Mercurial > repos > bgruening > autodock_vina
view docking.xml @ 6:0ae768a0e5c0 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
author | bgruening |
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date | Wed, 19 Jun 2019 06:43:41 -0400 |
parents | c410ffcabf9d |
children | 7b2f205b3f68 |
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<tool id="docking" name="Docking" version="0.2.1"> <description>tool to perform protein-ligand docking with Autodock Vina</description> <requirements> <requirement type="package" version="1.1.2">autodock-vina</requirement> <requirement type="package" version="2.4.1">openbabel</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 './output1.dat' --log './output2.dat' --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 './output1.dat' --log './output2.dat' --cpu \${GALAXY_SLOTS:-1} #if $config_params.exh != "": --exhaustiveness $config_params.exh #end if #end if #if $output_format == 'sdf': && python '$__tool_directory__/convert_pdbqt_to_sdf.py' './output1.dat' '$sdf_output' #else && mv ./output1.dat '$file_output1' && mv ./output2.dat '$file_output2' #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" /> <param type="integer" name="exh" label="Exhaustiveness" help="The number of poses to return from the docking job (optional, will override any value specified in the config file)" optional="true"/> </when> </conditional> <param type="select" name="output_format" label="Output format" help="Select a format for the output files"> <option value="pdbqt" selected="true">PDBQT (and separate log file with binding scores)</option> <option value="sdf">SDF</option> </param> </inputs> <outputs> <data name="file_output1" format="pdbqt"> <filter>output_format == 'pdbqt'</filter> </data> <data name="file_output2" format="txt"> <filter>output_format == 'pdbqt'</filter> </data> <data name="sdf_output" format="sdf"> <filter>output_format == 'sdf'</filter> </data> </outputs> <tests> <test expect_num_outputs="2"> <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="exhaustiveness" value="10" /> <param name="output_format" value="pdbqt" /> <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 expect_num_outputs="2"> <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"/> <param name="output_format" value="pdbqt" /> <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 expect_num_outputs="1"> <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"/> <param name="output_format" value="sdf" /> <output name="sdf_output" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.sdf" lines_diff="40"/> </test> </tests> <help><![CDATA[ This tool performs protein-ligand docking using the Autodock Vina program. ----- .. class:: infomark **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. A format for the output should also be selected: the available options are PDBQT or SDF. ----- .. class:: infomark **Outputs** Either PDBQT or SDF may be selected as output. **Option 1: SDF** An SDF file is produced as output. The binding affinity scores are also contained within the SDF file.:: OpenBabel06171915303D 23 23 0 0 0 0 0 0 0 0999 V2000 66.9030 73.3450 36.0040 O 0 0 0 0 0 0 0 0 0 0 0 0 66.8190 73.2170 37.2120 C 0 0 0 0 0 0 0 0 0 0 0 0 66.0490 72.3370 37.8940 O 0 0 0 0 0 0 0 0 0 0 0 0 66.2290 70.9500 37.5970 C 0 0 0 0 0 0 0 0 0 0 0 0 67.2070 70.4140 38.6010 C 0 0 0 0 0 0 0 0 0 0 0 0 68.5140 70.1440 38.3980 C 0 0 0 0 0 0 0 0 0 0 0 0 69.2150 70.3400 37.0800 C 0 0 0 0 0 0 0 0 0 0 0 0 69.3810 69.5970 39.5210 C 0 0 0 0 0 0 0 0 0 0 0 0 68.7730 69.8280 40.9100 C 0 0 0 0 0 0 0 0 0 0 0 0 69.3750 71.0120 41.6220 C 0 0 0 0 0 0 0 0 0 0 0 0 68.7550 72.1570 41.9760 C 0 0 0 0 0 0 0 0 0 0 0 0 67.3280 72.4970 41.6430 C 0 0 0 0 0 0 0 0 0 0 0 0 69.4770 73.2270 42.7560 C 0 0 0 0 0 0 0 0 0 0 0 0 67.5570 74.0540 38.1920 C 0 0 0 0 0 0 0 0 0 0 0 0 66.9010 75.0480 38.9340 C 0 0 0 0 0 0 0 0 0 0 0 0 67.6300 75.8170 39.8300 C 0 0 0 0 0 0 0 0 0 0 0 0 68.9950 75.5990 39.9980 C 0 0 0 0 0 0 0 0 0 0 0 0 69.6510 74.6060 39.2850 C 0 0 0 0 0 0 0 0 0 0 0 0 68.9300 73.8240 38.3800 C 0 0 0 0 0 0 0 0 0 0 0 0 67.0450 76.8040 40.5760 O 0 0 0 0 0 0 0 0 0 0 0 0 67.5560 77.4980 40.9760 H 0 0 0 0 0 0 0 0 0 0 0 0 69.7010 76.3670 40.8780 O 0 0 0 0 0 0 0 0 0 0 0 0 69.2520 76.7930 41.5990 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 2 14 1 0 0 0 0 4 3 1 0 0 0 0 4 5 1 0 0 0 0 6 5 2 0 0 0 0 6 8 1 0 0 0 0 7 6 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 13 1 0 0 0 0 12 11 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 20 1 0 0 0 0 17 22 1 0 0 0 0 18 17 2 0 0 0 0 19 18 1 0 0 0 0 20 21 1 0 0 0 0 22 23 1 0 0 0 0 M END > <MODEL> 1 > <REMARK> VINA RESULT: 0.0 0.000 0.000 9 active torsions: status: ('A' for Active; 'I' for Inactive) 1 A between atoms: C_2 and O_3 2 A between atoms: C_2 and C_14 3 A between atoms: O_3 and C_4 4 A between atoms: C_4 and C_5 5 A between atoms: C_6 and C_8 6 A between atoms: C_8 and C_9 7 A between atoms: C_9 and C_10 8 A between atoms: C_16 and O_17 9 A between atoms: C_19 and O_20 > <TORSDO> F 9 > <SCORE> 0.0 > <RMSD_LB> 0.000 > <RMSD_UB> 0.000 **Option 2: PDBQT** Two outputs are generated if PDBQT output is selected. 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>