Mercurial > repos > marcel > caddsuite_linux_x86_64
comparison CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml @ 3:ff6df146c0d5
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| author | marcel |
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| date | Sun, 26 Jun 2011 13:53:57 -0400 |
| parents | |
| children | b7a89b15646f |
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| 2:bbc4a2c1d276 | 3:ff6df146c0d5 |
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| 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> |