comparison CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml @ 3:ff6df146c0d5

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author marcel
date Sun, 26 Jun 2011 13:53:57 -0400
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2:bbc4a2c1d276 3:ff6df146c0d5
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="constraintsfinder" name="ConstraintsFinder" version="0.94">
4 <description>find strongly interacting residues</description>
5 <command interpreter="bash"><![CDATA[../../ConstraintsFinder
6 #if str( $rec ) != '' and str( $rec ) != 'None' :
7 -rec "$rec"
8 #end if
9 #if str( $rl ) != '' and str( $rl ) != 'None' :
10 -rl "$rl"
11 #end if
12 #if str( $ini ) != '' and str( $ini ) != 'None' :
13 -ini "$ini"
14 #end if
15 #if str( $o ) != '' and str( $o ) != 'None' :
16 -o "$o"
17 #end if
18 | tail -n 5
19 ]]></command>
20 <inputs>
21 <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
22 <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
23 <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
24 </inputs>
25 <outputs>
26 <data name="o" format="ini"/>
27 </outputs>
28 <help>This tool searches protein residues with which the reference ligand interacts strongly.
29 Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion.
30
31 As input we need:
32 * a file containing a protonated protein in pdb-format
33 * a file containing a reference ligand.
34 This reference ligand should be located in the binding pocket.
35 Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
36
37 Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.</help>
38 </tool>