fixing drug related bugs

ding-lab · Dec 5, 2017 · cf2dcd1 · cf2dcd1
2 parents 4532d89 + 8de6b5b
commit cf2dcd1
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Showing 4 changed files with 17 additions and 23 deletions.
diff --git a/HotSpot3D-1.8.2.tar.gz b/HotSpot3D-1.8.2.tar.gz
diff --git a/lib/TGI/Mutpro/Preprocess/Calpro.pm b/lib/TGI/Mutpro/Preprocess/Calpro.pm
@@ -300,11 +300,7 @@ sub writeProximityFile {
 			# Get AminoAcid object for residue in chain '$uniprotChain', 
 			# at position $position
 			$uniprotAminoAcidRef = $$peptideRef{$uniprotChain}->getAminoAcidObject( $residuePosition );
-			next if ( $$uniprotAminoAcidRef->isHOH() == 0 ); #skip water, but not other compounds
-			#my $thisIsProtein1 = 1;
-			#if ( not $$uniprotAminoAcidRef->isAA() ) {
-			#	$thisIsProtein1 = 0;
-			#}
+			next if ( $$uniprotAminoAcidRef->isHOH() == 1 );
 			$uniprotAaName = $$uniprotAminoAcidRef->name();
 			# 	Updated	170510 : use a hash with chain and regions for retrieving the offset
 			$uniprotChainOffset = getOffset( $allOffsets, $uniprotChain, $residuePosition );
@@ -343,11 +339,7 @@ sub writeProximityFile {
 				foreach $position ( sort {$a<=>$b} @tmp_array_positions ) {
 					$otherChainOffset = getOffset( $allOffsets, $chain, $position );
 					$aaObjRef = $$peptideRef{$chain}->getAminoAcidObject($position);
-					next if ( $$aaObjRef->isHOH() == 0 ); #skip water, but not other compounds
-					#my $thisIsProtein2 = 1;
-					#if ( not $$uniprotAminoAcidRef->isAA() ) {
-					#	$thisIsProtein2 = 0;
-					#}
+					next if ( $$aaObjRef->isHOH() == 1 );
 					if ( (defined $otherChainOffset) and ($otherChainOffset eq "N/A") ) { 
 						$correctedPosition = $position;
 					} else { 
@@ -535,8 +527,8 @@ sub checkOffsets {
 		#if not an AA, convertAA returns original value if length aminoAcid <= 3, 'Z' if length == 1, undef otherwise
 		$aminoAcidA = TGI::Mutpro::Preprocess::PdbStructure::convertAA( $aminoAcidA );
 		$aminoAcidB = TGI::Mutpro::Preprocess::PdbStructure::convertAA( $aminoAcidB );
-		next if ( !defined $aminoAcidA || !defined $aminoAcidB );
-		#check if position has an amino acid & whether its name is same as converted aminoAcid
+		next if ( !defined $aminoAcidA & !defined $aminoAcidB );
+		#next unless ( TGI::Mutpro::Preprocess::AminoAcid::checkAA( $aminoAcidA ) and TGI::Mutpro::Preprocess::AminoAcid::checkAA( $aminoAcidB )
 		if ( defined $pdbUniprotPosition{$pdbId}{$uniprotA}{$positionA+$offsetA} && $pdbUniprotPosition{$pdbId}{$uniprotA}{$positionA+$offsetA} ne $aminoAcidA ) {
 			print $coorfh "Inconsistent amino acids for $uniprotA position $positionA+$offsetA in $pdbId: '$pdbUniprotPosition{$pdbId}{$uniprotA}{$positionA+$offsetA}' and $aminoAcidA \n";
 		}

diff --git a/lib/TGI/Mutpro/Preprocess/PdbStructure.pm b/lib/TGI/Mutpro/Preprocess/PdbStructure.pm
@@ -533,6 +533,7 @@ sub convertAA {
     # Convert single amino acid code to triplet
     # or triplet to single amino acid code
     my $residue = $_[0];
+    my $convertedAA = undef;
     $residue = uc $residue;
     my %oneToThree =  (
 		       A => 'ALA',
@@ -559,15 +560,12 @@ sub convertAA {
     my %threeToOne;
     foreach (keys %oneToThree) { $threeToOne{$oneToThree{$_}} = $_; }
     if ( defined $oneToThree{$residue} ) {
-		return $oneToThree{$residue};
-    } elsif ( defined $threeToOne{$residue} ) {
-		return $threeToOne{$residue};
-    } elsif ( length( $residue ) <= 3 ) {
-        length( $residue ) == 1 ? return "Z" : return $residue;
-    } else {
-		carp "Unrecognized format for amino acid '$residue'";
-	}
-	return undef;
+	return $oneToThree{$residue};
+    }elsif ( defined $threeToOne{$residue} ) {
+	return $threeToOne{$residue};
+    }elsif ( length( $residue ) <= 3 ) {
+        length( $residue ) == 1 ? return "Z" : return $convertedAA;
+    } else { return $convertedAA; carp "Unrecognized format for amino acid '$residue'"; }
 }
 
 sub printStructure {

diff --git a/lib/TGI/Mutpro/Preprocess/Uppro.pm b/lib/TGI/Mutpro/Preprocess/Uppro.pm
@@ -22,6 +22,7 @@ use List::MoreUtils qw( uniq );
 
 use TGI::Mutpro::Preprocess::Uniprot;
 use TGI::Mutpro::Preprocess::HugoGeneMethods;
+use TGI::Files::File;
 use TGI::Files::MAF;
 use TGI::Files::List;
 
@@ -168,8 +169,8 @@ sub process {
         $fh->print( "\t$alias_list\n" );
     }
     $fh->close();
-	my $cmd_list_submit_file_fh;
-    unless( open ( $cmd_list_submit_file_fh, ">", $this->{'cmd_list_submit_file'} ) ) { die "HotSpot3D Uppro Error: Could not open cmd file (".$this->{'cmd_list_submit_file'}.")"; }
+	my $cmd_list_submit_file_fh = new FileHandle; #TGI::Files::File->new( $this->{'cmd_list_submit_file'} ) ;
+        unless( $cmd_list_submit_file_fh -> open ( $this->{'cmd_list_submit_file'}, "w" ) )  { die "HotSpot3D Uppro Error: Could not open cmd file (".$this->{'cmd_list_submit_file'}.")"; }
 	print STDOUT "Creating ".$this->{'cmd_list_submit_file'}."\n";
 	my $command = "";
 	if ( $this->{'parallel'} eq $BSUB ) {
@@ -215,12 +216,15 @@ sub makeBSUBCalproCommand {
 sub makeSerialCalproCommand {
 	my ( $this , $inpro_dir , $cmd_list_submit_file_fh , $uniprotid_toupdate ) = @_;
     my $log_dir = "$this->{'output_dir'}\/Logs\/";
+	my $serialCommand = "echo Serially Running Calpro Commands";
 	map {
 		system("touch $inpro_dir/$_.ProximityFile.csv");
 		my $command = $this->makeCalproCommand( $_ );
 		print STDOUT $command."\n"; 
 		$cmd_list_submit_file_fh->print( $command."\n" );
+		$serialCommand .= ";".$command;
 	} keys %{$uniprotid_toupdate};
+	return $serialCommand;
 }
 
 sub makeLocalCalproCommand {