Mercurial > repos > bgruening > autodock_vina

annotate docking.xml @ 8:7a871df65202 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:13:41 -0400
parents 7b2f205b3f68
children 90ea16534012
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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@">
7a871df65202 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.1.2</token>
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4 <token name="@GALAXY_VERSION@">0</token>
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5 </macros>
5
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6 <description>tool to perform protein-ligand docking with Autodock Vina</description>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">autodock-vina</requirement>
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9 <requirement type="package" version="3.1.1">openbabel</requirement>
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10 <requirement type="package" version="20200722">parallel</requirement>
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11 </requirements>
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12 <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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13 #if $ligands.is_of_type("sdf")
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14 obabel -isdf '$ligands' -O ligand.pdbqt -m -p $ph_value &&
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15 #else
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16 ln -s '$ligands' ligand1.pdbqt &&
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17 #end if
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18 mkdir output &&
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19 ls ligand*.pdbqt | parallel --will-cite -j \${GALAXY_SLOTS:-1} $'OUTNAME={.}_docked && vina
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20 --receptor \'$receptor\'
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21 --ligand {}
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22 --out ./\${OUTNAME}.pdbqt
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23 --log ./\${OUTNAME}.log
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24 --cpu 1
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25 #if $config_params.config_params == 'vals':
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26 --center_x $config_params.center_x
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27 --center_y $config_params.center_y
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28 --center_z $config_params.center_z
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29 --size_x $config_params.size_x
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30 --size_y $config_params.size_y
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31 --size_z $config_params.size_z
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32 #if $config_params.exh != "":
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33 --exhaustiveness $config_params.exh
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34 #end if
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35 #if $config_params.seed.seed == 'true':
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36 --seed $config_params.seed.seed_value
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37 #end if
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38 #else if $config_params.config_params == 'file':
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39 --config $config_params.box
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40 #if $config_params.exh != "":
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41 --exhaustiveness $config_params.exh
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42 #end if
6
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43 #end if
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44 && python \'$__tool_directory__/convert_pdbqt_to_sdf.py\' ./\${OUTNAME}.pdbqt output/\${OUTNAME}.sdf'
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45
2
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46 ]]></command>
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47 <inputs>
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48 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool." />
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49 <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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50 <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value for ligand protonation"
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51 help="Only used in case the input is a SD file."/>
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52 <conditional name="config_params">
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53 <param name="config_params" type="select" label="Specify parameters">
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54 <option value="file">Upload a config file to specify parameters</option>
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55 <option value="vals">Specify values directly</option>
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56 </param>
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57 <when value="vals">
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58 <param type="float" name="center_x" label="x coordinate" help="x coordinate of the binding site." value="0"/>
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59 <param type="float" name="center_y" label="y coordinate" help="y coordinate of the binding site." value="0"/>
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60 <param type="float" name="center_z" label="z coordinate" help="z coordinate of the binding site." value="0"/>
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61 <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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62 <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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63 <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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64 <param type="integer" name="exh" label="Exhaustiveness" optional="true"
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65 help="Exhaustiveness of global search (optional - if not specified a default of 8 is used)"/>
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66 <conditional name="seed">
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67 <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/>
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68 <when value="true">
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69 <param type="integer" name="seed_value" label="Random seed" help="Choose a seed value" value="1"/>
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70 </when>
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71 <when value="false"/>
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72 </conditional>
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73 </when>
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74 <when value="file">
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75 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" />
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76 <param type="integer" name="exh" label="Exhaustiveness" optional="true"
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77 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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78 </when>
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79 </conditional>
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80 </inputs>
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81 <outputs>
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82 <collection name="sdf_outputs" type="list" label="Docked ligands for ${on_string}" >
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83 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
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84 </collection>
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85 </outputs>
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86 <tests>
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87
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88 <test>
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89 <param name="receptor" value="protein.pdbqt"/>
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90 <param name="ligands" value="input_ligands.sdf"/>
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91 <param name="box" value="box.txt"/>
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92 <output_collection name="sdf_outputs" type="list" count="5">
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93 <element name="ligand1_docked" file="ligand1_docked.sdf" lines_diff="20"/>
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94 <element name="ligand2_docked" file="ligand2_docked.sdf" lines_diff="20"/>
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95 <!-- we check only the first 2 -->
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96 </output_collection>
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97 </test>
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98
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99 <test>
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100 <param name="receptor" value="protein.pdbqt"/>
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101 <param name="ligands" value="input_ligand.pdbqt"/>
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102 <param name="box" value="box.txt"/>
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103 <output_collection name="sdf_outputs" type="list" count="1">
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104 <element name="ligand1_docked" file="ligand_docked.sdf" lines_diff="1084"/>
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105 </output_collection>
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106 </test>
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107
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108 <!-- TODO - this should be able to use the same output as the previous test but there is inconsistency in
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109 how the parameters are handled that needs to be resolved so we use a different output file to compare to. -->
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110 <test>
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111 <param name="receptor" value="protein.pdbqt"/>
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112 <param name="ligands" value="input_ligand.pdbqt"/>
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113 <param name="config_params" value="vals"/>
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114 <param name="center_x" value="36.454" />
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115 <param name="center_y" value="-43.608000000000004" />
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116 <param name="center_z" value="75.176" />
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117 <param name="size_x" value="18.768" />
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118 <param name="size_y" value="10.205999999999996" />
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119 <param name="size_z" value="15.521999999999991" />
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120 <param name="seed" value="true" />
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121 <param name="seed_value" value="8" />
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122 <param name="exh" value="10" />
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123 <output_collection name="sdf_outputs" type="list" count="1">
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124 <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="1084"/>
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125 </output_collection>
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126 </test>
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127
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128 </tests>
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129 <help><![CDATA[
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130
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131 This tool performs protein-ligand docking using the Autodock Vina program.
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132
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133 -----
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134
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135 .. class:: infomark
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136
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137 **Inputs**
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138
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139 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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140 These files are produced by the receptor and ligand preparation tools.
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141 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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142 and those ligands are converted to individual PDBQT format files using openbabel as the first step of tool execution.
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143 You can specify the pH for protonation by openbabel
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144
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145 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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146 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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147 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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148 environment.
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149
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150 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should
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151 be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in
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152 which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be
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153 generated from the box parameter calculation file.
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154
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155
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156 -----
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157
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158 .. class:: infomark
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159
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160 **Outputs**
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161
7
7b2f205b3f68 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 6
diff changeset
162 SDF files are produced as output.
7b2f205b3f68 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 6
diff changeset
163 There is one file for each ligand in the input. Each entry in the file is a docked pose for that ligand.
7b2f205b3f68 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
bgruening
parents: 6
diff changeset
164 The binding affinity scores are contained within the SDF file.::
6
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
165
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
166 OpenBabel06171915303D
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
167
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
168 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
169 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
170 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
171 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
172 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
173 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
174 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
175 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
176 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
177 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
178 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
179 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
180 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
181 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
182 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
183 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
184 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
185 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
186 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
187 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
188 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
189 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
190 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
191 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
192 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
193 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
194 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
195 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
196 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
197 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
198 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
199 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
200 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
201 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
202 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
203 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
204 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
205 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
206 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
207 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
208 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
209 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
210 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
211 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
212 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
213 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
214 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
215 M END
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
216 > <MODEL>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
217 1
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
218
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
219 > <REMARK>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
220 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
221 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
222 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
223 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
224 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
225 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
226 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
227 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
228 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
229 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
230 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
231 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
232
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
233 > <TORSDO>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
234 F 9
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
235
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
236 > <SCORE>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
237 0.0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
238
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
239 > <RMSD_LB>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
240 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
241
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
242 > <RMSD_UB>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
243 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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diff changeset
244
2
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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245 ]]></help>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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246 <citations>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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247 <citation type="doi">10.1002/jcc.21334</citation>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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248 </citations>
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65ffed035ca8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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249 </tool>