<!--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="surfacematcher" name="SurfaceMatcher" version="1.5">
    <description>match two protein surfaces onto each other</description>
    <command interpreter="bash"><![CDATA[../../SurfaceMatcher 
#if str( $s1 ) != ''  and str( $s1 ) != 'None' :
   -s1 "$s1"
#end if
#if str( $s2 ) != ''  and str( $s2 ) != 'None' :
   -s2 "$s2"
#end if
#if str( $o1 ) != ''  and str( $o1 ) != 'None' :
   -o1 "$o1"
#end if
#if str( $o2 ) != ''  and str( $o2 ) != 'None' :
   -o2 "$o2"
#end if
#if str( $p1 ) != ''  and str( $p1 ) != 'None' :
   -p1 "$p1"
#end if
#if str( $p2 ) != ''  and str( $p2 ) != 'None' :
   -p2 "$p2"
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="s1" optional="false" label="protein surface 1, template" type="data" format="mol2/sdf/drf"/>
        <param name="s2" optional="false" label="protein surface 2, query" type="data" format="mol2/sdf/drf"/>
        <param name="p1" optional="true" label="pseudo atoms for template pocket" type="data" format="data"/>
        <param name="p2" optional="false" label="pseudo atoms for query pocket" type="data" format="data"/>
    </inputs>
    <outputs>
        <data name="o1" format="mol2/sdf/drf"/>
        <data name="o2" format="mol2/sdf/drf"/>
    </outputs>
    <help>SurfaceMatcher superposes two protein surfaces onto each other. This allows to examine the similarity of the binding pockets of two proteins of interest or search for pockets that are similar to a given pocket. The latter goal can be achieved by successively applying this tool to the studied pocket and a range of other protein-ligand binding pockets, e.g. all such pockets found in the PDB.

As input we need two files containing the receptor atoms that contribute the SES of the binding pocket of the respective protein, as generated by PocketCutter.
Furthermore, pocket pseudo-atoms as generated by PocketDetector should be specified. The information contained in these files helps to insure to minimize matching solvent-accessible space of one pocket onto that of the other pocket.

The output of SurfaceMatcher consists of two files that contain the matched surface atoms.</help>
</tool>