From f37976ca0f6ce86187322accb93c7da6ed59782e Mon Sep 17 00:00:00 2001
From: Adam David Scott <adam@adamscottphd.com>
Date: Mon, 16 Oct 2017 19:04:34 -0500
Subject: [PATCH] calpro calculates distances for drugs, small molecules, and
 amino acids but skips water.

---
 README.md                           |  6 +++---
 bin/hotspot3d                       |  4 ++--
 dist.ini                            |  2 +-
 lib/TGI/Mutpro/Preprocess/Calpro.pm | 12 ++++++++++--
 4 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 95d877b..87da186 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@ Usage
 
          Stable:     v0.6.0 
 
-           Beta:     up to v1.8.1
+           Beta:     up to v1.8.2
         
          Author:     Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta, & Amila Weerasinghe
 
@@ -86,9 +86,9 @@ For the latest stable version:
 
 For the latest beta version:
 
-	git pull origin v1.8.1
+	git pull origin v1.8.2
     
-	cpanm HotSpot3D-1.8.1.tar.gz
+	cpanm HotSpot3D-1.8.2.tar.gz
 
 Final note: Installations under some organizations may use an internal perl version. 
 To make use of the /usr/ perl, edit the first line of ~/perl5/bin/hotspot3d.
diff --git a/bin/hotspot3d b/bin/hotspot3d
index 5d4f83d..c4a3166 100755
--- 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: 1.8.1 $
+# $Revision: 1.8.2 $
 # $URL: $
 #----------------------------------
 use strict;
 use warnings;
 
-our $VERSION = 'V1.8.1';
+our $VERSION = 'V1.8.2';
 
 use Carp;
 use FileHandle;
diff --git a/dist.ini b/dist.ini
index 701b973..4660a87 100644
--- 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 = 1.8.1
+version = 1.8.2
 license = Perl_5
 copyright_holder = McDonnell Genome Institute at Washington University
 copyright_year   = 2017
diff --git a/lib/TGI/Mutpro/Preprocess/Calpro.pm b/lib/TGI/Mutpro/Preprocess/Calpro.pm
index c5e3cfc..bc93076 100644
--- a/lib/TGI/Mutpro/Preprocess/Calpro.pm
+++ b/lib/TGI/Mutpro/Preprocess/Calpro.pm
@@ -300,7 +300,11 @@ sub writeProximityFile {
 			# Get AminoAcid object for residue in chain '$uniprotChain', 
 			# at position $position
 			$uniprotAminoAcidRef = $$peptideRef{$uniprotChain}->getAminoAcidObject( $residuePosition );
-			next if ( $$uniprotAminoAcidRef->isAA() == 0 );
+			next if ( $$uniprotAminoAcidRef->isHOH() == 0 ); #skip water, but not other compounds
+			#my $thisIsProtein1 = 1;
+			#if ( not $$uniprotAminoAcidRef->isAA() ) {
+			#	$thisIsProtein1 = 0;
+			#}
 			$uniprotAaName = $$uniprotAminoAcidRef->name();
 			# 	Updated	170510 : use a hash with chain and regions for retrieving the offset
 			$uniprotChainOffset = getOffset( $allOffsets, $uniprotChain, $residuePosition );
@@ -339,7 +343,11 @@ sub writeProximityFile {
 				foreach $position ( sort {$a<=>$b} @tmp_array_positions ) {
 					$otherChainOffset = getOffset( $allOffsets, $chain, $position );
 					$aaObjRef = $$peptideRef{$chain}->getAminoAcidObject($position);
-					next if ( $$aaObjRef->isAA() == 0 );
+					next if ( $$aaObjRef->isHOH() == 0 ); #skip water, but not other compounds
+					#my $thisIsProtein2 = 1;
+					#if ( not $$uniprotAminoAcidRef->isAA() ) {
+					#	$thisIsProtein2 = 0;
+					#}
 					if ( (defined $otherChainOffset) and ($otherChainOffset eq "N/A") ) { 
 						$correctedPosition = $position;
 					} else {