Mercurial > repos > bgruening > rdock_rbcavity

comparison rbcavity.xml @ 0:06f376dc117a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:34:26 -0400
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children 7e5c2e4bc227
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-1:000000000000 0:06f376dc117a
1 <tool id="rdock_rbcavity" name="rDock cavity definition" version="0.1">
2 <description>- generate the active site definition needed for rDock docking</description>
3 <macros>
4 <import>rdock_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command><![CDATA[
8 ln -s '$receptor_prm' ./receptor.prm &&
9 ln -s '$receptor' receptor.mol2 &&
10 ln -s '$ligand' ligand.sdf &&
11 rbcavity -was -d -r receptor.prm
12 ]]></command>
13
14 <configfiles>
15 <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
16 RECEPTOR_FILE receptor.mol2
17 RECEPTOR_FLEX 3.0
18 SECTION MAPPER
19 SITE_MAPPER RbtLigandSiteMapper
20 REF_MOL ligand.sdf
21 RADIUS $radius
22 SMALL_SPHERE $sphere
23 MIN_VOLUME $min_volume
24 MAX_CAVITIES 1
25 VOL_INCR $vol_incr
26 GRIDSTEP $gridstep
27 END_SECTION
28 SECTION CAVITY
29 SCORING_FUNCTION RbtCavityGridSF
30 WEIGHT $weight
31 END_SECTION
32 </configfile>
33 </configfiles>
34
35 <inputs>
36 <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (Mol2 format)."/>
37 <param type="data" name="ligand" format="mol,sdf" label="Reference ligand" help="Single ligand in Mol or SDF format"/>
38 <param name="radius" type="float" value="6.0" min="0" label="Mapper sphere radius"
39 help="Mapper radius of large sphere in angstroms; rDock will search for cavities to the small sphere but not to the large sphere"/>
40 <param name="sphere" type="float" value="1.0" min="0" label="Mapper small sphere radius"
41 help="Mapper radius of small sphere in angstroms; rDock will search for cavities accessible to the small sphere but not to the large sphere"/>
42 <param name="min_volume" type="integer" value="100" min="0" label="Mapper minimum volume"
43 help="Mapper minimum volume in cubic angstroms. rDock will ignore cavities which are smaller than this value"/>
44 <param name="vol_incr" type="float" value="0.0" min="0" label="Mapper volume increment"
45 help="Mapper volume increment in angstroms. When excluding the volume occupied by the receptor from the cavity search, rDock will temporarily increase the radius of receptor atoms by this amount"/>
46 <param name="gridstep" type="float" value="0.5" min="0" label="Mapper grid step" help="Grid resolution for mapping in angstroms"/>
47 <param name="weight" type="float" value="1.0" min="0" label="Cavity weight" help="Cavity weight"/>
48 </inputs>
49 <outputs>
50 <data name="activesite" format="rdock_as" from_work_dir="receptor.as" label="rbcavity active site on ${on_string}"/>
51 </outputs>
52 <tests>
53 <test>
54 <param name="receptor" value="receptor.mol2"/>
55 <param name="ligand" value="ligand.sdf"/>
56 <output name="activesite" file="receptor.as" compare="sim_size"/>
57 </test>
58 <test>
59 <param name="receptor" value="receptor.mol2"/>
60 <param name="ligand" value="ligand.mol"/>
61 <output name="activesite" file="receptor.as" compare="sim_size"/>
62 </test>
63 </tests>
64 <help><![CDATA[
65
66 .. class:: infomark
67
68 This tool generates the cavity definition for rDock docking (the receptor.as file) using the rbcavity program.
69 See http://rdock.sourceforge.net/ for more details about rDock and associated programs.
70 Only a subset of the parameters are currently exposed. Read the rDock docs for a full understanding.
71
72 -----
73
74 .. class:: infomark
75
76 **Inputs**
77
78 1. The protein receptor to dock into as a file in Mol2 format.
79 2. A reference ligand used to define the location of the active site in Molfile or SDF format.
80 3. Various parameters for the mapper and cavity generation. Sensible defaults are provided for all.
81
82 -----
83
84 .. class:: infomark
85
86 **Outputs**
87
88 An active site definition binary file (receptor.as) that is needed by the rDock docking program to guide the docking.
89
90 ]]></help>
91 <expand macro="citations"/>
92 </tool>