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annotate CADDSuite-1.0.1/galaxyconfigs/tools/WaterFinder.xml @ 23:389056b8864a

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Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
author greg
date Mon, 14 Nov 2011 17:02:30 -0500
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23
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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1
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2 <!--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.-->
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3 <tool id="waterfinder" name="WaterFinder" version="1.0.1">
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4 <description>find strongly bound waters</description>
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5 <command interpreter="bash"><![CDATA[../../WaterFinder
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6 #if str( $rec ) != '' and str( $rec ) != 'None' :
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7 -rec "$rec"
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8 #end if
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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9 #if str( $rl ) != '' and str( $rl ) != 'None' :
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10 -rl "$rl"
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11 #end if
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12 #if str( $ini ) != '' and str( $ini ) != 'None' :
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13 -ini "$ini"
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14 #end if
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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15 #if str( $wat ) != '' and str( $wat ) != 'None' :
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16 -wat "$wat"
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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17 #end if
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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18 #if str( $o ) != '' and str( $o ) != 'None' :
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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19 -o "$o"
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20 #end if
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21 #if str( $ai ) != '' and str( $ai ) != 'None' :
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22 -ai
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23 #end if
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24 | tail -n 5
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25 ]]></command>
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26 <inputs>
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27 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
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28 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
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29 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
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30 <param name="wat" optional="true" label="input pdb-file containing water molecules (if not part of rec.-file)" type="data" format="pdb"/>
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31 <param name="ai" optional="true" label="use ab-initio water search (ignore water in pdb-file), experimental!" type="boolean" truevalue="true" falsevalue=""/>
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32 </inputs>
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33 <outputs>
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34 <data name="o" format="pdb"/>
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35 </outputs>
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36 <help>This tool searches for crystal waters that
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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37 * either interact very strongly with the receptor
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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38 * or that interact strongly with receptor and reference ligand,
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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39 thus functioning as a water bridge.
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40
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41 Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done.
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42
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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43 As input we need:
389056b8864a Uploaded https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.tar.gz
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44 * a file containing a protonated protein in pdb-format.
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45 This file should contain water molecules that are to be evaluated by this tool.
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46 However, you can also use a separate pdb-file as input for the water molecules (see below).
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47 * a file containing a reference ligand.
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48 This reference ligand should be located in the binding pocket.
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49 Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
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50 * optionally a file in pdb-format containing water molecules.
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51 If you specify such a file , all water molecules appearing in the
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52 protein input-file (if any) will be ignored.
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53
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54 Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.</help>
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55 </tool>