view CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml @ 3:bb26168c5715

author marcel
date Tue, 12 Jul 2011 10:53:07 -0400
children af446ca2d5c6
line wrap: on
line source

<!--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="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95">
    <description>define spatial constraint</description>
    <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner 
#if str( $ini ) != ''  and str( $ini ) != 'None' :
   -ini "$ini"
#end if
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $type ) != ''  and str( $type ) != 'None' :
   -type "$type"
#end if
#if str( $n ) != ''  and str( $n ) != 'None' :
   -n "$n"
#end if
#if str( $p ) != ''  and str( $p ) != 'None' :
   -p "$p"
#end if
 | tail -n 5
        <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
        <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
        <param name="type" optional="false" label="'fraction' or 'number' of compound atoms" type="select">
            <option value="fraction">fraction</option>
            <option value="number">number</option>
        <param name="n" optional="false" label="desired number/fraction of atoms in spatial area" type="text" area="true" size="1x5" value=""/>
        <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="1e11"/>
        <data name="o" format="ini"/>
    <help>This tool allows to define spatial constraints for docking or scoring.

For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.

Output of this tool is a ini-file that contains the desired spatial constraint.</help>