Mercurial > repos > bgruening > autodock_vina
view docking.xml @ 5:c410ffcabf9d draft
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 |
line wrap: on
line source
<tool id="docking" name="Docking" version="0.2.0"> <description>tool to perform protein-ligand docking with Autodock Vina</description> <requirements> <requirement type="package" version="1.1.2">autodock-vina</requirement> </requirements> <stdio> <exit_code range="1" /> </stdio> <command><![CDATA[ #if $config_params.config_params == 'vals': vina --center_x '$config_params.center_x' --center_y '$config_params.center_y' --center_z '$config_params.center_z' --size_x '$config_params.size_x' --size_y '$config_params.size_y' --size_z '$config_params.size_z' --exhaustiveness '$config_params.exh' --num_modes 9999 --energy_range 9999 --receptor '$receptor' --ligand '$ligand' --out '$file_output1' --log '$file_output2' --cpu \${GALAXY_SLOTS:-1} #if $config_params.seed.seed == 'true': --seed '$config_params.seed.seed_value' #end if #end if #if $config_params.config_params == 'file': vina --config '$config_params.box' --receptor '$receptor' --ligand '$ligand' --out '$file_output1' --log '$file_output2' --cpu \${GALAXY_SLOTS:-1} #end if ]]></command> <inputs> <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool." /> <param type="data" name="ligand" format="pdbqt" label="Ligand" help="Select a ligand (PDBQT format). This can be prepared using the ligand preparation tool." /> <conditional name="config_params"> <param name="config_params" type="select" label="Specify parameters"> <option value="file">Upload a config file to specify parameters</option> <option value="vals">Specify values directly</option> </param> <when value="vals"> <param type="float" name="center_x" label="x coordinate" help="x coordinate of the binding site." value="0"/> <param type="float" name="center_y" label="y coordinate" help="y coordinate of the binding site." value="0"/> <param type="float" name="center_z" label="z coordinate" help="z coordinate of the binding site." value="0"/> <param type="float" name="size_x" label="x size" help="Length of the binding site (Å) in the x direction." value="0"/> <param type="float" name="size_y" label="y size" help="Length of the binding site (Å) in the y direction." value="0"/> <param type="float" name="size_z" label="z size" help="Length of the binding site (Å) in the z direction." value="0"/> <param type="integer" name="exh" label="Exhaustiveness" help="The number of poses to return from the docking job" value="10"/> <conditional name="seed"> <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/> <when value="true"> <param type="integer" name="seed_value" label="Random seed" help="Choose a seed value" value="1"/> </when> <when value="false"/> </conditional> </when> <when value="file"> <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" /> </when> </conditional> </inputs> <outputs> <data name="file_output1" format="pdbqt" /> <data name="file_output2" format="txt" /> </outputs> <tests> <test> <param name="receptor" value="3u1i_for_DM.pdbqt"/> <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/> <param name="config_params" value="vals"/> <param name="center_x" value="70.92" /> <param name="center_y" value="70.57" /> <param name="center_z" value="36.86" /> <param name="size_x" value="20.00" /> <param name="size_y" value="18.40" /> <param name="size_z" value="23.60" /> <param name="seed" value="true" /> <param name="seed_value" value="1" /> <param name="exhaustivenesss" value="10" /> <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/> <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/> </test> <test> <param name="receptor" value="3u1i_for_DM.pdbqt"/> <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/> <param name="config_params" value="file"/> <param name="box" value="config_complexo_dm.txt"/> <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/> <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/> </test> </tests> <help><![CDATA[ This tool performs protein-ligand docking using the Autodock Vina program. **Inputs** 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. 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. **Outputs** 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:: MODEL 1 REMARK VINA RESULT: -0.0 0.000 0.000 REMARK 9 active torsions: REMARK status: ('A' for Active; 'I' for Inactive) REMARK 1 A between atoms: C_2 and O_3 REMARK 2 A between atoms: C_2 and C_14 REMARK 3 A between atoms: O_3 and C_4 REMARK 4 A between atoms: C_4 and C_5 REMARK 5 A between atoms: C_6 and C_8 REMARK 6 A between atoms: C_8 and C_9 REMARK 7 A between atoms: C_9 and C_10 REMARK 8 A between atoms: C_16 and O_17 REMARK 9 A between atoms: C_19 and O_20 ROOT ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C ENDROOT BRANCH 2 3 ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA BRANCH 3 4 ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C BRANCH 4 5 ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C BRANCH 6 8 ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C BRANCH 8 9 ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C BRANCH 9 10 ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C ATOM 12 C LIG d 1 75.833 75.151 40.104 0.00 0.00 0.042 C ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C ENDBRANCH 9 10 ENDBRANCH 8 9 ENDBRANCH 6 8 ENDBRANCH 4 5 ENDBRANCH 3 4 ENDBRANCH 2 3 BRANCH 2 14 ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A BRANCH 16 20 ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD ENDBRANCH 16 20 BRANCH 17 22 ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD ENDBRANCH 17 22 ENDBRANCH 2 14 TORSDOF 9 ENDMDL The second output is a log file containing the binding affinity scores, like the following:: ----------------------------------------------------------------- If you used AutoDock Vina in your work, please cite: O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461 DOI 10.1002/jcc.21334 Please see http://vina.scripps.edu for more information. ------------------------------------------------------------------ Reading input ... done. Setting up the scoring function ... done. Analyzing the binding site ... done. Using random seed: 1899908181 Performing search ... done. Refining results ... done. mode | affinity | dist from best mode | (kcal/mol) | rmsd l.b.| rmsd u.b. -----+------------+----------+---------- 1 -0.0 0.000 0.000 2 -0.0 2.046 2.443 3 -0.0 5.896 7.949 4 -0.0 2.518 3.100 5 -0.0 2.417 4.527 6 -0.0 5.686 7.689 7 -0.0 2.828 4.792 8 -0.0 5.547 7.086 9 -0.0 7.388 9.966 10 -0.0 7.877 11.352 11 -0.0 8.203 10.157 12 -0.0 5.163 7.653 13 -0.0 3.093 6.011 14 -0.0 7.998 11.146 15 -0.0 7.015 10.108 16 -0.0 8.795 11.682 17 -0.0 7.317 10.367 18 0.0 3.274 4.160 19 0.0 10.286 12.001 20 0.0 3.566 5.349 Writing output ... done. ]]></help> <citations> <citation type="doi">10.1002/jcc.21334</citation> </citations> </tool>