# HG changeset patch
# User greg
# Date 1321371100 18000
# Node ID c191531894866bc27f0bd5ae138250bf698e5972
# Parent  389056b8864a0d48ba51cd39d21d6576825f0b95
Deleted selected files

diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/AntitargetRescorer
--- a/CADDSuite-1.0.1/AntitargetRescorer	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/AntitargetRescorer.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/AutoModel
--- a/CADDSuite-1.0.1/AutoModel	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/AutoModel.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/BindingDBCleaner
--- a/CADDSuite-1.0.1/BindingDBCleaner	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/BindingDBCleaner.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/CADDSuite-description.txt
--- a/CADDSuite-1.0.1/CADDSuite-description.txt	Mon Nov 14 17:02:30 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-This package contains tools belonging to
-CADDSuite: A flexible and open framework for Computer-Aided Drug Design
-
-There are tools for the following tasks:
-
-Get Data:
-	- CombiLibGenerator: generate R-group decorated ligands
-	- DBExporter: fetch (filtered) molecules from DB
-
-Preparation of input:
-	- PDBCutter: separate ligand and receptor
-	- ProteinProtonator: protonate protein structures
-	- BindingDBCleaner: fix data from bindingdb.org
-	- EvenSplit: generate splits w/ equal property range
-	- PropertyModifier: modify property tags
-	- LigandFileSplitter: split molecule files
-	- Ligand3DGenerator: generate 3D coordinates for small molecules
-
-Structure checks and evaluations:
-	- ProteinCheck: evaluate protein quality
-	- LigCheck: chemical sanity check for ligands
-
-QuEasy (QSAR):
-	- InputReader: read molecules and generate features
-	- ModelCreator: create a QSAR model
-	- FeatureSelector: automatically select features of a QSAR model
-	- Validator: evaluate quality of a QSAR model
-	- MolPredictor: predict molecule activities with QSAR model
-	- AutoModel: automatically find best QSAR model
-
-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
-	- IMGDock: run Iterative Multi-Greedy Docking
-
-Rescoring:
-	- SimpleRescorer: rescore docking results 
-	- TaGRes-train: Target-specific Grid-Rescoring, training
-	- TaGRes: Target-specific Grid-Rescoring
-	- AntitargetRescoring: rescore w/ respect to antitarget
-
-Analysis:
-	- ScoreAnalyzer: generate ROC or enrichment plots
-	- SimilarityAnalyzer: analyze similarity between two molecule sets
-	- PropertyPlotter: plot molecule properties
-	- RMSDCalculator: calculate RMSD between conformations
-	- VendorFinder: search vendors for compounds
-
-Convert, combine and store:
-	- DockResultMerger: merge docking output files and/or filter them
-	- MolCombine: combine molecular files
-	- DBImporter: import molecules into DB
-	- Converter: interconvert molecular file-formats
-	- MolDepict: generate structure diagrams
-	- VendorFinder: search vendors for compounds
-
-For more information about an individual tool, please call the tool without any parameters (or with '-help').
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/CombiLibGenerator
--- a/CADDSuite-1.0.1/CombiLibGenerator	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/CombiLibGenerator.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/ConstraintsFinder
--- a/CADDSuite-1.0.1/ConstraintsFinder	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/ConstraintsFinder.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/Converter
--- a/CADDSuite-1.0.1/Converter	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/Converter.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/DBExporter
--- a/CADDSuite-1.0.1/DBExporter	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/DBExporter.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/DBImporter
--- a/CADDSuite-1.0.1/DBImporter	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/DBImporter.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/DockResultMerger
--- a/CADDSuite-1.0.1/DockResultMerger	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/DockResultMerger.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/EvenSplit
--- a/CADDSuite-1.0.1/EvenSplit	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/EvenSplit.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/FeatureSelector
--- a/CADDSuite-1.0.1/FeatureSelector	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/FeatureSelector.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/GalaxyConfigGenerator
--- a/CADDSuite-1.0.1/GalaxyConfigGenerator	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/GridBuilder
--- a/CADDSuite-1.0.1/GridBuilder	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/GridBuilder.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/IMGDock
--- a/CADDSuite-1.0.1/IMGDock	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/IMGDock.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/InputPartitioner
--- a/CADDSuite-1.0.1/InputPartitioner	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/InputPartitioner.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/InputReader
--- a/CADDSuite-1.0.1/InputReader	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/InputReader.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/InteractionConstraintDefiner
--- a/CADDSuite-1.0.1/InteractionConstraintDefiner	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/LigCheck
--- a/CADDSuite-1.0.1/LigCheck	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/LigCheck.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/Ligand3DGenerator
--- a/CADDSuite-1.0.1/Ligand3DGenerator	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/Ligand3DGenerator.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/LigandFileSplitter
--- a/CADDSuite-1.0.1/LigandFileSplitter	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/LigandFileSplitter.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/ModelCreator
--- a/CADDSuite-1.0.1/ModelCreator	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/ModelCreator.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/MolCombine
--- a/CADDSuite-1.0.1/MolCombine	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/MolCombine.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/MolDepict
--- a/CADDSuite-1.0.1/MolDepict	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/MolDepict.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/MolFilter
--- a/CADDSuite-1.0.1/MolFilter	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/MolFilter.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/MolPredictor
--- a/CADDSuite-1.0.1/MolPredictor	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/MolPredictor.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/PDBCutter
--- a/CADDSuite-1.0.1/PDBCutter	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/PDBCutter.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/PDBDownload
--- a/CADDSuite-1.0.1/PDBDownload	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/PDBDownload.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/PartialChargesCopy
--- a/CADDSuite-1.0.1/PartialChargesCopy	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/PartialChargesCopy.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/PocketDetector
--- a/CADDSuite-1.0.1/PocketDetector	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/PocketDetector.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/Predictor
--- a/CADDSuite-1.0.1/Predictor	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/Predictor.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/PropertyModifier
--- a/CADDSuite-1.0.1/PropertyModifier	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/PropertyModifier.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/PropertyPlotter
--- a/CADDSuite-1.0.1/PropertyPlotter	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/PropertyPlotter.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/ProteinCheck
--- a/CADDSuite-1.0.1/ProteinCheck	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/ProteinCheck.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/ProteinProtonator
--- a/CADDSuite-1.0.1/ProteinProtonator	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/ProteinProtonator.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/README
--- a/CADDSuite-1.0.1/README	Mon Nov 14 17:02:30 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
------------------------------------------------------------------------
-   CADDSuite - A flexible and open framework and workflow system
-               for computer-aided drug design
------------------------------------------------------------------------
-
-This package contains all tools belonging to CADDSuite.
-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 '-help').
-
-
-
---------------------------------------------------------------------
-Instructions for integration of CADDSuite into the workflow-system
-Galaxy (http://getgalaxy.org)
---------------------------------------------------------------------
-
-
-In order to install CADDSuite into your Galaxy installation, please to the following:
-
-Let's assume $galaxybase is the base-folder of your Galaxy installation.
-If you don't have a galaxy-installation yet, download a version from http://getgalaxy.org and follow the installation instructions shown there first.
-
-
--- Extract the CADDSuite archive into a new folder $galaxybase/tools/CADDSuite, or extract it somewhere else and create a link named $galaxybase/tools/CADDSuite that points to this destination.
-
-After this, you need to copy a few files that you find in the galaxyconfig/ subfolder of this archive to the destinations specified below:
-
--- Copy tool_conf.xml and datatypes_conf.xml to $galaxybase if you want to setup your Galaxy instance for exclusive use of CADDSuite, or copy the contents of those files into the files already existing in $galaxybase if you want to keep using tools that came along with the Galaxy installation.
-
--- Copy molFiles.py, confFiles.py and countResidues.sh to $galaxybase/lib/galaxy/datatypes/
-
--- Add "#import molFiles, confFiles.py" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py
-
-
-
-Last but not least, restart Galaxy.
-All CADDSuite tools should now appear in your Galaxy webinterface.
-
-
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/RMSDCalculator
--- a/CADDSuite-1.0.1/RMSDCalculator	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/RMSDCalculator.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/ScoreAnalyzer
--- a/CADDSuite-1.0.1/ScoreAnalyzer	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/ScoreAnalyzer.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/SimilarityAnalyzer
--- a/CADDSuite-1.0.1/SimilarityAnalyzer	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/SimpleRescorer
--- a/CADDSuite-1.0.1/SimpleRescorer	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/SimpleRescorer.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/SpatialConstraintDefiner
--- a/CADDSuite-1.0.1/SpatialConstraintDefiner	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/TaGRes
--- a/CADDSuite-1.0.1/TaGRes	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/TaGRes.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/TaGRes-train
--- a/CADDSuite-1.0.1/TaGRes-train	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/TaGRes-train.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/Validator
--- a/CADDSuite-1.0.1/Validator	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/Validator.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/VendorFinder
--- a/CADDSuite-1.0.1/VendorFinder	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/VendorFinder.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/WaterFinder
--- a/CADDSuite-1.0.1/WaterFinder	Mon Nov 14 17:02:30 2011 -0500
+++ /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
-		"$BASE_DIR"/bin/WaterFinder.bin "$@" 
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/changelog.txt
--- a/CADDSuite-1.0.1/changelog.txt	Mon Nov 14 17:02:30 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-Version 1.0.1, 11-06-2011:
-	- In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules
-	- Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions
-	- Display meaningful error if automatic QSAR model creation is attempted with data not containing any response variables
-
-Version 1.0, 11-04-2011:
-	- Added support for advanced parameters and parameter sections
-	- Added some missing 'supported_formats' and 'tool_category' tags
-	- Fixed tar compression on Mac
-	- Fix for use of libsvm 3.1
-	- Fix for use of created release packages on MacOS 10.7
-	- Added missing flag to MolPredictor.
-
-Version 0.9.6, 08-20-2011:
-	- MolFilter: Use union of SMARTS matches instead of intersection
-	- Support for reading and writing compressed molecule files (*.gz)
-	- Added optional parameter for output log-file to DBImporter
-	- Added flag for disabling uniqueness-check to LigCheck
-	- mol2-files: disabled gaff atom-typing for speed-up
-	- drf-files: automatically add new protein-conformations
-	- Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable
-	- InputReader: made sure to always calculate correct set of features
-	- Fixed a nan problem during centering of QSAR data
-
-Version 0.9.5, 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 0.9.4, 06-27-2011:
-	- Fixed tool-startup script for pathes containing whitespaces
-	- New tool SpatialConstraintDefiner
-	- New tool InteractionConstraintDefiner
-	- Removed superficial pathes from startup-script
-	- Slight change in ParamFile format (i.e. the files written with -write_par)
-	- Renamed IMeedyDock to IMGDock
-
-Version 0.9.3, 05-30-2011:
-	- Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring)
-	- Allow to optionally specify output filenames to LigandFileSplitter
-	- Fixed creation of galaxy-scripts for tools with inputfile-lists
-	- Fixed creation of galaxy-scripts for Converter and DockResultMerger
-	- Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive
-	- New tool MolFilter
-	- Fixed some gnuplot issues
-	- Added PDBDownload tool
-	- Slight change of format of ParamFile
-	- Added some missing tool-manuals
-	- Disable B-factor check for hydrogens in ProteinCheck
-	- Added safeguards to several tools
-	- Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator
-	- Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used)
-	- Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file)
-	- Enhanced several tool manuals
-	- Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles.
-
-Version 0.9.2, 05-17-2011:
-	- Speed-up of ob-mol generation
-	- Support build on Windows
-	- ProteinCheck now generates protein-quality report as pdf
-	- Added info about mandatory parameters and parameter-restrictions to parameter xml-file
-	- Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file)
-	- Simplified use of some other tools by merging several flags into one string-parameter that has restrictions.
-	- New tool MolDepict. It generates structure diagrams for small molecules by using openbabel's svg-writer and merges them to one pdf-file (3 on 5).
-	- Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script
-	- Write information about supported file-formats to parameter xml-file
-	- new tool ProteinProtonator
-	- new tool Ligand3DGenerator
-	- new tool GalaxyConfigGenerator
-	- allow to open file that do not have an extension (by searching for format-specific keywords)
-
-Version 0.9.1, 04-12-2011:
-	- All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par)
-
-Version 0.9
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/install.sh
--- a/CADDSuite-1.0.1/install.sh	Mon Nov 14 17:02:30 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-#!/bin/bash
-
-QT_DIR=""
-INSTALL_DIR=""
-#OPT="Linux_x86_64"
-
-
-checkDir()
-{
-	echo -n "checking for "$1" ... "
-	if [ -f $QT_DIR/$1 ]; then
-		echo $QT_DIR/$1
-		return 1
-	else
-		echo "not found!"
-		return 0
-	fi
-}
-
-echo
-cat license.txt
-echo
-echo -n "Do you agree to this license?! (y/n) "
-read license_accepted
-echo
-
-if [ "$license_accepted" != "y" ] && [ "$license_accepted" != "yes" ]; then
-	echo "License was not accepted, aborting."
-	exit 1
-fi
-
-echo -n "Please enter *absolute* path to install target-directory: "
-
-read INSTALL_DIR
-if [ ! -d $INSTALL_DIR ]; then 
-	mkdir $INSTALL_DIR
-fi
-
-if [ ! -d $INSTALL_DIR ]; then
-	echo
-	echo "[Error:] The desired install-directory does not exist and could also not be created!"
-	echo "Perhaps there was a typo or you do not have permission to create this folder."
-	echo "Aborting install."
-	echo
-	exit 1
-fi
-
-# if [ -f /usr/lib/libQtCore.so.4 ] && [ -f  /usr/lib/libQtGui.so.4 ]; then
-# 	QT_DIR=/usr/lib 
-# else 
-# 	echo "Please enter absolute path to the directory containing"
-# 	echo -n "your Qt4 libraries (version>=4.3.5): "
-# 	read QT_DIR
-# fi
-
-# checkDir libQtCore.so.4; ok=$?;
-# checkDir libQtGui.so.4;  if [ $ok = 1 ]; then let ok $?; fi
-# #checkDir libQtOpenGL.so; if [ $ok = 1 ]; then ok=$?; fi
-# 
-# if [ $ok != 1 ]; then
-# 	echo "Aborting installation due to missing Qt4!"
-# 	exit 1
-# fi
-
-cd bin
-programs=`ls *.bin`
-cd ..
-for i in $programs; do
-	chmod +x ${i:0:${#i}-4}
-done
-
-
-mv * $INSTALL_DIR/
-
-if [ -f $INSTALL_DIR/CADDSuite-description.txt ]; then
-	echo
-	echo
-	cat $INSTALL_DIR/CADDSuite-description.txt
-fi
-
-echo
-echo "Installation finished."
-echo "You can find all installed programs in $INSTALL_DIR."
-echo
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/license.txt
--- a/CADDSuite-1.0.1/license.txt	Mon Nov 14 17:02:30 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
--------------------------------------------------------------------------------
-   CADDSuite - A flexible and open framework and workflow system
-               for computer-aided drug design
--------------------------------------------------------------------------------
-
-Copyright (C) 2011  Marcel Schumann
-
-CADDSuite is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 3 of the License, or (at
-your option) any later version.
-
-CADDSuite is distributed in the hope that it will be useful, but
-WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program; if not, see <http://www.gnu.org/licenses/>.
-
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/setPathes.sh
--- a/CADDSuite-1.0.1/setPathes.sh	Mon Nov 14 17:02:30 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#!/bin/bash
-export LD_LIBRARY_PATH="$BASE_DIR"/lib
-export DYLD_LIBRARY_PATH="$BASE_DIR"/lib:/System/Library/Frameworks/Accelerate.framework/Versions/Current/
-export BALL_DATA_PATH="$BASE_DIR"/data
-export BABEL_DATADIR="$BASE_DIR"/data/OpenBabel/
-export QT_PLUGIN_PATH="$BASE_DIR"/lib/plugins/
-export PATH="$BASE_DIR"/bin:$PATH
-export GDFONTPATH="$BASE_DIR"/data/gnuplot
-export GNUPLOT_DEFAULT_GDFONT=FreeSans
-export GNUPLOT_PS_DIR="$BASE_DIR"/data/gnuplot
-
diff -r 389056b8864a -r c19153189486 CADDSuite-1.0.1/suite_config.xml
--- a/CADDSuite-1.0.1/suite_config.xml	Mon Nov 14 17:02:30 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,140 +0,0 @@
-<suite id="CADDSuite_toolsuite" name="CADDSuite" version="1.0.1">
-
-<description>
-CADDSuite: A flexible and open framework for Computer-Aided Drug Design
-</description>
-<tool id="cadds_upload" name="Upload File" version="1.1.2">
-    <description>from your computer</description>
-</tool>
-<tool id="antitargetrescorer" name="AntitargetRescorer" version="1.0.1">
-    <description>rescore w/ anti-target dock-results</description>
-</tool>
-<tool id="automodel" name="AutoModel" version="1.0.1">
-    <description>automatically find best QSAR model</description>
-</tool>
-<tool id="bindingdbcleaner" name="BindingDBCleaner" version="1.0.1">
-    <description>fix bindingdb.org downloads</description>
-</tool>
-<tool id="combilibgenerator" name="CombiLibGenerator" version="1.0.1">
-    <description>generate combinatorial lib</description>
-</tool>
-<tool id="constraintsfinder" name="ConstraintsFinder" version="1.0.1">
-    <description>find strongly interacting residues</description>
-</tool>
-<tool id="converter" name="Converter" version="1.0.1">
-    <description>interconvert molecular file-formats</description>
-</tool>
-<tool id="dbexporter" name="DBExporter" version="1.0.1 (ob)">
-    <description>export molecules from data base</description>
-</tool>
-<tool id="dbimporter" name="DBImporter" version="1.0.1 (ob)">
-    <description>import molecules into data base</description>
-</tool>
-<tool id="dockresultmerger" name="DockResultMerger" version="1.0.1">
-    <description>merge docking output files</description>
-</tool>
-<tool id="evensplit" name="EvenSplit" version="1.0.1">
-    <description>generate splits w/ equal property range</description>
-</tool>
-<tool id="featureselector" name="FeatureSelector" version="1.0.1">
-    <description>run feature-selection on a QSAR model</description>
-</tool>
-<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="1.0.1">
-    <description>generate galaxy tool-config files</description>
-</tool>
-<tool id="gridbuilder" name="GridBuilder" version="1.0.1">
-    <description>create score-grids for docking</description>
-</tool>
-<tool id="imeedydock" name="IMGDock" version="1.0.1">
-    <description>Iterative Multi-Greedy Docking</description>
-</tool>
-<tool id="inputpartitioner" name="InputPartitioner" version="1.0.1">
-    <description>split QSAR data set</description>
-</tool>
-<tool id="inputreader" name="InputReader" version="1.0.1">
-    <description>generate QSAR data set</description>
-</tool>
-<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="1.0.1">
-    <description>define interaction constraint</description>
-</tool>
-<tool id="ligcheck" name="LigCheck" version="1.0.1">
-    <description>check molecules for errors</description>
-</tool>
-<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="1.0.1">
-    <description>generate 3D coordinates for small molecules</description>
-</tool>
-<tool id="ligandfilesplitter" name="LigandFileSplitter" version="1.0.1">
-    <description>split molecule files</description>
-</tool>
-<tool id="modelcreator" name="ModelCreator" version="1.1">
-    <description>create a QSAR model</description>
-</tool>
-<tool id="molcombine" name="MolCombine" version="1.0.1">
-    <description>combine molecular files</description>
-</tool>
-<tool id="moldepict" name="MolDepict" version="1.0.1">
-    <description>create structure diagrams</description>
-</tool>
-<tool id="molfilter" name="MolFilter" version="0.9">
-    <description>filter molecule files</description>
-</tool>
-<tool id="molpredictor" name="MolPredictor" version="1.0.1">
-    <description>predict molecule activities with QSAR model</description>
-</tool>
-<tool id="pdbcutter" name="PDBCutter" version="1.0.1">
-    <description>separate ligand and receptor</description>
-</tool>
-<tool id="pdbdownload" name="PDBDownload" version="1.0.1">
-    <description>retrieve pdb-file from pdb.org</description>
-</tool>
-<tool id="partialchargescopy" name="PartialChargesCopy" version="1.0.1">
-    <description>transfer part. charges between files</description>
-</tool>
-<tool id="pocketdetector" name="PocketDetector" version="1.0.1">
-    <description>detect binding pocket</description>
-</tool>
-<tool id="predictor" name="Predictor" version="1.0.1">
-    <description>predict activities with QSAR model</description>
-</tool>
-<tool id="propertymodifier" name="PropertyModifier" version="1.0.1">
-    <description>modify molecule property tags</description>
-</tool>
-<tool id="propertyplotter" name="PropertyPlotter" version="1.0.1">
-    <description>plot molecule properties</description>
-</tool>
-<tool id="proteincheck" name="ProteinCheck" version="1.0.1">
-    <description>quality check for proteins structures</description>
-</tool>
-<tool id="proteinprotonator" name="ProteinProtonator" version="1.0.1">
-    <description>protonate protein structures</description>
-</tool>
-<tool id="rmsdcalculator" name="RMSDCalculator" version="1.0.1">
-    <description>calculate RMSD between poses</description>
-</tool>
-<tool id="scoreanalyzer" name="ScoreAnalyzer" version="1.0.1">
-    <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="1.0.1">
-    <description>rescore docking results</description>
-</tool>
-<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="1.0.1">
-    <description>define spatial constraint</description>
-</tool>
-<tool id="tagres-train" name="TaGRes-train" version="1.0.1">
-    <description>Target-specific Grid-Rescoring, training</description>
-</tool>
-<tool id="tagres" name="TaGRes" version="1.0.1">
-    <description>Target-specific Grid-Rescoring</description>
-</tool>
-<tool id="validator" name="Validator" version="1.0.1">
-    <description>evaluate quality of a QSAR model</description>
-</tool>
-<tool id="vendorfinder" name="VendorFinder" version="1.0.1">
-    <description>search vendors for compounds</description>
-</tool>
-<tool id="waterfinder" name="WaterFinder" version="1.0.1">
-    <description>find strongly bound waters</description>
-</tool></suite>