annotate CADDSuite-1.0.1/galaxyconfigs/tools/WaterFinder.xml @ 5:e30a41af9d2b

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<!--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="1.0.1">
    <description>find strongly bound waters</description>
    <command interpreter="bash"><![CDATA[../../WaterFinder 
#if str( $rec ) != ''  and str( $rec ) != 'None' :
   -rec "$rec"
#end if
#if str( $rl ) != ''  and str( $rl ) != 'None' :
   -rl "$rl"
#end if
#if str( $ini ) != ''  and str( $ini ) != 'None' :
   -ini "$ini"
#end if
#if str( $wat ) != ''  and str( $wat ) != 'None' :
   -wat "$wat"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $ai ) != ''  and str( $ai ) != 'None' :
   -ai
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
        <param name="rl" optional="false" label="reference-ligand" type="data" format="mol2/sdf/drf"/>
        <param name="ini" optional="true" label="configuration file" type="data" format="ini"/>
        <param name="wat" optional="true" label="input pdb-file containing water molecules (if not part of rec.-file)" type="data" format="pdb"/>
        <param name="ai" optional="true" label="use ab-initio water search (ignore water in pdb-file), experimental!" type="boolean" truevalue="true" falsevalue=""/>
    </inputs>
    <outputs>
        <data name="o" format="pdb"/>
    </outputs>
    <help>This tool searches for crystal waters that
    * either interact very strongly with the receptor
    * or that interact strongly with receptor and reference ligand, 
      thus functioning as a water bridge.

Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done.

As input we need:
    * a file containing a protonated protein in pdb-format.
      This file should contain water molecules that are to be evaluated by this tool.
      However, you can also use a separate pdb-file as input for the water molecules (see below).
    * a file containing a reference ligand.
      This reference ligand should be located in the binding pocket.
      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
    * optionally a file in pdb-format containing water molecules.
      If you specify such a file , all water molecules appearing in the
      protein input-file (if any) will be ignored.

Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.</help>
</tool>