Mercurial > repos > bgruening > rdock_rbdock

annotate rbdock.xml @ 9:c362398df83b draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:43:58 -0400
parents 07fa39ed62c7
children
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rev   line source
9
c362398df83b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="rdock_rbdock" name="rDock docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" 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>
9
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5 <token name="@GALAXY_VERSION@">0</token>
0
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command><![CDATA[
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9 ln -s '$active_site' receptor.as &&
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10 ln -s '$receptor' receptor.mol2 &&
6
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11
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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12 #if $custom_rec.custom_rec_select == 'true':
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13 ## simple check that the receptor file name is correct
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14 grep -q 'RECEPTOR_FILE receptor.mol2' $custom_rec.prm_file || (echo "Error: a custom receptor.prm file must contain the line 'RECEPTOR_FILE receptor.mol2'" >&2 && exit 1) &&
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15 ln -s '$custom_rec.prm_file' receptor.prm &&
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16 #else
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17 ln -s '$receptor_prm' receptor.prm &&
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18 #end if
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19
0
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20 #if $name == 'Y':
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21 sdmodify -f_REC '$ligands' > ligands.sdf &&
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22 #else
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23 ln -s '$ligands' ligands.sdf &&
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24 #end if
4
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25
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26 python '$__tool_directory__/rbdock.py'
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27 -n '$num'
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28 #if $seed:
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29 -s '$seed'
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30 #end if
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31 &&
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32
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
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33 cat rdock_output.sd
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34
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35 #if $filter.filter_select == "filter":
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36 #if $filter.score:
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37 | sdfilter -f'\$SCORE <= ${filter.score}'
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38 #end if
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39 #if $filter.nscore:
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40 | sdfilter -f'\$SCORE.norm <= ${filter.nscore}'
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41 #end if
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42 #if $filter.top
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43 | sdsort -n -s -fSCORE | sdfilter -f'\$_COUNT <= $filter.top'
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44 #end if
0
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45 #end if
4
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46
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47 > '$output'
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48
0
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49 ]]></command>
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50
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51 <configfiles>
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52 <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
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53 RECEPTOR_FILE receptor.mol2
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54 #if $custom_rec.custom_rec_select == 'false':
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55 RECEPTOR_FLEX $custom_rec.flex
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56 #end if
0
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57 </configfile>
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58 </configfiles>
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59
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60 <inputs>
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61 <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/>
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62 <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/>
2
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63 <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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64 <conditional name="custom_rec">
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65 <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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66 <option value="true">Use custom receptor.prm file</option>
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67 <option value="false" selected="true">Use default options (no user upload required)</option>
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68 </param>
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69 <when value="true">
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70 <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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71 </when>
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72 <when value="false">
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73 <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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74 </when>
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75 </conditional>
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76
0
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77 <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/>
4
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78 <conditional name="filter">
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79 <param name="filter_select" type="select" label="Filter the docking results" help="Using sdfilter">
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80 <option value="filter">Show filter options</option>
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81 <option value="no_filter">No filtering</option>
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82 </param>
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83 <when value="filter">
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84 <param name="score" type="float" optional="true" label="Score filter"
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85 help="Exclude poses with 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
86 <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"
bgruening
parents: 2
diff changeset
87 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
88 <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
89 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
90 </when>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
91 <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
92 </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
93 <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
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diff changeset
94 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
95 <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
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diff changeset
96 </inputs>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
97 <outputs>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
98 <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
99 </outputs>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
100 <tests>
4
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
101 <!-- broken ligand test -->
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
102 <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
103 <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
104 <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
105 <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
106 <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
107 <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
108 <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
109 <conditional name="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="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
111 <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
112 </conditional>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
113 <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
114 </test>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
115 <test>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
116 <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
117 <param name="ligands" value="ligands_names.sdf"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
118 <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
119 <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
120 <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
121 <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
122 <conditional name="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="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
124 <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
125 </conditional>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
126 <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
127 <output name="output">
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
128 <assert_contents>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
129 <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
130 <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
131 </assert_contents>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
132 </output>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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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 <test>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
135 <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
136 <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
137 <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
138 <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
139 <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
140 <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
141 <conditional name="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="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
143 <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
144 </conditional>
0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
145 <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
146 <output name="output">
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
147 <assert_contents>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
148 <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
149 <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
150 </assert_contents>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
151 </output>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
152 </test>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
153 <!-- no filter test -->
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
154 <test>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
155 <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
156 <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
157 <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
158 <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
159 <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
160 <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
161 <conditional name="filter">
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
162 <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
163 </conditional>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
164 <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
165 <output name="output">
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
166 <assert_contents>
a428230b38f6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit db567a29443284f2cec1444ec9db9aa6bd913fad"
bgruening
parents: 2
diff changeset
167 <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
168 <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
169 </assert_contents>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
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diff changeset
170 </output>
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 <test>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
173 <param name="receptor" value="receptor.mol2"/>
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="ligands" value="ligands_names.sdf"/>
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175 <param name="active_site" value="receptor.as"/>
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176 <param name="num" value="1"/>
6
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177 <param name="flex" value="3"/>
4
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178 <param name="seed" value="3"/>
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179 <conditional name="filter">
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180 <param name="filter_select" value="filter"/>
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181 <param name="score" value="10"/>
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182 <param name="nscore" value="1"/>
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183 </conditional>
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184 <param name="name"/>
0
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185 <output name="output">
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186 <assert_contents>
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187 <has_text text="Rbt.Current_Directory"/>
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188 <has_n_lines n="352"/>
0
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189 </assert_contents>
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190 </output>
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191 </test>
6
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192 <!-- test with custom receptor.prm -->
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193 <test>
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194 <param name="receptor" value="receptor.mol2"/>
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195 <param name="ligands" value="ligands_names.sdf"/>
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196 <param name="active_site" value="receptor.as"/>
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197 <param name="custom_rec_select" value="true"/>
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198 <param name="prm_file" value="receptor.prm"/>
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199 <param name="num" value="1"/>
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200 <param name="seed" value="3"/>
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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201 <conditional name="filter">
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202 <param name="filter_select" value="filter"/>
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203 <param name="score" value="10"/>
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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204 <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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205 </conditional>
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206 <param name="name"/>
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207 <output name="output">
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208 <assert_contents>
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209 <has_text text="Rbt.Current_Directory"/>
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210 <has_n_lines n="352"/>
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211 </assert_contents>
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212 </output>
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213 </test>
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214 <!-- test with custom but broken receptor.prm -->
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215 <test expect_failure="true" expect_exit_code="1">
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216 <param name="receptor" value="receptor.mol2"/>
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217 <param name="ligands" value="ligands_names.sdf"/>
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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218 <param name="active_site" value="receptor.as"/>
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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219 <param name="custom_rec_select" value="true"/>
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220 <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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221 <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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222 <param name="seed" value="3"/>
07fa39ed62c7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit e9c627440028cfd2c743462927672e0c5e3576aa"
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223 <conditional name="filter">
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224 <param name="filter_select" value="no_filter"/>
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225 </conditional>
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226 <param name="name"/>
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227 </test>
0
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228 </tests>
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229 <help><![CDATA[
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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230
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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231 .. class:: infomark
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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232
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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233 This tool performs protein-ligand docking using the rDock program.
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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234 See http://rdock.sourceforge.net/ for more details about rDock and associated programs.
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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
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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238 .. class:: infomark
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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239
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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240 **Inputs**
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241
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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242 1. The protein receptor to dock into as a file in Mol2 format.
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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243 2. The active site definition as a file as generated by the rbcavity tool.
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244 3. A set of ligands (collection or single file) to dock as a file in SDF format.
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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245 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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246 5. The number of best scoring dockings to keep (integer).
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247 6. The max score that is allowed. Poses with scores greater than this are excluded (float, optional).
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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248 7. The max normalised score (the score normalised by the number of heavy atoms) that is allowed.
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249 Poses with normalised scores greater than this are excluded (float, optional).
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250 8. Optionally generate the name field in the ligands SDF (this is the first line in the entry).
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251 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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252 then the name field is probably absent and must be generated.
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253
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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254 You will need to perform some test dockings to establish suitable values for the score filters.
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255 The score is a number with lower values being better. Values can be negative.
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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
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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259 .. class:: infomark
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260
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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261 **Outputs**
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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262
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
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263 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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264
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
265 1-pyrimethamine
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
266 rDOCK(R) 3D
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
267 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
268 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
269 -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
270 -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
271 -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
272 -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
273 -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
274 -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
275 -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
276 -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
277 -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
278 -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
279 -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
280 -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
281 -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
282 -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
283 -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
284 -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
285 -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
286 -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
287 -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
288 -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
289 -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
290 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
291 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
292 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
293 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
294 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
295 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
296 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
297 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
298 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
299 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
300 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
301 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
302 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
303 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
304 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
305 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
306 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
307 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
308 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
309 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
310 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
311 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
312 M END
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
313 > <CHROM.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
314 -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
315
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
316 > <CHROM.1>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
317 -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
318 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
319
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
320 > <Rbt.Current_Directory>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
321 /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
322
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
323 > <Rbt.Executable>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
324 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
325
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
326 > <Rbt.Library>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
327 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
328
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
329 > <Rbt.Parameter_File>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
330 /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
331
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
332 > <Rbt.Receptor>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
333 receptor.prm
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
334
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
335 > <SCORE>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
336 0.445364
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
337
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
338 > <SCORE.INTER>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
339 8.4
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
340
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
341 > <SCORE.INTER.CONST>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
342 1
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
343
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
344 > <SCORE.INTER.POLAR>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
345 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
346
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
347 > <SCORE.INTER.REPUL>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
348 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
349
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
350 > <SCORE.INTER.ROT>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
351 3
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
352
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
353 > <SCORE.INTER.VDW>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
354 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
355
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
356 > <SCORE.INTER.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
357 0.494118
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
358
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
359 > <SCORE.INTRA>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
360 -1.38672
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
361
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
362 > <SCORE.INTRA.DIHEDRAL>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
363 -0.818539
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
364
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
365 > <SCORE.INTRA.DIHEDRAL.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
366 6.01924
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
367
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
368 > <SCORE.INTRA.POLAR>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
369 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
370
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
371 > <SCORE.INTRA.POLAR.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
372 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
373
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
374 > <SCORE.INTRA.REPUL>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
375 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
376
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
377 > <SCORE.INTRA.REPUL.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
378 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
379
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
380 > <SCORE.INTRA.VDW>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
381 -0.977448
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
382
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
383 > <SCORE.INTRA.VDW.0>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
384 -1.0079
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
385
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
386 > <SCORE.INTRA.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
387 -0.0815716
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
388
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
389 > <SCORE.RESTR>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
390
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
391 > <SCORE.RESTR.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
392 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
393
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
394 > <SCORE.SYSTEM>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
395 -6.56792
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
396
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
397 > <SCORE.SYSTEM.CONST>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
398 0
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
399
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
400 > <SCORE.SYSTEM.DIHEDRAL>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
401 1.50415
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
402
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
403 > <SCORE.SYSTEM.POLAR>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
404 -2.3289
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
405
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
406 > <SCORE.SYSTEM.VDW>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
407 0.59827
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
408
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
409 > <SCORE.SYSTEM.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
410 -0.386348
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
411
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
412 > <SCORE.heavy>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
413 17
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
414
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
415 > <SCORE.norm>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
416 0.0261979
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
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
420 ]]></help>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
421 <expand macro="citations"/>
1a1600fde77a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents:
diff changeset
422 </tool>