annotate CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml @ 1:0dcf542923ab

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<!--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="combilibgenerator" name="CombiLibGenerator" version="0.94">
    <description>generate combinatorial lib</description>
    <command interpreter="bash"><![CDATA[../../CombiLibGenerator 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" label="input combi-lib file" optional="false" type="data" format="data"/>
    </inputs>
    <outputs>
        <data name="o" format="mol2/sdf/drf"/>
    </outputs>
    <help>This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties.

As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need:

&lt;scaffold&gt;
      Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3
      Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3
&lt;moietyR1&gt;
      [R1]C(C)(C)C
&lt;moietyR2&gt;
      [R2]OC(C)(C)C

Output of CombiLibGenerator is a file containing created topologies. Note that this tool does *not* generate any conformations but only topologies, so that all coordinates in the output file will be zero. Thus, apply Ligand3DGenerator to the output generated by CombiLibGenerator if you need 3D conformations.</help>
</tool>