|
7
|
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="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.95">
|
|
|
4 <description>define spatial constraint</description>
|
|
|
5 <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner
|
|
|
6 #if str( $ini ) != '' and str( $ini ) != 'None' :
|
|
|
7 -ini "$ini"
|
|
|
8 #end if
|
|
|
9 #if str( $i ) != '' and str( $i ) != 'None' :
|
|
|
10 -i "$i"
|
|
|
11 #end if
|
|
|
12 #if str( $o ) != '' and str( $o ) != 'None' :
|
|
|
13 -o "$o"
|
|
|
14 #end if
|
|
|
15 #if str( $type ) != '' and str( $type ) != 'None' :
|
|
|
16 -type "$type"
|
|
|
17 #end if
|
|
|
18 #if str( $n ) != '' and str( $n ) != 'None' :
|
|
|
19 -n "$n"
|
|
|
20 #end if
|
|
|
21 #if str( $p ) != '' and str( $p ) != 'None' :
|
|
|
22 -p "$p"
|
|
|
23 #end if
|
|
|
24 | tail -n 5
|
|
|
25 ]]></command>
|
|
|
26 <inputs>
|
|
|
27 <param name="ini" optional="true" label="input configuration file" type="data" format="ini"/>
|
|
|
28 <param name="i" optional="false" label="input molecule file" type="data" format="mol2/sdf/drf"/>
|
|
|
29 <param name="type" optional="false" label="'fraction' or 'number' of compound atoms" type="select">
|
|
|
30 <option value="fraction">fraction</option>
|
|
|
31 <option value="number">number</option>
|
|
|
32 </param>
|
|
|
33 <param name="n" optional="false" label="desired number/fraction of atoms in spatial area" type="text" area="true" size="1x5" value=""/>
|
|
|
34 <param name="p" optional="false" label="penalty value" type="text" area="true" size="1x5" value="1e11"/>
|
|
|
35 </inputs>
|
|
|
36 <outputs>
|
|
|
37 <data name="o" format="ini"/>
|
|
|
38 </outputs>
|
|
|
39 <help>This tool allows to define spatial constraints for docking or scoring.
|
|
|
40
|
|
|
41 For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
|
|
|
42 Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.
|
|
|
43
|
|
|
44 Output of this tool is a ini-file that contains the desired spatial constraint.</help>
|
|
|
45 </tool> |
