Mercurial > repos > bgruening > autodock_vina

annotate docking.xml @ 7:7b2f205b3f68 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:49:30 -0400
parents 0ae768a0e5c0
children 7a871df65202
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7b2f205b3f68 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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1 <tool id="docking" name="VINA Docking" version="0.3.0">
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2 <description>tool to perform protein-ligand docking with Autodock Vina</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.2">autodock-vina</requirement>
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5 <requirement type="package" version="2.4.1">openbabel</requirement>
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6 <requirement type="package" version="20190722">parallel</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $ligands.is_of_type("sdf")
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10 obabel -isdf '$ligands' -O ligand.pdbqt -m -p $ph_value &&
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11 #else
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12 ln -s '$ligands' ligand1.pdbqt &&
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13 #end if
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14 mkdir output &&
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15 ls ligand*.pdbqt | parallel --will-cite -j \${GALAXY_SLOTS:-1} $'OUTNAME={.}_docked && vina
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16 --receptor \'$receptor\'
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17 --ligand {}
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18 --out ./\${OUTNAME}.pdbqt
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19 --log ./\${OUTNAME}.log
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20 --cpu 1
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21 #if $config_params.config_params == 'vals':
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22 --center_x $config_params.center_x
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23 --center_y $config_params.center_y
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24 --center_z $config_params.center_z
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25 --size_x $config_params.size_x
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26 --size_y $config_params.size_y
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27 --size_z $config_params.size_z
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28 #if $config_params.exh != "":
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29 --exhaustiveness $config_params.exh
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30 #end if
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31 #if $config_params.seed.seed == 'true':
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32 --seed $config_params.seed.seed_value
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33 #end if
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34 #else if $config_params.config_params == 'file':
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35 --config $config_params.box
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36 #if $config_params.exh != "":
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37 --exhaustiveness $config_params.exh
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38 #end if
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39 #end if
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40 && python \'$__tool_directory__/convert_pdbqt_to_sdf.py\' ./\${OUTNAME}.pdbqt output/\${OUTNAME}.sdf'
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41
2
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42 ]]></command>
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43 <inputs>
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44 <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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45 <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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46 <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value for ligand protonation"
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47 help="Only used in case the input is a SD file."/>
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48 <conditional name="config_params">
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49 <param name="config_params" type="select" label="Specify parameters">
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50 <option value="file">Upload a config file to specify parameters</option>
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51 <option value="vals">Specify values directly</option>
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52 </param>
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53 <when value="vals">
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54 <param type="float" name="center_x" label="x coordinate" help="x coordinate of the binding site." value="0"/>
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55 <param type="float" name="center_y" label="y coordinate" help="y coordinate of the binding site." value="0"/>
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56 <param type="float" name="center_z" label="z coordinate" help="z coordinate of the binding site." value="0"/>
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57 <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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58 <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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59 <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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60 <param type="integer" name="exh" label="Exhaustiveness" optional="true"
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61 help="Exhaustiveness of global search (optional - if not specified a default of 8 is used)"/>
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62 <conditional name="seed">
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63 <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/>
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64 <when value="true">
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65 <param type="integer" name="seed_value" label="Random seed" help="Choose a seed value" value="1"/>
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66 </when>
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67 <when value="false"/>
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68 </conditional>
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69 </when>
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70 <when value="file">
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71 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" />
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72 <param type="integer" name="exh" label="Exhaustiveness" optional="true"
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73 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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74 </when>
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75 </conditional>
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76 </inputs>
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77 <outputs>
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78 <collection name="sdf_outputs" type="list" label="Docked ligands for ${on_string}" >
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79 <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" />
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80 </collection>
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81 </outputs>
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82 <tests>
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83
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84 <test>
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85 <param name="receptor" value="protein.pdbqt"/>
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86 <param name="ligands" value="input_ligands.sdf"/>
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87 <param name="box" value="box.txt"/>
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88 <output_collection name="sdf_outputs" type="list" count="5">
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89 <element name="ligand1_docked" file="ligand1_docked.sdf" lines_diff="20"/>
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90 <element name="ligand2_docked" file="ligand2_docked.sdf" lines_diff="20"/>
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91 <!-- we check only the first 2 -->
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92 </output_collection>
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93 </test>
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94
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95 <test>
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96 <param name="receptor" value="protein.pdbqt"/>
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97 <param name="ligands" value="input_ligand.pdbqt"/>
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98 <param name="box" value="box.txt"/>
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99 <output_collection name="sdf_outputs" type="list" count="1">
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100 <element name="ligand1_docked" file="ligand1_docked.sdf" lines_diff="20"/>
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101 </output_collection>
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102 </test>
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103
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104 <!-- TODO - this should be able to use the same output as the previous test but there is inconsistency in
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105 how the parameters are handled that needs to be resolved so we use a different output file to compare to. -->
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106 <test>
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107 <param name="receptor" value="protein.pdbqt"/>
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108 <param name="ligands" value="input_ligand.pdbqt"/>
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109 <param name="config_params" value="vals"/>
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110 <param name="center_x" value="36.454" />
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111 <param name="center_y" value="-43.608000000000004" />
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112 <param name="center_z" value="75.176" />
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113 <param name="size_x" value="18.768" />
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114 <param name="size_y" value="10.205999999999996" />
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115 <param name="size_z" value="15.521999999999991" />
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116 <param name="seed" value="true" />
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117 <param name="seed_value" value="1" />
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118 <param name="exh" value="10" />
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119 <output_collection name="sdf_outputs" type="list" count="1">
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120 <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="20"/>
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121 </output_collection>
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122 </test>
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123
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124 </tests>
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125 <help><![CDATA[
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126
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127 This tool performs protein-ligand docking using the Autodock Vina program.
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128
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129 -----
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130
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131 .. class:: infomark
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132
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133 **Inputs**
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134
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135 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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136 These files are produced by the receptor and ligand preparation tools.
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137 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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138 and those ligands are converted to individual PDBQT format files using openbabel as the first step of tool execution.
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139 You can specify the pH for protonation by openbabel
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140
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141 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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142 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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143 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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144 environment.
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145
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146 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should
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147 be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in
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148 which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be
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149 generated from the box parameter calculation file.
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150
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151
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152 -----
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153
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154 .. class:: infomark
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155
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156 **Outputs**
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157
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158 SDF files are produced as output.
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159 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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160 The binding affinity scores are contained within the SDF file.::
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161
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
162 OpenBabel06171915303D
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
163
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
164 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
165 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
166 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
167 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
168 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
169 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
170 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
171 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
172 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
173 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
174 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
175 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
176 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
177 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
178 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
179 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
180 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
181 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
182 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
183 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
184 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
185 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
186 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
187 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
188 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
189 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
190 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
191 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
192 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
193 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
194 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
195 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
196 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
197 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
198 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
199 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
200 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
201 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
202 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
203 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
204 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
205 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
206 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
207 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
208 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
209 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
210 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
211 M END
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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212 > <MODEL>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
213 1
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
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214
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
215 > <REMARK>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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parents: 5
diff changeset
216 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
217 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
218 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
219 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
220 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
221 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
222 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
223 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
224 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
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225 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
226 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
227 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
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228
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
229 > <TORSDO>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
230 F 9
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
231
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
232 > <SCORE>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
233 0.0
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
234
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
235 > <RMSD_LB>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
236 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
237
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
238 > <RMSD_UB>
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
bgruening
parents: 5
diff changeset
239 0.000
0ae768a0e5c0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
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240
2
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
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241 ]]></help>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
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242 <citations>
18dec59e29ae planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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243 <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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244 </citations>
3
65ffed035ca8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
bgruening
parents: 2
diff changeset
245 </tool>