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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="ligcheck" name="LigCheck" version="0.95">
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4 <description>check molecules for errors</description>
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5 <command interpreter="bash"><![CDATA[../../LigCheck
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $o ) != '' and str( $o ) != 'None' :
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10 -o "$o"
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11 #end if
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12 #if str( $ef ) != '' and str( $ef ) != 'None' :
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13 -ef "$ef"
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14 #end if
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15 #if str( $ri ) != '' and str( $ri ) != 'None' :
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16 -ri
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17 #end if
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18 #if str( $ut ) != '' and str( $ut ) != 'None' :
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19 -ut
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20 #end if
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21 | tail -n 5
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22 ]]></command>
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23 <inputs>
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24 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
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25 <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"/>
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26 <param name="ri" optional="true" label="remove invalid molecules." type="boolean" truevalue="true" falsevalue="" checked="true"/>
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27 <param name="ut" optional="true" label="check for unique topologies (default: check only for unique conformation)" type="boolean" truevalue="true" falsevalue=""/>
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28 </inputs>
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29 <outputs>
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30 <data name="o" format="mol2/sdf/drf" format_source="i"/>
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31 </outputs>
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32 <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
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33
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34 The following checks are done for each molecule:
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35
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36 * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem)
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37 * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
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38 * each atom must have a valid assigned element
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39 * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
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40 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
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41 * partial charges may not contain completely senseless values (>5 or <-5).
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42 * 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.
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43
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44 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>
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45 </tool> |
