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annotate CADDSuite-1.5/galaxyconfigs/tools/ConstraintsFinder.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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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="constraintsfinder" name="ConstraintsFinder" version="1.5">
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4 <description>find strongly interacting residues</description>
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5 <command interpreter="bash"><![CDATA[../../ConstraintsFinder
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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
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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
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15 #if str( $o ) != '' and str( $o ) != 'None' :
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16 -o "$o"
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17 #end if
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18 | tail -n 5
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19 ]]></command>
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20 <inputs>
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21 <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
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22 <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
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23 <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
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24 </inputs>
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25 <outputs>
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26 <data name="o" format="ini"/>
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27 </outputs>
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28 <help>This tool searches protein residues with which the reference ligand interacts strongly.
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29 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.
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30
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31 As input we need:
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32 * a file containing a protonated protein in pdb-format
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33 * a file containing a reference ligand.
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34 This reference ligand should be located in the binding pocket.
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35 Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
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36
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37 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>
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38 </tool>