Mercurial > repos > bgruening > autodock_vina
annotate docking.xml @ 2:18dec59e29ae draft
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
| author | bgruening |
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| date | Fri, 03 Jun 2016 16:49:49 -0400 |
| parents | |
| children | 65ffed035ca8 |
| rev | line source |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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1 <tool id="docking" name="Docking" version="0.1.0"> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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2 <description>- Tool to running molecular docking with Autodock Vina</description> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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3 <requirements> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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4 <requirement type="package" version="1.1.2">autodock-vina</requirement> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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5 </requirements> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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6 <stdio> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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7 <exit_code range="1" /> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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8 </stdio> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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9 <command><![CDATA[ |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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10 vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2" |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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11 ]]></command> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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12 <inputs> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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13 <param type="data" name="box" format="txt" label="Box configuration: " help="Select a text file with the box configurations" /> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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14 <param type="data" name="receptor" format="pdbqt" label="Receptor: " help="Select a receptor pdbqt file" /> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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15 <param type="data" name="ligand" format="pdbqt" label="Ligand: " help="Select a ligand pdbqt file" /> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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16 </inputs> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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17 <outputs> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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18 <data name="file_output1" format="pdbqt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.pdbqt" /> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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19 <data name="file_output2" format="txt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.log" /> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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20 </outputs> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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21 <tests> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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22 <test> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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23 <param name="box" value="config_complexo_dm.txt"/> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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24 <param name="receptor" value="3u1i_for_DM.pdbqt"/> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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25 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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26 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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27 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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28 </test> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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29 </tests> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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30 <help><![CDATA[ |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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31 ** What it does? ** |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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32 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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33 This tool performs molecular docking with Autodock Vina program. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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34 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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35 ** inputs ** |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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36 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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37 Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example: |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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38 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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39 size_x = 20.00 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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40 size_y = 18.40 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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41 size_z = 23.60 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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42 center_x = 70.92 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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43 center_y = 70.57 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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44 center_z = 36.86 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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45 num_modes = 9999 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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46 energy_range = 9999 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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47 exhaustiveness = 10 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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48 cpu = 4 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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49 seed = 1 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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50 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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51 Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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52 The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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53 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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54 The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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55 The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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56 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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57 ** outputs ** |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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58 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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59 Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like the following example: |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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60 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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61 MODEL 1 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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62 REMARK VINA RESULT: -0.0 0.000 0.000 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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63 REMARK 9 active torsions: |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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64 REMARK status: ('A' for Active; 'I' for Inactive) |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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65 REMARK 1 A between atoms: C_2 and O_3 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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66 REMARK 2 A between atoms: C_2 and C_14 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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67 REMARK 3 A between atoms: O_3 and C_4 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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68 REMARK 4 A between atoms: C_4 and C_5 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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69 REMARK 5 A between atoms: C_6 and C_8 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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70 REMARK 6 A between atoms: C_8 and C_9 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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71 REMARK 7 A between atoms: C_9 and C_10 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
72 REMARK 8 A between atoms: C_16 and O_17 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
73 REMARK 9 A between atoms: C_19 and O_20 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
74 ROOT |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
75 ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
76 ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
77 ENDROOT |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
78 BRANCH 2 3 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
79 ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
80 BRANCH 3 4 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
81 ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
82 BRANCH 4 5 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
83 ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
84 ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
85 ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
86 BRANCH 6 8 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
87 ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
88 BRANCH 8 9 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
89 ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
90 BRANCH 9 10 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
91 ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
92 ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
93 ATOM 12 C LIG d 1 75.833 75.151 40.104 0.00 0.00 0.042 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
94 ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
95 ENDBRANCH 9 10 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
96 ENDBRANCH 8 9 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
97 ENDBRANCH 6 8 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
98 ENDBRANCH 4 5 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
99 ENDBRANCH 3 4 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
100 ENDBRANCH 2 3 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
101 BRANCH 2 14 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
102 ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
103 ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
104 ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
105 ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
106 ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
107 ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
108 BRANCH 16 20 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
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|
109 ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
110 ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
111 ENDBRANCH 16 20 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
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|
112 BRANCH 17 22 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
113 ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
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|
114 ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
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|
115 ENDBRANCH 17 22 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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116 ENDBRANCH 2 14 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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117 TORSDOF 9 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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118 ENDMDL |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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119 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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120 The last is a log file with the binding affinity scores, this file looks like the following example: |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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121 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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122 ----------------------------------------------------------------- |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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123 If you used AutoDock Vina in your work, please cite: |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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124 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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125 O. Trott, A. J. Olson, |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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126 AutoDock Vina: improving the speed and accuracy of docking |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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127 with a new scoring function, efficient optimization and |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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|
128 multithreading, Journal of Computational Chemistry 31 (2010) |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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129 455-461 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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130 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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131 DOI 10.1002/jcc.21334 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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132 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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133 Please see http://vina.scripps.edu for more information. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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134 ------------------------------------------------------------------ |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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135 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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136 Reading input ... done. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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137 Setting up the scoring function ... done. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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138 Analyzing the binding site ... done. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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139 Using random seed: 1899908181 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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140 Performing search ... done. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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141 Refining results ... done. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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142 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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143 mode | affinity | dist from best mode |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
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changeset
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144 | (kcal/mol) | rmsd l.b.| rmsd u.b. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
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145 -----+------------+----------+---------- |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
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146 1 -0.0 0.000 0.000 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
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147 2 -0.0 2.046 2.443 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
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148 3 -0.0 5.896 7.949 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
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149 4 -0.0 2.518 3.100 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
150 5 -0.0 2.417 4.527 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
151 6 -0.0 5.686 7.689 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
152 7 -0.0 2.828 4.792 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
153 8 -0.0 5.547 7.086 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
154 9 -0.0 7.388 9.966 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
155 10 -0.0 7.877 11.352 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
156 11 -0.0 8.203 10.157 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
157 12 -0.0 5.163 7.653 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
158 13 -0.0 3.093 6.011 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
159 14 -0.0 7.998 11.146 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
160 15 -0.0 7.015 10.108 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
161 16 -0.0 8.795 11.682 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
162 17 -0.0 7.317 10.367 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
163 18 0.0 3.274 4.160 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
164 19 0.0 10.286 12.001 |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff
changeset
|
165 20 0.0 3.566 5.349 |
|
18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
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166 Writing output ... done. |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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167 ]]></help> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
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168 <citations> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
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169 <citation type="doi">10.1002/jcc.21334</citation> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
bgruening
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170 </citations> |
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18dec59e29ae
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
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171 </tool> |