Mercurial > repos > bgruening > rdock_rbdock

annotate rbdock.xml @ 8:a22969b08177 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit dff183f4eb2d3df42917ec4fed0fbdb2ea11e19a"
author bgruening
date Thu, 21 May 2020 10:54:15 -0400
parents 07fa39ed62c7
children c362398df83b
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07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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1 <tool id="rdock_rbdock" name="rDock docking" version="0.1.4" profile="19.01">
0
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2 <description>- perform protein-ligand docking with rDock</description>
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3 <macros>
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4 <import>rdock_macros.xml</import>
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5 </macros>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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6 <expand macro="requirements"/>
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7 <command><![CDATA[
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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8 ln -s '$active_site' receptor.as &&
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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9 ln -s '$receptor' receptor.mol2 &&
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07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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11 #if $custom_rec.custom_rec_select == 'true':
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12 ## simple check that the receptor file name is correct
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13 grep -q 'RECEPTOR_FILE receptor.mol2' $custom_rec.prm_file || (echo "Error: a custom receptor.prm file must contain the line 'RECEPTOR_FILE receptor.mol2'" >&2 && exit 1) &&
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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14 ln -s '$custom_rec.prm_file' receptor.prm &&
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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15 #else
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16 ln -s '$receptor_prm' receptor.prm &&
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17 #end if
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18
0
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19 #if $name == 'Y':
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20 sdmodify -f_REC '$ligands' > ligands.sdf &&
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21 #else
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22 ln -s '$ligands' ligands.sdf &&
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23 #end if
4
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24
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
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25 python '$__tool_directory__/rbdock.py'
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26 -n '$num'
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27 #if $seed:
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28 -s '$seed'
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29 #end if
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30 &&
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a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
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32 cat rdock_output.sd
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33
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
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34 #if $filter.filter_select == "filter":
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35 #if $filter.score:
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36 | sdfilter -f'\$SCORE <= ${filter.score}'
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37 #end if
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38 #if $filter.nscore:
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39 | sdfilter -f'\$SCORE.norm <= ${filter.nscore}'
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40 #end if
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41 #if $filter.top
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42 | sdsort -n -s -fSCORE | sdfilter -f'\$_COUNT <= $filter.top'
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43 #end if
0
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44 #end if
4
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45
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46 > '$output'
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47
0
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48 ]]></command>
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49
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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50 <configfiles>
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51 <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
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52 RECEPTOR_FILE receptor.mol2
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53 #if $custom_rec.custom_rec_select == 'false':
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54 RECEPTOR_FLEX $custom_rec.flex
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55 #end if
0
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56 </configfile>
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57 </configfiles>
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58
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59 <inputs>
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60 <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/>
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61 <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/>
2
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62 <param type="data" name="ligands" format="sdf,mol" label="Ligands" help="Ligands in SDF format (or single ligand in MOL format)"/>
6
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63 <conditional name="custom_rec">
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64 <param name="custom_rec_select" type="select" label="Use a custom receptor.prm file?" help="Useful for more advanced use-cases, such as tethered docking.">
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65 <option value="true">Use custom receptor.prm file</option>
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66 <option value="false" selected="true">Use default options (no user upload required)</option>
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67 </param>
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68 <when value="true">
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69 <param type="data" name="prm_file" format="txt" label="Receptor prm file" help="Note the file must contain the line 'RECEPTOR_FILE receptor.mol2', else the tool will fail."/>
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70 </when>
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71 <when value="false">
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72 <param name="flex" type="float" value="3.0" min="0.0" label="Receptor flex" help="Value for RECEPTOR_FLEX (default 3)"/>
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73 </when>
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74 </conditional>
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75
0
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76 <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/>
4
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77 <conditional name="filter">
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78 <param name="filter_select" type="select" label="Filter the docking results" help="Using sdfilter">
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79 <option value="filter">Show filter options</option>
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80 <option value="no_filter">No filtering</option>
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81 </param>
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82 <when value="filter">
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83 <param name="score" type="float" optional="true" label="Score filter"
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84 help="Exclude poses with score greater than this value"/>
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85 <param name="nscore" type="float" optional="true" label="Normalised score filter"
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
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parents: 2
diff changeset
86 help="Exclude poses with normalised score greater than this value"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
87 <param name="top" type="integer" value="1" optional="true" min="1" label="Number of best poses"
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
88 help="Number of best scoring poses to keep"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
89 </when>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
90 <when value="no_filter"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
91 </conditional>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
92 <param name="name" type="boolean" label="Generate name field" truevalue="Y" falsevalue="N" checked="false"
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
93 help="Generate the name field (first line) for cases where this is empty"/>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
94 <param argument="-seed" type="integer" optional="true" label="Random seed" help=""/>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
95 </inputs>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
96 <outputs>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
97 <data name="output" format="sdf" label="rDock on ${on_string}"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
98 </outputs>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
99 <tests>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
100 <!-- broken ligand test -->
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
101 <test expect_failure="true" expect_exit_code="23">
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
102 <param name="receptor" value="receptor.mol2"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
103 <param name="ligands" value="broken_ligand.sdf"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
104 <param name="active_site" value="receptor.as"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
105 <param name="num" value="3"/>
6
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
bgruening
parents: 4
diff changeset
106 <param name="flex" value="3"/>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
107 <param name="seed" value="3"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
108 <conditional name="filter">
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
109 <param name="filter_select" value="filter"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
110 <param name="top" value="1"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
111 </conditional>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
112 <param name="name" value="false"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
113 </test>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
114 <test>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
115 <param name="receptor" value="receptor.mol2"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
116 <param name="ligands" value="ligands_names.sdf"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
117 <param name="active_site" value="receptor.as"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
118 <param name="num" value="3"/>
6
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
bgruening
parents: 4
diff changeset
119 <param name="flex" value="3"/>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
120 <param name="seed" value="3"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
121 <conditional name="filter">
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
122 <param name="filter_select" value="filter"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
123 <param name="top" value="1"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
124 </conditional>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
125 <param name="name" value="false"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
126 <output name="output">
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
127 <assert_contents>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
128 <has_text text="Rbt.Current_Directory"/>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
129 <has_n_lines n="352"/>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
130 </assert_contents>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
131 </output>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
132 </test>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
133 <test>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
134 <param name="receptor" value="receptor.mol2"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
135 <param name="ligands" value="ligands_nonames.sdf"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
136 <param name="active_site" value="receptor.as"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
137 <param name="num" value="3"/>
6
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
bgruening
parents: 4
diff changeset
138 <param name="flex" value="3"/>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
139 <param name="seed" value="3"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
140 <conditional name="filter">
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
141 <param name="filter_select" value="filter"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
142 <param name="top" value="1"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
143 </conditional>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
144 <param name="name" value="true"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
145 <output name="output">
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
146 <assert_contents>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
147 <has_text text="Rbt.Current_Directory"/>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
148 <has_n_lines n="352"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
149 </assert_contents>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
150 </output>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
151 </test>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
152 <!-- no filter test -->
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
153 <test>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
154 <param name="receptor" value="receptor.mol2"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
155 <param name="ligands" value="ligands_nonames.sdf"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
156 <param name="active_site" value="receptor.as"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
157 <param name="num" value="3"/>
6
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
bgruening
parents: 4
diff changeset
158 <param name="flex" value="3"/>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
159 <param name="seed" value="3"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
160 <conditional name="filter">
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
161 <param name="filter_select" value="no_filter"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
162 </conditional>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
163 <param name="name" value="true"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
164 <output name="output">
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
165 <assert_contents>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
166 <has_text text="Rbt.Current_Directory"/>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
167 <has_n_lines n="1056"/>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
168 </assert_contents>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
169 </output>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
170 </test>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
171 <test>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
172 <param name="receptor" value="receptor.mol2"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
173 <param name="ligands" value="ligands_names.sdf"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
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174 <param name="active_site" value="receptor.as"/>
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175 <param name="num" value="1"/>
6
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176 <param name="flex" value="3"/>
4
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177 <param name="seed" value="3"/>
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178 <conditional name="filter">
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179 <param name="filter_select" value="filter"/>
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180 <param name="score" value="10"/>
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181 <param name="nscore" value="1"/>
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182 </conditional>
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183 <param name="name"/>
0
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184 <output name="output">
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185 <assert_contents>
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186 <has_text text="Rbt.Current_Directory"/>
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187 <has_n_lines n="352"/>
0
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188 </assert_contents>
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189 </output>
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190 </test>
6
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191 <!-- test with custom receptor.prm -->
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192 <test>
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193 <param name="receptor" value="receptor.mol2"/>
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194 <param name="ligands" value="ligands_names.sdf"/>
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195 <param name="active_site" value="receptor.as"/>
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196 <param name="custom_rec_select" value="true"/>
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197 <param name="prm_file" value="receptor.prm"/>
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198 <param name="num" value="1"/>
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199 <param name="seed" value="3"/>
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200 <conditional name="filter">
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201 <param name="filter_select" value="filter"/>
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202 <param name="score" value="10"/>
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203 <param name="nscore" value="1"/>
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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204 </conditional>
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205 <param name="name"/>
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206 <output name="output">
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207 <assert_contents>
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208 <has_text text="Rbt.Current_Directory"/>
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209 <has_n_lines n="352"/>
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210 </assert_contents>
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211 </output>
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212 </test>
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213 <!-- test with custom but broken receptor.prm -->
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214 <test expect_failure="true" expect_exit_code="1">
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215 <param name="receptor" value="receptor.mol2"/>
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216 <param name="ligands" value="ligands_names.sdf"/>
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217 <param name="active_site" value="receptor.as"/>
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218 <param name="custom_rec_select" value="true"/>
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219 <param name="prm_file" value="wrong_receptor.prm"/>
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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220 <param name="num" value="1"/>
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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221 <param name="seed" value="3"/>
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222 <conditional name="filter">
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223 <param name="filter_select" value="no_filter"/>
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224 </conditional>
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225 <param name="name"/>
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226 </test>
0
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227 </tests>
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228 <help><![CDATA[
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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229
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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230 .. class:: infomark
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231
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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232 This tool performs protein-ligand docking using the rDock program.
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233 See http://rdock.sourceforge.net/ for more details about rDock and associated programs.
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234
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235 -----
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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236
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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237 .. class:: infomark
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238
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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239 **Inputs**
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240
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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241 1. The protein receptor to dock into as a file in Mol2 format.
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242 2. The active site definition as a file as generated by the rbcavity tool.
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243 3. A set of ligands (collection or single file) to dock as a file in SDF format.
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244 4. The number of docking poses to generate (integer).
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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245 5. The number of best scoring dockings to keep (integer).
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246 6. The max score that is allowed. Poses with scores greater than this are excluded (float, optional).
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247 7. The max normalised score (the score normalised by the number of heavy atoms) that is allowed.
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248 Poses with normalised scores greater than this are excluded (float, optional).
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249 8. Optionally generate the name field in the ligands SDF (this is the first line in the entry).
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250 This field must be present and be unique for sorting and filtering to work. If your results contain only one record
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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251 then the name field is probably absent and must be generated.
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252
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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253 You will need to perform some test dockings to establish suitable values for the score filters.
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254 The score is a number with lower values being better. Values can be negative.
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255
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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256 -----
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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257
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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258 .. class:: infomark
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259
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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260 **Outputs**
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261
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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262 An SDF file is produced as output. The binding affinity scores are contained within the SDF file.::
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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263
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264 1-pyrimethamine
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parents:
diff changeset
265 rDOCK(R) 3D
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
266 libRbt.so/2013.1/901 2013/11/27
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
267 21 22 0 0 0 0 0 0 0 0999 V2000
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
268 -5.1897 17.8912 17.9590 N 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
269 -3.9121 17.9973 18.3210 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
270 -3.2404 19.1465 18.3804 N 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
271 -3.8989 20.2829 18.0453 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
272 -5.2389 20.2802 17.6553 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
273 -5.8448 19.0235 17.6464 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
274 -5.9601 21.5065 17.2850 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
275 -6.2108 22.5074 18.2382 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
276 -6.8903 23.6771 17.8851 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
277 -7.3267 23.8556 16.5746 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
278 -7.0903 22.8744 15.6151 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
279 -6.4107 21.7051 15.9695 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
280 -3.2455 16.8582 18.6507 N 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
281 -7.1550 18.8446 17.2393 N 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
282 -8.1626 25.2957 16.1391 Cl 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
283 -2.9891 22.1828 19.5033 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
284 -3.1112 21.5771 18.1096 C 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
285 -2.2766 16.9101 18.9273 H 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
286 -3.7237 15.9703 18.6154 H 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
287 -7.8809 19.3992 17.6807 H 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
288 -7.4159 17.8951 16.9940 H 0 0 0 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
289 1 2 2 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
290 1 6 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
291 2 3 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
292 2 13 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
293 3 4 2 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
294 4 5 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
295 4 17 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
296 5 6 2 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
297 5 7 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
298 6 14 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
299 7 8 2 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
300 7 12 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
301 8 9 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
302 9 10 2 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
303 10 11 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
304 10 15 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
305 11 12 2 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
306 13 18 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
307 13 19 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
308 14 20 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
309 14 21 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
310 16 17 1 0 0 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
311 M END
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
312 > <CHROM.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
313 -177.71086620,1.45027861,170.39044546,46.02877151,68.76956623,70.55425150
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
314
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
315 > <CHROM.1>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
316 -81.34718191,-65.90186149,129.45748660,-5.61305786,21.23281353,17.50152835
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
317 0.96119776,0.49809360,-3.12917831
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
318
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
319 > <Rbt.Current_Directory>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
320 /home/timbo/github/im/docking-validation/targets/dhfr/expts/vs-simple-rdock
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
321
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
322 > <Rbt.Executable>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
323 rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
324
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
325 > <Rbt.Library>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
326 libRbt.so (2013.1, Build901 2013/11/27)
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
327
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
328 > <Rbt.Parameter_File>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
329 /rDock_2013.1/data/scripts/dock.prm
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
330
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
331 > <Rbt.Receptor>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
332 receptor.prm
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
333
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
334 > <SCORE>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
335 0.445364
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
336
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
337 > <SCORE.INTER>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
338 8.4
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
339
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
340 > <SCORE.INTER.CONST>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
341 1
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
342
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
343 > <SCORE.INTER.POLAR>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
344 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
345
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
346 > <SCORE.INTER.REPUL>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
347 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
348
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
349 > <SCORE.INTER.ROT>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
350 3
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
351
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
352 > <SCORE.INTER.VDW>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
353 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
354
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
355 > <SCORE.INTER.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
356 0.494118
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
357
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
358 > <SCORE.INTRA>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
359 -1.38672
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
360
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
361 > <SCORE.INTRA.DIHEDRAL>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
362 -0.818539
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
363
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
364 > <SCORE.INTRA.DIHEDRAL.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
365 6.01924
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
366
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
367 > <SCORE.INTRA.POLAR>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
368 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
369
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
370 > <SCORE.INTRA.POLAR.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
371 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
372
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
373 > <SCORE.INTRA.REPUL>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
374 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
375
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
376 > <SCORE.INTRA.REPUL.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
377 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
378
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
379 > <SCORE.INTRA.VDW>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
380 -0.977448
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
381
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
382 > <SCORE.INTRA.VDW.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
383 -1.0079
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
384
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
385 > <SCORE.INTRA.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
386 -0.0815716
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
387
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
388 > <SCORE.RESTR>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
389
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
390 > <SCORE.RESTR.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
391 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
392
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
393 > <SCORE.SYSTEM>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
394 -6.56792
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
395
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
396 > <SCORE.SYSTEM.CONST>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
397 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
398
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
399 > <SCORE.SYSTEM.DIHEDRAL>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
400 1.50415
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
401
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
402 > <SCORE.SYSTEM.POLAR>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
403 -2.3289
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
404
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
405 > <SCORE.SYSTEM.VDW>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
406 0.59827
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
407
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
408 > <SCORE.SYSTEM.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
409 -0.386348
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
410
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
411 > <SCORE.heavy>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
412 17
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
413
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
414 > <SCORE.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
415 0.0261979
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
416
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
417 $$$$
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
418
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
419 ]]></help>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
420 <expand macro="citations"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
421 </tool>