|
0
|
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="ligcheck" name="LigCheck" version="0.94">
|
|
|
4 <description>check molecules for errors</description>
|
|
|
5 <command interpreter="bash"><![CDATA[../../LigCheck
|
|
|
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( $ef ) != '' and str( $ef ) != 'None' :
|
|
|
13 -ef "$ef"
|
|
|
14 #end if
|
|
|
15 #if str( $ri ) != '' and str( $ri ) != 'None' :
|
|
|
16 -ri
|
|
|
17 #end if
|
|
|
18 #if str( $ut ) != '' and str( $ut ) != 'None' :
|
|
|
19 -ut
|
|
|
20 #end if
|
|
|
21 | tail -n 5
|
|
|
22 ]]></command>
|
|
|
23 <inputs>
|
|
|
24 <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
|
|
|
25 <param name="ef" label="error fraction; print error if fraction of invalid mols is larger" optional="true" type="text" area="true" size="1x5" value="0.5"/>
|
|
|
26 <param name="ri" label="remove invalid molecules." optional="true" type="boolean" truevalue="true" falsevalue=""/>
|
|
|
27 <param name="ut" label="check for unique topologies (default: check only for unique conformation)" optional="true" type="boolean" truevalue="true" falsevalue=""/>
|
|
|
28 </inputs>
|
|
|
29 <outputs>
|
|
|
30 <data name="o" format="mol2/sdf/drf" format_source="i"/>
|
|
|
31 </outputs>
|
|
|
32 <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
|
|
|
33
|
|
|
34 The following checks are done for each molecule:
|
|
|
35
|
|
|
36 * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem)
|
|
|
37 * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
|
|
|
38 * each atom must have a valid assigned element
|
|
|
39 * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
|
|
|
40 * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
|
|
|
41 * partial charges may not contain completely senseless values (>5 or <-5).
|
|
|
42 * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.
|
|
|
43
|
|
|
44 If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.</help>
|
|
|
45 </tool> |
