changeset 2:bbc4a2c1d276

Deleted selected files

--- a/CADDSuite/CADDSuite-description.txt	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +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
-	- ConstraintsFinder: find strongly interacting residues
-	- PocketDetector: detect ligand binding pocket
-	- GridBuilder: precalculate grids for docking
-	- IMeedyDock: 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').

--- a/CADDSuite/IMGDock	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/IMGDock.bin "$@" 

--- a/CADDSuite/InteractionConstraintDefiner	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@" 

--- a/CADDSuite/SpatialConstraintDefiner	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-#!/bin/bash
-	export BASE_DIR=`dirname "$0"`
-	. "$BASE_DIR"/setPathes.sh
-	"$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@" 

Binary file CADDSuite/bin/AntitargetRescorer.bin has changed

Binary file CADDSuite/bin/AutoModel.bin has changed

Binary file CADDSuite/bin/BindingDBCleaner.bin has changed

Binary file CADDSuite/bin/CombiLibGenerator.bin has changed

Binary file CADDSuite/bin/ConstraintsFinder.bin has changed

Binary file CADDSuite/bin/Converter.bin has changed

Binary file CADDSuite/bin/DBExporter.bin has changed

Binary file CADDSuite/bin/DBImporter.bin has changed

Binary file CADDSuite/bin/DockResultMerger.bin has changed

Binary file CADDSuite/bin/EvenSplit.bin has changed

Binary file CADDSuite/bin/FeatureSelector.bin has changed

Binary file CADDSuite/bin/GalaxyConfigGenerator.bin has changed

Binary file CADDSuite/bin/GridBuilder.bin has changed

Binary file CADDSuite/bin/IMGDock.bin has changed

Binary file CADDSuite/bin/InputPartitioner.bin has changed

Binary file CADDSuite/bin/InputReader.bin has changed

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Binary file CADDSuite/bin/PropertyPlotter.bin has changed

Binary file CADDSuite/bin/ProteinCheck.bin has changed

Binary file CADDSuite/bin/ProteinProtonator.bin has changed

Binary file CADDSuite/bin/RMSDCalculator.bin has changed

Binary file CADDSuite/bin/ScoreAnalyzer.bin has changed

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Binary file CADDSuite/bin/SimpleRescorer.bin has changed

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Binary file CADDSuite/bin/TaGRes-train.bin has changed

Binary file CADDSuite/bin/TaGRes.bin has changed

Binary file CADDSuite/bin/Validator.bin has changed

Binary file CADDSuite/bin/VendorFinder.bin has changed

Binary file CADDSuite/bin/WaterFinder.bin has changed

--- a/CADDSuite/changelog.txt	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-Version 0.94, 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 0.93, 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 0.92, 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 0.91, 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

--- a/CADDSuite/galaxyconfigs/tool_conf.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<?xml version="1.0"?>
-<toolbox>
-  <label text="CADDSuite" id="cadds" />
-
-  <section name="Get Data" id="getext">
-    <tool file="data_source/upload.xml"/>
-    <tool file="CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml"/>
-    <tool file="CADDSuite/galaxyconfigs/tools/PDBDownload.xml"/>
-    <tool file="CADDSuite/galaxyconfigs/tools/DBExporter.xml"/>
-  </section>
-
-  <section name="Data preparation" id="dataPrep">
-	<tool file="CADDSuite/galaxyconfigs/tools/PDBCutter.xml" />
-	<tool file="CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml" />
-	<tool file="CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml" />
-	<tool file="CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml" />
-   <tool file="CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml"/>
-   <tool file="CADDSuite/galaxyconfigs/tools/EvenSplit.xml"/>
-   <tool file="CADDSuite/galaxyconfigs/tools/PropertyModifier.xml"/>
-   <tool file="CADDSuite/galaxyconfigs/tools/MolFilter.xml"/>
-  </section>
-
-  <section name="Checks and evaluations" id="checks">
-	<tool file="CADDSuite/galaxyconfigs/tools/ProteinCheck.xml" />
-	<tool file="CADDSuite/galaxyconfigs/tools/LigCheck.xml" />
-  </section>
-
-  <section name="Docking" id="dockingTools">
-	 <tool file="CADDSuite/galaxyconfigs/tools/WaterFinder.xml" />
-	 <tool file="CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml" />
-	 <tool file="CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml" />
-	 <tool file="CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml"/>
-	 <tool file="CADDSuite/galaxyconfigs/tools/PocketDetector.xml"/>
-    <tool file="CADDSuite/galaxyconfigs/tools/GridBuilder.xml" />
-    <tool file="CADDSuite/galaxyconfigs/tools/IMeedyDock.xml" />
-  </section>
-
-  <section name="Rescoring" id="rescoringsection">
-	<tool file="CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml"/>
-	<tool file="CADDSuite/galaxyconfigs/tools/TaGRes-train.xml"/>
-	<tool file="CADDSuite/galaxyconfigs/tools/TaGRes.xml"/>
-	<tool file="CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml" />
-  </section>
-
-	<section name="QuEasy (QSAR)" id="queasy">
-		<tool file="CADDSuite/galaxyconfigs/tools/InputReader.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/ModelCreator.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/FeatureSelector.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/Validator.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/MolPredictor.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/AutoModel.xml" />
-	</section>
-
-	<section name="Analysis" id="analysis">
-		<tool file="CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml"/>
-		<tool file="CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml"/>
-		<tool file="CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml"/>
-		<tool file="CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml"/>
-	</section>
-
-	<section name="Convert, combine and store" id="storeData">
-		<tool file="CADDSuite/galaxyconfigs/tools/Converter.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/MolCombine.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/DockResultMerger.xml"/>
-		<tool file="CADDSuite/galaxyconfigs/tools/Filter.xml"/>
-		<tool file="CADDSuite/galaxyconfigs/tools/MolDepict.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/DBImporter.xml" />
-		<tool file="CADDSuite/galaxyconfigs/tools/VendorFinder.xml" />
-	</section>
-
-</toolbox>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94">
-    <description>rescore w/ anti-target dock-results</description>
-    <command interpreter="bash"><![CDATA[../../AntitargetRescorer 
-#if str( $t ) != ''  and str( $t ) != 'None' :
-   -t "$t"
-#end if
-#if str( $at ) != ''  and str( $at ) != 'None' :
-   -at "$at"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="t" label="input file w/ target dock-results" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="at" label="input file w/ anti-target dock-results" optional="false" type="data" format="mol2/sdf/drf"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="t"/>
-    </outputs>
-    <help>This tool rescores docking output poses.
-AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file.
-
-As input we need:
-    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docket into the specified protein (i.e. the target).
-    * a file containing the same compounds docked into the antitarget.
-
-Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 'antitarget_rescore'.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94">
-    <description>fix bindingdb.org downloads</description>
-    <command interpreter="bash"><![CDATA[../../BindingDBCleaner 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $type ) != ''  and str( $type ) != 'None' :
-   -type "$type"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $target ) != ''  and str( $target ) != 'None' :
-   -target "$target"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="type" label="type of contained activity values: 'Ki' or 'IC50'" optional="false" type="select">
-            <option value="IC50">IC50</option>
-            <option value="Ki">Ki</option>
-        </param>
-        <param name="target" label="binding-DB target name" optional="false" area="true" type="text" size="1x15"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool cleans up the sd-properties contained in sd-files downloaded from bindingdb.org.
-
-For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'.
-
-All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94">
-    <description>generate combinatorial lib</description>
-    <command interpreter="bash"><![CDATA[../../CombiLibGenerator 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input combi-lib file" optional="false" type="data" format="data"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf"/>
-    </outputs>
-    <help>This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties.
-
-As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need:
-
-&lt;scaffold&gt;
-      Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3
-      Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3
-&lt;moietyR1&gt;
-      [R1]C(C)(C)C
-&lt;moietyR2&gt;
-      [R2]OC(C)(C)C
-
-Output of CombiLibGenerator is a file containing created topologies. Note that this tool does *not* generate any conformations but only topologies, so that all coordinates in the output file will be zero. Thus, apply Ligand3DGenerator to the output generated by CombiLibGenerator if you need 3D conformations.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94">
-    <description>find strongly interacting residues</description>
-    <command interpreter="bash"><![CDATA[../../ConstraintsFinder 
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $rl ) != ''  and str( $rl ) != 'None' :
-   -rl "$rl"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="ini"/>
-    </outputs>
-    <help>This tool searches protein residues with which the reference ligand interacts strongly.
-Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion.
-
-As input we need:
-    * a file containing a protonated protein in pdb-format
-    * a file containing a reference ligand.
-      This reference ligand should be located in the binding pocket.
-      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-
-Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/Converter.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="converter" name="Converter" version="0.94">
-    <description>interconvert molecular file-formats</description>
-    <command interpreter="bash"><![CDATA[../../Converter 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $f ) != ''  and str( $f ) != 'None' :
-   -f "$f"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="f" label="output format" optional="true" type="select">
-            <option value="mol2">mol2</option>
-            <option value="sdf">sdf</option>
-            <option value="drf">drf</option>
-            <option value="pdb">pdb</option>
-            <option value="ac">ac</option>
-            <option value="ent">ent</option>
-            <option value="brk">brk</option>
-            <option value="hin">hin</option>
-            <option value="mol">mol</option>
-            <option value="xyz">xyz</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf">
-            <change_format>
-                <when input="f" value="mol2" format="mol2"/>
-                <when input="f" value="sdf" format="sdf"/>
-                <when input="f" value="drf" format="drf"/>
-                <when input="f" value="pdb" format="pdb"/>
-                <when input="f" value="ac" format="ac"/>
-                <when input="f" value="ent" format="ent"/>
-                <when input="f" value="brk" format="brk"/>
-                <when input="f" value="hin" format="hin"/>
-                <when input="f" value="mol" format="mol"/>
-                <when input="f" value="xyz" format="xyz"/>
-            </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>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/DBExporter.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,97 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="dbexporter" name="DBExporter" version="0.94 (ob)">
-    <description>export molecules from data base</description>
-    <command interpreter="bash"><![CDATA[../../DBExporter 
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $start_id ) != ''  and str( $start_id ) != 'None' :
-   -start_id "$start_id"
-#end if
-#if str( $end_id ) != ''  and str( $end_id ) != 'None' :
-   -end_id "$end_id"
-#end if
-#if str( $min_logP ) != ''  and str( $min_logP ) != 'None' :
-   -min_logP "$min_logP"
-#end if
-#if str( $max_logP ) != ''  and str( $max_logP ) != 'None' :
-   -max_logP "$max_logP"
-#end if
-#if str( $min_MW ) != ''  and str( $min_MW ) != 'None' :
-   -min_MW "$min_MW"
-#end if
-#if str( $max_MW ) != ''  and str( $max_MW ) != 'None' :
-   -max_MW "$max_MW"
-#end if
-#if str( $max_mols ) != ''  and str( $max_mols ) != 'None' :
-   -max_mols "$max_mols"
-#end if
-#if str( $target ) != ''  and str( $target ) != 'None' :
-   -target "$target"
-#end if
-#if str( $q ) != ''  and str( $q ) != 'None' :
-   -q "$q"
-#end if
-#if str( $min_sim ) != ''  and str( $min_sim ) != 'None' :
-   -min_sim "$min_sim"
-#end if
-#if str( $max_sim ) != ''  and str( $max_sim ) != 'None' :
-   -max_sim "$max_sim"
-#end if
-#if str( $smarts ) != ''  and str( $smarts ) != 'None' :
-   -smarts "$smarts"
-#end if
-#if str( $smarts_file ) != ''  and str( $smarts_file ) != 'None' :
-   -smarts_file "$smarts_file"
-#end if
-#if str( $uck ) != ''  and str( $uck ) != 'None' :
-   -uck "$uck"
-#end if
-#if str( $d ) != ''  and str( $d ) != 'None' :
-   -d "$d"
-#end if
-#if str( $u ) != ''  and str( $u ) != 'None' :
-   -u "$u"
-#end if
-#if str( $h ) != ''  and str( $h ) != 'None' :
-   -h "$h"
-#end if
-#if str( $port ) != ''  and str( $port ) != 'None' :
-   -port "$port"
-#end if
-#if str( $p ) != ''  and str( $p ) != 'None' :
-   -p "$p"
-#end if
-#if str( $s ) != ''  and str( $s ) != 'None' :
-   -s
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="mol2/sdf/drf"/>
-        <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/>
-        <param name="start_id" label="ID of the first conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="end_id" label="ID of the last conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="min_logP" label="minimal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
-        <param name="max_logP" label="maximal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
-        <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max_mols" label="max. number of molecules to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/>
-        <param name="min_sim" label="minimal average similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
-        <param name="max_sim" label="maximal similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
-        <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/>
-        <param name="uck" label="UCK key" optional="true" area="true" type="text" size="1x15"/>
-        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
-        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
-        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
-        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
-        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
-        <param name="s" label="show summary of datasets in database" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf"/>
-    </outputs>
-    <help>This tool exports compounds from a database to a molecular file. Compounds can be filtered according to (among others) SMARTS expressions, logP, molecular weight, or similarity to query molecule(s) and dataset name.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/DBImporter.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="dbimporter" name="DBImporter" version="0.94 (ob)">
-    <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( $target ) != ''  and str( $target ) != 'None' :
-   -target "$target"
-#end if
-#if str( $d ) != ''  and str( $d ) != 'None' :
-   -d "$d"
-#end if
-#if str( $u ) != ''  and str( $u ) != 'None' :
-   -u "$u"
-#end if
-#if str( $h ) != ''  and str( $h ) != 'None' :
-   -h "$h"
-#end if
-#if str( $port ) != ''  and str( $port ) != 'None' :
-   -port "$port"
-#end if
-#if str( $p ) != ''  and str( $p ) != 'None' :
-   -p "$p"
-#end if
-#if str( $vn ) != ''  and str( $vn ) != 'None' :
-   -vn "$vn"
-#end if
-#if str( $vid ) != ''  and str( $vid ) != 'None' :
-   -vid "$vid"
-#end if
-#if str( $vd ) != ''  and str( $vd ) != 'None' :
-   -vd "$vd"
-#end if
-#if str( $vu ) != ''  and str( $vu ) != 'None' :
-   -vu "$vu"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/>
-        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
-        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
-        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
-        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
-        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
-        <param name="vn" label="name of compound vendor" optional="true" area="true" type="text" size="1x15"/>
-        <param name="vid" label="name of vendor's compound-ID tag in sd-file" optional="true" area="true" type="text" size="1x15"/>
-        <param name="vd" label="vendor library date or version" optional="true" area="true" type="text" size="1x15"/>
-        <param name="vu" label="url from wich vendor library was obtained" optional="true" area="true" type="text" size="1x15"/>
-    </inputs>
-    <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

--- a/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="dockresultmerger" name="DockResultMerger" version="0.94">
-    <description>merge docking output files</description>
-    <command interpreter="bash"><![CDATA[../../DockResultMerger 
-#for $s in $series_i 
-   #if str( "${s.i.file_name}" ) != ''  and str( "${s.i.file_name}" ) != 'None' :
-      -i "${s.i.file_name}"
-   #end if
-#end for 
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $score ) != ''  and str( $score ) != 'None' :
-   -score "$score"
-#end if
-#if str( $min ) != ''  and str( $min ) != 'None' :
-   -min "$min"
-#end if
-#if str( $max ) != ''  and str( $max ) != 'None' :
-   -max "$max"
-#end if
-#if str( $k ) != ''  and str( $k ) != 'None' :
-   -k "$k"
-#end if
-#if str( $rm ) != ''  and str( $rm ) != 'None' :
-   -rm
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <repeat name="series_i" title="input files" min="1">
-            <param name="i" label="input files" optional="false" type="data" format="mol2/sdf/drf"/>
-        </repeat>
-        <param name="score" label="score property name" optional="true" area="true" type="text" size="1x15" value="score"/>
-        <param name="min" label="minimal score value" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="max" label="maximal score value" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="k" label="number of output molecules" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="rm" label="remove input files after merging" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool merges and sorts molecule files as generated by docking or rescoring.
-
-You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.
-
- Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/EvenSplit.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="evensplit" name="EvenSplit" version="0.94">
-    <description>generate splits w/ equal property range</description>
-    <command interpreter="bash"><![CDATA[../../EvenSplit 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o1 ) != ''  and str( $o1 ) != 'None' :
-   -o1 "$o1"
-#end if
-#if str( $o2 ) != ''  and str( $o2 ) != 'None' :
-   -o2 "$o2"
-#end if
-#if str( $n ) != ''  and str( $n ) != 'None' :
-   -n "$n"
-#end if
-#if str( $offset ) != ''  and str( $offset ) != 'None' :
-   -offset "$offset"
-#end if
-#if str( $k ) != ''  and str( $k ) != 'None' :
-   -k "$k"
-#end if
-#if str( $prop ) != ''  and str( $prop ) != 'None' :
-   -prop "$prop"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="n" label="number of compounds to use from input file" optional="true" type="text" area="true" size="1x5" value=""/>
-        <param name="offset" label="extract each (i+offset)%k == 0 for o2" optional="true" type="text" area="true" size="1x5" value="0"/>
-        <param name="k" label="extract each k'th compound for 2nd output file" optional="true" type="text" area="true" size="1x5" value="2"/>
-        <param name="prop" label="property name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
-    </inputs>
-    <outputs>
-        <data name="o1" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o2" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool splits a molecule file into two subsets in such a way that each of them convers an equal range of a property. The property with respect to which this is to be done should be specified with '-prop'.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94">
-    <description>generate galaxy tool-config files</description>
-    <command interpreter="bash"><![CDATA[../../GalaxyConfigGenerator 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ignore ) != ''  and str( $ignore ) != 'None' :
-   -ignore "$ignore"
-#end if
-#if str( $s ) != ''  and str( $s ) != 'None' :
-   -s "$s"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input par-file" optional="false" type="data" format="data"/>
-        <param name="ignore" label="tool-parameter to be ignored, i.e. those for which no galaxy config entry should be created" optional="true" area="true" size="1x5"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="xml"/>
-        <data name="s" format="data"/>
-    </outputs>
-    <help>This tool can be used to create galaxy tool-configuration files.
-As input, please supply a parameter-file as written by '-write_par' by all of our tools.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/GridBuilder.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="gridbuilder" name="GridBuilder" version="0.94">
-    <description>create score-grids for docking</description>
-    <command interpreter="bash"><![CDATA[../../GridBuilder 
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $rl ) != ''  and str( $rl ) != 'None' :
-   -rl "$rl"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $grd ) != ''  and str( $grd ) != 'None' :
-   -grd "$grd"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-    </inputs>
-    <outputs>
-        <data name="grd" format="grd.tgz"/>
-    </outputs>
-    <help>This tool precalculates a score-grid for a binding pocket of a given receptor.
-
-As input we need:
-    * a file containing a protonated protein in pdb-format
-    * a file containing a reference ligand.
-      This reference ligand should be located in the binding pocket, 
-      so that a grid can be precalculated around it.
-      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-
-Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock).</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/IMGDock.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="imeedydock" name="IMGDock" version="0.94">
-    <description>Iterative Multi-Greedy Docking</description>
-    <command interpreter="bash"><![CDATA[../../IMGDock 
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $rl ) != ''  and str( $rl ) != 'None' :
-   -rl "$rl"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $grd ) != ''  and str( $grd ) != 'None' :
-   -grd "$grd"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="compounds to be docked" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="grd" label="ScoreGrid file" optional="false" type="data" format="grd.tgz"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach.
-As input we need:
-
-    * a file containing a protonated protein in pdb-format
-    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-    * a score-grid file generated by GridBuilder. This grid must have been precalculated for the same receptor and reference ligand as those that are to be used here.
-    * a file containing the compounds that are to be docked. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). These molecules must have been assigned 3D coordinates (e.g. by Ligand3DGenerator) and should have been checked for errors using LigCheck.
-
-Output of this tool is a file containing all compounds docked into the binding pocket, with a property-tag named 'score' indicating the score obtained for each compound.
-
-Tip: If you want to parallelize docking, use LigandFileSplitter to separate your input file containing the compounds to be docked into several batches, dock each batch with this tool and merge the output files with DockResultMerger.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94">
-    <description>define interaction constraint</description>
-    <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner 
-#if str( $res ) != ''  and str( $res ) != 'None' :
-   -res "$res"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $s ) != ''  and str( $s ) != 'None' :
-   -s "$s"
-#end if
-#if str( $p ) != ''  and str( $p ) != 'None' :
-   -p "$p"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/>
-        <param name="res" label="residue ID" optional="false" area="true" type="text" size="1x15"/>
-        <param name="s" label="desired minimal interation (score) between ligand and specified residue(s)" optional="false" type="text" area="true" size="1x5" value="-2.0"/>
-        <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="10"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="ini"/>
-    </outputs>
-    <help>This tool allows to define interaction constraints for docking or scoring.
-
-The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: &lt;chain-ID&gt;:&lt;residue-ID&gt;, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17.
-
-Output of this tool is a ini-file that contains the desired interaction constraint.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="ligcheck" name="LigCheck" version="0.94">
-    <description>check molecules for errors</description>
-    <command interpreter="bash"><![CDATA[../../LigCheck 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ef ) != ''  and str( $ef ) != 'None' :
-   -ef "$ef"
-#end if
-#if str( $ri ) != ''  and str( $ri ) != 'None' :
-   -ri
-#end if
-#if str( $ut ) != ''  and str( $ut ) != 'None' :
-   -ut
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ef" label="error fraction; print error if fraction of invalid mols is larger" optional="true" type="text" area="true" size="1x5" value="0.5"/>
-        <param name="ri" label="remove invalid molecules." optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="ut" label="check for unique topologies (default: check only for unique conformation)" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-
-The following checks are done for each molecule:
-
-    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
-    * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
-    * each atom must have a valid assigned element
-    * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
-    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
-    * partial charges may not contain completely senseless values (&gt;5 or &lt;-5).
-    * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.
-
-If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94">
-    <description>generate 3D coordinates for small molecules</description>
-    <command interpreter="bash"><![CDATA[../../Ligand3DGenerator 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ph ) != ''  and str( $ph ) != 'None' :
-   -ph "$ph"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool generates 3D conformations for small molecules and adds hydrogens to them.
-As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary.
-
-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>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94">
-    <description>split molecule files</description>
-    <command interpreter="bash"><![CDATA[../../LigandFileSplitter 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $no ) != ''  and str( $no ) != 'None' :
-   -no "$no"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $o2 ) != ''  and str( $o2 ) != 'None' :
-   -o "$o2"
-#end if
-#if str( $o3 ) != ''  and str( $o3 ) != 'None' :
-   -o "$o3"
-#end if
-#if str( $o4 ) != ''  and str( $o4 ) != 'None' :
-   -o "$o4"
-#end if
-#if str( $o5 ) != ''  and str( $o5 ) != 'None' :
-   -o "$o5"
-#end if
-#if str( $o6 ) != ''  and str( $o6 ) != 'None' :
-   -o "$o6"
-#end if
-#if str( $o7 ) != ''  and str( $o7 ) != 'None' :
-   -o "$o7"
-#end if
-#if str( $o8 ) != ''  and str( $o8 ) != 'None' :
-   -o "$o8"
-#end if
-#if str( $o9 ) != ''  and str( $o9 ) != 'None' :
-   -o "$o9"
-#end if
-#if str( $o10 ) != ''  and str( $o10 ) != 'None' :
-   -o "$o10"
-#end if
-#if str( $o11 ) != ''  and str( $o11 ) != 'None' :
-   -o "$o11"
-#end if
-#if str( $o12 ) != ''  and str( $o12 ) != 'None' :
-   -o "$o12"
-#end if
-#if str( $o13 ) != ''  and str( $o13 ) != 'None' :
-   -o "$o13"
-#end if
-#if str( $o14 ) != ''  and str( $o14 ) != 'None' :
-   -o "$o14"
-#end if
-#if str( $o15 ) != ''  and str( $o15 ) != 'None' :
-   -o "$o15"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="no" label="no. of splits to be created" optional="false" type="hidden" area="true" size="1x5" value="15"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o2" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o3" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o4" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o5" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o6" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o7" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o8" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o9" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o10" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o11" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o12" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o13" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o14" format="mol2/sdf/drf" format_source="i"/>
-        <data name="o15" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>LigandFileSplitter splits a molecule file into a given number of subsets.
-Note that the molecules are not sorted in any way for this.
-
-Since Galaxy does not support a flexible number of output-files, we will create 15 output files when you use LigandFileSplitter in Galaxy.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/MolCombine.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="molcombine" name="MolCombine" version="0.94">
-    <description>combine molecular files</description>
-    <command interpreter="bash"><![CDATA[../../MolCombine 
-#if str( $i1 ) != ''  and str( $i1 ) != 'None' :
-   -i1 "$i1"
-#end if
-#if str( $i2 ) != ''  and str( $i2 ) != 'None' :
-   -i2 "$i2"
-#end if
-#if str( $mode ) != ''  and str( $mode ) != 'None' :
-   -mode "$mode"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ignH ) != ''  and str( $ignH ) != 'None' :
-   -ignH
-#end if
-#if str( $replace_prop ) != ''  and str( $replace_prop ) != 'None' :
-   -replace_prop
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i1" label="input molecule file A" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="i2" label="input molecule file B" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="mode" label="'intersection', 'union' or 'b_not_a'" optional="false" type="select">
-            <option value="intersection">intersection</option>
-            <option value="union">union</option>
-            <option value="b_not_a">b_not_a</option>
-        </param>
-        <param name="ignH" label="ignore hydrogens, i.e. match molecules to any protonation state." optional="true" type="boolean" truevalue="true" falsevalue=""/>
-        <param name="replace_prop" label="replace properties from file 1 w/ those from file 2" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i1"/>
-    </outputs>
-    <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.
-
-If you want to match molecules regardless of their protonation state, use option '-ignH'.
-
-Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/MolDepict.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="moldepict" name="MolDepict" version="0.94">
-    <description>create structure diagrams</description>
-    <command interpreter="bash"><![CDATA[../../MolDepict 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $max ) != ''  and str( $max ) != 'None' :
-   -max "$max"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="max" label="maximal number of pictures (default=60, 0=unlimited)" optional="true" type="text" area="true" size="1x5" value="60"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="pdf"/>
-    </outputs>
-    <help>This tool create structure diagrams for small molecules.
-Supported input-formats are mol, mol2, sdf, drf.
-
-Output of this tool is one pdf-file containing the structure diagrams for all molecules in the input-file.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/PDBCutter.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="pdbcutter" name="PDBCutter" version="0.94">
-    <description>separate ligand and receptor</description>
-    <command interpreter="bash"><![CDATA[../../PDBCutter 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $lig ) != ''  and str( $lig ) != 'None' :
-   -lig "$lig"
-#end if
-#if str( $lig_chain ) != ''  and str( $lig_chain ) != 'None' :
-   -lig_chain "$lig_chain"
-#end if
-#if str( $lig_name ) != ''  and str( $lig_name ) != 'None' :
-   -lig_name "$lig_name"
-#end if
-#if str( $rm_ch ) != ''  and str( $rm_ch ) != 'None' :
-   -rm_ch "$rm_ch"
-#end if
-#if str( $rm_res ) != ''  and str( $rm_res ) != 'None' :
-   -rm_res "$rm_res"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="lig_chain" label="chain-name of ligand" optional="false" area="true" type="text" size="1x15"/>
-        <param name="lig_name" label="ligand name" optional="false" area="true" type="text" size="1x15"/>
-        <param name="rm_ch" label="protein chains that are to be deleted" optional="true" area="true" type="text" size="1x15"/>
-        <param name="rm_res" label="pdb-residues that are to be deleted (e.g. water or ions)" optional="true" area="true" type="text" size="1x15"/>
-    </inputs>
-    <outputs>
-        <data name="rec" format="pdb"/>
-        <data name="lig" format="pdb"/>
-    </outputs>
-    <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
-
-The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
-Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.
-
-Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/PDBDownload.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="pdbdownload" name="PDBDownload" version="0.94">
-    <description>retrieve pdb-file from pdb.org</description>
-    <command interpreter="bash"><![CDATA[../../PDBDownload 
-#if str( $id ) != ''  and str( $id ) != 'None' :
-   -id "$id"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $p ) != ''  and str( $p ) != 'None' :
-   -p "$p"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="id" label="PDB ID for desired structure" optional="false" area="true" type="text" size="1x15"/>
-        <param name="p" label="proxy" optional="true" area="true" type="text" size="1x15"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="pdb"/>
-    </outputs>
-    <help>Download a pdb-file from the pdb data bank (http://www.pdb.org/) using the specified ID of the desired protein structure.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94">
-    <description>transfer part. charges between files</description>
-    <command interpreter="bash"><![CDATA[../../PartialChargesCopy 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $chr ) != ''  and str( $chr ) != 'None' :
-   -chr "$chr"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="chr" label="file containing the same molecules as the input file, but with (different) partial charges" optional="false" type="data" format="mol2"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2" format_source="i"/>
-    </outputs>
-    <help>This tool copies partial charges from a given file to the conformations read from a different file.
-This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/PocketDetector.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="pocketdetector" name="PocketDetector" version="0.94">
-    <description>detect binding pocket</description>
-    <command interpreter="bash"><![CDATA[../../PocketDetector 
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $rl ) != ''  and str( $rl ) != 'None' :
-   -rl "$rl"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="input ini file" optional="true" type="data" format="ini"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="ini"/>
-    </outputs>
-    <help>This tool tries to detect the binding pocket in which the reference ligand is located.
-Therefore, probe atoms are placed above the protein surface at positions of relative deep burial. The cluster of probe atoms around the geometric center of the reference ligand is used for the description of the binding pocket.
-
-As input we need:
-    * a file containing a protonated protein in pdb-format. Furthermore, it should contain only relevant (i.e. strongly bound) water molecules as detected by WaterFinder.
-    * a file containing a reference ligand.
-      This reference ligand should be located in the binding pocket.
-      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-
-Output of this tool is a docking configuration file that contains the description of the detected binding pocket. This file should in following pipeline steps be specified for docking and rescoring.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="propertymodifier" name="PropertyModifier" version="0.94">
-    <description>modify molecule property tags</description>
-    <command interpreter="bash"><![CDATA[../../PropertyModifier 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $mode ) != ''  and str( $mode ) != 'None' :
-   -mode "$mode"
-#end if
-#if str( $name ) != ''  and str( $name ) != 'None' :
-   -name "$name"
-#end if
-#if str( $value ) != ''  and str( $value ) != 'None' :
-   -value "$value"
-#end if
-#if str( $new_name ) != ''  and str( $new_name ) != 'None' :
-   -new_name "$new_name"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="mode" label="'delete', 'add' or 'rename' properties" optional="false" type="select">
-            <option value="add">add</option>
-            <option value="rename">rename</option>
-            <option value="delete">delete</option>
-        </param>
-        <param name="name" label="property name ('all' will erase all properties if in delete-mode)" optional="false" area="true" type="text" size="1x15"/>
-        <param name="value" label="property value (in case of prop. adding only)" optional="true" area="true" type="text" size="1x15"/>
-        <param name="new_name" label="new property name (in case of renaming only)" optional="true" area="true" type="text" size="1x15"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>With this tools you can add, rename or delete molecule property tags.
-These tags can for example contain information about scores, binding-free-energy, IDs or names for the resp. molecule.
-The output of this tool is a molecule file in which the desired property tags have been added/renamed/deleted (as chosen).</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="propertyplotter" name="PropertyPlotter" version="0.94">
-    <description>plot molecule properties</description>
-    <command interpreter="bash"><![CDATA[../../PropertyPlotter 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $p1 ) != ''  and str( $p1 ) != 'None' :
-   -p1 "$p1"
-#end if
-#if str( $p2 ) != ''  and str( $p2 ) != 'None' :
-   -p2 "$p2"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
--quiet 
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="p1" label="name of property 1" optional="false" area="true" type="text" size="1x15"/>
-        <param name="p2" label="name of property 2" optional="true" area="true" type="text" size="1x15"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="png"/>
-    </outputs>
-    <help>PropertyPlotter can be used to generate distribution- or scatter-plots of data contained in molecule property-tags.
-
-In case you want to create a scatter-plot, specify the name of both property-tags to be used with '-p1' and '-p2'. If you want to generate a distribution plot, just specify '-p1'.
-The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
-
-The output of this tool is a plot in form of an eps or png-file (as chosen).</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="proteincheck" name="ProteinCheck" version="0.94">
-    <description>quality check for proteins structures</description>
-    <command interpreter="bash"><![CDATA[../../ProteinCheck 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $bc ) != ''  and str( $bc ) != 'None' :
-   -bc
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="bc" label="ignore broken chains" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="pdf"/>
-    </outputs>
-    <help>Check a given protein structure for the following errors:
-    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
-    * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked.
-    * each atom must have a valid assigned element
-    * the protein must be protonated (since this is necessary for docking/(re-)scoring).
-    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
-    * there may be no senseless temperature factors (&lt;1 or &gt;100)
-    * there may be no sterical clashes between atoms
-
-A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="proteinprotonator" name="ProteinProtonator" version="0.94">
-    <description>protonate protein structures</description>
-    <command interpreter="bash"><![CDATA[../../ProteinProtonator 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ph ) != ''  and str( $ph ) != 'None' :
-   -ph "$ph"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="pdb"/>
-        <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="pdb" format_source="i"/>
-    </outputs>
-    <help>ProteinProtonator allows you add hydrogens to a protein structure.
-
-Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed.
-
-Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
-    <description>calculate RMSD between poses</description>
-    <command interpreter="bash"><![CDATA[../../RMSDCalculator 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $org ) != ''  and str( $org ) != 'None' :
-   -org "$org"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
--quiet 
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="org" label="molecule file containing the original ('true') poses" optional="false" type="data" format="mol2/sdf/drf"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool calculates the RMSD between different conformations of the same molecule.
-
-Therefore this tool can for example be used to evaluate the different between ligands taken from co-crystal structures and their poses generated by a docking.
-Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
-
-Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94">
-    <description>generate ROC or enrichment plots</description>
-    <command interpreter="bash"><![CDATA[../../ScoreAnalyzer 
-#if str( $mode ) != ''  and str( $mode ) != 'None' :
-   -mode "$mode"
-#end if
-#if str( $title ) != ''  and str( $title ) != 'None' :
-   -title "$title"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $s ) != ''  and str( $s ) != 'None' :
-   -s "$s"
-#end if
-#if str( $e ) != ''  and str( $e ) != 'None' :
-   -e "$e"
-#end if
-#if str( $t ) != ''  and str( $t ) != 'None' :
-   -t "$t"
-#end if
-#if str( $b ) != ''  and str( $b ) != 'None' :
-   -b
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="mode" label="'roc', 'top50', 'scatter' or 'enrichment'" optional="false" type="select">
-            <option value="roc">roc</option>
-            <option value="top50">top50</option>
-            <option value="scatter">scatter</option>
-            <option value="enrichment">enrichment</option>
-        </param>
-        <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/>
-        <param name="s" label="score label" optional="false" area="true" type="text" size="1x15" value="score"/>
-        <param name="e" label="binding-free-energy/class label name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
-        <param name="t" label="only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" optional="true" area="true" type="text" size="1x15"/>
-        <param name="b" label="binary experimental activity data" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="png"/>
-    </outputs>
-    <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.
-
-The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'.
-The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
-
-The output of this tool is a plot in form of an eps or png-file (as chosen).</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="simplerescorer" name="SimpleRescorer" version="0.94">
-    <description>rescore docking results</description>
-    <command interpreter="bash"><![CDATA[../../SimpleRescorer 
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $rl ) != ''  and str( $rl ) != 'None' :
-   -rl "$rl"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $function ) != ''  and str( $function ) != 'None' :
-   -function "$function"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="function" label="scoring function: 'MM', 'PLP' or 'PB'" optional="true" type="select">
-            <option value="MM">MM</option>
-            <option value="PLP">PLP</option>
-            <option value="PB">PB</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool rescores docking output poses.
-A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified).
-
-As input we need:
-    * a file containing a protonated protein in pdb-format
-    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
-
-Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94">
-    <description>define spatial constraint</description>
-    <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner 
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $type ) != ''  and str( $type ) != 'None' :
-   -type "$type"
-#end if
-#if str( $n ) != ''  and str( $n ) != 'None' :
-   -n "$n"
-#end if
-#if str( $p ) != ''  and str( $p ) != 'None' :
-   -p "$p"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="type" label="'fraction' or 'number' of compound atoms" optional="false" type="select">
-            <option value="fraction">fraction</option>
-            <option value="number">number</option>
-        </param>
-        <param name="n" label="desired number/fraction of atoms in spatial area" optional="false" type="text" area="true" size="1x5" value=""/>
-        <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="1e11"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="ini"/>
-    </outputs>
-    <help>This tool allows to define spatial constraints for docking or scoring.
-
-For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
-Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.
-
-Output of this tool is a ini-file that contains the desired spatial constraint.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="tagres-train" name="TaGRes-train" version="0.94">
-    <description>Target-specific Grid-Rescoring, training</description>
-    <command interpreter="bash"><![CDATA[../../TaGRes-train 
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $rl ) != ''  and str( $rl ) != 'None' :
-   -rl "$rl"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $method ) != ''  and str( $method ) != 'None' :
-   -method "$method"
-#end if
-#if str( $function ) != ''  and str( $function ) != 'None' :
-   -function "$function"
-#end if
-#if str( $exp ) != ''  and str( $exp ) != 'None' :
-   -exp "$exp"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
-            <option value="Rescoring3D">Rescoring3D</option>
-            <option value="Rescoring4D">Rescoring4D</option>
-            <option value="Rescoring1D">Rescoring1D</option>
-        </param>
-        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
-            <option value="MM">MM</option>
-            <option value="PLP">PLP</option>
-        </param>
-        <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
-    </inputs>
-    <outputs>
-        <data name="o" format="mod"/>
-    </outputs>
-    <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes).
-As input we need:
-
-    * a file containing a protonated protein in pdb-format
-    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-    * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein.
-
-A scoring function is applied and an interaction-grid thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it.
-
-The output of this TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/TaGRes.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="tagres" name="TaGRes" version="0.94">
-    <description>Target-specific Grid-Rescoring</description>
-    <command interpreter="bash"><![CDATA[../../TaGRes 
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $rl ) != ''  and str( $rl ) != 'None' :
-   -rl "$rl"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $mod ) != ''  and str( $mod ) != 'None' :
-   -mod "$mod"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $method ) != ''  and str( $method ) != 'None' :
-   -method "$method"
-#end if
-#if str( $function ) != ''  and str( $function ) != 'None' :
-   -function "$function"
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="mod" label="model-file generated by TaGRes-train" optional="false" type="data" format="data"/>
-        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
-            <option value="Rescoring3D">Rescoring3D</option>
-            <option value="Rescoring4D">Rescoring4D</option>
-            <option value="Rescoring1D">Rescoring1D</option>
-        </param>
-        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
-            <option value="MM">MM</option>
-            <option value="PLP">PLP</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="o" format="mol2/sdf/drf" format_source="i"/>
-    </outputs>
-    <help>This tool rescores docking output poses using Target-specific Grid-Rescoring.
-Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool.
-As input TaGRes needs:
-
-    * a file containing a protonated protein in pdb-format
-    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
-    * a regression model file as generated by TaGRes-train for same protein target than the one specified here.
-
-TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy.
-
-Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/VendorFinder.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="vendorfinder" name="VendorFinder" version="0.94">
-    <description>search vendors for compounds</description>
-    <command interpreter="bash"><![CDATA[../../VendorFinder 
-#if str( $i ) != ''  and str( $i ) != 'None' :
-   -i "$i"
-#end if
-#if str( $d ) != ''  and str( $d ) != 'None' :
-   -d "$d"
-#end if
-#if str( $u ) != ''  and str( $u ) != 'None' :
-   -u "$u"
-#end if
-#if str( $h ) != ''  and str( $h ) != 'None' :
-   -h "$h"
-#end if
-#if str( $port ) != ''  and str( $port ) != 'None' :
-   -port "$port"
-#end if
-#if str( $p ) != ''  and str( $p ) != 'None' :
-   -p "$p"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $opt ) != ''  and str( $opt ) != 'None' :
-   -opt
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="i" label="input file containing compounds" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
-        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
-        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
-        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
-        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
-        <param name="opt" label="optimize purchase, i.e. select cheapest sources and sort by vendor" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="txt"/>
-    </outputs>
-    <help>This tool can be used to fetch information about vendors for each compound in the given input file from a data base.
-
-Of course, vendors can only be found if they have been stored in the database that is to be used here. Use DBImporter with molecules files obtained from the compound vendors of your choice in order to create such a database.
-
-Output of this tool is a text-file containing a list of vendor-name and vendor's compound-ID for each compound in the input file for which vendor-information was found in the database.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/WaterFinder.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-
-<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
-<tool id="waterfinder" name="WaterFinder" version="0.94">
-    <description>find strongly bound waters</description>
-    <command interpreter="bash"><![CDATA[../../WaterFinder 
-#if str( $rec ) != ''  and str( $rec ) != 'None' :
-   -rec "$rec"
-#end if
-#if str( $rl ) != ''  and str( $rl ) != 'None' :
-   -rl "$rl"
-#end if
-#if str( $ini ) != ''  and str( $ini ) != 'None' :
-   -ini "$ini"
-#end if
-#if str( $wat ) != ''  and str( $wat ) != 'None' :
-   -wat "$wat"
-#end if
-#if str( $o ) != ''  and str( $o ) != 'None' :
-   -o "$o"
-#end if
-#if str( $ai ) != ''  and str( $ai ) != 'None' :
-   -ai
-#end if
- | tail -n 5
-]]></command>
-    <inputs>
-        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
-        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
-        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
-        <param name="wat" label="input pdb-file containing water molecules (if not part of rec.-file)" optional="true" type="data" format="pdb"/>
-        <param name="ai" label="use ab-initio water search (ignore water in pdb-file), experimental!" optional="true" type="boolean" truevalue="true" falsevalue=""/>
-    </inputs>
-    <outputs>
-        <data name="o" format="pdb"/>
-    </outputs>
-    <help>This tool searches for crystal waters that
-    * either interact very strongly with the receptor
-    * or that interact strongly with receptor and reference ligand, 
-      thus functioning as a water bridge.
-
-Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done.
-
-As input we need:
-    * a file containing a protonated protein in pdb-format.
-      This file should contain water molecules that are to be evaluated by this tool.
-      However, you can also use a separate pdb-file as input for the water molecules (see below).
-    * a file containing a reference ligand.
-      This reference ligand should be located in the binding pocket.
-      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
-    * optionally a file in pdb-format containing water molecules.
-      If you specify such a file , all water molecules appearing in the
-      protein input-file (if any) will be ignored.
-
-Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.</help>
-</tool>
\ No newline at end of file

--- a/CADDSuite/galaxyconfigs/tools/upload.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<?xml version="1.0"?>
-
-<tool name="Upload File" id="cadds_upload" version="1.1.2">
-  <description>
-    from your computer  
-  </description>
-  <action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
-  <command interpreter="python">
-      ../../../data_source/upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile
-    #set $outnum = 0
-    #while $varExists('output%i' % $outnum):
-        #set $output = $getVar('output%i' % $outnum)
-        #set $outnum += 1
-        ${output.dataset.dataset.id}:${output.files_path}:${output}
-    #end while
-  </command>
-  <inputs nginx_upload="true">
-    <param name="file_type" type="select" label="File Format" help="Which format? See help below">
-      <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ &quot;%s%s%s&quot; % ( line, self.separator, line ) for line in obj ]">
-        <column name="value" index="1"/>
-        <column name="name" index="0"/>
-        <filter type="sort_by" column="0"/>
-        <filter type="add_value" name="Auto-detect" value="auto" index="0"/>
-      </options>
-    </param>
-    <param name="async_datasets" type="hidden" value="None"/>
-    <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
-      <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: For NGS and other large files (>~2GB), uploading via HTTP/FTP URL (below) is the most reliable method.">
-        <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs -->
-      </param>
-      <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> 
-      <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/>
-      <!--
-      <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."> 
-        <option value="Yes">Yes</option>
-      </param>
-      -->
-    </upload_dataset>
-    <!--<param name="dbkey" type="genomebuild" label="Genome" />-->
-    <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />
-    <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> -->
-  </inputs>
-  <help>
-
-  </help>
-</tool>

--- a/CADDSuite/install.sh	Sun Jun 26 13:45:14 2011 -0400
+++ /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

Binary file CADDSuite/lib/libBALL.so.1.4 has changed

Binary file CADDSuite/lib/libQtCore.so.4 has changed

Binary file CADDSuite/lib/libQtNetwork.so.4 has changed

Binary file CADDSuite/lib/libQtSql.so.4 has changed

Binary file CADDSuite/lib/libQtXml.so.4 has changed

Binary file CADDSuite/lib/libmysqlclient_r.so.16 has changed

Binary file CADDSuite/lib/libnsl.so.1 has changed

--- a/CADDSuite/setPathes.sh	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#!/bin/bash
-export LD_LIBRARY_PATH="$BASE_DIR"/lib
-export DYLD_LIBRARY_PATH="$BASE_DIR"/lib
-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/fonts
-export GNUPLOT_DEFAULT_GDFONT=FreeSans
-

--- a/CADDSuite/suite_config.xml	Sun Jun 26 13:45:14 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,140 +0,0 @@
-<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.94">
-
-<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="0.94">
-    <description>rescore w/ anti-target dock-results</description>
-</tool>
-<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94">
-    <description>fix bindingdb.org downloads</description>
-</tool>
-<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94">
-    <description>generate combinatorial lib</description>
-</tool>
-<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94">
-    <description>find strongly interacting residues</description>
-</tool>
-<tool id="converter" name="Converter" version="0.94">
-    <description>interconvert molecular file-formats</description>
-</tool>
-<tool id="dbexporter" name="DBExporter" version="0.94 (ob)">
-    <description>export molecules from data base</description>
-</tool>
-<tool id="dbimporter" name="DBImporter" version="0.94 (ob)">
-    <description>import molecules into data base</description>
-</tool>
-<tool id="dockresultmerger" name="DockResultMerger" version="0.94">
-    <description>merge docking output files</description>
-</tool>
-<tool id="evensplit" name="EvenSplit" version="0.94">
-    <description>generate splits w/ equal property range</description>
-</tool>
-<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94">
-    <description>generate galaxy tool-config files</description>
-</tool>
-<tool id="gridbuilder" name="GridBuilder" version="0.94">
-    <description>create score-grids for docking</description>
-</tool>
-<tool id="imeedydock" name="IMGDock" version="0.94">
-    <description>Iterative Multi-Greedy Docking</description>
-</tool>
-<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94">
-    <description>define interaction constraint</description>
-</tool>
-<tool id="ligcheck" name="LigCheck" version="0.94">
-    <description>check molecules for errors</description>
-</tool>
-<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94">
-    <description>generate 3D coordinates for small molecules</description>
-</tool>
-<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94">
-    <description>split molecule files</description>
-</tool>
-<tool id="molcombine" name="MolCombine" version="0.94">
-    <description>combine molecular files</description>
-</tool>
-<tool id="moldepict" name="MolDepict" version="0.94">
-    <description>create structure diagrams</description>
-</tool>
-<tool id="molfilter" name="MolFilter" version="0.9">
-    <description>filter molecule files</description>
-</tool>
-<tool id="pdbcutter" name="PDBCutter" version="0.94">
-    <description>separate ligand and receptor</description>
-</tool>
-<tool id="pdbdownload" name="PDBDownload" version="0.94">
-    <description>retrieve pdb-file from pdb.org</description>
-</tool>
-<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94">
-    <description>transfer part. charges between files</description>
-</tool>
-<tool id="pocketdetector" name="PocketDetector" version="0.94">
-    <description>detect binding pocket</description>
-</tool>
-<tool id="propertymodifier" name="PropertyModifier" version="0.94">
-    <description>modify molecule property tags</description>
-</tool>
-<tool id="propertyplotter" name="PropertyPlotter" version="0.94">
-    <description>plot molecule properties</description>
-</tool>
-<tool id="proteincheck" name="ProteinCheck" version="0.94">
-    <description>quality check for proteins structures</description>
-</tool>
-<tool id="proteinprotonator" name="ProteinProtonator" version="0.94">
-    <description>protonate protein structures</description>
-</tool>
-<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
-    <description>calculate RMSD between poses</description>
-</tool>
-<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94">
-    <description>generate ROC or enrichment plots</description>
-</tool>
-<tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9">
-    <description>analyze similarity between molecule files</description>
-</tool>
-<tool id="simplerescorer" name="SimpleRescorer" version="0.94">
-    <description>rescore docking results</description>
-</tool>
-<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94">
-    <description>define spatial constraint</description>
-</tool>
-<tool id="tagres-train" name="TaGRes-train" version="0.94">
-    <description>Target-specific Grid-Rescoring, training</description>
-</tool>
-<tool id="tagres" name="TaGRes" version="0.94">
-    <description>Target-specific Grid-Rescoring</description>
-</tool>
-<tool id="vendorfinder" name="VendorFinder" version="0.94">
-    <description>search vendors for compounds</description>
-</tool>
-<tool id="waterfinder" name="WaterFinder" version="0.94">
-    <description>find strongly bound waters</description>
-</tool>
-<tool id="automodel" name="AutoModel" version="1.1">
-    <description>automatically find best QSAR model</description>
-</tool>
-<tool id="featureselector" name="FeatureSelector" version="1.1">
-    <description>run feature-selection on a QSAR model</description>
-</tool>
-<tool id="inputpartitioner" name="InputPartitioner" version="1.1">
-    <description>split QSAR data set</description>
-</tool>
-<tool id="inputreader" name="InputReader" version="1.1">
-    <description>generate QSAR data set</description>
-</tool>
-<tool id="modelcreator" name="ModelCreator" version="1.1">
-    <description>create a QSAR model</description>
-</tool>
-<tool id="molpredictor" name="MolPredictor" version="1.1">
-    <description>predict molecule activities with QSAR model</description>
-</tool>
-<tool id="predictor" name="Predictor" version="1.1">
-    <description>predict activities with QSAR model</description>
-</tool>
-<tool id="validator" name="Validator" version="1.1">
-    <description>evaluate quality of a QSAR model</description>
-</tool></suite>