Mercurial > repos > marcel > caddsuite_linux_x86_64

annotate CADDSuite-1.5/suite_config.xml @ 16:1a24aef40d01 draft

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author marcel
date Tue, 24 Jul 2012 11:10:07 -0400
parents ac342506cd4e
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15
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
1 <suite id="CADDSuite_toolsuite" name="CADDSuite" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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2
ac342506cd4e CADDSuite version 1.5
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3 <description>
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4 CADDSuite: A flexible and open framework for Computer-Aided Drug Design
ac342506cd4e CADDSuite version 1.5
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5 </description>
ac342506cd4e CADDSuite version 1.5
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6 <tool id="cadds_upload" name="Upload File" version="1.1.2">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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7 <description>from your computer</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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8 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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9 <tool id="antitargetrescorer" name="AntitargetRescorer" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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10 <description>rescore w/ anti-target dock-results</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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11 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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12 <tool id="automodel" name="AutoModel" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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13 <description>automatically find best QSAR model</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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14 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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15 <tool id="bindingdbcleaner" name="BindingDBCleaner" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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16 <description>fix bindingdb.org downloads</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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17 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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18 <tool id="combilibgenerator" name="CombiLibGenerator" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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19 <description>generate combinatorial lib</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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20 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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21 <tool id="constraintsfinder" name="ConstraintsFinder" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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22 <description>find strongly interacting residues</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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23 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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24 <tool id="converter" name="Converter" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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25 <description>interconvert molecular file-formats</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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26 </tool>
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27 <tool id="dbexporter" name="DBExporter" version="1.5 (ob)">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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28 <description>export molecules from data base</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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29 </tool>
ac342506cd4e CADDSuite version 1.5
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30 <tool id="dbimporter" name="DBImporter" version="1.5 (ob)">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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31 <description>import molecules into data base</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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32 </tool>
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33 <tool id="dockresultmerger" name="DockResultMerger" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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34 <description>merge docking output files</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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35 </tool>
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36 <tool id="evensplit" name="EvenSplit" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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37 <description>generate splits w/ equal property range</description>
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38 </tool>
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39 <tool id="featureselector" name="FeatureSelector" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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40 <description>run feature-selection on a QSAR model</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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41 </tool>
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Marcel Schumann <schumann.marcel@gmail.com>
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42 <tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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43 <description>generate galaxy tool-config files</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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44 </tool>
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Marcel Schumann <schumann.marcel@gmail.com>
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45 <tool id="gridbuilder" name="GridBuilder" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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46 <description>create score-grids for docking</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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47 </tool>
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48 <tool id="imeedydock" name="IMGDock" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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49 <description>Iterative Multi-Greedy Docking</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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50 </tool>
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Marcel Schumann <schumann.marcel@gmail.com>
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51 <tool id="inputpartitioner" name="InputPartitioner" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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52 <description>split QSAR data set</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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53 </tool>
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Marcel Schumann <schumann.marcel@gmail.com>
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54 <tool id="inputreader" name="InputReader" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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55 <description>generate QSAR data set</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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56 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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57 <tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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58 <description>define interaction constraint</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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59 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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60 <tool id="ligand3dgenerator" name="Ligand3DGenerator" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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61 <description>generate 3D coordinates for small molecules</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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62 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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63 <tool id="ligandfilesplitter" name="LigandFileSplitter" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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64 <description>split molecule files</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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65 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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66 <tool id="ligcheck" name="LigCheck" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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67 <description>check molecules for errors</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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68 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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69 <tool id="modelcreator" name="ModelCreator" version="1.1">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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70 <description>create a QSAR model</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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71 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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72 <tool id="molcombine" name="MolCombine" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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73 <description>combine molecular files</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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74 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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75 <tool id="moldepict" name="MolDepict" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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76 <description>create structure diagrams</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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77 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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78 <tool id="molfilter" name="MolFilter" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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79 <description>filter molecule files</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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80 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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81 <tool id="molpredictor" name="MolPredictor" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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82 <description>predict molecule activities with QSAR model</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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83 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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84 <tool id="partialchargescopy" name="PartialChargesCopy" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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85 <description>transfer part. charges between files</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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86 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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87 <tool id="pdbcutter" name="PDBCutter" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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88 <description>separate ligand and receptor</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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89 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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90 <tool id="pdbdownload" name="PDBDownload" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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91 <description>retrieve pdb-file from pdb.org</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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92 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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93 <tool id="pocketcutter" name="PocketCutter" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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94 <description>cut binding pocket surface</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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95 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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96 <tool id="pocketdetector" name="PocketDetector" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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97 <description>detect binding pocket</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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98 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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99 <tool id="predictor" name="Predictor" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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100 <description>predict activities with QSAR model</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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101 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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102 <tool id="propertymodifier" name="PropertyModifier" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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103 <description>modify molecule property tags</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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104 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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105 <tool id="propertyplotter" name="PropertyPlotter" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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106 <description>plot molecule properties</description>
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107 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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108 <tool id="proteincheck" name="ProteinCheck" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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109 <description>quality check for proteins structures</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
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110 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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111 <tool id="proteinprotonator" name="ProteinProtonator" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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112 <description>protonate protein structures</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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113 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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114 <tool id="rmsdcalculator" name="RMSDCalculator" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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115 <description>calculate RMSD between poses</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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116 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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117 <tool id="scoreanalyzer" name="ScoreAnalyzer" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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118 <description>generate ROC or enrichment plots</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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119 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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120 <tool id="similarityanalyzer" name="SimilarityAnalyzer" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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121 <description>analyze similarity between molecule files</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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122 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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123 <tool id="simplerescorer" name="SimpleRescorer" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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124 <description>rescore docking results</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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125 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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126 <tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
127 <description>define spatial constraint</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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128 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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129 <tool id="surfacematcher" name="SurfaceMatcher" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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130 <description>match two protein surfaces onto each other</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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131 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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132 <tool id="tagres" name="TaGRes" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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133 <description>Target-specific Grid-Rescoring</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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134 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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135 <tool id="tagres-train" name="TaGRes-train" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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136 <description>Target-specific Grid-Rescoring, training</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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137 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
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138 <tool id="validator" name="Validator" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
139 <description>evaluate quality of a QSAR model</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
140 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
141 <tool id="vendorfinder" name="VendorFinder" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
142 <description>search vendors for compounds</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
143 </tool>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
144 <tool id="waterfinder" name="WaterFinder" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
145 <description>find strongly bound waters</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
146 </tool></suite>