exponentials weight coefficient to wi. exponentials centroids chosen …

…by score magnitude.
ding-lab · Sep 27, 2017 · e3ee4f7 · e3ee4f7
1 parent f4e4dfb
commit e3ee4f7
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Showing 4 changed files with 13 additions and 8 deletions.
diff --git a/HotSpot3D-1.8.0.tar.gz → HotSpot3D-1.8.0.0.tar.gz b/HotSpot3D-1.8.0.tar.gz → HotSpot3D-1.8.0.0.tar.gz
diff --git a/bin/hotspot3d b/bin/hotspot3d
@@ -2,13 +2,13 @@
 #----------------------------------
 # $Authors: Beifang Niu & Adam D Scott
 # $Date: 2013-08-08 13:22:08 -0500 (Thu Aug  8 13:22:08 CDT 2013) $
-# $Revision: 1.8.0 $
+# $Revision: 1.8.0.0 $
 # $URL: $
 #----------------------------------
 use strict;
 use warnings;
 
-our $VERSION = 'V1.8.0';
+our $VERSION = 'V1.8.0.0';
 
 use Carp;
 use FileHandle;

diff --git a/dist.ini b/dist.ini
@@ -1,6 +1,6 @@
 name    = HotSpot3D
 author  = Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta, Amila Weerasinghe, & Matthew H Bailey from McDonnell Genome Institute of Washington University at St. Louis
-version = 1.8.0
+version = 1.8.0.0
 license = Perl_5
 copyright_holder = McDonnell Genome Institute at Washington University
 copyright_year   = 2017

diff --git a/lib/TGI/Mutpro/Main/Network.pm b/lib/TGI/Mutpro/Main/Network.pm
@@ -346,8 +346,14 @@ sub isRadiusOkay {
 sub determineCentroid {
 	my ( $this , $mutationKey , $newScore , 
 		 $currentCentroid , $currentScore ) = @_;
-	if ( $newScore > $currentScore ) {
-		return ( $mutationKey , $newScore );
+	if ( $this->{'vertex_score'} eq $EXPONENTIALS ) {
+		if ( abs( $newScore ) > abs( $currentScore ) ) {
+			return ( $mutationKey , $newScore );
+		}
+	} else {
+		if ( $newScore > $currentScore ) {
+			return ( $mutationKey , $newScore );
+		}
 	}
 	return ( $currentCentroid , $currentScore );
 }
@@ -359,7 +365,7 @@ sub determineSubClusters {
 	my $subClusterID = -1;
 	while ( $moreToFind == 1 ) {
 		my $score = 0;
-		my $centroidScore = $MAXWEIGHT - 2*$MAXWEIGHT;
+		my $centroidScore = 0;
 		my $centroid;
 		$subClusterID++;
 		print "Finding subcluster: ".$subClusterID."\n";
@@ -496,8 +502,7 @@ sub exponential {
 	my ( $this , $weight , $geodesic ) = @_;
 	my $weightExp = abs( $weight / $this->{'weight_scale'} );
 	my $geodesicExp = $geodesic / $this->{'length_scale'};
-	my $weightShifted = $weight + $MAXWEIGHT + 1;
-	my $score = $weightShifted * exp( $weightExp - $geodesicExp );
+	my $score = $weight * exp( $weightExp - $geodesicExp );
 	return $score;
 }