Mercurial > repos > bgruening > autodock_vina

annotate docking.xml @ 9:90ea16534012 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
author bgruening
date Tue, 21 Dec 2021 14:18:33 +0000
parents 7a871df65202
children
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7a871df65202 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="docking" name="VINA Docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>tool to perform protein-ligand docking with Autodock Vina</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.2.3</token>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">vina</requirement>
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9 <requirement type="package" version="3.9">python</requirement>
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10 <requirement type="package" version="3.1.1">openbabel</requirement>
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11 <requirement type="package" version="20211022">parallel</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
7b2f205b3f68 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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14 #if $ligands.is_of_type("sdf")
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15 obabel -isdf '$ligands' -O ligand.pdbqt -m -p $ph_value &&
7b2f205b3f68 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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16 #else
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17 ln -s '$ligands' ligand1.pdbqt &&
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18 #end if
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19 mkdir output &&
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20 ls ligand*.pdbqt | parallel --will-cite -j \${GALAXY_SLOTS:-1} $'OUTNAME={.}_docked && vina
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21 --receptor \'$receptor\'
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22 #if $flex:
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23 --flex \'$flex\'
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24 #end if
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25 --ligand {}
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26 --out ./\${OUTNAME}.pdbqt
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27 --cpu 1
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28 --verbosity 2
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29 #if $config_params.config_params == "vals":
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30 --center_x $config_params.center_x
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31 --center_y $config_params.center_y
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32 --center_z $config_params.center_z
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33 --size_x $config_params.size_x
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34 --size_y $config_params.size_y
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35 --size_z $config_params.size_z
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36 #if $config_params.exh != "":
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37 --exhaustiveness $config_params.exh
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38 #end if
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39 #if $config_params.seed.seed == "true":
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40 --seed $config_params.seed.seed_value
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41 #end if
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42 #else if $config_params.config_params == "file":
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43 --config $config_params.box
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44 #if $config_params.exh != "":
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45 --exhaustiveness $config_params.exh
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46 #end if
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47 #end if
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48 #if $settings.scoring:
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49 --scoring \'$settings.scoring\'
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50 #end if
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51 #if $settings.num_modes:
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52 --num_modes \'$settings.num_modes\'
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53 #end if
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54 #if $settings.min_rmsd:
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55 --min_rmsd \'$settings.min_rmsd\'
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56 #end if
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57 #if $settings.energy_range:
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58 --energy_range \'$settings.energy_range\'
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59 #end if
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60 #if $output == "sdf":
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61 && python \'$__tool_directory__/convert_pdbqt_to_sdf.py\' ./\${OUTNAME}.pdbqt output/\${OUTNAME}.sdf
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62 #end if
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63 '
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64 #if $output == "pdbqt":
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65 && mv *docked.pdbqt output/
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66 #end if
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67 ]]></command>
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68 <inputs>
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69 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool. If the 'Flexible side chains' option is chosen, it should contain only the rigid part of the receptor." />
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70 <param type="data" name="ligands" format="sdf,pdbqt" label="Ligands" help="Select ligands (SDF format with multiple ligands or PDBQT format with single ligand)." />
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71 <param type="data" name="flex" format="pdbqt" optional="true" label="Flexible side chains" help="Part of the receptor which should be treated flexibly (PDBQT format)." />
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72 <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value for ligand protonation"
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73 help="Only used if the input is a SD file."/>
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74 <conditional name="config_params">
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75 <param name="config_params" type="select" label="Specify parameters">
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76 <option value="file">Upload a config file to specify parameters</option>
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77 <option value="vals">Specify values directly</option>
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78 </param>
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79 <when value="vals">
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80 <param type="float" name="center_x" label="x coordinate" help="x coordinate of the binding site." value="0"/>
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81 <param type="float" name="center_y" label="y coordinate" help="y coordinate of the binding site." value="0"/>
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82 <param type="float" name="center_z" label="z coordinate" help="z coordinate of the binding site." value="0"/>
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83 <param type="float" name="size_x" label="x size" help="Length of the binding site (Å) in the x direction." value="0"/>
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84 <param type="float" name="size_y" label="y size" help="Length of the binding site (Å) in the y direction." value="0"/>
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85 <param type="float" name="size_z" label="z size" help="Length of the binding site (Å) in the z direction." value="0"/>
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86 <param type="integer" name="exh" label="Exhaustiveness" optional="true"
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87 help="Exhaustiveness of global search (optional - if not specified a default of 8 is used)"/>
5
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88 <conditional name="seed">
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89 <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/>
c410ffcabf9d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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90 <when value="true">
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91 <param type="integer" name="seed_value" label="Random seed" help="Choose a seed value" value="1"/>
c410ffcabf9d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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92 </when>
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93 <when value="false"/>
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94 </conditional>
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95 </when>
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96 <when value="file">
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97 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" />
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98 <param type="integer" name="exh" label="Exhaustiveness" optional="true"
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99 help="Exhaustiveness of global search (optional - if not specified a default of 8 is used, if specified will override any value specified in the config file)"/>
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100 </when>
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101 </conditional>
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102
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103 <section name="settings" title="Optional settings" expanded="true" help="All these settings can also be specified in the config file. Specifying them additionally here overrides the config file.">
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104 <param type="select" name="scoring" label="Scoring function" optional="true" help="Function to use for scoring the poses." value="vina">
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105 <option value="vina">vina</option>
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106 <option value="ad4">ad4</option>
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107 <option value="vinardo">vinardo</option>
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108 </param>
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109 <param type="integer" name="num_modes" optional="true" label="Number of poses" help="Maximum number of binding poses to generate (default 9)" />
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110 <param type="float" name="min_rmsd" optional="true" label="Minimum RMSD between output poses (default 1)" />
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111 <param type="float" name="energy_range" optional="true" label="Energy range" help="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) (default 3)"/>
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112 </section>
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113 <param type="select" name="output" label="Output format" help="Format for the docking poses.">
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114 <option value="sdf" selected="true">SDF</option>
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115 <option value="pdbqt">PDBQT</option>
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116 </param>
2
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117 </inputs>
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118 <outputs>
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119 <collection name="sdf_outputs" type="list" label="Docked ligands for ${on_string}" >
7b2f205b3f68 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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120 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
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121 <filter>output == "sdf"</filter>
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122 </collection>
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123 <collection name="pdbqt_outputs" type="list" label="Docked structures for ${on_string}" >
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124 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
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125 <filter>output == "pdbqt"</filter>
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126 </collection>
2
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127 </outputs>
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128 <tests>
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129 <test>
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130 <param name="receptor" value="protein.pdbqt"/>
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131 <param name="ligands" value="input_ligands.sdf"/>
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132 <param name="box" value="box.txt"/>
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133 <output_collection name="sdf_outputs" type="list" count="5">
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134 <!-- linesdiff because there is a time stamp for each of the 9 poses -->
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135 <element name="ligand1_docked" file="ligand1_docked.sdf" lines_diff="18"/>
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136 <element name="ligand2_docked" file="ligand2_docked.sdf" lines_diff="18"/>
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137 <!-- we check only the first 2 -->
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138 </output_collection>
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139 </test>
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140
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141 <test>
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142 <param name="receptor" value="protein.pdbqt"/>
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143 <param name="ligands" value="input_ligand.pdbqt"/>
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144 <param name="box" value="box.txt"/>
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145 <output_collection name="sdf_outputs" type="list" count="1">
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146 <element name="ligand1_docked" file="ligand_docked.sdf" lines_diff="18"/>
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147 </output_collection>
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148 </test>
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149
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150 <!-- test with optional params -->
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151 <test>
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152 <param name="receptor" value="protein.pdbqt"/>
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153 <param name="ligands" value="input_ligand.pdbqt"/>
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154 <param name="box" value="box.txt"/>
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155 <param name="scoring" value="vinardo"/>
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156 <param name="energy_range" value="5"/>
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157 <param name="num_modes" value="20"/>
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158 <param name="min_rmsd" value="0.5"/>
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159 <output_collection name="sdf_outputs" type="list" count="1">
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160 <element name="ligand1_docked" file="ligand_docked_opt.sdf" lines_diff="40"/>
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161 </output_collection>
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162 </test>
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163
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164 <!-- TODO - this should be able to use the same output as the previous test but there is inconsistency in
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165 how the parameters are handled that needs to be resolved so we use a different output file to compare to. -->
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166 <test>
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167 <param name="receptor" value="protein.pdbqt"/>
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168 <param name="ligands" value="input_ligand.pdbqt"/>
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169 <param name="config_params" value="vals"/>
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170 <param name="center_x" value="36.454" />
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171 <param name="center_y" value="-43.608000000000004" />
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172 <param name="center_z" value="75.176" />
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173 <param name="size_x" value="18.768" />
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174 <param name="size_y" value="10.205999999999996" />
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175 <param name="size_z" value="15.521999999999991" />
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176 <param name="seed" value="true" />
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177 <param name="seed_value" value="8" />
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178 <param name="exh" value="10" />
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179 <output_collection name="sdf_outputs" type="list" count="1">
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180 <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="18"/>
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181 </output_collection>
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182 </test>
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183
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184 <!-- flexible docking -->
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185 <test>
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186 <param name="receptor" value="protein_rigid.pdbqt"/>
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187 <param name="flex" value="protein_flex.pdbqt"/>
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188 <param name="ligands" value="input_ligands.sdf"/>
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189 <param name="config_params" value="vals"/>
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190 <param name="center_x" value="15.2" />
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191 <param name="center_y" value="53.9" />
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192 <param name="center_z" value="16.9" />
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193 <param name="size_x" value="20" />
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194 <param name="size_y" value="20" />
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195 <param name="size_z" value="20" />
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196 <param name="seed" value="true" />
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197 <param name="seed_value" value="8" />
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198 <param name="exh" value="10" />
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199 <param name="output" value="pdbqt"/>
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200 <output_collection name="pdbqt_outputs" type="list" count="5">
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201 <element name="ligand1_docked" file="ligand1_docked_flex.pdbqt"/>
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202 <element name="ligand2_docked" file="ligand2_docked_flex.pdbqt"/>
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203 <!-- we check only the first 2 -->
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204 </output_collection>
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205 </test>
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206 </tests>
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207 <help><![CDATA[
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208
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209 This tool performs protein-ligand docking using the Autodock Vina program.
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210
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211 -----
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212
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213 .. class:: infomark
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214
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215 **Inputs**
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216
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217 The first two inputs required are files describing the receptor (in the pdbqt format) and ligands (in SDF of PDBQT format) respectively.
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218 These files are produced by the receptor and ligand preparation tools.
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219 If using PDBQT format for the ligands only a single ligand can be specified. If using SDF you can include multiple ligands
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220 and those ligands are converted to individual PDBQT format files using openbabel as the first step of tool execution.
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221 You can specify the pH for protonation by openbabel
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222
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223 VINA will dock each of the ligands in the SDF file sequentially. If there are a large number of ligands then first split
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224 them into a collection of smaller files e.g. using the splitter tool. This allows each split chunk of molecules to be docked
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225 as a separate task. The optimal size of the chunk will depend on the number of ligands and the capacity of the execution
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226 environment.
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227
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228 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should
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229 be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in
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230 which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be
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231 generated from the box parameter calculation file.
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232
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233
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234 -----
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235
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236 .. class:: infomark
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237
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238 **Outputs**
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239
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240 SDF files are produced as output.
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241 There is one file for each ligand in the input. Each entry in the file is a docked pose for that ligand.
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242 The binding affinity scores are contained within the SDF file.::
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243
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244 OpenBabel06171915303D
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245
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
246 23 23 0 0 0 0 0 0 0 0999 V2000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
247 66.9030 73.3450 36.0040 O 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
248 66.8190 73.2170 37.2120 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
249 66.0490 72.3370 37.8940 O 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
250 66.2290 70.9500 37.5970 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
251 67.2070 70.4140 38.6010 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
252 68.5140 70.1440 38.3980 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
253 69.2150 70.3400 37.0800 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
254 69.3810 69.5970 39.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
255 68.7730 69.8280 40.9100 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
256 69.3750 71.0120 41.6220 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
257 68.7550 72.1570 41.9760 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
258 67.3280 72.4970 41.6430 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
259 69.4770 73.2270 42.7560 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
260 67.5570 74.0540 38.1920 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
261 66.9010 75.0480 38.9340 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
262 67.6300 75.8170 39.8300 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
263 68.9950 75.5990 39.9980 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
264 69.6510 74.6060 39.2850 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
265 68.9300 73.8240 38.3800 C 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
266 67.0450 76.8040 40.5760 O 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
267 67.5560 77.4980 40.9760 H 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
268 69.7010 76.3670 40.8780 O 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
269 69.2520 76.7930 41.5990 H 0 0 0 0 0 0 0 0 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
270 1 2 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
271 2 3 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
272 2 14 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
273 4 3 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
274 4 5 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
275 6 5 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
276 6 8 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
277 7 6 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
278 8 9 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
279 9 10 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
280 10 11 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
281 11 13 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
282 12 11 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
283 14 19 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
284 14 15 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
285 15 16 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
286 16 17 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
287 16 20 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
288 17 22 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
289 18 17 2 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
290 19 18 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
291 20 21 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
292 22 23 1 0 0 0 0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
293 M END
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
294 > <MODEL>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
295 1
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
296
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
297 > <REMARK>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
298 VINA RESULT: 0.0 0.000 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
299 9 active torsions:
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
300 status: ('A' for Active; 'I' for Inactive)
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
301 1 A between atoms: C_2 and O_3
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
302 2 A between atoms: C_2 and C_14
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
303 3 A between atoms: O_3 and C_4
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
304 4 A between atoms: C_4 and C_5
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
305 5 A between atoms: C_6 and C_8
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
306 6 A between atoms: C_8 and C_9
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
307 7 A between atoms: C_9 and C_10
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
308 8 A between atoms: C_16 and O_17
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
309 9 A between atoms: C_19 and O_20
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
310
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
311 > <TORSDO>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
312 F 9
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
313
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
314 > <SCORE>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
315 0.0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
316
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
317 > <RMSD_LB>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
318 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
319
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
320 > <RMSD_UB>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
321 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
322
2
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
323 ]]></help>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
324 <citations>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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parents:
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325 <citation type="doi">10.1002/jcc.21334</citation>
9
90ea16534012 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
bgruening
parents: 8
diff changeset
326 <citation type="doi">10.1021/acs.jcim.1c00203</citation>
2
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
327 </citations>
3
65ffed035ca8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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parents: 2
diff changeset
328 </tool>