Mercurial > repos > marcel > caddsuite_linux_x86_64
changeset 8:9ab6da6cd36c
Uploaded
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--- a/CADDSuite/changelog.txt Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/changelog.txt Fri Sep 02 08:48:21 2011 -0400 @@ -1,4 +1,15 @@ -Version 0.95, 07-12-2011: +Version 0.9.6, 08-20-2011: + - MolFilter: Use union of SMARTS matches instead of intersection + - Support for reading and writing compressed molecule files (*.gz) + - Added optional parameter for output log-file to DBImporter + - Added flag for disabling uniqueness-check to LigCheck + - mol2-files: disabled gaff atom-typing for speed-up + - drf-files: automatically add new protein-conformations + - Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable + - InputReader: made sure to always calculate correct set of features + - Fixed a nan problem during centering of QSAR data + +Version 0.9.5, 07-12-2011: - Let rescoring search for correct LigCheck molecule property-tags - Indicate optional parameters in galaxy interface - Fixed compilation with disabled QuEasyViz @@ -6,7 +17,7 @@ - Set some default values for flags for use in GUIs - Clarified EvenSplit docu -Version 0.94, 06-27-2011: +Version 0.9.4, 06-27-2011: - Fixed tool-startup script for pathes containing whitespaces - New tool SpatialConstraintDefiner - New tool InteractionConstraintDefiner @@ -14,7 +25,7 @@ - Slight change in ParamFile format (i.e. the files written with -write_par) - Renamed IMeedyDock to IMGDock -Version 0.93, 05-30-2011: +Version 0.9.3, 05-30-2011: - Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring) - Allow to optionally specify output filenames to LigandFileSplitter - Fixed creation of galaxy-scripts for tools with inputfile-lists @@ -33,7 +44,7 @@ - Enhanced several tool manuals - Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles. -Version 0.92, 05-17-2011: +Version 0.9.2, 05-17-2011: - Speed-up of ob-mol generation - Support build on Windows - ProteinCheck now generates protein-quality report as pdf @@ -48,7 +59,7 @@ - new tool GalaxyConfigGenerator - allow to open file that do not have an extension (by searching for format-specific keywords) -Version 0.91, 04-12-2011: - - All tools now write a manual text to cout as well as to parameter xml-file (as generated by 'write_par) +Version 0.9.1, 04-12-2011: + - All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par) Version 0.9
--- a/CADDSuite/galaxyconfigs/tool_conf.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tool_conf.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <toolbox> - <label text="CADDSuite 0.95" id="cadds" /> + <label text="CADDSuite 0.9.6" id="cadds" /> <section name="Get Data" id="getext"> <tool file="CADDSuite/galaxyconfigs/tools/upload.xml"/>
--- a/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.95"> +<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.9.6"> <description>rescore w/ anti-target dock-results</description> <command interpreter="bash"><![CDATA[../../AntitargetRescorer #if str( $t ) != '' and str( $t ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/AutoModel.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="automodel" name="AutoModel" version="0.95"> +<tool id="automodel" name="AutoModel" version="0.9.6"> <description>automatically find best QSAR model</description> <command interpreter="bash"><![CDATA[../../AutoModel #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.95"> +<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.9.6"> <description>fix bindingdb.org downloads</description> <command interpreter="bash"><![CDATA[../../BindingDBCleaner #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="combilibgenerator" name="CombiLibGenerator" version="0.95"> +<tool id="combilibgenerator" name="CombiLibGenerator" version="0.9.6"> <description>generate combinatorial lib</description> <command interpreter="bash"><![CDATA[../../CombiLibGenerator #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="constraintsfinder" name="ConstraintsFinder" version="0.95"> +<tool id="constraintsfinder" name="ConstraintsFinder" version="0.9.6"> <description>find strongly interacting residues</description> <command interpreter="bash"><![CDATA[../../ConstraintsFinder #if str( $rec ) != '' and str( $rec ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/Converter.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/Converter.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="converter" name="Converter" version="0.95"> +<tool id="converter" name="Converter" version="0.9.6"> <description>interconvert molecular file-formats</description> <command interpreter="bash"><![CDATA[../../Converter #if str( $i ) != '' and str( $i ) != 'None' : @@ -12,6 +12,9 @@ #if str( $f ) != '' and str( $f ) != 'None' : -f "$f" #end if +#if str( $rm ) != '' and str( $rm ) != 'None' : + -rm +#end if | tail -n 5 ]]></command> <inputs> @@ -27,7 +30,18 @@ <option value="hin">hin</option> <option value="mol">mol</option> <option value="xyz">xyz</option> + <option value="mol2.gz">mol2.gz</option> + <option value="sdf.gz">sdf.gz</option> + <option value="drf.gz">drf.gz</option> + <option value="pdb.gz">pdb.gz</option> + <option value="ac.gz">ac.gz</option> + <option value="ent.gz">ent.gz</option> + <option value="brk.gz">brk.gz</option> + <option value="hin.gz">hin.gz</option> + <option value="mol.gz">mol.gz</option> + <option value="xyz.gz">xyz.gz</option> </param> + <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf"> @@ -42,9 +56,19 @@ <when input="f" value="hin" format="hin"/> <when input="f" value="mol" format="mol"/> <when input="f" value="xyz" format="xyz"/> + <when input="f" value="mol2.gz" format="mol2.gz"/> + <when input="f" value="sdf.gz" format="sdf.gz"/> + <when input="f" value="drf.gz" format="drf.gz"/> + <when input="f" value="pdb.gz" format="pdb.gz"/> + <when input="f" value="ac.gz" format="ac.gz"/> + <when input="f" value="ent.gz" format="ent.gz"/> + <when input="f" value="brk.gz" format="brk.gz"/> + <when input="f" value="hin.gz" format="hin.gz"/> + <when input="f" value="mol.gz" format="mol.gz"/> + <when input="f" value="xyz.gz" format="xyz.gz"/> </change_format> </data> </outputs> <help>This tool can be used to convert between different molecular file-formats. -Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help> +Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz, mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.</help> </tool> \ No newline at end of file
--- a/CADDSuite/galaxyconfigs/tools/DBExporter.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="dbexporter" name="DBExporter" version="0.95 (ob)"> +<tool id="dbexporter" name="DBExporter" version="0.9.6 (ob)"> <description>export molecules from data base</description> <command interpreter="bash"><![CDATA[../../DBExporter #if str( $o ) != '' and str( $o ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/DBImporter.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,11 +1,14 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="dbimporter" name="DBImporter" version="0.95 (ob)"> +<tool id="dbimporter" name="DBImporter" version="0.9.6 (ob)"> <description>import molecules into data base</description> <command interpreter="bash"><![CDATA[../../DBImporter #if str( $i ) != '' and str( $i ) != 'None' : -i "$i" #end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if #if str( $target ) != '' and str( $target ) != 'None' : -target "$target" #end if @@ -51,7 +54,9 @@ <param name="vd" optional="true" label="Optional: vendor library date or version" area="true" type="text" size="1x15"/> <param name="vu" optional="true" label="Optional: url from wich vendor library was obtained" area="true" type="text" size="1x15"/> </inputs> - <outputs/> + <outputs> + <data name="o" format="data"/> + </outputs> <help>This tool imports molecules into a database. As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help> </tool> \ No newline at end of file
--- a/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="dockresultmerger" name="DockResultMerger" version="0.95"> +<tool id="dockresultmerger" name="DockResultMerger" version="0.9.6"> <description>merge docking output files</description> <command interpreter="bash"><![CDATA[../../DockResultMerger #for $s in $series_i
--- a/CADDSuite/galaxyconfigs/tools/EvenSplit.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="evensplit" name="EvenSplit" version="0.95"> +<tool id="evensplit" name="EvenSplit" version="0.9.6"> <description>generate splits w/ equal property range</description> <command interpreter="bash"><![CDATA[../../EvenSplit #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="featureselector" name="FeatureSelector" version="0.95"> +<tool id="featureselector" name="FeatureSelector" version="0.9.6"> <description>run feature-selection on a QSAR model</description> <command interpreter="bash"><![CDATA[../../FeatureSelector #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.95"> +<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.9.6"> <description>generate galaxy tool-config files</description> <command interpreter="bash"><![CDATA[../../GalaxyConfigGenerator #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/GridBuilder.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="gridbuilder" name="GridBuilder" version="0.95"> +<tool id="gridbuilder" name="GridBuilder" version="0.9.6"> <description>create score-grids for docking</description> <command interpreter="bash"><![CDATA[../../GridBuilder #if str( $rec ) != '' and str( $rec ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/IMGDock.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/IMGDock.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="imeedydock" name="IMGDock" version="0.95"> +<tool id="imeedydock" name="IMGDock" version="0.9.6"> <description>Iterative Multi-Greedy Docking</description> <command interpreter="bash"><![CDATA[../../IMGDock #if str( $rec ) != '' and str( $rec ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="inputpartitioner" name="InputPartitioner" version="0.95"> +<tool id="inputpartitioner" name="InputPartitioner" version="0.9.6"> <description>split QSAR data set</description> <command interpreter="bash"><![CDATA[../../InputPartitioner #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/InputReader.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="inputreader" name="InputReader" version="0.95"> +<tool id="inputreader" name="InputReader" version="0.9.6"> <description>generate QSAR data set</description> <command interpreter="bash"><![CDATA[../../InputReader #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.95"> +<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.9.6"> <description>define interaction constraint</description> <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner #if str( $res ) != '' and str( $res ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/LigCheck.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="ligcheck" name="LigCheck" version="0.95"> +<tool id="ligcheck" name="LigCheck" version="0.9.6"> <description>check molecules for errors</description> <command interpreter="bash"><![CDATA[../../LigCheck #if str( $i ) != '' and str( $i ) != 'None' : @@ -18,13 +18,21 @@ #if str( $ut ) != '' and str( $ut ) != 'None' : -ut #end if +#if str( $nc ) != '' and str( $nc ) != 'None' : + -nc +#end if +#if str( $rm ) != '' and str( $rm ) != 'None' : + -rm +#end if | tail -n 5 ]]></command> <inputs> <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/> <param name="ef" optional="true" label="Optional: error fraction; print error if fraction of invalid mols is larger" type="text" area="true" size="1x5" value="0.5"/> <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/> - <param name="ut" optional="true" label="check for unique topologies (default: check only for unique conformation)" type="boolean" truevalue="true" falsevalue=""/> + <param name="ut" optional="true" label="check for unique topologies" type="boolean" truevalue="true" falsevalue=""/> + <param name="nc" optional="true" label="no not check for unique conformations" type="boolean" truevalue="true" falsevalue=""/> + <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.95"> +<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.9.6"> <description>generate 3D coordinates for small molecules</description> <command interpreter="bash"><![CDATA[../../Ligand3DGenerator #if str( $i ) != '' and str( $i ) != 'None' : @@ -12,11 +12,15 @@ #if str( $ph ) != '' and str( $ph ) != 'None' : -ph "$ph" #end if +#if str( $rm ) != '' and str( $rm ) != 'None' : + -rm +#end if | tail -n 5 ]]></command> <inputs> <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/> <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/> + <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/> @@ -26,5 +30,5 @@ Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other. -Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help> +Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz, mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.</help> </tool> \ No newline at end of file
--- a/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.95"> +<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.9.6"> <description>split molecule files</description> <command interpreter="bash"><![CDATA[../../LigandFileSplitter #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/MolCombine.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="molcombine" name="MolCombine" version="0.95"> +<tool id="molcombine" name="MolCombine" version="0.9.6"> <description>combine molecular files</description> <command interpreter="bash"><![CDATA[../../MolCombine #if str( $i1 ) != '' and str( $i1 ) != 'None' : @@ -21,6 +21,9 @@ #if str( $replace_prop ) != '' and str( $replace_prop ) != 'None' : -replace_prop #end if +#if str( $rm ) != '' and str( $rm ) != 'None' : + -rm +#end if | tail -n 5 ]]></command> <inputs> @@ -33,6 +36,7 @@ </param> <param name="ignH" optional="true" label="ignore hydrogens, i.e. match molecules to any protonation state." type="boolean" truevalue="true" falsevalue="" checked="true"/> <param name="replace_prop" optional="true" label="replace properties from file 1 w/ those from file 2" type="boolean" truevalue="true" falsevalue=""/> + <param name="rm" optional="true" label="remove input files when finished" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i1"/>
--- a/CADDSuite/galaxyconfigs/tools/MolDepict.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="moldepict" name="MolDepict" version="0.95"> +<tool id="moldepict" name="MolDepict" version="0.9.6"> <description>create structure diagrams</description> <command interpreter="bash"><![CDATA[../../MolDepict #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/MolFilter.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml Fri Sep 02 08:48:21 2011 -0400 @@ -37,6 +37,9 @@ -o "$o" #end if -quiet +#if str( $rm ) != '' and str( $rm ) != 'None' : + -rm +#end if | tail -n 5 ]]></command> <inputs> @@ -50,6 +53,7 @@ <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" area="true" size="1x5" value=""/> <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" area="true" size="1x5" value=""/> <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/> + <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="mol2/sdf/drf" format_source="i"/>
--- a/CADDSuite/galaxyconfigs/tools/MolPredictor.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="molpredictor" name="MolPredictor" version="0.95"> +<tool id="molpredictor" name="MolPredictor" version="0.9.6"> <description>predict molecule activities with QSAR model</description> <command interpreter="bash"><![CDATA[../../MolPredictor #if str( $i ) != '' and str( $i ) != 'None' : @@ -27,6 +27,9 @@ #if str( $csv_dl ) != '' and str( $csv_dl ) != 'None' : -csv_dl #end if +#if str( $rm ) != '' and str( $rm ) != 'None' : + -rm +#end if | tail -n 5 ]]></command> <inputs> @@ -37,6 +40,7 @@ <param name="csv_sep" optional="true" label="Optional: separator symbol in csv-file" type="text" area="true" size="1x5" value=""/> <param name="csv_cl" optional="true" label="csv-file has compound (row) labels" type="boolean" truevalue="true" falsevalue=""/> <param name="csv_dl" optional="true" label="csv-file has descriptor (column) labels" type="boolean" truevalue="true" falsevalue=""/> + <param name="rm" optional="true" label="remove input sd-file when finished" type="boolean" truevalue="true" falsevalue=""/> </inputs> <outputs> <data name="o" format="sdf"/>
--- a/CADDSuite/galaxyconfigs/tools/PDBCutter.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="pdbcutter" name="PDBCutter" version="0.95"> +<tool id="pdbcutter" name="PDBCutter" version="0.9.6"> <description>separate ligand and receptor</description> <command interpreter="bash"><![CDATA[../../PDBCutter #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/PDBDownload.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="pdbdownload" name="PDBDownload" version="0.95"> +<tool id="pdbdownload" name="PDBDownload" version="0.9.6"> <description>retrieve pdb-file from pdb.org</description> <command interpreter="bash"><![CDATA[../../PDBDownload #if str( $id ) != '' and str( $id ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="partialchargescopy" name="PartialChargesCopy" version="0.95"> +<tool id="partialchargescopy" name="PartialChargesCopy" version="0.9.6"> <description>transfer part. charges between files</description> <command interpreter="bash"><![CDATA[../../PartialChargesCopy #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/PocketDetector.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="pocketdetector" name="PocketDetector" version="0.95"> +<tool id="pocketdetector" name="PocketDetector" version="0.9.6"> <description>detect binding pocket</description> <command interpreter="bash"><![CDATA[../../PocketDetector #if str( $rec ) != '' and str( $rec ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/Predictor.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="predictor" name="Predictor" version="0.95"> +<tool id="predictor" name="Predictor" version="0.9.6"> <description>predict activities with QSAR model</description> <command interpreter="bash"><![CDATA[../../Predictor #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="propertymodifier" name="PropertyModifier" version="0.95"> +<tool id="propertymodifier" name="PropertyModifier" version="0.9.6"> <description>modify molecule property tags</description> <command interpreter="bash"><![CDATA[../../PropertyModifier #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="propertyplotter" name="PropertyPlotter" version="0.95"> +<tool id="propertyplotter" name="PropertyPlotter" version="0.9.6"> <description>plot molecule properties</description> <command interpreter="bash"><![CDATA[../../PropertyPlotter #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="proteincheck" name="ProteinCheck" version="0.95"> +<tool id="proteincheck" name="ProteinCheck" version="0.9.6"> <description>quality check for proteins structures</description> <command interpreter="bash"><![CDATA[../../ProteinCheck #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="proteinprotonator" name="ProteinProtonator" version="0.95"> +<tool id="proteinprotonator" name="ProteinProtonator" version="0.9.6"> <description>protonate protein structures</description> <command interpreter="bash"><![CDATA[../../ProteinProtonator #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="rmsdcalculator" name="RMSDCalculator" version="0.95"> +<tool id="rmsdcalculator" name="RMSDCalculator" version="0.9.6"> <description>calculate RMSD between poses</description> <command interpreter="bash"><![CDATA[../../RMSDCalculator #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.95"> +<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.9.6"> <description>generate ROC or enrichment plots</description> <command interpreter="bash"><![CDATA[../../ScoreAnalyzer #if str( $mode ) != '' and str( $mode ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="simplerescorer" name="SimpleRescorer" version="0.95"> +<tool id="simplerescorer" name="SimpleRescorer" version="0.9.6"> <description>rescore docking results</description> <command interpreter="bash"><![CDATA[../../SimpleRescorer #if str( $rec ) != '' and str( $rec ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95"> +<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.9.6"> <description>define spatial constraint</description> <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner #if str( $ini ) != '' and str( $ini ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="tagres-train" name="TaGRes-train" version="0.95"> +<tool id="tagres-train" name="TaGRes-train" version="0.9.6"> <description>Target-specific Grid-Rescoring, training</description> <command interpreter="bash"><![CDATA[../../TaGRes-train #if str( $rec ) != '' and str( $rec ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/TaGRes.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="tagres" name="TaGRes" version="0.95"> +<tool id="tagres" name="TaGRes" version="0.9.6"> <description>Target-specific Grid-Rescoring</description> <command interpreter="bash"><![CDATA[../../TaGRes #if str( $rec ) != '' and str( $rec ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/Validator.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/Validator.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="validator" name="Validator" version="0.95"> +<tool id="validator" name="Validator" version="0.9.6"> <description>evaluate quality of a QSAR model</description> <command interpreter="bash"><![CDATA[../../Validator #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/VendorFinder.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="vendorfinder" name="VendorFinder" version="0.95"> +<tool id="vendorfinder" name="VendorFinder" version="0.9.6"> <description>search vendors for compounds</description> <command interpreter="bash"><![CDATA[../../VendorFinder #if str( $i ) != '' and str( $i ) != 'None' :
--- a/CADDSuite/galaxyconfigs/tools/WaterFinder.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,6 +1,6 @@ <!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> -<tool id="waterfinder" name="WaterFinder" version="0.95"> +<tool id="waterfinder" name="WaterFinder" version="0.9.6"> <description>find strongly bound waters</description> <command interpreter="bash"><![CDATA[../../WaterFinder #if str( $rec ) != '' and str( $rec ) != 'None' :
--- a/CADDSuite/suite_config.xml Tue Jul 12 10:29:49 2011 -0400 +++ b/CADDSuite/suite_config.xml Fri Sep 02 08:48:21 2011 -0400 @@ -1,4 +1,4 @@ -<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.95"> +<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.9.6"> <description> CADDSuite: A flexible and open framework for Computer-Aided Drug Design @@ -6,135 +6,135 @@ <tool id="cadds_upload" name="Upload File" version="1.1.2"> <description>from your computer</description> </tool> -<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.95"> +<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.9.6"> <description>rescore w/ anti-target dock-results</description> </tool> -<tool id="automodel" name="AutoModel" version="0.95"> +<tool id="automodel" name="AutoModel" version="0.9.6"> <description>automatically find best QSAR model</description> </tool> -<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.95"> +<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.9.6"> <description>fix bindingdb.org downloads</description> </tool> -<tool id="combilibgenerator" name="CombiLibGenerator" version="0.95"> +<tool id="combilibgenerator" name="CombiLibGenerator" version="0.9.6"> <description>generate combinatorial lib</description> </tool> -<tool id="constraintsfinder" name="ConstraintsFinder" version="0.95"> +<tool id="constraintsfinder" name="ConstraintsFinder" version="0.9.6"> <description>find strongly interacting residues</description> </tool> -<tool id="converter" name="Converter" version="0.95"> +<tool id="converter" name="Converter" version="0.9.6"> <description>interconvert molecular file-formats</description> </tool> -<tool id="dbexporter" name="DBExporter" version="0.95 (ob)"> +<tool id="dbexporter" name="DBExporter" version="0.9.6 (ob)"> <description>export molecules from data base</description> </tool> -<tool id="dbimporter" name="DBImporter" version="0.95 (ob)"> +<tool id="dbimporter" name="DBImporter" version="0.9.6 (ob)"> <description>import molecules into data base</description> </tool> -<tool id="dockresultmerger" name="DockResultMerger" version="0.95"> +<tool id="dockresultmerger" name="DockResultMerger" version="0.9.6"> <description>merge docking output files</description> </tool> -<tool id="evensplit" name="EvenSplit" version="0.95"> +<tool id="evensplit" name="EvenSplit" version="0.9.6"> <description>generate splits w/ equal property range</description> </tool> -<tool id="featureselector" name="FeatureSelector" version="0.95"> +<tool id="featureselector" name="FeatureSelector" version="0.9.6"> <description>run feature-selection on a QSAR model</description> </tool> -<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.95"> +<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.9.6"> <description>generate galaxy tool-config files</description> </tool> -<tool id="gridbuilder" name="GridBuilder" version="0.95"> +<tool id="gridbuilder" name="GridBuilder" version="0.9.6"> <description>create score-grids for docking</description> </tool> -<tool id="imeedydock" name="IMGDock" version="0.95"> +<tool id="imeedydock" name="IMGDock" version="0.9.6"> <description>Iterative Multi-Greedy Docking</description> </tool> -<tool id="inputpartitioner" name="InputPartitioner" version="0.95"> +<tool id="inputpartitioner" name="InputPartitioner" version="0.9.6"> <description>split QSAR data set</description> </tool> -<tool id="inputreader" name="InputReader" version="0.95"> +<tool id="inputreader" name="InputReader" version="0.9.6"> <description>generate QSAR data set</description> </tool> -<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.95"> +<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.9.6"> <description>define interaction constraint</description> </tool> -<tool id="ligcheck" name="LigCheck" version="0.95"> +<tool id="ligcheck" name="LigCheck" version="0.9.6"> <description>check molecules for errors</description> </tool> -<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.95"> +<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.9.6"> <description>generate 3D coordinates for small molecules</description> </tool> -<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.95"> +<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.9.6"> <description>split molecule files</description> </tool> <tool id="modelcreator" name="ModelCreator" version="1.1"> <description>create a QSAR model</description> </tool> -<tool id="molcombine" name="MolCombine" version="0.95"> +<tool id="molcombine" name="MolCombine" version="0.9.6"> <description>combine molecular files</description> </tool> -<tool id="moldepict" name="MolDepict" version="0.95"> +<tool id="moldepict" name="MolDepict" version="0.9.6"> <description>create structure diagrams</description> </tool> <tool id="molfilter" name="MolFilter" version="0.9"> <description>filter molecule files</description> </tool> -<tool id="molpredictor" name="MolPredictor" version="0.95"> +<tool id="molpredictor" name="MolPredictor" version="0.9.6"> <description>predict molecule activities with QSAR model</description> </tool> -<tool id="pdbcutter" name="PDBCutter" version="0.95"> +<tool id="pdbcutter" name="PDBCutter" version="0.9.6"> <description>separate ligand and receptor</description> </tool> -<tool id="pdbdownload" name="PDBDownload" version="0.95"> +<tool id="pdbdownload" name="PDBDownload" version="0.9.6"> <description>retrieve pdb-file from pdb.org</description> </tool> -<tool id="partialchargescopy" name="PartialChargesCopy" version="0.95"> +<tool id="partialchargescopy" name="PartialChargesCopy" version="0.9.6"> <description>transfer part. charges between files</description> </tool> -<tool id="pocketdetector" name="PocketDetector" version="0.95"> +<tool id="pocketdetector" name="PocketDetector" version="0.9.6"> <description>detect binding pocket</description> </tool> -<tool id="predictor" name="Predictor" version="0.95"> +<tool id="predictor" name="Predictor" version="0.9.6"> <description>predict activities with QSAR model</description> </tool> -<tool id="propertymodifier" name="PropertyModifier" version="0.95"> +<tool id="propertymodifier" name="PropertyModifier" version="0.9.6"> <description>modify molecule property tags</description> </tool> -<tool id="propertyplotter" name="PropertyPlotter" version="0.95"> +<tool id="propertyplotter" name="PropertyPlotter" version="0.9.6"> <description>plot molecule properties</description> </tool> -<tool id="proteincheck" name="ProteinCheck" version="0.95"> +<tool id="proteincheck" name="ProteinCheck" version="0.9.6"> <description>quality check for proteins structures</description> </tool> -<tool id="proteinprotonator" name="ProteinProtonator" version="0.95"> +<tool id="proteinprotonator" name="ProteinProtonator" version="0.9.6"> <description>protonate protein structures</description> </tool> -<tool id="rmsdcalculator" name="RMSDCalculator" version="0.95"> +<tool id="rmsdcalculator" name="RMSDCalculator" version="0.9.6"> <description>calculate RMSD between poses</description> </tool> -<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.95"> +<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.9.6"> <description>generate ROC or enrichment plots</description> </tool> <tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9"> <description>analyze similarity between molecule files</description> </tool> -<tool id="simplerescorer" name="SimpleRescorer" version="0.95"> +<tool id="simplerescorer" name="SimpleRescorer" version="0.9.6"> <description>rescore docking results</description> </tool> -<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95"> +<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.9.6"> <description>define spatial constraint</description> </tool> -<tool id="tagres-train" name="TaGRes-train" version="0.95"> +<tool id="tagres-train" name="TaGRes-train" version="0.9.6"> <description>Target-specific Grid-Rescoring, training</description> </tool> -<tool id="tagres" name="TaGRes" version="0.95"> +<tool id="tagres" name="TaGRes" version="0.9.6"> <description>Target-specific Grid-Rescoring</description> </tool> -<tool id="validator" name="Validator" version="0.95"> +<tool id="validator" name="Validator" version="0.9.6"> <description>evaluate quality of a QSAR model</description> </tool> -<tool id="vendorfinder" name="VendorFinder" version="0.95"> +<tool id="vendorfinder" name="VendorFinder" version="0.9.6"> <description>search vendors for compounds</description> </tool> -<tool id="waterfinder" name="WaterFinder" version="0.95"> +<tool id="waterfinder" name="WaterFinder" version="0.9.6"> <description>find strongly bound waters</description> </tool></suite>