view CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml @ 4:af446ca2d5c6

author marcel
date Fri, 02 Sep 2011 08:54:17 -0400
parents bb26168c5715
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<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy ( This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
<tool id="constraintsfinder" name="ConstraintsFinder" version="0.9.6">
    <description>find strongly interacting residues</description>
    <command interpreter="bash"><![CDATA[../../ConstraintsFinder 
#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( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
 | tail -n 5
        <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"/>
        <data name="o" format="ini"/>
    <help>This tool searches protein residues with which the reference ligand interacts strongly.
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.

As input we need:
    * a file containing a protonated protein in pdb-format
    * 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).

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>