Mercurial > repos > bgruening > autodock_vina

annotate docking.xml @ 5:c410ffcabf9d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:31:43 -0400
parents 3c8e86318a81
children 0ae768a0e5c0
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5
c410ffcabf9d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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1 <tool id="docking" name="Docking" version="0.2.0">
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2 <description>tool to perform protein-ligand docking with Autodock Vina</description>
2
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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 </requirements>
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6 <stdio>
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7 <exit_code range="1" />
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8 </stdio>
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9 <command><![CDATA[
5
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10 #if $config_params.config_params == 'vals':
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11 vina
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12 --center_x '$config_params.center_x'
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13 --center_y '$config_params.center_y'
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14 --center_z '$config_params.center_z'
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15 --size_x '$config_params.size_x'
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16 --size_y '$config_params.size_y'
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17 --size_z '$config_params.size_z'
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18 --exhaustiveness '$config_params.exh'
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19 --num_modes 9999
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20 --energy_range 9999
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21 --receptor '$receptor'
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22 --ligand '$ligand'
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23 --out '$file_output1'
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24 --log '$file_output2'
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25 --cpu \${GALAXY_SLOTS:-1}
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26 #if $config_params.seed.seed == 'true':
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27 --seed '$config_params.seed.seed_value'
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28 #end if
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29 #end if
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30 #if $config_params.config_params == 'file':
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31 vina
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32 --config '$config_params.box'
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33 --receptor '$receptor'
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34 --ligand '$ligand'
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35 --out '$file_output1'
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36 --log '$file_output2'
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37 --cpu \${GALAXY_SLOTS:-1}
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38
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39 #end if
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40
2
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41 ]]></command>
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42 <inputs>
5
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43 <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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44 <param type="data" name="ligand" format="pdbqt" label="Ligand" help="Select a ligand (PDBQT format). This can be prepared using the ligand preparation tool." />
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45 <conditional name="config_params">
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46 <param name="config_params" type="select" label="Specify parameters">
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47 <option value="file">Upload a config file to specify parameters</option>
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48 <option value="vals">Specify values directly</option>
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49 </param>
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50 <when value="vals">
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51 <param type="float" name="center_x" label="x coordinate" help="x coordinate of the binding site." value="0"/>
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52 <param type="float" name="center_y" label="y coordinate" help="y coordinate of the binding site." value="0"/>
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53 <param type="float" name="center_z" label="z coordinate" help="z coordinate of the binding site." value="0"/>
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54 <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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55 <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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56 <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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57 <param type="integer" name="exh" label="Exhaustiveness" help="The number of poses to return from the docking job" value="10"/>
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58 <conditional name="seed">
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59 <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/>
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60 <when value="true">
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61 <param type="integer" name="seed_value" label="Random seed" help="Choose a seed value" value="1"/>
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62 </when>
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63 <when value="false"/>
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64 </conditional>
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65 </when>
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66 <when value="file">
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67 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" />
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68 </when>
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69 </conditional>
2
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70 </inputs>
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71 <outputs>
3
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72 <data name="file_output1" format="pdbqt" />
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73 <data name="file_output2" format="txt" />
2
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
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78 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
5
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79 <param name="config_params" value="vals"/>
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80 <param name="center_x" value="70.92" />
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81 <param name="center_y" value="70.57" />
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82 <param name="center_z" value="36.86" />
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83 <param name="size_x" value="20.00" />
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84 <param name="size_y" value="18.40" />
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85 <param name="size_z" value="23.60" />
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86 <param name="seed" value="true" />
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87 <param name="seed_value" value="1" />
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88 <param name="exhaustivenesss" value="10" />
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89 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
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90 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
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91 </test>
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92 <test>
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93 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
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94 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
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95 <param name="config_params" value="file"/>
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96 <param name="box" value="config_complexo_dm.txt"/>
2
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97 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
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98 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
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99 </test>
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100 </tests>
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101 <help><![CDATA[
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102
5
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103 This tool performs protein-ligand docking using the Autodock Vina program.
2
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104
4
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105 **Inputs**
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106
5
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107 The first two inputs required are files (in the pdbqt format) describing the receptor and ligand respectively. These files are produced by the receptor and ligand preparation tools.
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108
5
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109 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be generated from the box parameter calculation file.
2
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110
4
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111 **Outputs**
2
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112
5
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113 Two outputs are generated by this tool. The first is another pdbqt file containing the molecular structure resulting from docking, such as the following example::
2
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114
4
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115 MODEL 1
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116 REMARK VINA RESULT: -0.0 0.000 0.000
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117 REMARK 9 active torsions:
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118 REMARK status: ('A' for Active; 'I' for Inactive)
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119 REMARK 1 A between atoms: C_2 and O_3
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120 REMARK 2 A between atoms: C_2 and C_14
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121 REMARK 3 A between atoms: O_3 and C_4
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122 REMARK 4 A between atoms: C_4 and C_5
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123 REMARK 5 A between atoms: C_6 and C_8
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124 REMARK 6 A between atoms: C_8 and C_9
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125 REMARK 7 A between atoms: C_9 and C_10
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126 REMARK 8 A between atoms: C_16 and O_17
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127 REMARK 9 A between atoms: C_19 and O_20
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128 ROOT
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129 ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA
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130 ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C
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131 ENDROOT
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132 BRANCH 2 3
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133 ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA
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134 BRANCH 3 4
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135 ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C
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136 BRANCH 4 5
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137 ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C
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138 ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C
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139 ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C
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140 BRANCH 6 8
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141 ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C
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142 BRANCH 8 9
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143 ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C
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144 BRANCH 9 10
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145 ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C
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146 ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C
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147 ATOM 12 C LIG d 1 75.833 75.151 40.104 0.00 0.00 0.042 C
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148 ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C
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149 ENDBRANCH 9 10
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150 ENDBRANCH 8 9
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151 ENDBRANCH 6 8
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152 ENDBRANCH 4 5
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153 ENDBRANCH 3 4
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154 ENDBRANCH 2 3
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155 BRANCH 2 14
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156 ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A
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157 ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A
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158 ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A
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159 ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A
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160 ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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161 ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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162 BRANCH 16 20
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163 ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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164 ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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165 ENDBRANCH 16 20
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166 BRANCH 17 22
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167 ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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168 ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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169 ENDBRANCH 17 22
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170 ENDBRANCH 2 14
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171 TORSDOF 9
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172 ENDMDL
2
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173
5
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174 The second output is a log file containing the binding affinity scores, like the following::
2
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175
4
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176 -----------------------------------------------------------------
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177 If you used AutoDock Vina in your work, please cite:
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178
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179 O. Trott, A. J. Olson,
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180 AutoDock Vina: improving the speed and accuracy of docking
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181 with a new scoring function, efficient optimization and
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182 multithreading, Journal of Computational Chemistry 31 (2010)
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183 455-461
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184
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185 DOI 10.1002/jcc.21334
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186
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187 Please see http://vina.scripps.edu for more information.
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188 ------------------------------------------------------------------
2
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189
4
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190 Reading input ... done.
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191 Setting up the scoring function ... done.
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192 Analyzing the binding site ... done.
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193 Using random seed: 1899908181
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194 Performing search ... done.
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195 Refining results ... done.
2
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196
4
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197 mode | affinity | dist from best mode
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198 | (kcal/mol) | rmsd l.b.| rmsd u.b.
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199 -----+------------+----------+----------
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200 1 -0.0 0.000 0.000
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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201 2 -0.0 2.046 2.443
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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202 3 -0.0 5.896 7.949
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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203 4 -0.0 2.518 3.100
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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204 5 -0.0 2.417 4.527
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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205 6 -0.0 5.686 7.689
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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206 7 -0.0 2.828 4.792
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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207 8 -0.0 5.547 7.086
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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208 9 -0.0 7.388 9.966
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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209 10 -0.0 7.877 11.352
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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210 11 -0.0 8.203 10.157
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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211 12 -0.0 5.163 7.653
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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212 13 -0.0 3.093 6.011
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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213 14 -0.0 7.998 11.146
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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214 15 -0.0 7.015 10.108
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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215 16 -0.0 8.795 11.682
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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216 17 -0.0 7.317 10.367
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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217 18 0.0 3.274 4.160
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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218 19 0.0 10.286 12.001
3c8e86318a81 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787
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219 20 0.0 3.566 5.349
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220 Writing output ... done.
2
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221 ]]></help>
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222 <citations>
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223 <citation type="doi">10.1002/jcc.21334</citation>
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224 </citations>
3
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225 </tool>