif ($line_s =~ /Final Precision-score for input query structures:\s*(\S*)/) {
+			$precision_n = sprintf "%.3f", $1;
+			push(@precision_s, $precision_n); 
+		} elsif ($line_s =~ /F-score of input query structures:\s*(\S+)/) {
+			$f_measure_n = $1;
+			push(@fmeasure_s, $f_measure_n); 
+		} elsif ($line_s =~ /DP-Score:\s*(\S+)/) {
+			$dp_score_n = sprintf "%.3f", $1;
+			push(@dp_s, $dp_score_n); 
+		}
+	}
+	close(SF);
+	#	print "Recall: $recall_n, Precision: $precision_n, F-measure: $f_measure_n, DP-Score: $dp_score_n \n" ;  
+	#print "  Recall Precision F-measure  DP-Score \n" ;
+	print "     R       P        F       DP \n" ;
+	foreach (@dp_s) {
+		printf " %7.3f %7.3f  %7.3f %7.3f \n", $recall_s[$i], $precision_s[$i], $fmeasure_s[$i], $dp_s[$i]  ;
+		$i++ ; 
+	}
+
+}
+exit ; 
+
+

Scripts/GetRPF_Scores.pl.00

@@ -0,0 +1,47 @@
+#!/usr/bin/perl
+
+use strict; 
+
+my $rpf = $ARGV[0] ;
+my @recall_s ; 
+my @precision_s ;
+my @fmeasure_s ; 
+my @dp_s ; 
+my $i = 0 ;
+
+my $recsum = 0 ; 
+my $precsum = 0 ;
+my $fmsum = 0 ; 
+my $dpsum = 0 ; 
+
+# extract and write out RPF scores
+if (open(SF, "<$rpf")) {
+	my ($recall_n, $precision_n, $f_measure_n, $dp_score_n) = (0, 0, 0, 0);
+	while (my $line_s = <SF>) {
+		next if $line_s !~ (/input query structures:/ || /DP-Score:/); 
+		if ($line_s =~ /Final Recall-score for input query structures:\s*(\S+)/) {
+			$recall_n = sprintf "%.3f", $1;
+			push(@recall_s, $recall_n); 
+		} elsif ($line_s =~ /Final Precision-score for input query structures:\s*(\S*)/) {
+			$precision_n = sprintf "%.3f", $1;
+			push(@precision_s, $precision_n); 
+		} elsif ($line_s =~ /F-score of input query structures:\s*(\S+)/) {
+			$f_measure_n = $1;
+			push(@fmeasure_s, $f_measure_n); 
+		} elsif ($line_s =~ /DP-Score:\s*(\S+)/) {
+			$dp_score_n = sprintf "%.3f", $1;
+			push(@dp_s, $dp_score_n); 
+		}
+	}
+	close(SF);
+	#	print "Recall: $recall_n, Precision: $precision_n, F-measure: $f_measure_n, DP-Score: $dp_score_n \n" ;  
+	print " Recall Precision F-measure  DP-Score \n" ;
+	foreach (@dp_s) {
+		print " $recall_s[$i]     $precision_s[$i]    $fmeasure_s[$i]    $dp_s[$i] \n" ;
+		$i++ ; 
+	}
+
+}
+exit ; 
+
+