diff CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml @ 3:bb26168c5715

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Tue Jul 12 10:53:07 2011 -0400
@@ -0,0 +1,30 @@
+
+<!--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>
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