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annotate CADDSuite-1.5/galaxyconfigs/tools/Ligand3DGenerator.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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2 <!--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.-->
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3 <tool id="ligand3dgenerator" name="Ligand3DGenerator" version="1.5">
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4 <description>generate 3D coordinates for small molecules</description>
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5 <command interpreter="bash"><![CDATA[../../Ligand3DGenerator
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $o ) != '' and str( $o ) != 'None' :
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10 -o "$o"
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11 #end if
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12 #if str( $ph ) != '' and str( $ph ) != 'None' :
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13 -ph "$ph"
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14 #end if
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15 #if str( $rm ) != '' and str( $rm ) != 'None' :
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16 -rm
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17 #end if
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18 | tail -n 5
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19 ]]></command>
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20 <inputs>
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21 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
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22 <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
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23 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
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24 </inputs>
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25 <outputs>
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26 <data name="o" format="mol2/sdf/drf" format_source="i"/>
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27 </outputs>
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28 <help>This tool generates 3D conformations for small molecules and adds hydrogens to them.
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29 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.
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31 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.
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33 Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz, mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.</help>
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34 </tool>