<!--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="ligand3dgenerator" name="Ligand3DGenerator" version="0.95">
    <description>generate 3D coordinates for small molecules</description>
    <command interpreter="bash"><![CDATA[../../Ligand3DGenerator 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $ph ) != ''  and str( $ph ) != 'None' :
   -ph "$ph"
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
        <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
    </inputs>
    <outputs>
        <data name="o" format="mol2/sdf/drf" format_source="i"/>
    </outputs>
    <help>This tool generates 3D conformations for small molecules and adds hydrogens to them.
As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary.

Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other.

Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help>
</tool>