Mercurial > repos > bgruening > rxdock_rbcavity

annotate rbcavity.xml @ 0:e99f861ba68a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
author bgruening
date Sat, 04 Apr 2020 15:04:13 -0400
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children 583dcdbdbf42
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e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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1 <tool id="rxdock_rbcavity" name="rxDock cavity definition" version="0.1">
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2 <description>- generate the active site definition needed for rxDock docking</description>
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3 <macros>
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4 <import>rdock_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command><![CDATA[
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8 ln -s '$receptor_prm' receptor.prm &&
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9 ln -s '$receptor' receptor.mol2 &&
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10 ln -s '$ligand' ligand.sdf &&
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11 rbcavity -W -d -r receptor.prm &&
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12 ls -l
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13 ]]></command>
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14
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15 <configfiles>
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16 <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
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17 RECEPTOR_FILE receptor.mol2
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18 RECEPTOR_FLEX 3.0
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19 SECTION MAPPER
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20 SITE_MAPPER RbtLigandSiteMapper
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21 REF_MOL ligand.sdf
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22 RADIUS $radius
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23 SMALL_SPHERE $sphere
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24 MIN_VOLUME $min_volume
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25 MAX_CAVITIES 1
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26 VOL_INCR $vol_incr
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27 GRIDSTEP $gridstep
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28 END_SECTION
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29 SECTION CAVITY
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30 SCORING_FUNCTION RbtCavityGridSF
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31 WEIGHT $weight
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32 END_SECTION
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33 </configfile>
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34 </configfiles>
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35
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36 <inputs>
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37 <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (Mol2 format)."/>
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38 <param type="data" name="ligand" format="mol,sdf" label="Reference ligand" help="Single ligand in Mol or SDF format"/>
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39 <param name="radius" type="float" value="6.0" min="0" label="Mapper sphere radius"
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40 help="Mapper radius of large sphere in angstroms; rxDock will search for cavities to the small sphere but not to the large sphere"/>
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41 <param name="sphere" type="float" value="1.0" min="0" label="Mapper small sphere radius"
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42 help="Mapper radius of small sphere in angstroms; rxDock will search for cavities accessible to the small sphere but not to the large sphere"/>
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43 <param name="min_volume" type="integer" value="100" min="0" label="Mapper minimum volume"
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44 help="Mapper minimum volume in cubic angstroms. rxDock will ignore cavities which are smaller than this value"/>
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45 <param name="vol_incr" type="float" value="0.0" min="0" label="Mapper volume increment"
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46 help="Mapper volume increment in angstroms. When excluding the volume occupied by the receptor from the cavity search, rxDock will temporarily increase the radius of receptor atoms by this amount"/>
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47 <param name="gridstep" type="float" value="0.5" min="0" label="Mapper grid step" help="Grid resolution for mapping in angstroms"/>
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48 <param name="weight" type="float" value="1.0" min="0" label="Cavity weight" help="Cavity weight"/>
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49 </inputs>
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50 <outputs>
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51 <data name="activesite" format="rdock_as" from_work_dir="receptor.as" label="rbcavity active site on ${on_string}"/>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="receptor" value="receptor.mol2"/>
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56 <param name="ligand" value="ligand.sdf"/>
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57 <output name="activesite" file="receptor.as" compare="sim_size"/>
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58 </test>
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59 <test>
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60 <param name="receptor" value="receptor.mol2"/>
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61 <param name="ligand" value="ligand.mol"/>
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62 <output name="activesite" file="receptor.as" compare="sim_size"/>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66
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67 .. class:: infomark
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68
e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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69 This tool generates the cavity definition for rxDock docking (the receptor.as file) using the rbcavity program.
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70 See https://www.rxdock.org for more details about rxDock and associated programs.
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71 Only a subset of the parameters are currently exposed. Read the rxDock docs for a full understanding.
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72
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73 -----
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74
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75 .. class:: infomark
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76
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77 **Inputs**
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78
e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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79 1. The protein receptor to dock into as a file in Mol2 format.
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80 2. A reference ligand used to define the location of the active site in Molfile or SDF format.
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81 3. Various parameters for the mapper and cavity generation. Sensible defaults are provided for all.
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82
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83 -----
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84
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85 .. class:: infomark
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86
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87 **Outputs**
e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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88
e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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89 An active site definition binary file (receptor.as) that is needed by the rxDock docking program to guide the docking.
e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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90
e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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91 ]]></help>
e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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92 <expand macro="citations"/>
e99f861ba68a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit bb19570293b920983b6856b30b42203a09543bc5"
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93 </tool>