|
9
|
1
|
|
|
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.-->
|
|
|
3 <tool id="ligand3dgenerator" name="Ligand3DGenerator" version="1.0.1">
|
|
|
4 <description>generate 3D coordinates for small molecules</description>
|
|
|
5 <command interpreter="bash"><![CDATA[../../Ligand3DGenerator
|
|
|
6 #if str( $i ) != '' and str( $i ) != 'None' :
|
|
|
7 -i "$i"
|
|
|
8 #end if
|
|
|
9 #if str( $o ) != '' and str( $o ) != 'None' :
|
|
|
10 -o "$o"
|
|
|
11 #end if
|
|
|
12 #if str( $ph ) != '' and str( $ph ) != 'None' :
|
|
|
13 -ph "$ph"
|
|
|
14 #end if
|
|
|
15 #if str( $rm ) != '' and str( $rm ) != 'None' :
|
|
|
16 -rm
|
|
|
17 #end if
|
|
|
18 | tail -n 5
|
|
|
19 ]]></command>
|
|
|
20 <inputs>
|
|
|
21 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
|
|
|
22 <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
|
|
|
23 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
|
|
|
24 </inputs>
|
|
|
25 <outputs>
|
|
|
26 <data name="o" format="mol2/sdf/drf" format_source="i"/>
|
|
|
27 </outputs>
|
|
|
28 <help>This tool generates 3D conformations for small molecules and adds hydrogens to them.
|
|
|
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.
|
|
|
30
|
|
|
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.
|
|
|
32
|
|
|
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>
|
|
|
34 </tool> |
