# HG changeset patch
# User marcel
# Date 1310480613 14400
# Node ID b7a89b15646f0b3d874c8bd5c9862de0d43e566b
# Parent  02c8570cde57068d130bf8040fb863acf29905c5
Uploaded

diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/AntitargetRescorer
--- a/CADDSuite/AntitargetRescorer	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/AntitargetRescorer	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/AntitargetRescorer.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/AntitargetRescorer.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/AutoModel
--- a/CADDSuite/AutoModel	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/AutoModel	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/AutoModel.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/AutoModel.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/BindingDBCleaner
--- a/CADDSuite/BindingDBCleaner	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/BindingDBCleaner	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/BindingDBCleaner.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/BindingDBCleaner.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/CADDSuite-description.txt
--- a/CADDSuite/CADDSuite-description.txt	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/CADDSuite-description.txt	Tue Jul 12 10:23:33 2011 -0400
@@ -31,10 +31,11 @@
 Docking:
 	- WaterFinder: find strongly bound water molecules
 	- SpatialConstraintDefiner: define spatial constraint
+	- InteractionConstraintDefiner: define interaction constraint
 	- ConstraintsFinder: find strongly interacting residues
 	- PocketDetector: detect ligand binding pocket
 	- GridBuilder: precalculate grids for docking
-	- IMeedyDock: run Iterative Multi-Greedy Docking
+	- IMGDock: run Iterative Multi-Greedy Docking
 
 Rescoring:
 	- SimpleRescorer: rescore docking results 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/CombiLibGenerator
--- a/CADDSuite/CombiLibGenerator	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/CombiLibGenerator	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/CombiLibGenerator.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/CombiLibGenerator.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/ConstraintsFinder
--- a/CADDSuite/ConstraintsFinder	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/ConstraintsFinder	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/ConstraintsFinder.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ConstraintsFinder.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/Converter
--- a/CADDSuite/Converter	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/Converter	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/Converter.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/Converter.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/DBExporter
--- a/CADDSuite/DBExporter	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/DBExporter	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/DBExporter.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/DBExporter.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/DBImporter
--- a/CADDSuite/DBImporter	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/DBImporter	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/DBImporter.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/DBImporter.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/DockResultMerger
--- a/CADDSuite/DockResultMerger	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/DockResultMerger	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/DockResultMerger.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/DockResultMerger.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/EvenSplit
--- a/CADDSuite/EvenSplit	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/EvenSplit	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/EvenSplit.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/EvenSplit.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/FeatureSelector
--- a/CADDSuite/FeatureSelector	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/FeatureSelector	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/FeatureSelector.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/FeatureSelector.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/GalaxyConfigGenerator
--- a/CADDSuite/GalaxyConfigGenerator	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/GalaxyConfigGenerator	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/GridBuilder
--- a/CADDSuite/GridBuilder	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/GridBuilder	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/GridBuilder.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/GridBuilder.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/IMGDock
--- a/CADDSuite/IMGDock	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/IMGDock	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/IMGDock.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/IMGDock.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/InputPartitioner
--- a/CADDSuite/InputPartitioner	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/InputPartitioner	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/InputPartitioner.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/InputPartitioner.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/InputReader
--- a/CADDSuite/InputReader	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/InputReader	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/InputReader.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/InputReader.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/InteractionConstraintDefiner
--- a/CADDSuite/InteractionConstraintDefiner	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/InteractionConstraintDefiner	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/LigCheck
--- a/CADDSuite/LigCheck	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/LigCheck	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/LigCheck.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/LigCheck.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/Ligand3DGenerator
--- a/CADDSuite/Ligand3DGenerator	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/Ligand3DGenerator	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/Ligand3DGenerator.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/Ligand3DGenerator.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/LigandFileSplitter
--- a/CADDSuite/LigandFileSplitter	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/LigandFileSplitter	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/LigandFileSplitter.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/LigandFileSplitter.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/ModelCreator
--- a/CADDSuite/ModelCreator	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/ModelCreator	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/ModelCreator.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ModelCreator.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/MolCombine
--- a/CADDSuite/MolCombine	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/MolCombine	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/MolCombine.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/MolCombine.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/MolDepict
--- a/CADDSuite/MolDepict	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/MolDepict	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/MolDepict.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/MolDepict.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/MolFilter
--- a/CADDSuite/MolFilter	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/MolFilter	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/MolFilter.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/MolFilter.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/MolPredictor
--- a/CADDSuite/MolPredictor	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/MolPredictor	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/MolPredictor.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/MolPredictor.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/PDBCutter
--- a/CADDSuite/PDBCutter	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/PDBCutter	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/PDBCutter.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PDBCutter.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/PDBDownload
--- a/CADDSuite/PDBDownload	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/PDBDownload	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/PDBDownload.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PDBDownload.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/PartialChargesCopy
--- a/CADDSuite/PartialChargesCopy	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/PartialChargesCopy	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/PartialChargesCopy.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PartialChargesCopy.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/PocketDetector
--- a/CADDSuite/PocketDetector	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/PocketDetector	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/PocketDetector.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PocketDetector.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/Predictor
--- a/CADDSuite/Predictor	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/Predictor	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/Predictor.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/Predictor.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/PropertyModifier
--- a/CADDSuite/PropertyModifier	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/PropertyModifier	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/PropertyModifier.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PropertyModifier.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/PropertyPlotter
--- a/CADDSuite/PropertyPlotter	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/PropertyPlotter	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/PropertyPlotter.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PropertyPlotter.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/ProteinCheck
--- a/CADDSuite/ProteinCheck	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/ProteinCheck	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/ProteinCheck.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ProteinCheck.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/ProteinProtonator
--- a/CADDSuite/ProteinProtonator	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/ProteinProtonator	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/ProteinProtonator.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ProteinProtonator.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/QuEasyRun
--- a/CADDSuite/QuEasyRun	Tue Jun 28 10:37:20 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/QuEasyRun.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/README
--- a/CADDSuite/README	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/README	Tue Jul 12 10:23:33 2011 -0400
@@ -7,7 +7,7 @@
 For an overview over the contained tools, please see CADDSuite-description.txt.
 After extraction the package, you can directly start the applications using the startup-scripts in the base-folder.
 
-For more information about an individual tool, please call the tool without any parameters (or with '-h').
+For more information about an individual tool, please call the tool without any parameters (or with '-help').
 
 
 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/RMSDCalculator
--- a/CADDSuite/RMSDCalculator	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/RMSDCalculator	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/RMSDCalculator.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/RMSDCalculator.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/ScoreAnalyzer
--- a/CADDSuite/ScoreAnalyzer	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/ScoreAnalyzer	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/ScoreAnalyzer.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ScoreAnalyzer.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/SideChainGridBuilder
--- a/CADDSuite/SideChainGridBuilder	Tue Jun 28 10:37:20 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/SideChainGridBuilder.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/SimilarityAnalyzer
--- a/CADDSuite/SimilarityAnalyzer	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/SimilarityAnalyzer	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/SimpleRescorer
--- a/CADDSuite/SimpleRescorer	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/SimpleRescorer	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/SimpleRescorer.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/SimpleRescorer.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/SpatialConstraintDefiner
--- a/CADDSuite/SpatialConstraintDefiner	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/SpatialConstraintDefiner	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/TaGRes
--- a/CADDSuite/TaGRes	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/TaGRes	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/TaGRes.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/TaGRes.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/TaGRes-train
--- a/CADDSuite/TaGRes-train	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/TaGRes-train	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/TaGRes-train.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/TaGRes-train.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/Validator
--- a/CADDSuite/Validator	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/Validator	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/Validator.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/Validator.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/VendorFinder
--- a/CADDSuite/VendorFinder	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/VendorFinder	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/VendorFinder.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/VendorFinder.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/WaterFinder
--- a/CADDSuite/WaterFinder	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/WaterFinder	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
 #!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/WaterFinder.bin "$@" 
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/WaterFinder.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/AntitargetRescorer.bin
Binary file CADDSuite/bin/AntitargetRescorer.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/AutoModel.bin
Binary file CADDSuite/bin/AutoModel.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/BindingDBCleaner.bin
Binary file CADDSuite/bin/BindingDBCleaner.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/CombiLibGenerator.bin
Binary file CADDSuite/bin/CombiLibGenerator.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/ConstraintsFinder.bin
Binary file CADDSuite/bin/ConstraintsFinder.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/Converter.bin
Binary file CADDSuite/bin/Converter.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/DBExporter.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/DBImporter.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/DockResultMerger.bin
Binary file CADDSuite/bin/DockResultMerger.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/EvenSplit.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/FeatureSelector.bin
Binary file CADDSuite/bin/FeatureSelector.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/GalaxyConfigGenerator.bin
Binary file CADDSuite/bin/GalaxyConfigGenerator.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/GridBuilder.bin
Binary file CADDSuite/bin/GridBuilder.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/IMGDock.bin
Binary file CADDSuite/bin/IMGDock.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/InputPartitioner.bin
Binary file CADDSuite/bin/InputPartitioner.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/InputReader.bin
Binary file CADDSuite/bin/InputReader.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/InteractionConstraintDefiner.bin
Binary file CADDSuite/bin/InteractionConstraintDefiner.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/LigCheck.bin
Binary file CADDSuite/bin/LigCheck.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/Ligand3DGenerator.bin
Binary file CADDSuite/bin/Ligand3DGenerator.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/LigandFileSplitter.bin
Binary file CADDSuite/bin/LigandFileSplitter.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/ModelCreator.bin
Binary file CADDSuite/bin/ModelCreator.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/MolCombine.bin
Binary file CADDSuite/bin/MolCombine.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/MolDepict.bin
Binary file CADDSuite/bin/MolDepict.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/MolFilter.bin
Binary file CADDSuite/bin/MolFilter.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/MolPredictor.bin
Binary file CADDSuite/bin/MolPredictor.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/PDBCutter.bin
Binary file CADDSuite/bin/PDBCutter.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/PDBDownload.bin
Binary file CADDSuite/bin/PDBDownload.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/PartialChargesCopy.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/PocketDetector.bin
Binary file CADDSuite/bin/PocketDetector.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/Predictor.bin
Binary file CADDSuite/bin/Predictor.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/PropertyModifier.bin
Binary file CADDSuite/bin/PropertyModifier.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/PropertyPlotter.bin
Binary file CADDSuite/bin/PropertyPlotter.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/ProteinCheck.bin
Binary file CADDSuite/bin/ProteinCheck.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/ProteinProtonator.bin
Binary file CADDSuite/bin/ProteinProtonator.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/RMSDCalculator.bin
Binary file CADDSuite/bin/RMSDCalculator.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/ScoreAnalyzer.bin
Binary file CADDSuite/bin/ScoreAnalyzer.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/SimilarityAnalyzer.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/SimpleRescorer.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/SpatialConstraintDefiner.bin
Binary file CADDSuite/bin/SpatialConstraintDefiner.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/TaGRes-train.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/TaGRes.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/Validator.bin
Binary file CADDSuite/bin/Validator.bin has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/VendorFinder.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/bin/WaterFinder.bin
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diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/changelog.txt
--- a/CADDSuite/changelog.txt	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/changelog.txt	Tue Jul 12 10:23:33 2011 -0400
@@ -1,3 +1,11 @@
+Version 0.95, 07-12-2011:
+	- Let rescoring search for correct LigCheck molecule property-tags
+	- Indicate optional parameters in galaxy interface
+	- Fixed compilation with disabled QuEasyViz
+	- Added missing gnuplot data file to release archive
+	- Set some default values for flags for use in GUIs
+	- Clarified EvenSplit docu
+
 Version 0.94, 06-27-2011:
 	- Fixed tool-startup script for pathes containing whitespaces
 	- New tool SpatialConstraintDefiner
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/data/fonts/FreeSans.ttf
Binary file CADDSuite/data/fonts/FreeSans.ttf has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/data/gnuplot/FreeSans.ttf
Binary file CADDSuite/data/gnuplot/FreeSans.ttf has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/data/gnuplot/prologue.ps
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/gnuplot/prologue.ps	Tue Jul 12 10:23:33 2011 -0400
@@ -0,0 +1,371 @@
+%
+% Gnuplot Prolog Version 4.4 (January 2010)
+%
+%/SuppressPDFMark true def
+%
+/M {moveto} bind def
+/L {lineto} bind def
+/R {rmoveto} bind def
+/V {rlineto} bind def
+/N {newpath moveto} bind def
+/Z {closepath} bind def
+/C {setrgbcolor} bind def
+/f {rlineto fill} bind def
+/Gshow {show} def   % May be redefined later in the file to support UTF-8
+/vpt2 vpt 2 mul def
+/hpt2 hpt 2 mul def
+/Lshow {currentpoint stroke M 0 vshift R 
+	Blacktext {gsave 0 setgray show grestore} {show} ifelse} def
+/Rshow {currentpoint stroke M dup stringwidth pop neg vshift R
+	Blacktext {gsave 0 setgray show grestore} {show} ifelse} def
+/Cshow {currentpoint stroke M dup stringwidth pop -2 div vshift R 
+	Blacktext {gsave 0 setgray show grestore} {show} ifelse} def
+/UP {dup vpt_ mul /vpt exch def hpt_ mul /hpt exch def
+  /hpt2 hpt 2 mul def /vpt2 vpt 2 mul def} def
+/DL {Color {setrgbcolor Solid {pop []} if 0 setdash}
+ {pop pop pop 0 setgray Solid {pop []} if 0 setdash} ifelse} def
+/BL {stroke userlinewidth 2 mul setlinewidth
+	Rounded {1 setlinejoin 1 setlinecap} if} def
+/AL {stroke userlinewidth 2 div setlinewidth
+	Rounded {1 setlinejoin 1 setlinecap} if} def
+/UL {dup gnulinewidth mul /userlinewidth exch def
+	dup 1 lt {pop 1} if 10 mul /udl exch def} def
+/PL {stroke userlinewidth setlinewidth
+	Rounded {1 setlinejoin 1 setlinecap} if} def
+% Default Line colors
+/LCw {1 1 1} def
+/LCb {0 0 0} def
+/LCa {0 0 0} def
+/LC0 {1 0 0} def
+/LC1 {0 1 0} def
+/LC2 {0 0 1} def
+/LC3 {1 0 1} def
+/LC4 {0 1 1} def
+/LC5 {1 1 0} def
+/LC6 {0 0 0} def
+/LC7 {1 0.3 0} def
+/LC8 {0.5 0.5 0.5} def
+% Default Line Types
+/LTw {PL [] 1 setgray} def
+/LTb {BL [] LCb DL} def
+/LTa {AL [1 udl mul 2 udl mul] 0 setdash LCa setrgbcolor} def
+/LT0 {PL [] LC0 DL} def
+/LT1 {PL [4 dl1 2 dl2] LC1 DL} def
+/LT2 {PL [2 dl1 3 dl2] LC2 DL} def
+/LT3 {PL [1 dl1 1.5 dl2] LC3 DL} def
+/LT4 {PL [6 dl1 2 dl2 1 dl1 2 dl2] LC4 DL} def
+/LT5 {PL [3 dl1 3 dl2 1 dl1 3 dl2] LC5 DL} def
+/LT6 {PL [2 dl1 2 dl2 2 dl1 6 dl2] LC6 DL} def
+/LT7 {PL [1 dl1 2 dl2 6 dl1 2 dl2 1 dl1 2 dl2] LC7 DL} def
+/LT8 {PL [2 dl1 2 dl2 2 dl1 2 dl2 2 dl1 2 dl2 2 dl1 4 dl2] LC8 DL} def
+/Pnt {stroke [] 0 setdash gsave 1 setlinecap M 0 0 V stroke grestore} def
+/Dia {stroke [] 0 setdash 2 copy vpt add M
+  hpt neg vpt neg V hpt vpt neg V
+  hpt vpt V hpt neg vpt V closepath stroke
+  Pnt} def
+/Pls {stroke [] 0 setdash vpt sub M 0 vpt2 V
+  currentpoint stroke M
+  hpt neg vpt neg R hpt2 0 V stroke
+ } def
+/Box {stroke [] 0 setdash 2 copy exch hpt sub exch vpt add M
+  0 vpt2 neg V hpt2 0 V 0 vpt2 V
+  hpt2 neg 0 V closepath stroke
+  Pnt} def
+/Crs {stroke [] 0 setdash exch hpt sub exch vpt add M
+  hpt2 vpt2 neg V currentpoint stroke M
+  hpt2 neg 0 R hpt2 vpt2 V stroke} def
+/TriU {stroke [] 0 setdash 2 copy vpt 1.12 mul add M
+  hpt neg vpt -1.62 mul V
+  hpt 2 mul 0 V
+  hpt neg vpt 1.62 mul V closepath stroke
+  Pnt} def
+/Star {2 copy Pls Crs} def
+/BoxF {stroke [] 0 setdash exch hpt sub exch vpt add M
+  0 vpt2 neg V hpt2 0 V 0 vpt2 V
+  hpt2 neg 0 V closepath fill} def
+/TriUF {stroke [] 0 setdash vpt 1.12 mul add M
+  hpt neg vpt -1.62 mul V
+  hpt 2 mul 0 V
+  hpt neg vpt 1.62 mul V closepath fill} def
+/TriD {stroke [] 0 setdash 2 copy vpt 1.12 mul sub M
+  hpt neg vpt 1.62 mul V
+  hpt 2 mul 0 V
+  hpt neg vpt -1.62 mul V closepath stroke
+  Pnt} def
+/TriDF {stroke [] 0 setdash vpt 1.12 mul sub M
+  hpt neg vpt 1.62 mul V
+  hpt 2 mul 0 V
+  hpt neg vpt -1.62 mul V closepath fill} def
+/DiaF {stroke [] 0 setdash vpt add M
+  hpt neg vpt neg V hpt vpt neg V
+  hpt vpt V hpt neg vpt V closepath fill} def
+/Pent {stroke [] 0 setdash 2 copy gsave
+  translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
+  closepath stroke grestore Pnt} def
+/PentF {stroke [] 0 setdash gsave
+  translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
+  closepath fill grestore} def
+/Circle {stroke [] 0 setdash 2 copy
+  hpt 0 360 arc stroke Pnt} def
+/CircleF {stroke [] 0 setdash hpt 0 360 arc fill} def
+/C0 {BL [] 0 setdash 2 copy moveto vpt 90 450 arc} bind def
+/C1 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 0 90 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C2 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 90 180 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C3 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 0 180 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C4 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 180 270 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C5 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 0 90 arc
+	2 copy moveto
+	2 copy vpt 180 270 arc closepath fill
+	vpt 0 360 arc} bind def
+/C6 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 90 270 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C7 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 0 270 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C8 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 270 360 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C9 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 270 450 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C10 {BL [] 0 setdash 2 copy 2 copy moveto vpt 270 360 arc closepath fill
+	2 copy moveto
+	2 copy vpt 90 180 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C11 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 0 180 arc closepath fill
+	2 copy moveto
+	2 copy vpt 270 360 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C12 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 180 360 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C13 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 0 90 arc closepath fill
+	2 copy moveto
+	2 copy vpt 180 360 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/C14 {BL [] 0 setdash 2 copy moveto
+	2 copy vpt 90 360 arc closepath fill
+	vpt 0 360 arc} bind def
+/C15 {BL [] 0 setdash 2 copy vpt 0 360 arc closepath fill
+	vpt 0 360 arc closepath} bind def
+/Rec {newpath 4 2 roll moveto 1 index 0 rlineto 0 exch rlineto
+	neg 0 rlineto closepath} bind def
+/Square {dup Rec} bind def
+/Bsquare {vpt sub exch vpt sub exch vpt2 Square} bind def
+/S0 {BL [] 0 setdash 2 copy moveto 0 vpt rlineto BL Bsquare} bind def
+/S1 {BL [] 0 setdash 2 copy vpt Square fill Bsquare} bind def
+/S2 {BL [] 0 setdash 2 copy exch vpt sub exch vpt Square fill Bsquare} bind def
+/S3 {BL [] 0 setdash 2 copy exch vpt sub exch vpt2 vpt Rec fill Bsquare} bind def
+/S4 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt Square fill Bsquare} bind def
+/S5 {BL [] 0 setdash 2 copy 2 copy vpt Square fill
+	exch vpt sub exch vpt sub vpt Square fill Bsquare} bind def
+/S6 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt vpt2 Rec fill Bsquare} bind def
+/S7 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt vpt2 Rec fill
+	2 copy vpt Square fill Bsquare} bind def
+/S8 {BL [] 0 setdash 2 copy vpt sub vpt Square fill Bsquare} bind def
+/S9 {BL [] 0 setdash 2 copy vpt sub vpt vpt2 Rec fill Bsquare} bind def
+/S10 {BL [] 0 setdash 2 copy vpt sub vpt Square fill 2 copy exch vpt sub exch vpt Square fill
+	Bsquare} bind def
+/S11 {BL [] 0 setdash 2 copy vpt sub vpt Square fill 2 copy exch vpt sub exch vpt2 vpt Rec fill
+	Bsquare} bind def
+/S12 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill Bsquare} bind def
+/S13 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill
+	2 copy vpt Square fill Bsquare} bind def
+/S14 {BL [] 0 setdash 2 copy exch vpt sub exch vpt sub vpt2 vpt Rec fill
+	2 copy exch vpt sub exch vpt Square fill Bsquare} bind def
+/S15 {BL [] 0 setdash 2 copy Bsquare fill Bsquare} bind def
+/D0 {gsave translate 45 rotate 0 0 S0 stroke grestore} bind def
+/D1 {gsave translate 45 rotate 0 0 S1 stroke grestore} bind def
+/D2 {gsave translate 45 rotate 0 0 S2 stroke grestore} bind def
+/D3 {gsave translate 45 rotate 0 0 S3 stroke grestore} bind def
+/D4 {gsave translate 45 rotate 0 0 S4 stroke grestore} bind def
+/D5 {gsave translate 45 rotate 0 0 S5 stroke grestore} bind def
+/D6 {gsave translate 45 rotate 0 0 S6 stroke grestore} bind def
+/D7 {gsave translate 45 rotate 0 0 S7 stroke grestore} bind def
+/D8 {gsave translate 45 rotate 0 0 S8 stroke grestore} bind def
+/D9 {gsave translate 45 rotate 0 0 S9 stroke grestore} bind def
+/D10 {gsave translate 45 rotate 0 0 S10 stroke grestore} bind def
+/D11 {gsave translate 45 rotate 0 0 S11 stroke grestore} bind def
+/D12 {gsave translate 45 rotate 0 0 S12 stroke grestore} bind def
+/D13 {gsave translate 45 rotate 0 0 S13 stroke grestore} bind def
+/D14 {gsave translate 45 rotate 0 0 S14 stroke grestore} bind def
+/D15 {gsave translate 45 rotate 0 0 S15 stroke grestore} bind def
+/DiaE {stroke [] 0 setdash vpt add M
+  hpt neg vpt neg V hpt vpt neg V
+  hpt vpt V hpt neg vpt V closepath stroke} def
+/BoxE {stroke [] 0 setdash exch hpt sub exch vpt add M
+  0 vpt2 neg V hpt2 0 V 0 vpt2 V
+  hpt2 neg 0 V closepath stroke} def
+/TriUE {stroke [] 0 setdash vpt 1.12 mul add M
+  hpt neg vpt -1.62 mul V
+  hpt 2 mul 0 V
+  hpt neg vpt 1.62 mul V closepath stroke} def
+/TriDE {stroke [] 0 setdash vpt 1.12 mul sub M
+  hpt neg vpt 1.62 mul V
+  hpt 2 mul 0 V
+  hpt neg vpt -1.62 mul V closepath stroke} def
+/PentE {stroke [] 0 setdash gsave
+  translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
+  closepath stroke grestore} def
+/CircE {stroke [] 0 setdash 
+  hpt 0 360 arc stroke} def
+/Opaque {gsave closepath 1 setgray fill grestore 0 setgray closepath} def
+/DiaW {stroke [] 0 setdash vpt add M
+  hpt neg vpt neg V hpt vpt neg V
+  hpt vpt V hpt neg vpt V Opaque stroke} def
+/BoxW {stroke [] 0 setdash exch hpt sub exch vpt add M
+  0 vpt2 neg V hpt2 0 V 0 vpt2 V
+  hpt2 neg 0 V Opaque stroke} def
+/TriUW {stroke [] 0 setdash vpt 1.12 mul add M
+  hpt neg vpt -1.62 mul V
+  hpt 2 mul 0 V
+  hpt neg vpt 1.62 mul V Opaque stroke} def
+/TriDW {stroke [] 0 setdash vpt 1.12 mul sub M
+  hpt neg vpt 1.62 mul V
+  hpt 2 mul 0 V
+  hpt neg vpt -1.62 mul V Opaque stroke} def
+/PentW {stroke [] 0 setdash gsave
+  translate 0 hpt M 4 {72 rotate 0 hpt L} repeat
+  Opaque stroke grestore} def
+/CircW {stroke [] 0 setdash 
+  hpt 0 360 arc Opaque stroke} def
+/BoxFill {gsave Rec 1 setgray fill grestore} def
+/Density {
+  /Fillden exch def
+  currentrgbcolor
+  /ColB exch def /ColG exch def /ColR exch def
+  /ColR ColR Fillden mul Fillden sub 1 add def
+  /ColG ColG Fillden mul Fillden sub 1 add def
+  /ColB ColB Fillden mul Fillden sub 1 add def
+  ColR ColG ColB setrgbcolor} def
+/BoxColFill {gsave Rec PolyFill} def
+/PolyFill {gsave Density fill grestore grestore} def
+/h {rlineto rlineto rlineto gsave closepath fill grestore} bind def
+%
+% PostScript Level 1 Pattern Fill routine for rectangles
+% Usage: x y w h s a XX PatternFill
+%	x,y = lower left corner of box to be filled
+%	w,h = width and height of box
+%	  a = angle in degrees between lines and x-axis
+%	 XX = 0/1 for no/yes cross-hatch
+%
+/PatternFill {gsave /PFa [ 9 2 roll ] def
+  PFa 0 get PFa 2 get 2 div add PFa 1 get PFa 3 get 2 div add translate
+  PFa 2 get -2 div PFa 3 get -2 div PFa 2 get PFa 3 get Rec
+  gsave 1 setgray fill grestore clip
+  currentlinewidth 0.5 mul setlinewidth
+  /PFs PFa 2 get dup mul PFa 3 get dup mul add sqrt def
+  0 0 M PFa 5 get rotate PFs -2 div dup translate
+  0 1 PFs PFa 4 get div 1 add floor cvi
+	{PFa 4 get mul 0 M 0 PFs V} for
+  0 PFa 6 get ne {
+	0 1 PFs PFa 4 get div 1 add floor cvi
+	{PFa 4 get mul 0 2 1 roll M PFs 0 V} for
+ } if
+  stroke grestore} def
+%
+/languagelevel where
+ {pop languagelevel} {1} ifelse
+ 2 lt
+	{/InterpretLevel1 true def}
+	{/InterpretLevel1 Level1 def}
+ ifelse
+%
+% PostScript level 2 pattern fill definitions
+%
+/Level2PatternFill {
+/Tile8x8 {/PaintType 2 /PatternType 1 /TilingType 1 /BBox [0 0 8 8] /XStep 8 /YStep 8}
+	bind def
+/KeepColor {currentrgbcolor [/Pattern /DeviceRGB] setcolorspace} bind def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke} 
+>> matrix makepattern
+/Pat1 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke
+	0 4 M 4 8 L 8 4 L 4 0 L 0 4 L stroke}
+>> matrix makepattern
+/Pat2 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 0 0 M 0 8 L
+	8 8 L 8 0 L 0 0 L fill}
+>> matrix makepattern
+/Pat3 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop -4 8 M 8 -4 L
+	0 12 M 12 0 L stroke}
+>> matrix makepattern
+/Pat4 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop -4 0 M 8 12 L
+	0 -4 M 12 8 L stroke}
+>> matrix makepattern
+/Pat5 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop -2 8 M 4 -4 L
+	0 12 M 8 -4 L 4 12 M 10 0 L stroke}
+>> matrix makepattern
+/Pat6 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop -2 0 M 4 12 L
+	0 -4 M 8 12 L 4 -4 M 10 8 L stroke}
+>> matrix makepattern
+/Pat7 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 8 -2 M -4 4 L
+	12 0 M -4 8 L 12 4 M 0 10 L stroke}
+>> matrix makepattern
+/Pat8 exch def
+<< Tile8x8
+ /PaintProc {0.5 setlinewidth pop 0 -2 M 12 4 L
+	-4 0 M 12 8 L -4 4 M 8 10 L stroke}
+>> matrix makepattern
+/Pat9 exch def
+/Pattern1 {PatternBgnd KeepColor Pat1 setpattern} bind def
+/Pattern2 {PatternBgnd KeepColor Pat2 setpattern} bind def
+/Pattern3 {PatternBgnd KeepColor Pat3 setpattern} bind def
+/Pattern4 {PatternBgnd KeepColor Landscape {Pat5} {Pat4} ifelse setpattern} bind def
+/Pattern5 {PatternBgnd KeepColor Landscape {Pat4} {Pat5} ifelse setpattern} bind def
+/Pattern6 {PatternBgnd KeepColor Landscape {Pat9} {Pat6} ifelse setpattern} bind def
+/Pattern7 {PatternBgnd KeepColor Landscape {Pat8} {Pat7} ifelse setpattern} bind def
+} def
+%
+%
+%End of PostScript Level 2 code
+%
+/PatternBgnd {
+  TransparentPatterns {} {gsave 1 setgray fill grestore} ifelse
+} def
+%
+% Substitute for Level 2 pattern fill codes with
+% grayscale if Level 2 support is not selected.
+%
+/Level1PatternFill {
+/Pattern1 {0.250 Density} bind def
+/Pattern2 {0.500 Density} bind def
+/Pattern3 {0.750 Density} bind def
+/Pattern4 {0.125 Density} bind def
+/Pattern5 {0.375 Density} bind def
+/Pattern6 {0.625 Density} bind def
+/Pattern7 {0.875 Density} bind def
+} def
+%
+% Now test for support of Level 2 code
+%
+Level1 {Level1PatternFill} {Level2PatternFill} ifelse
+%
+/Symbol-Oblique /Symbol findfont [1 0 .167 1 0 0] makefont
+dup length dict begin {1 index /FID eq {pop pop} {def} ifelse} forall
+currentdict end definefont pop
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tool_conf.xml
--- a/CADDSuite/galaxyconfigs/tool_conf.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tool_conf.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <toolbox>
-  <label text="CADDSuite  0.94" id="cadds" />
+  <label text="CADDSuite 0.95" id="cadds" />
 
   <section name="Get Data" id="getext">
-    <tool file="data_source/upload.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/upload.xml"/>
     <tool file="CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml"/>
     <tool file="CADDSuite/galaxyconfigs/tools/PDBDownload.xml"/>
     <tool file="CADDSuite/galaxyconfigs/tools/DBExporter.xml"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml
--- a/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94">
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.95">
     <description>rescore w/ anti-target dock-results</description>
     <command interpreter="bash"><![CDATA[../../AntitargetRescorer 
 #if str( $t ) != ''  and str( $t ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="t" label="input file w/ target dock-results" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="at" label="input file w/ anti-target dock-results" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="t" optional="false" label="input file w/ target dock-results" type="data" format="mol2/sdf/drf"/>
+        <param name="at" optional="false" label="input file w/ anti-target dock-results" type="data" format="mol2/sdf/drf"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="t"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/AutoModel.xml
--- a/CADDSuite/galaxyconfigs/tools/AutoModel.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="automodel" name="AutoModel" version="1.1">
+<tool id="automodel" name="AutoModel" version="0.95">
     <description>automatically find best QSAR model</description>
     <command interpreter="bash"><![CDATA[../../AutoModel 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input data-file" optional="false" type="data" format="dat"/>
-        <param name="min_quality" label="minimal desired quality (default: 0.3)" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value="0.3"/>
+        <param name="i" optional="false" label="input data-file" type="data" format="dat"/>
+        <param name="min_quality" optional="true" label="Optional: minimal desired quality (default: 0.3)" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value="0.3"/>
     </inputs>
     <outputs>
         <data name="o" format="mod"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml
--- a/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94">
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.95">
     <description>fix bindingdb.org downloads</description>
     <command interpreter="bash"><![CDATA[../../BindingDBCleaner 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -18,12 +18,12 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="type" label="type of contained activity values: 'Ki' or 'IC50'" optional="false" type="select">
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="type" optional="false" label="type of contained activity values: 'Ki' or 'IC50'" type="select">
             <option value="IC50">IC50</option>
             <option value="Ki">Ki</option>
         </param>
-        <param name="target" label="binding-DB target name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="target" optional="false" label="binding-DB target name" area="true" type="text" size="1x15"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml
--- a/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94">
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.95">
     <description>generate combinatorial lib</description>
     <command interpreter="bash"><![CDATA[../../CombiLibGenerator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -12,7 +12,7 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input combi-lib file" optional="false" type="data" format="data"/>
+        <param name="i" optional="false" label="input combi-lib file" type="data" format="data"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf"/>
@@ -23,7 +23,6 @@
 
 &lt;scaffold&gt;
       Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3
-      Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3
 &lt;moietyR1&gt;
       [R1]C(C)(C)C
 &lt;moietyR2&gt;
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml
--- a/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94">
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.95">
     <description>find strongly interacting residues</description>
     <command interpreter="bash"><![CDATA[../../ConstraintsFinder 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -18,9 +18,9 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
     </inputs>
     <outputs>
         <data name="o" format="ini"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/Converter.xml
--- a/CADDSuite/galaxyconfigs/tools/Converter.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Converter.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="converter" name="Converter" version="0.94">
+<tool id="converter" name="Converter" version="0.95">
     <description>interconvert molecular file-formats</description>
     <command interpreter="bash"><![CDATA[../../Converter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="f" label="output format" optional="true" type="select">
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="f" optional="true" label="output format" type="select">
             <option value="mol2">mol2</option>
             <option value="sdf">sdf</option>
             <option value="drf">drf</option>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/DBExporter.xml
--- a/CADDSuite/galaxyconfigs/tools/DBExporter.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="dbexporter" name="DBExporter" version="0.94 (ob)">
+<tool id="dbexporter" name="DBExporter" version="0.95 (ob)">
     <description>export molecules from data base</description>
     <command interpreter="bash"><![CDATA[../../DBExporter 
 #if str( $o ) != ''  and str( $o ) != 'None' :
@@ -69,26 +69,26 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="mol2/sdf/drf"/>
-        <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/>
-        <param name="start_id" label="ID of the first conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="end_id" label="ID of the last conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="min_logP" label="minimal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
-        <param name="max_logP" label="maximal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
-        <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max_mols" label="max. number of molecules to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/>
-        <param name="min_sim" label="minimal average similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
-        <param name="max_sim" label="maximal similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
-        <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/>
-        <param name="uck" label="UCK key" optional="true" area="true" type="text" size="1x15"/>
-        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
-        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
-        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
-        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
-        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
-        <param name="s" label="show summary of datasets in database" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="mol2/sdf/drf"/>
+        <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="data"/>
+        <param name="start_id" optional="true" label="Optional: ID of the first conformation to be exported" type="text" area="true" size="1x5" value=""/>
+        <param name="end_id" optional="true" label="Optional: ID of the last conformation to be exported" type="text" area="true" size="1x5" value=""/>
+        <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
+        <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
+        <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/>
+        <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/>
+        <param name="max_mols" optional="true" label="Optional: max. number of molecules to be exported" type="text" area="true" size="1x5" value=""/>
+        <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/>
+        <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
+        <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
+        <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
+        <param name="uck" optional="true" label="Optional: UCK key" area="true" type="text" size="1x15"/>
+        <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/>
+        <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/>
+        <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/>
+        <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
+        <param name="s" optional="true" label="show summary of datasets in database" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/DBImporter.xml
--- a/CADDSuite/galaxyconfigs/tools/DBImporter.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="dbimporter" name="DBImporter" version="0.94 (ob)">
+<tool id="dbimporter" name="DBImporter" version="0.95 (ob)">
     <description>import molecules into data base</description>
     <command interpreter="bash"><![CDATA[../../DBImporter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -39,17 +39,17 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/>
-        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
-        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
-        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
-        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
-        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
-        <param name="vn" label="name of compound vendor" optional="true" area="true" type="text" size="1x15"/>
-        <param name="vid" label="name of vendor's compound-ID tag in sd-file" optional="true" area="true" type="text" size="1x15"/>
-        <param name="vd" label="vendor library date or version" optional="true" area="true" type="text" size="1x15"/>
-        <param name="vu" label="url from wich vendor library was obtained" optional="true" area="true" type="text" size="1x15"/>
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/>
+        <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/>
+        <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/>
+        <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/>
+        <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
+        <param name="vn" optional="true" label="Optional: name of compound vendor" area="true" type="text" size="1x15"/>
+        <param name="vid" optional="true" label="Optional: name of vendor's compound-ID tag in sd-file" area="true" type="text" size="1x15"/>
+        <param name="vd" optional="true" label="Optional: vendor library date or version" area="true" type="text" size="1x15"/>
+        <param name="vu" optional="true" label="Optional: url from wich vendor library was obtained" area="true" type="text" size="1x15"/>
     </inputs>
     <outputs/>
     <help>This tool imports molecules into a database.
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/DockResultMerger.xml
--- a/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="dockresultmerger" name="DockResultMerger" version="0.94">
+<tool id="dockresultmerger" name="DockResultMerger" version="0.95">
     <description>merge docking output files</description>
     <command interpreter="bash"><![CDATA[../../DockResultMerger 
 #for $s in $series_i 
@@ -30,13 +30,13 @@
 ]]></command>
     <inputs>
         <repeat name="series_i" title="input files" min="1">
-            <param name="i" label="input files" optional="false" type="data" format="mol2/sdf/drf"/>
+            <param name="i" optional="false" label="input files" type="data" format="mol2/sdf/drf"/>
         </repeat>
-        <param name="score" label="score property name" optional="true" area="true" type="text" size="1x15" value="score"/>
-        <param name="min" label="minimal score value" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max" label="maximal score value" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="k" label="number of output molecules" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="rm" label="remove input files after merging" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="score" optional="true" label="Optional: score property name" area="true" type="text" size="1x15" value="score"/>
+        <param name="min" optional="true" label="Optional: minimal score value" type="text" area="true" size="1x5" value=""/>
+        <param name="max" optional="true" label="Optional: maximal score value" type="text" area="true" size="1x5" value=""/>
+        <param name="k" optional="true" label="Optional: number of output molecules" type="text" area="true" size="1x5" value=""/>
+        <param name="rm" optional="true" label="remove input files after merging" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/EvenSplit.xml
--- a/CADDSuite/galaxyconfigs/tools/EvenSplit.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="evensplit" name="EvenSplit" version="0.94">
+<tool id="evensplit" name="EvenSplit" version="0.95">
     <description>generate splits w/ equal property range</description>
     <command interpreter="bash"><![CDATA[../../EvenSplit 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -12,26 +12,26 @@
 #if str( $o2 ) != ''  and str( $o2 ) != 'None' :
    -o2 "$o2"
 #end if
+#if str( $prop ) != ''  and str( $prop ) != 'None' :
+   -prop "$prop"
+#end if
 #if str( $n ) != ''  and str( $n ) != 'None' :
    -n "$n"
 #end if
-#if str( $offset ) != ''  and str( $offset ) != 'None' :
-   -offset "$offset"
-#end if
 #if str( $k ) != ''  and str( $k ) != 'None' :
    -k "$k"
 #end if
-#if str( $prop ) != ''  and str( $prop ) != 'None' :
-   -prop "$prop"
+#if str( $offset ) != ''  and str( $offset ) != 'None' :
+   -offset "$offset"
 #end if
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="n" label="number of compounds to use from input file" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="offset" label="extract each (i+offset)%k == 0 for o2" optional="true" type="text" area="true" size="1x5" value="0"/>
-        <param name="k" label="extract each k'th compound for 2nd output file" optional="true" type="text" area="true" size="1x5" value="2"/>
-        <param name="prop" label="property name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="prop" optional="false" label="property name" area="true" type="text" size="1x15" value="binding_free_energy"/>
+        <param name="n" optional="true" label="Optional: max. number of compounds to use from input file" type="text" area="true" size="1x5" value=""/>
+        <param name="k" optional="true" label="Optional: extract each k'th compound to 2nd output file" type="text" area="true" size="1x5" value="2"/>
+        <param name="offset" optional="true" label="Optional: offset; extract each (i+offset)%k == 0 to 2nd output file" type="text" area="true" size="1x5" value="0"/>
     </inputs>
     <outputs>
         <data name="o1" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/FeatureSelector.xml
--- a/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="featureselector" name="FeatureSelector" version="1.1">
+<tool id="featureselector" name="FeatureSelector" version="0.95">
     <description>run feature-selection on a QSAR model</description>
     <command interpreter="bash"><![CDATA[../../FeatureSelector 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -18,9 +18,9 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
-        <param name="dat" label="data-file" optional="false" type="data" format="dat"/>
-        <param name="type" label="feature-selection type" optional="false" type="select">
+        <param name="i" optional="false" label="input mod-file" type="data" format="mod"/>
+        <param name="dat" optional="false" label="data-file" type="data" format="dat"/>
+        <param name="type" optional="false" label="feature-selection type" type="select">
             <option value="remove_correlated">remove_correlated</option>
             <option value="forward_selection">forward_selection</option>
             <option value="backward_selection">backward_selection</option>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml
--- a/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94">
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.95">
     <description>generate galaxy tool-config files</description>
     <command interpreter="bash"><![CDATA[../../GalaxyConfigGenerator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -18,8 +18,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input par-file" optional="false" type="data" format="data"/>
-        <param name="ignore" label="tool-parameter to be ignored, i.e. those for which no galaxy config entry should be created" optional="true" area="true" size="1x5"/>
+        <param name="i" optional="false" label="input par-file" type="data" format="data"/>
+        <param name="ignore" optional="true" label="Optional: tool-parameter to be ignored, i.e. those for which no galaxy config entry should be created" area="true" size="1x5"/>
     </inputs>
     <outputs>
         <data name="o" format="xml"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/GridBuilder.xml
--- a/CADDSuite/galaxyconfigs/tools/GridBuilder.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="gridbuilder" name="GridBuilder" version="0.94">
+<tool id="gridbuilder" name="GridBuilder" version="0.95">
     <description>create score-grids for docking</description>
     <command interpreter="bash"><![CDATA[../../GridBuilder 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -18,9 +18,9 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
     </inputs>
     <outputs>
         <data name="grd" format="grd.tgz"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/IMGDock.xml
--- a/CADDSuite/galaxyconfigs/tools/IMGDock.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/IMGDock.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="imeedydock" name="IMGDock" version="0.94">
+<tool id="imeedydock" name="IMGDock" version="0.95">
     <description>Iterative Multi-Greedy Docking</description>
     <command interpreter="bash"><![CDATA[../../IMGDock 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -24,11 +24,11 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="compounds to be docked" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="grd" label="ScoreGrid file" optional="false" type="data" format="grd.tgz"/>
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
+        <param name="i" optional="false" label="compounds to be docked" type="data" format="mol2/sdf/drf"/>
+        <param name="grd" optional="false" label="ScoreGrid file" type="data" format="grd.tgz"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/InputPartitioner.xml
--- a/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="inputpartitioner" name="InputPartitioner" version="1.1">
+<tool id="inputpartitioner" name="InputPartitioner" version="0.95">
     <description>split QSAR data set</description>
     <command interpreter="bash"><![CDATA[../../InputPartitioner 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input data-file" optional="false" type="data" format="dat"/>
-        <param name="n" label="number of partitions" optional="false" type="text" area="true" size="1x5" value=""/>
+        <param name="i" optional="false" label="input data-file" type="data" format="dat"/>
+        <param name="n" optional="false" label="number of partitions" type="text" area="true" size="1x5" value=""/>
     </inputs>
     <outputs>
         <data name="o" format="dat"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/InputReader.xml
--- a/CADDSuite/galaxyconfigs/tools/InputReader.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="inputreader" name="InputReader" version="1.1">
+<tool id="inputreader" name="InputReader" version="0.95">
     <description>generate QSAR data set</description>
     <command interpreter="bash"><![CDATA[../../InputReader 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -39,16 +39,16 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
-        <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
-        <param name="act" label="sd-property containing response values" optional="true" area="true" type="text" size="1x15"/>
-        <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="sdp" label="use sd-properties as additional descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="no_cd" label="do not center descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="no_cr" label="do not center response values" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="i" optional="false" label="input sd-file" type="data" format="sdf"/>
+        <param name="csv" optional="true" label="input csv-file w/ additional descriptors" type="data" format="csv"/>
+        <param name="act" optional="true" label="Optional: sd-property containing response values" area="true" type="text" size="1x15"/>
+        <param name="csv_nr" optional="true" label="Optional: no. of response variables in csv-file" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_sep" optional="true" label="Optional: separator symbol in csv-file" type="text" area="true" size="1x5" value=""/>
+        <param name="sdp" optional="true" label="use sd-properties as additional descriptors" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="no_cd" optional="true" label="do not center descriptors" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="no_cr" optional="true" label="do not center response values" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_cl" optional="true" label="csv-file has compound (row) labels" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_dl" optional="true" label="csv-file has descriptor (column) labels" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="dat"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml
--- a/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94">
+<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.95">
     <description>define interaction constraint</description>
     <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner 
 #if str( $res ) != ''  and str( $res ) != 'None' :
@@ -21,10 +21,10 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/>
-        <param name="res" label="residue ID" optional="false" area="true" type="text" size="1x15"/>
-        <param name="s" label="desired minimal interation (score) between ligand and specified residue(s)" optional="false" type="text" area="true" size="1x5" value="-2.0"/>
-        <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="10"/>
+        <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
+        <param name="res" optional="false" label="residue ID" area="true" type="text" size="1x15"/>
+        <param name="s" optional="false" label="desired minimal interation (score) between ligand and specified residue(s)" type="text" area="true" size="1x5" value="-2.0"/>
+        <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="10"/>
     </inputs>
     <outputs>
         <data name="o" format="ini"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/LigCheck.xml
--- a/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="ligcheck" name="LigCheck" version="0.94">
+<tool id="ligcheck" name="LigCheck" version="0.95">
     <description>check molecules for errors</description>
     <command interpreter="bash"><![CDATA[../../LigCheck 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -21,10 +21,10 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ef" label="error fraction; print error if fraction of invalid mols is larger" optional="true" type="text" area="true" size="1x5" value="0.5"/>
-        <param name="ri" label="remove invalid molecules." optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="ut" label="check for unique topologies (default: check only for unique conformation)" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
+        <param name="ef" optional="true" label="Optional: error fraction; print error if fraction of invalid mols is larger" type="text" area="true" size="1x5" value="0.5"/>
+        <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/>
+        <param name="ut" optional="true" label="check for unique topologies (default: check only for unique conformation)" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml
--- a/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94">
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.95">
     <description>generate 3D coordinates for small molecules</description>
     <command interpreter="bash"><![CDATA[../../Ligand3DGenerator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/>
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml
--- a/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94">
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.95">
     <description>split molecule files</description>
     <command interpreter="bash"><![CDATA[../../LigandFileSplitter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -57,8 +57,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="no" label="no. of splits to be created" optional="false" type="hidden" area="true" size="1x5" value="15"/>
+        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
+        <param name="no" optional="false" label="no. of splits to be created" type="hidden" area="true" size="1x5" value="15"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/ModelCreator.xml
--- a/CADDSuite/galaxyconfigs/tools/ModelCreator.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ModelCreator.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -18,8 +18,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input dat-file" optional="false" type="data" format="dat"/>
-        <param name="type" label="model type" optional="false" type="select">
+        <param name="i" optional="false" label="input dat-file" type="data" format="dat"/>
+        <param name="type" optional="false" label="model type" type="select">
             <option value="MLR">MLR</option>
             <option value="RR">RR</option>
             <option value="PCR">PCR</option>
@@ -34,7 +34,7 @@
             <option value="snB">snB</option>
             <option value="nB">nB</option>
         </param>
-        <param name="kernel" label="kernel type (in case of kernel-model)" optional="true" type="select">
+        <param name="kernel" optional="true" label="kernel type (in case of kernel-model)" type="select">
             <option value="none">none</option>
             <option value="polynomial">polynomial</option>
             <option value="rbf">rbf</option>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/MolCombine.xml
--- a/CADDSuite/galaxyconfigs/tools/MolCombine.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="molcombine" name="MolCombine" version="0.94">
+<tool id="molcombine" name="MolCombine" version="0.95">
     <description>combine molecular files</description>
     <command interpreter="bash"><![CDATA[../../MolCombine 
 #if str( $i1 ) != ''  and str( $i1 ) != 'None' :
@@ -24,15 +24,15 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i1" label="input molecule file A" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="i2" label="input molecule file B" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="mode" label="'intersection', 'union' or 'b_not_a'" optional="false" type="select">
+        <param name="i1" optional="false" label="input molecule file A" type="data" format="mol2/sdf/drf"/>
+        <param name="i2" optional="false" label="input molecule file B" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" optional="false" label="'intersection', 'union' or 'b_not_a'" type="select">
             <option value="intersection">intersection</option>
             <option value="union">union</option>
             <option value="b_not_a">b_not_a</option>
         </param>
-        <param name="ignH" label="ignore hydrogens, i.e. match molecules to any protonation state." optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="replace_prop" label="replace properties from file 1 w/ those from file 2" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/>
+        <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i1"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/MolDepict.xml
--- a/CADDSuite/galaxyconfigs/tools/MolDepict.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="moldepict" name="MolDepict" version="0.94">
+<tool id="moldepict" name="MolDepict" version="0.95">
     <description>create structure diagrams</description>
     <command interpreter="bash"><![CDATA[../../MolDepict 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="max" label="maximal number of pictures (default=60, 0=unlimited)" optional="true" type="text" area="true" size="1x5" value="60"/>
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="max" optional="true" label="Optional: maximal number of pictures (default=60, 0=unlimited)" type="text" area="true" size="1x5" value="60"/>
     </inputs>
     <outputs>
         <data name="o" format="pdf"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/MolFilter.xml
--- a/CADDSuite/galaxyconfigs/tools/MolFilter.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -40,16 +40,16 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input molecule-file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="txt"/>
-        <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/>
-        <param name="min_logP" label="minimal logP value" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max_logP" label="maximal logP value" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="min_sim" label="minimal average similarity" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max_sim" label="maximal similarity" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/>
+        <param name="i" optional="false" label="input molecule-file" type="data" format="mol2/sdf/drf"/>
+        <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="txt"/>
+        <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="data"/>
+        <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" area="true" size="1x5" value=""/>
+        <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" area="true" size="1x5" value=""/>
+        <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/>
+        <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/>
+        <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" area="true" size="1x5" value=""/>
+        <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" area="true" size="1x5" value=""/>
+        <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/MolPredictor.xml
--- a/CADDSuite/galaxyconfigs/tools/MolPredictor.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="molpredictor" name="MolPredictor" version="1.1">
+<tool id="molpredictor" name="MolPredictor" version="0.95">
     <description>predict molecule activities with QSAR model</description>
     <command interpreter="bash"><![CDATA[../../MolPredictor 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -30,13 +30,13 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
-        <param name="mod" label="file containing QSAR model" optional="false" type="data" format="mod"/>
-        <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
-        <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="i" optional="false" label="input sd-file" type="data" format="sdf"/>
+        <param name="mod" optional="false" label="file containing QSAR model" type="data" format="mod"/>
+        <param name="csv" optional="true" label="input csv-file w/ additional descriptors" type="data" format="csv"/>
+        <param name="csv_nr" optional="true" label="Optional: no. of response variables in csv-file" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_sep" optional="true" label="Optional: separator symbol in csv-file" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_cl" optional="true" label="csv-file has compound (row) labels" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_dl" optional="true" label="csv-file has descriptor (column) labels" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="sdf"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/PDBCutter.xml
--- a/CADDSuite/galaxyconfigs/tools/PDBCutter.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="pdbcutter" name="PDBCutter" version="0.94">
+<tool id="pdbcutter" name="PDBCutter" version="0.95">
     <description>separate ligand and receptor</description>
     <command interpreter="bash"><![CDATA[../../PDBCutter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -27,11 +27,11 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="lig_chain" label="chain-name of ligand" optional="false" area="true" type="text" size="1x15"/>
-        <param name="lig_name" label="ligand name" optional="false" area="true" type="text" size="1x15"/>
-        <param name="rm_ch" label="protein chains that are to be deleted" optional="true" area="true" type="text" size="1x15"/>
-        <param name="rm_res" label="pdb-residues that are to be deleted (e.g. water or ions)" optional="true" area="true" type="text" size="1x15"/>
+        <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
+        <param name="lig_chain" optional="false" label="chain-name of ligand" area="true" type="text" size="1x15"/>
+        <param name="lig_name" optional="false" label="ligand name" area="true" type="text" size="1x15"/>
+        <param name="rm_ch" optional="true" label="Optional: protein chains that are to be deleted" area="true" type="text" size="1x15"/>
+        <param name="rm_res" optional="true" label="Optional: pdb-residues that are to be deleted (e.g. water or ions)" area="true" type="text" size="1x15"/>
     </inputs>
     <outputs>
         <data name="rec" format="pdb"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/PDBDownload.xml
--- a/CADDSuite/galaxyconfigs/tools/PDBDownload.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="pdbdownload" name="PDBDownload" version="0.94">
+<tool id="pdbdownload" name="PDBDownload" version="0.95">
     <description>retrieve pdb-file from pdb.org</description>
     <command interpreter="bash"><![CDATA[../../PDBDownload 
 #if str( $id ) != ''  and str( $id ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="id" label="PDB ID for desired structure" optional="false" area="true" type="text" size="1x15"/>
-        <param name="p" label="proxy" optional="true" area="true" type="text" size="1x15"/>
+        <param name="id" optional="false" label="PDB ID for desired structure" area="true" type="text" size="1x15"/>
+        <param name="p" optional="true" label="Optional: proxy" area="true" type="text" size="1x15"/>
     </inputs>
     <outputs>
         <data name="o" format="pdb"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml
--- a/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94">
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.95">
     <description>transfer part. charges between files</description>
     <command interpreter="bash"><![CDATA[../../PartialChargesCopy 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="chr" label="file containing the same molecules as the input file, but with (different) partial charges" optional="false" type="data" format="mol2"/>
+        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
+        <param name="chr" optional="false" label="file containing the same molecules as the input file, but with (different) partial charges" type="data" format="mol2"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/PocketDetector.xml
--- a/CADDSuite/galaxyconfigs/tools/PocketDetector.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="pocketdetector" name="PocketDetector" version="0.94">
+<tool id="pocketdetector" name="PocketDetector" version="0.95">
     <description>detect binding pocket</description>
     <command interpreter="bash"><![CDATA[../../PocketDetector 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -18,9 +18,9 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="input ini file" optional="true" type="data" format="ini"/>
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="input ini file" type="data" format="ini"/>
     </inputs>
     <outputs>
         <data name="o" format="ini"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/Predictor.xml
--- a/CADDSuite/galaxyconfigs/tools/Predictor.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="predictor" name="Predictor" version="1.1">
+<tool id="predictor" name="Predictor" version="0.95">
     <description>predict activities with QSAR model</description>
     <command interpreter="bash"><![CDATA[../../Predictor 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
-        <param name="dat" label="data-file containing prediction data set" optional="false" type="data" format="dat"/>
+        <param name="i" optional="false" label="input mod-file" type="data" format="mod"/>
+        <param name="dat" optional="false" label="data-file containing prediction data set" type="data" format="dat"/>
     </inputs>
     <outputs>
         <data name="o" format="txt"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/PropertyModifier.xml
--- a/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="propertymodifier" name="PropertyModifier" version="0.94">
+<tool id="propertymodifier" name="PropertyModifier" version="0.95">
     <description>modify molecule property tags</description>
     <command interpreter="bash"><![CDATA[../../PropertyModifier 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -24,15 +24,15 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="mode" label="'delete', 'add' or 'rename' properties" optional="false" type="select">
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" optional="false" label="'delete', 'add' or 'rename' properties" type="select">
             <option value="add">add</option>
             <option value="rename">rename</option>
             <option value="delete">delete</option>
         </param>
-        <param name="name" label="property name ('all' will erase all properties if in delete-mode)" optional="false" area="true" type="text" size="1x15"/>
-        <param name="value" label="property value (in case of prop. adding only)" optional="true" area="true" type="text" size="1x15"/>
-        <param name="new_name" label="new property name (in case of renaming only)" optional="true" area="true" type="text" size="1x15"/>
+        <param name="name" optional="false" label="property name ('all' will erase all properties if in delete-mode)" area="true" type="text" size="1x15"/>
+        <param name="value" optional="true" label="Optional: property value (in case of prop. adding only)" area="true" type="text" size="1x15"/>
+        <param name="new_name" optional="true" label="Optional: new property name (in case of renaming only)" area="true" type="text" size="1x15"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml
--- a/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="propertyplotter" name="PropertyPlotter" version="0.94">
+<tool id="propertyplotter" name="PropertyPlotter" version="0.95">
     <description>plot molecule properties</description>
     <command interpreter="bash"><![CDATA[../../PropertyPlotter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -19,9 +19,9 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="p1" label="name of property 1" optional="false" area="true" type="text" size="1x15"/>
-        <param name="p2" label="name of property 2" optional="true" area="true" type="text" size="1x15"/>
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="p1" optional="false" label="name of property 1" area="true" type="text" size="1x15"/>
+        <param name="p2" optional="true" label="Optional: name of property 2" area="true" type="text" size="1x15"/>
     </inputs>
     <outputs>
         <data name="o" format="png"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/ProteinCheck.xml
--- a/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="proteincheck" name="ProteinCheck" version="0.94">
+<tool id="proteincheck" name="ProteinCheck" version="0.95">
     <description>quality check for proteins structures</description>
     <command interpreter="bash"><![CDATA[../../ProteinCheck 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="bc" label="ignore broken chains" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
+        <param name="bc" optional="true" label="ignore broken chains" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="pdf"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml
--- a/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="proteinprotonator" name="ProteinProtonator" version="0.94">
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.95">
     <description>protonate protein structures</description>
     <command interpreter="bash"><![CDATA[../../ProteinProtonator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -15,8 +15,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="pdb"/>
-        <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/>
+        <param name="i" optional="false" label="input file" type="data" format="pdb"/>
+        <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
     </inputs>
     <outputs>
         <data name="o" format="pdb" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml
--- a/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.95">
     <description>calculate RMSD between poses</description>
     <command interpreter="bash"><![CDATA[../../RMSDCalculator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -16,8 +16,8 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="org" label="molecule file containing the original ('true') poses" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
+        <param name="org" optional="false" label="molecule file containing the original ('true') poses" type="data" format="mol2/sdf/drf"/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml
--- a/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94">
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.95">
     <description>generate ROC or enrichment plots</description>
     <command interpreter="bash"><![CDATA[../../ScoreAnalyzer 
 #if str( $mode ) != ''  and str( $mode ) != 'None' :
@@ -30,18 +30,18 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="mode" label="'roc', 'top50', 'scatter' or 'enrichment'" optional="false" type="select">
+        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" optional="false" label="'roc', 'top50', 'scatter' or 'enrichment'" type="select">
             <option value="roc">roc</option>
             <option value="top50">top50</option>
             <option value="scatter">scatter</option>
             <option value="enrichment">enrichment</option>
         </param>
-        <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/>
-        <param name="s" label="score label" optional="false" area="true" type="text" size="1x15" value="score"/>
-        <param name="e" label="binding-free-energy/class label name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
-        <param name="t" label="only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" optional="true" area="true" type="text" size="1x15"/>
-        <param name="b" label="binary experimental activity data" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/>
+        <param name="s" optional="false" label="score label" area="true" type="text" size="1x15" value="score"/>
+        <param name="e" optional="false" label="binding-free-energy/class label name" area="true" type="text" size="1x15" value="binding_free_energy"/>
+        <param name="t" optional="true" label="Optional: only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" area="true" type="text" size="1x15"/>
+        <param name="b" optional="true" label="binary experimental activity data" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="png"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml
--- a/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -19,9 +19,9 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i1" label="input molecule file 1" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="i2" label="input molecule file 2" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/>
+        <param name="i1" optional="false" label="input molecule file 1" type="data" format="mol2/sdf/drf"/>
+        <param name="i2" optional="false" label="input molecule file 2" type="data" format="mol2/sdf/drf"/>
+        <param name="title" optional="true" label="Optional: plot title" area="true" type="text" size="1x15"/>
     </inputs>
     <outputs>
         <data name="o" format="png"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml
--- a/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="simplerescorer" name="SimpleRescorer" version="0.94">
+<tool id="simplerescorer" name="SimpleRescorer" version="0.95">
     <description>rescore docking results</description>
     <command interpreter="bash"><![CDATA[../../SimpleRescorer 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -24,11 +24,11 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="function" label="scoring function: 'MM', 'PLP' or 'PB'" optional="true" type="select">
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
+        <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/>
+        <param name="function" optional="true" label="scoring function: 'MM', 'PLP' or 'PB'" type="select">
             <option value="MM">MM</option>
             <option value="PLP">PLP</option>
             <option value="PB">PB</option>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml
--- a/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94">
+<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95">
     <description>define spatial constraint</description>
     <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner 
 #if str( $ini ) != ''  and str( $ini ) != 'None' :
@@ -24,14 +24,14 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="type" label="'fraction' or 'number' of compound atoms" optional="false" type="select">
+        <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
+        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
+        <param name="type" optional="false" label="'fraction' or 'number' of compound atoms" type="select">
             <option value="fraction">fraction</option>
             <option value="number">number</option>
         </param>
-        <param name="n" label="desired number/fraction of atoms in spatial area" optional="false" type="text" area="true" size="1x5" value=""/>
-        <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="1e11"/>
+        <param name="n" optional="false" label="desired number/fraction of atoms in spatial area" type="text" area="true" size="1x5" value=""/>
+        <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="1e11"/>
     </inputs>
     <outputs>
         <data name="o" format="ini"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/TaGRes-train.xml
--- a/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="tagres-train" name="TaGRes-train" version="0.94">
+<tool id="tagres-train" name="TaGRes-train" version="0.95">
     <description>Target-specific Grid-Rescoring, training</description>
     <command interpreter="bash"><![CDATA[../../TaGRes-train 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -30,20 +30,20 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
+        <param name="i" optional="false" label="training compound data set" type="data" format="mol2/sdf/drf"/>
+        <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select">
             <option value="Rescoring3D">Rescoring3D</option>
             <option value="Rescoring4D">Rescoring4D</option>
             <option value="Rescoring1D">Rescoring1D</option>
         </param>
-        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
+        <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select">
             <option value="MM">MM</option>
             <option value="PLP">PLP</option>
         </param>
-        <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+        <param name="exp" optional="false" label="property-tag name containing experimentally determined binding-free-energies" area="true" type="text" size="1x15" value="binding_free_energy"/>
     </inputs>
     <outputs>
         <data name="o" format="mod"/>
@@ -55,7 +55,7 @@
     * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
     * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein.
 
-A scoring function is applied and an interaction-grid thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it.
+A scoring function is applied and an interaction-grid is thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it.
 
-The output of this TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help>
+The output of TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help>
 </tool>
\ No newline at end of file
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/TaGRes.xml
--- a/CADDSuite/galaxyconfigs/tools/TaGRes.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="tagres" name="TaGRes" version="0.94">
+<tool id="tagres" name="TaGRes" version="0.95">
     <description>Target-specific Grid-Rescoring</description>
     <command interpreter="bash"><![CDATA[../../TaGRes 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -18,6 +18,9 @@
 #if str( $mod ) != ''  and str( $mod ) != 'None' :
    -mod "$mod"
 #end if
+#if str( $tf ) != ''  and str( $tf ) != 'None' :
+   -tf "$tf"
+#end if
 #if str( $o ) != ''  and str( $o ) != 'None' :
    -o "$o"
 #end if
@@ -30,17 +33,18 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="mod" label="model-file generated by TaGRes-train" optional="false" type="data" format="data"/>
-        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
+        <param name="i" optional="false" label="compounds to be rescored" type="data" format="mol2/sdf/drf"/>
+        <param name="mod" optional="false" label="model-file generated by TaGRes-train" type="data" format="data"/>
+        <param name="tf" optional="true" label="Optional: top-scored fraction of compounds not to be rescored" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
+        <param name="method" optional="false" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" type="select">
             <option value="Rescoring3D">Rescoring3D</option>
             <option value="Rescoring4D">Rescoring4D</option>
             <option value="Rescoring1D">Rescoring1D</option>
         </param>
-        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
+        <param name="function" optional="true" label="scoring function: 'MM' or 'PLP'" type="select">
             <option value="MM">MM</option>
             <option value="PLP">PLP</option>
         </param>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/Validator.xml
--- a/CADDSuite/galaxyconfigs/tools/Validator.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Validator.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="validator" name="Validator" version="1.1">
+<tool id="validator" name="Validator" version="0.95">
     <description>evaluate quality of a QSAR model</description>
     <command interpreter="bash"><![CDATA[../../Validator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -18,9 +18,9 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
-        <param name="dat" label="data-file" optional="false" type="data" format="dat"/>
-        <param name="type" label="feature-selection type" optional="false" type="select">
+        <param name="i" optional="false" label="input mod-file" type="data" format="mod"/>
+        <param name="dat" optional="false" label="data-file" type="data" format="dat"/>
+        <param name="type" optional="false" label="feature-selection type" type="select">
             <option value="cross validation">cross validation</option>
             <option value="bootstrapping">bootstrapping</option>
             <option value="response permutation">response permutation</option>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/VendorFinder.xml
--- a/CADDSuite/galaxyconfigs/tools/VendorFinder.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="vendorfinder" name="VendorFinder" version="0.94">
+<tool id="vendorfinder" name="VendorFinder" version="0.95">
     <description>search vendors for compounds</description>
     <command interpreter="bash"><![CDATA[../../VendorFinder 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -30,13 +30,13 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="i" label="input file containing compounds" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
-        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
-        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
-        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
-        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
-        <param name="opt" label="optimize purchase, i.e. select cheapest sources and sort by vendor" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="i" optional="false" label="input file containing compounds" type="data" format="mol2/sdf/drf"/>
+        <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/>
+        <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/>
+        <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/>
+        <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/>
+        <param name="opt" optional="true" label="optimize purchase, i.e. select cheapest sources and sort by vendor" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="txt"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/galaxyconfigs/tools/WaterFinder.xml
--- a/CADDSuite/galaxyconfigs/tools/WaterFinder.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,6 +1,6 @@
 
 <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="waterfinder" name="WaterFinder" version="0.94">
+<tool id="waterfinder" name="WaterFinder" version="0.95">
     <description>find strongly bound waters</description>
     <command interpreter="bash"><![CDATA[../../WaterFinder 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
@@ -24,11 +24,11 @@
  | tail -n 5
 ]]></command>
     <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="wat" label="input pdb-file containing water molecules (if not part of rec.-file)" optional="true" type="data" format="pdb"/>
-        <param name="ai" label="use ab-initio water search (ignore water in pdb-file), experimental!" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
+        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
+        <param name="wat" optional="true" label="input pdb-file containing water molecules (if not part of rec.-file)" type="data" format="pdb"/>
+        <param name="ai" optional="true" label="use ab-initio water search (ignore water in pdb-file), experimental!" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="pdb"/>
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/lib/libBALL.so.1.4
Binary file CADDSuite/lib/libBALL.so.1.4 has changed
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/rescoring_common
--- a/CADDSuite/rescoring_common	Tue Jun 28 10:37:20 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/rescoring_common.bin "$@" 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/setPathes.sh
--- a/CADDSuite/setPathes.sh	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/setPathes.sh	Tue Jul 12 10:23:33 2011 -0400
@@ -5,6 +5,7 @@
 export BABEL_DATADIR="$BASE_DIR"/data/OpenBabel/
 export QT_PLUGIN_PATH="$BASE_DIR"/lib/plugins/
 export PATH="$BASE_DIR"/bin:$PATH
-export GDFONTPATH="$BASE_DIR"/data/fonts
+export GDFONTPATH="$BASE_DIR"/data/gnuplot
 export GNUPLOT_DEFAULT_GDFONT=FreeSans
+export GNUPLOT_PS_DIR="$BASE_DIR"/data/gnuplot
 
diff -r 02c8570cde57 -r b7a89b15646f CADDSuite/suite_config.xml
--- a/CADDSuite/suite_config.xml	Tue Jun 28 10:37:20 2011 -0400
+++ b/CADDSuite/suite_config.xml	Tue Jul 12 10:23:33 2011 -0400
@@ -1,4 +1,4 @@
-<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.94">
+<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.95">
 
 <description>
 CADDSuite: A flexible and open framework for Computer-Aided Drug Design
@@ -6,135 +6,135 @@
 <tool id="cadds_upload" name="Upload File" version="1.1.2">
     <description>from your computer</description>
 </tool>
-<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94">
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.95">
     <description>rescore w/ anti-target dock-results</description>
 </tool>
-<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94">
+<tool id="automodel" name="AutoModel" version="0.95">
+    <description>automatically find best QSAR model</description>
+</tool>
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.95">
     <description>fix bindingdb.org downloads</description>
 </tool>
-<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94">
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.95">
     <description>generate combinatorial lib</description>
 </tool>
-<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94">
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.95">
     <description>find strongly interacting residues</description>
 </tool>
-<tool id="converter" name="Converter" version="0.94">
+<tool id="converter" name="Converter" version="0.95">
     <description>interconvert molecular file-formats</description>
 </tool>
-<tool id="dbexporter" name="DBExporter" version="0.94 (ob)">
+<tool id="dbexporter" name="DBExporter" version="0.95 (ob)">
     <description>export molecules from data base</description>
 </tool>
-<tool id="dbimporter" name="DBImporter" version="0.94 (ob)">
+<tool id="dbimporter" name="DBImporter" version="0.95 (ob)">
     <description>import molecules into data base</description>
 </tool>
-<tool id="dockresultmerger" name="DockResultMerger" version="0.94">
+<tool id="dockresultmerger" name="DockResultMerger" version="0.95">
     <description>merge docking output files</description>
 </tool>
-<tool id="evensplit" name="EvenSplit" version="0.94">
+<tool id="evensplit" name="EvenSplit" version="0.95">
     <description>generate splits w/ equal property range</description>
 </tool>
-<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94">
+<tool id="featureselector" name="FeatureSelector" version="0.95">
+    <description>run feature-selection on a QSAR model</description>
+</tool>
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.95">
     <description>generate galaxy tool-config files</description>
 </tool>
-<tool id="gridbuilder" name="GridBuilder" version="0.94">
+<tool id="gridbuilder" name="GridBuilder" version="0.95">
     <description>create score-grids for docking</description>
 </tool>
-<tool id="imeedydock" name="IMGDock" version="0.94">
+<tool id="imeedydock" name="IMGDock" version="0.95">
     <description>Iterative Multi-Greedy Docking</description>
 </tool>
-<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94">
+<tool id="inputpartitioner" name="InputPartitioner" version="0.95">
+    <description>split QSAR data set</description>
+</tool>
+<tool id="inputreader" name="InputReader" version="0.95">
+    <description>generate QSAR data set</description>
+</tool>
+<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.95">
     <description>define interaction constraint</description>
 </tool>
-<tool id="ligcheck" name="LigCheck" version="0.94">
+<tool id="ligcheck" name="LigCheck" version="0.95">
     <description>check molecules for errors</description>
 </tool>
-<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94">
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.95">
     <description>generate 3D coordinates for small molecules</description>
 </tool>
-<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94">
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.95">
     <description>split molecule files</description>
 </tool>
-<tool id="molcombine" name="MolCombine" version="0.94">
+<tool id="modelcreator" name="ModelCreator" version="1.1">
+    <description>create a QSAR model</description>
+</tool>
+<tool id="molcombine" name="MolCombine" version="0.95">
     <description>combine molecular files</description>
 </tool>
-<tool id="moldepict" name="MolDepict" version="0.94">
+<tool id="moldepict" name="MolDepict" version="0.95">
     <description>create structure diagrams</description>
 </tool>
 <tool id="molfilter" name="MolFilter" version="0.9">
     <description>filter molecule files</description>
 </tool>
-<tool id="pdbcutter" name="PDBCutter" version="0.94">
+<tool id="molpredictor" name="MolPredictor" version="0.95">
+    <description>predict molecule activities with QSAR model</description>
+</tool>
+<tool id="pdbcutter" name="PDBCutter" version="0.95">
     <description>separate ligand and receptor</description>
 </tool>
-<tool id="pdbdownload" name="PDBDownload" version="0.94">
+<tool id="pdbdownload" name="PDBDownload" version="0.95">
     <description>retrieve pdb-file from pdb.org</description>
 </tool>
-<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94">
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.95">
     <description>transfer part. charges between files</description>
 </tool>
-<tool id="pocketdetector" name="PocketDetector" version="0.94">
+<tool id="pocketdetector" name="PocketDetector" version="0.95">
     <description>detect binding pocket</description>
 </tool>
-<tool id="propertymodifier" name="PropertyModifier" version="0.94">
+<tool id="predictor" name="Predictor" version="0.95">
+    <description>predict activities with QSAR model</description>
+</tool>
+<tool id="propertymodifier" name="PropertyModifier" version="0.95">
     <description>modify molecule property tags</description>
 </tool>
-<tool id="propertyplotter" name="PropertyPlotter" version="0.94">
+<tool id="propertyplotter" name="PropertyPlotter" version="0.95">
     <description>plot molecule properties</description>
 </tool>
-<tool id="proteincheck" name="ProteinCheck" version="0.94">
+<tool id="proteincheck" name="ProteinCheck" version="0.95">
     <description>quality check for proteins structures</description>
 </tool>
-<tool id="proteinprotonator" name="ProteinProtonator" version="0.94">
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.95">
     <description>protonate protein structures</description>
 </tool>
-<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.95">
     <description>calculate RMSD between poses</description>
 </tool>
-<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94">
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.95">
     <description>generate ROC or enrichment plots</description>
 </tool>
 <tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9">
     <description>analyze similarity between molecule files</description>
 </tool>
-<tool id="simplerescorer" name="SimpleRescorer" version="0.94">
+<tool id="simplerescorer" name="SimpleRescorer" version="0.95">
     <description>rescore docking results</description>
 </tool>
-<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94">
+<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95">
     <description>define spatial constraint</description>
 </tool>
-<tool id="tagres-train" name="TaGRes-train" version="0.94">
+<tool id="tagres-train" name="TaGRes-train" version="0.95">
     <description>Target-specific Grid-Rescoring, training</description>
 </tool>
-<tool id="tagres" name="TaGRes" version="0.94">
+<tool id="tagres" name="TaGRes" version="0.95">
     <description>Target-specific Grid-Rescoring</description>
 </tool>
-<tool id="vendorfinder" name="VendorFinder" version="0.94">
+<tool id="validator" name="Validator" version="0.95">
+    <description>evaluate quality of a QSAR model</description>
+</tool>
+<tool id="vendorfinder" name="VendorFinder" version="0.95">
     <description>search vendors for compounds</description>
 </tool>
-<tool id="waterfinder" name="WaterFinder" version="0.94">
+<tool id="waterfinder" name="WaterFinder" version="0.95">
     <description>find strongly bound waters</description>
-</tool>
-<tool id="automodel" name="AutoModel" version="1.1">
-    <description>automatically find best QSAR model</description>
-</tool>
-<tool id="featureselector" name="FeatureSelector" version="1.1">
-    <description>run feature-selection on a QSAR model</description>
-</tool>
-<tool id="inputpartitioner" name="InputPartitioner" version="1.1">
-    <description>split QSAR data set</description>
-</tool>
-<tool id="inputreader" name="InputReader" version="1.1">
-    <description>generate QSAR data set</description>
-</tool>
-<tool id="modelcreator" name="ModelCreator" version="1.1">
-    <description>create a QSAR model</description>
-</tool>
-<tool id="molpredictor" name="MolPredictor" version="1.1">
-    <description>predict molecule activities with QSAR model</description>
-</tool>
-<tool id="predictor" name="Predictor" version="1.1">
-    <description>predict activities with QSAR model</description>
-</tool>
-<tool id="validator" name="Validator" version="1.1">
-    <description>evaluate quality of a QSAR model</description>
 </tool></suite>