<!--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="1.6">
    <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( $p1 ) != ''  and str( $p1 ) != 'None' :
   -p1 "$p1"
#end if
#if str( $s1_full ) != ''  and str( $s1_full ) != 'None' :
   -s1_full "$s1_full"
#end if
#if str( $s2 ) != ''  and str( $s2 ) != 'None' :
   -s2 "$s2"
#end if
#if str( $p2 ) != ''  and str( $p2 ) != 'None' :
   -p2 "$p2"
#end if
#if str( $s2_full ) != ''  and str( $s2_full ) != 'None' :
   -s2_full "$s2_full"
#end if
#if str( $max_id ) != ''  and str( $max_id ) != 'None' :
   -max_id "$max_id"
#end if
#if str( $max_sec_id ) != ''  and str( $max_sec_id ) != 'None' :
   -max_sec_id "$max_sec_id"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#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="p1" optional="true" label="pseudo atoms for template pocket" type="data" format="data"/>
        <param name="s1_full" optional="true" label="full-length template protein" type="data" format="mol2/sdf/drf"/>
        <param name="s2" optional="false" label="protein surface 2, query" type="data" format="mol2/sdf/drf"/>
        <param name="p2" optional="false" label="pseudo atoms for query pocket" type="data" format="data"/>
        <param name="s2_full" optional="true" label="full-length query protein (for sequence ident. check only)" type="data" format="data"/>
        <param name="max_id" optional="true" label="Optional: maximal allowed sequence identity between full-length proteins (in percent); do nothing if threshold is exceeded" type="text" area="true" size="1x5" value=""/>
        <param name="max_sec_id" optional="true" label="Optional: maximal allowed secondary structure identity between full-length proteins (in percent); do nothing if threshold is exceeded" type="text" area="true" size="1x5" value=""/>
    </inputs>
    <outputs>
        <data name="o" 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 a file containing the matched template surface atoms. Alternatively, the full-length template protein can be passed to this tool, in which case it will be transform and written to the specified output. However, even in this case only the surfaces (and not the full-length protein) will be used to compute the actual superposition and similarity.</help>
</tool>