# HG changeset patch
# User marcel
# Date 1314968057 14400
# Node ID af446ca2d5c6d0a5fcbcec0b905e26e550974a1b
# Parent  bb26168c571599555ed45a1fc81c98556686a2d7
Uploaded

diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/AntitargetRescorer.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/AutoModel.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/BindingDBCleaner.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/CombiLibGenerator.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/ConstraintsFinder.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/Converter.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/DBExporter.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/DBImporter.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/DockResultMerger.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/EvenSplit.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/FeatureSelector.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/GalaxyConfigGenerator.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/GridBuilder.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/IMGDock.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/InputPartitioner.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/InputReader.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/InteractionConstraintDefiner.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/LigCheck.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/Ligand3DGenerator.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/LigandFileSplitter.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/ModelCreator.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/MolCombine.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/MolDepict.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/MolFilter.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/MolPredictor.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/PDBCutter.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/PDBDownload.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/PartialChargesCopy.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/PocketDetector.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/Predictor.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/PropertyModifier.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/PropertyPlotter.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/ProteinCheck.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/ProteinProtonator.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/RMSDCalculator.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/ScoreAnalyzer.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/SimilarityAnalyzer.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/SimpleRescorer.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/SpatialConstraintDefiner.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/TaGRes-train.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/TaGRes.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/Validator.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/VendorFinder.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/bin/WaterFinder.bin
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diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/changelog.txt
--- a/CADDSuite/changelog.txt	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/changelog.txt	Fri Sep 02 08:54:17 2011 -0400
@@ -1,4 +1,15 @@
-Version 0.95, 07-12-2011:
+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
@@ -6,7 +17,7 @@
 	- Set some default values for flags for use in GUIs
 	- Clarified EvenSplit docu
 
-Version 0.94, 06-27-2011:
+Version 0.9.4, 06-27-2011:
 	- Fixed tool-startup script for pathes containing whitespaces
 	- New tool SpatialConstraintDefiner
 	- New tool InteractionConstraintDefiner
@@ -14,7 +25,7 @@
 	- Slight change in ParamFile format (i.e. the files written with -write_par)
 	- Renamed IMeedyDock to IMGDock
 
-Version 0.93, 05-30-2011:
+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
@@ -33,7 +44,7 @@
 	- 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 0.92, 05-17-2011:
+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
@@ -48,7 +59,7 @@
 	- new tool GalaxyConfigGenerator
 	- allow to open file that do not have an extension (by searching for format-specific keywords)
 
-Version 0.91, 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 0.9.1, 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 bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tool_conf.xml
--- a/CADDSuite/galaxyconfigs/tool_conf.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tool_conf.xml	Fri Sep 02 08:54:17 2011 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <toolbox>
-  <label text="CADDSuite 0.95" id="cadds" />
+  <label text="CADDSuite 0.9.6" id="cadds" />
 
   <section name="Get Data" id="getext">
     <tool file="CADDSuite/galaxyconfigs/tools/upload.xml"/>
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml
--- a/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.9.6">
     <description>rescore w/ anti-target dock-results</description>
     <command interpreter="bash"><![CDATA[../../AntitargetRescorer 
 #if str( $t ) != ''  and str( $t ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/AutoModel.xml
--- a/CADDSuite/galaxyconfigs/tools/AutoModel.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="automodel" name="AutoModel" version="0.9.6">
     <description>automatically find best QSAR model</description>
     <command interpreter="bash"><![CDATA[../../AutoModel 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml
--- a/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.9.6">
     <description>fix bindingdb.org downloads</description>
     <command interpreter="bash"><![CDATA[../../BindingDBCleaner 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml
--- a/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.9.6">
     <description>generate combinatorial lib</description>
     <command interpreter="bash"><![CDATA[../../CombiLibGenerator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml
--- a/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.9.6">
     <description>find strongly interacting residues</description>
     <command interpreter="bash"><![CDATA[../../ConstraintsFinder 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/Converter.xml
--- a/CADDSuite/galaxyconfigs/tools/Converter.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Converter.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="converter" name="Converter" version="0.9.6">
     <description>interconvert molecular file-formats</description>
     <command interpreter="bash"><![CDATA[../../Converter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -12,6 +12,9 @@
 #if str( $f ) != ''  and str( $f ) != 'None' :
    -f "$f"
 #end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
  | tail -n 5
 ]]></command>
     <inputs>
@@ -27,7 +30,18 @@
             <option value="hin">hin</option>
             <option value="mol">mol</option>
             <option value="xyz">xyz</option>
+            <option value="mol2.gz">mol2.gz</option>
+            <option value="sdf.gz">sdf.gz</option>
+            <option value="drf.gz">drf.gz</option>
+            <option value="pdb.gz">pdb.gz</option>
+            <option value="ac.gz">ac.gz</option>
+            <option value="ent.gz">ent.gz</option>
+            <option value="brk.gz">brk.gz</option>
+            <option value="hin.gz">hin.gz</option>
+            <option value="mol.gz">mol.gz</option>
+            <option value="xyz.gz">xyz.gz</option>
         </param>
+        <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf">
@@ -42,9 +56,19 @@
                 <when input="f" value="hin" format="hin"/>
                 <when input="f" value="mol" format="mol"/>
                 <when input="f" value="xyz" format="xyz"/>
+                <when input="f" value="mol2.gz" format="mol2.gz"/>
+                <when input="f" value="sdf.gz" format="sdf.gz"/>
+                <when input="f" value="drf.gz" format="drf.gz"/>
+                <when input="f" value="pdb.gz" format="pdb.gz"/>
+                <when input="f" value="ac.gz" format="ac.gz"/>
+                <when input="f" value="ent.gz" format="ent.gz"/>
+                <when input="f" value="brk.gz" format="brk.gz"/>
+                <when input="f" value="hin.gz" format="hin.gz"/>
+                <when input="f" value="mol.gz" format="mol.gz"/>
+                <when input="f" value="xyz.gz" format="xyz.gz"/>
             </change_format>
         </data>
     </outputs>
     <help>This tool can be used to convert between different molecular file-formats.
-Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help>
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz, mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.</help>
 </tool>
\ No newline at end of file
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/DBExporter.xml
--- a/CADDSuite/galaxyconfigs/tools/DBExporter.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml	Fri Sep 02 08:54:17 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="0.95 (ob)">
+<tool id="dbexporter" name="DBExporter" version="0.9.6 (ob)">
     <description>export molecules from data base</description>
     <command interpreter="bash"><![CDATA[../../DBExporter 
 #if str( $o ) != ''  and str( $o ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/DBImporter.xml
--- a/CADDSuite/galaxyconfigs/tools/DBImporter.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml	Fri Sep 02 08:54:17 2011 -0400
@@ -1,11 +1,14 @@
 
 <!--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="0.95 (ob)">
+<tool id="dbimporter" name="DBImporter" version="0.9.6 (ob)">
     <description>import molecules into data base</description>
     <command interpreter="bash"><![CDATA[../../DBImporter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
    -i "$i"
 #end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
 #if str( $target ) != ''  and str( $target ) != 'None' :
    -target "$target"
 #end if
@@ -51,7 +54,9 @@
         <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/>
+    <outputs>
+        <data name="o" format="data"/>
+    </outputs>
     <help>This tool imports molecules into a database.
 As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help>
 </tool>
\ No newline at end of file
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/DockResultMerger.xml
--- a/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="dockresultmerger" name="DockResultMerger" version="0.9.6">
     <description>merge docking output files</description>
     <command interpreter="bash"><![CDATA[../../DockResultMerger 
 #for $s in $series_i 
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/EvenSplit.xml
--- a/CADDSuite/galaxyconfigs/tools/EvenSplit.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="evensplit" name="EvenSplit" version="0.9.6">
     <description>generate splits w/ equal property range</description>
     <command interpreter="bash"><![CDATA[../../EvenSplit 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/FeatureSelector.xml
--- a/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="featureselector" name="FeatureSelector" version="0.9.6">
     <description>run feature-selection on a QSAR model</description>
     <command interpreter="bash"><![CDATA[../../FeatureSelector 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml
--- a/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.9.6">
     <description>generate galaxy tool-config files</description>
     <command interpreter="bash"><![CDATA[../../GalaxyConfigGenerator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/GridBuilder.xml
--- a/CADDSuite/galaxyconfigs/tools/GridBuilder.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="gridbuilder" name="GridBuilder" version="0.9.6">
     <description>create score-grids for docking</description>
     <command interpreter="bash"><![CDATA[../../GridBuilder 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/IMGDock.xml
--- a/CADDSuite/galaxyconfigs/tools/IMGDock.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/IMGDock.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="imeedydock" name="IMGDock" version="0.9.6">
     <description>Iterative Multi-Greedy Docking</description>
     <command interpreter="bash"><![CDATA[../../IMGDock 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/InputPartitioner.xml
--- a/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="inputpartitioner" name="InputPartitioner" version="0.9.6">
     <description>split QSAR data set</description>
     <command interpreter="bash"><![CDATA[../../InputPartitioner 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/InputReader.xml
--- a/CADDSuite/galaxyconfigs/tools/InputReader.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="inputreader" name="InputReader" version="0.9.6">
     <description>generate QSAR data set</description>
     <command interpreter="bash"><![CDATA[../../InputReader 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml
--- a/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.9.6">
     <description>define interaction constraint</description>
     <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner 
 #if str( $res ) != ''  and str( $res ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/LigCheck.xml
--- a/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="ligcheck" name="LigCheck" version="0.9.6">
     <description>check molecules for errors</description>
     <command interpreter="bash"><![CDATA[../../LigCheck 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -18,13 +18,21 @@
 #if str( $ut ) != ''  and str( $ut ) != 'None' :
    -ut
 #end if
+#if str( $nc ) != ''  and str( $nc ) != 'None' :
+   -nc
+#end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
  | tail -n 5
 ]]></command>
     <inputs>
         <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=""/>
+        <param name="ut" optional="true" label="check for unique topologies" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="nc" optional="true" label="no not check for unique conformations" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml
--- a/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.9.6">
     <description>generate 3D coordinates for small molecules</description>
     <command interpreter="bash"><![CDATA[../../Ligand3DGenerator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -12,11 +12,15 @@
 #if str( $ph ) != ''  and str( $ph ) != 'None' :
    -ph "$ph"
 #end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
  | tail -n 5
 ]]></command>
     <inputs>
         <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"/>
+        <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
@@ -26,5 +30,5 @@
 
 Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other.
 
-Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help>
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz, mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.</help>
 </tool>
\ No newline at end of file
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml
--- a/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.9.6">
     <description>split molecule files</description>
     <command interpreter="bash"><![CDATA[../../LigandFileSplitter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/MolCombine.xml
--- a/CADDSuite/galaxyconfigs/tools/MolCombine.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="molcombine" name="MolCombine" version="0.9.6">
     <description>combine molecular files</description>
     <command interpreter="bash"><![CDATA[../../MolCombine 
 #if str( $i1 ) != ''  and str( $i1 ) != 'None' :
@@ -21,6 +21,9 @@
 #if str( $replace_prop ) != ''  and str( $replace_prop ) != 'None' :
    -replace_prop
 #end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
  | tail -n 5
 ]]></command>
     <inputs>
@@ -33,6 +36,7 @@
         </param>
         <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=""/>
+        <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i1"/>
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/MolDepict.xml
--- a/CADDSuite/galaxyconfigs/tools/MolDepict.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="moldepict" name="MolDepict" version="0.9.6">
     <description>create structure diagrams</description>
     <command interpreter="bash"><![CDATA[../../MolDepict 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/MolFilter.xml
--- a/CADDSuite/galaxyconfigs/tools/MolFilter.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml	Fri Sep 02 08:54:17 2011 -0400
@@ -37,6 +37,9 @@
    -o "$o"
 #end if
 -quiet 
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
  | tail -n 5
 ]]></command>
     <inputs>
@@ -50,6 +53,7 @@
         <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"/>
+        <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="mol2/sdf/drf" format_source="i"/>
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/MolPredictor.xml
--- a/CADDSuite/galaxyconfigs/tools/MolPredictor.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="molpredictor" name="MolPredictor" version="0.9.6">
     <description>predict molecule activities with QSAR model</description>
     <command interpreter="bash"><![CDATA[../../MolPredictor 
 #if str( $i ) != ''  and str( $i ) != 'None' :
@@ -27,6 +27,9 @@
 #if str( $csv_dl ) != ''  and str( $csv_dl ) != 'None' :
    -csv_dl
 #end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
  | tail -n 5
 ]]></command>
     <inputs>
@@ -37,6 +40,7 @@
         <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=""/>
+        <param name="rm" optional="true" label="remove input sd-file when finished" type="boolean" truevalue="true" falsevalue=""/>
     </inputs>
     <outputs>
         <data name="o" format="sdf"/>
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/PDBCutter.xml
--- a/CADDSuite/galaxyconfigs/tools/PDBCutter.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="pdbcutter" name="PDBCutter" version="0.9.6">
     <description>separate ligand and receptor</description>
     <command interpreter="bash"><![CDATA[../../PDBCutter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/PDBDownload.xml
--- a/CADDSuite/galaxyconfigs/tools/PDBDownload.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="pdbdownload" name="PDBDownload" version="0.9.6">
     <description>retrieve pdb-file from pdb.org</description>
     <command interpreter="bash"><![CDATA[../../PDBDownload 
 #if str( $id ) != ''  and str( $id ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml
--- a/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.9.6">
     <description>transfer part. charges between files</description>
     <command interpreter="bash"><![CDATA[../../PartialChargesCopy 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/PocketDetector.xml
--- a/CADDSuite/galaxyconfigs/tools/PocketDetector.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="pocketdetector" name="PocketDetector" version="0.9.6">
     <description>detect binding pocket</description>
     <command interpreter="bash"><![CDATA[../../PocketDetector 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/Predictor.xml
--- a/CADDSuite/galaxyconfigs/tools/Predictor.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="predictor" name="Predictor" version="0.9.6">
     <description>predict activities with QSAR model</description>
     <command interpreter="bash"><![CDATA[../../Predictor 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/PropertyModifier.xml
--- a/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="propertymodifier" name="PropertyModifier" version="0.9.6">
     <description>modify molecule property tags</description>
     <command interpreter="bash"><![CDATA[../../PropertyModifier 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml
--- a/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="propertyplotter" name="PropertyPlotter" version="0.9.6">
     <description>plot molecule properties</description>
     <command interpreter="bash"><![CDATA[../../PropertyPlotter 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/ProteinCheck.xml
--- a/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="proteincheck" name="ProteinCheck" version="0.9.6">
     <description>quality check for proteins structures</description>
     <command interpreter="bash"><![CDATA[../../ProteinCheck 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml
--- a/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.9.6">
     <description>protonate protein structures</description>
     <command interpreter="bash"><![CDATA[../../ProteinProtonator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml
--- a/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.9.6">
     <description>calculate RMSD between poses</description>
     <command interpreter="bash"><![CDATA[../../RMSDCalculator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml
--- a/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.9.6">
     <description>generate ROC or enrichment plots</description>
     <command interpreter="bash"><![CDATA[../../ScoreAnalyzer 
 #if str( $mode ) != ''  and str( $mode ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml
--- a/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="simplerescorer" name="SimpleRescorer" version="0.9.6">
     <description>rescore docking results</description>
     <command interpreter="bash"><![CDATA[../../SimpleRescorer 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml
--- a/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.9.6">
     <description>define spatial constraint</description>
     <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner 
 #if str( $ini ) != ''  and str( $ini ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/TaGRes-train.xml
--- a/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="tagres-train" name="TaGRes-train" version="0.9.6">
     <description>Target-specific Grid-Rescoring, training</description>
     <command interpreter="bash"><![CDATA[../../TaGRes-train 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/TaGRes.xml
--- a/CADDSuite/galaxyconfigs/tools/TaGRes.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="tagres" name="TaGRes" version="0.9.6">
     <description>Target-specific Grid-Rescoring</description>
     <command interpreter="bash"><![CDATA[../../TaGRes 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/Validator.xml
--- a/CADDSuite/galaxyconfigs/tools/Validator.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/Validator.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="validator" name="Validator" version="0.9.6">
     <description>evaluate quality of a QSAR model</description>
     <command interpreter="bash"><![CDATA[../../Validator 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/VendorFinder.xml
--- a/CADDSuite/galaxyconfigs/tools/VendorFinder.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="vendorfinder" name="VendorFinder" version="0.9.6">
     <description>search vendors for compounds</description>
     <command interpreter="bash"><![CDATA[../../VendorFinder 
 #if str( $i ) != ''  and str( $i ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/galaxyconfigs/tools/WaterFinder.xml
--- a/CADDSuite/galaxyconfigs/tools/WaterFinder.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml	Fri Sep 02 08:54:17 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="0.95">
+<tool id="waterfinder" name="WaterFinder" version="0.9.6">
     <description>find strongly bound waters</description>
     <command interpreter="bash"><![CDATA[../../WaterFinder 
 #if str( $rec ) != ''  and str( $rec ) != 'None' :
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/lib/libBALL.1.4.dylib
Binary file CADDSuite/lib/libBALL.1.4.dylib has changed
diff -r bb26168c5715 -r af446ca2d5c6 CADDSuite/suite_config.xml
--- a/CADDSuite/suite_config.xml	Tue Jul 12 10:53:07 2011 -0400
+++ b/CADDSuite/suite_config.xml	Fri Sep 02 08:54:17 2011 -0400
@@ -1,4 +1,4 @@
-<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.95">
+<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.9.6">
 
 <description>
 CADDSuite: A flexible and open framework for Computer-Aided Drug Design
@@ -7,135 +7,135 @@
     <description>from your computer</description>
 </tool>
 
-<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.95">
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.9.6">
     <description>rescore w/ anti-target dock-results</description>
 </tool>
-<tool id="automodel" name="AutoModel" version="0.95">
+<tool id="automodel" name="AutoModel" version="0.9.6">
     <description>automatically find best QSAR model</description>
 </tool>
-<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.95">
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.9.6">
     <description>fix bindingdb.org downloads</description>
 </tool>
-<tool id="combilibgenerator" name="CombiLibGenerator" version="0.95">
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.9.6">
     <description>generate combinatorial lib</description>
 </tool>
-<tool id="constraintsfinder" name="ConstraintsFinder" version="0.95">
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.9.6">
     <description>find strongly interacting residues</description>
 </tool>
-<tool id="converter" name="Converter" version="0.95">
+<tool id="converter" name="Converter" version="0.9.6">
     <description>interconvert molecular file-formats</description>
 </tool>
-<tool id="dbexporter" name="DBExporter" version="0.95 (ob)">
+<tool id="dbexporter" name="DBExporter" version="0.9.6 (ob)">
     <description>export molecules from data base</description>
 </tool>
-<tool id="dbimporter" name="DBImporter" version="0.95 (ob)">
+<tool id="dbimporter" name="DBImporter" version="0.9.6 (ob)">
     <description>import molecules into data base</description>
 </tool>
-<tool id="dockresultmerger" name="DockResultMerger" version="0.95">
+<tool id="dockresultmerger" name="DockResultMerger" version="0.9.6">
     <description>merge docking output files</description>
 </tool>
-<tool id="evensplit" name="EvenSplit" version="0.95">
+<tool id="evensplit" name="EvenSplit" version="0.9.6">
     <description>generate splits w/ equal property range</description>
 </tool>
-<tool id="featureselector" name="FeatureSelector" version="0.95">
+<tool id="featureselector" name="FeatureSelector" version="0.9.6">
     <description>run feature-selection on a QSAR model</description>
 </tool>
-<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.95">
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.9.6">
     <description>generate galaxy tool-config files</description>
 </tool>
-<tool id="gridbuilder" name="GridBuilder" version="0.95">
+<tool id="gridbuilder" name="GridBuilder" version="0.9.6">
     <description>create score-grids for docking</description>
 </tool>
-<tool id="imeedydock" name="IMGDock" version="0.95">
+<tool id="imeedydock" name="IMGDock" version="0.9.6">
     <description>Iterative Multi-Greedy Docking</description>
 </tool>
-<tool id="inputpartitioner" name="InputPartitioner" version="0.95">
+<tool id="inputpartitioner" name="InputPartitioner" version="0.9.6">
     <description>split QSAR data set</description>
 </tool>
-<tool id="inputreader" name="InputReader" version="0.95">
+<tool id="inputreader" name="InputReader" version="0.9.6">
     <description>generate QSAR data set</description>
 </tool>
-<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.95">
+<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.9.6">
     <description>define interaction constraint</description>
 </tool>
-<tool id="ligcheck" name="LigCheck" version="0.95">
+<tool id="ligcheck" name="LigCheck" version="0.9.6">
     <description>check molecules for errors</description>
 </tool>
-<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.95">
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.9.6">
     <description>generate 3D coordinates for small molecules</description>
 </tool>
-<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.95">
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.9.6">
     <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="0.95">
+<tool id="molcombine" name="MolCombine" version="0.9.6">
     <description>combine molecular files</description>
 </tool>
-<tool id="moldepict" name="MolDepict" version="0.95">
+<tool id="moldepict" name="MolDepict" version="0.9.6">
     <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="0.95">
+<tool id="molpredictor" name="MolPredictor" version="0.9.6">
     <description>predict molecule activities with QSAR model</description>
 </tool>
-<tool id="pdbcutter" name="PDBCutter" version="0.95">
+<tool id="pdbcutter" name="PDBCutter" version="0.9.6">
     <description>separate ligand and receptor</description>
 </tool>
-<tool id="pdbdownload" name="PDBDownload" version="0.95">
+<tool id="pdbdownload" name="PDBDownload" version="0.9.6">
     <description>retrieve pdb-file from pdb.org</description>
 </tool>
-<tool id="partialchargescopy" name="PartialChargesCopy" version="0.95">
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.9.6">
     <description>transfer part. charges between files</description>
 </tool>
-<tool id="pocketdetector" name="PocketDetector" version="0.95">
+<tool id="pocketdetector" name="PocketDetector" version="0.9.6">
     <description>detect binding pocket</description>
 </tool>
-<tool id="predictor" name="Predictor" version="0.95">
+<tool id="predictor" name="Predictor" version="0.9.6">
     <description>predict activities with QSAR model</description>
 </tool>
-<tool id="propertymodifier" name="PropertyModifier" version="0.95">
+<tool id="propertymodifier" name="PropertyModifier" version="0.9.6">
     <description>modify molecule property tags</description>
 </tool>
-<tool id="propertyplotter" name="PropertyPlotter" version="0.95">
+<tool id="propertyplotter" name="PropertyPlotter" version="0.9.6">
     <description>plot molecule properties</description>
 </tool>
-<tool id="proteincheck" name="ProteinCheck" version="0.95">
+<tool id="proteincheck" name="ProteinCheck" version="0.9.6">
     <description>quality check for proteins structures</description>
 </tool>
-<tool id="proteinprotonator" name="ProteinProtonator" version="0.95">
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.9.6">
     <description>protonate protein structures</description>
 </tool>
-<tool id="rmsdcalculator" name="RMSDCalculator" version="0.95">
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.9.6">
     <description>calculate RMSD between poses</description>
 </tool>
-<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.95">
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.9.6">
     <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="0.95">
+<tool id="simplerescorer" name="SimpleRescorer" version="0.9.6">
     <description>rescore docking results</description>
 </tool>
-<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95">
+<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.9.6">
     <description>define spatial constraint</description>
 </tool>
-<tool id="tagres-train" name="TaGRes-train" version="0.95">
+<tool id="tagres-train" name="TaGRes-train" version="0.9.6">
     <description>Target-specific Grid-Rescoring, training</description>
 </tool>
-<tool id="tagres" name="TaGRes" version="0.95">
+<tool id="tagres" name="TaGRes" version="0.9.6">
     <description>Target-specific Grid-Rescoring</description>
 </tool>
-<tool id="validator" name="Validator" version="0.95">
+<tool id="validator" name="Validator" version="0.9.6">
     <description>evaluate quality of a QSAR model</description>
 </tool>
-<tool id="vendorfinder" name="VendorFinder" version="0.95">
+<tool id="vendorfinder" name="VendorFinder" version="0.9.6">
     <description>search vendors for compounds</description>
 </tool>
-<tool id="waterfinder" name="WaterFinder" version="0.95">
+<tool id="waterfinder" name="WaterFinder" version="0.9.6">
     <description>find strongly bound waters</description>
 </tool></suite>