Mercurial > repos > bgruening > autodock_vina
view docking.xml @ 9:90ea16534012 draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 8ae58ec16b3b6d62b47022745211f11181ad78ea"
| author | bgruening |
|---|---|
| date | Tue, 21 Dec 2021 14:18:33 +0000 |
| parents | 7a871df65202 |
| children |
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<tool id="docking" name="VINA Docking" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>tool to perform protein-ligand docking with Autodock Vina</description> <macros> <token name="@TOOL_VERSION@">1.2.3</token> <token name="@GALAXY_VERSION@">0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">vina</requirement> <requirement type="package" version="3.9">python</requirement> <requirement type="package" version="3.1.1">openbabel</requirement> <requirement type="package" version="20211022">parallel</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if $ligands.is_of_type("sdf") obabel -isdf '$ligands' -O ligand.pdbqt -m -p $ph_value && #else ln -s '$ligands' ligand1.pdbqt && #end if mkdir output && ls ligand*.pdbqt | parallel --will-cite -j \${GALAXY_SLOTS:-1} $'OUTNAME={.}_docked && vina --receptor \'$receptor\' #if $flex: --flex \'$flex\' #end if --ligand {} --out ./\${OUTNAME}.pdbqt --cpu 1 --verbosity 2 #if $config_params.config_params == "vals": --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 #if $config_params.exh != "": --exhaustiveness $config_params.exh #end if #if $config_params.seed.seed == "true": --seed $config_params.seed.seed_value #end if #else if $config_params.config_params == "file": --config $config_params.box #if $config_params.exh != "": --exhaustiveness $config_params.exh #end if #end if #if $settings.scoring: --scoring \'$settings.scoring\' #end if #if $settings.num_modes: --num_modes \'$settings.num_modes\' #end if #if $settings.min_rmsd: --min_rmsd \'$settings.min_rmsd\' #end if #if $settings.energy_range: --energy_range \'$settings.energy_range\' #end if #if $output == "sdf": && python \'$__tool_directory__/convert_pdbqt_to_sdf.py\' ./\${OUTNAME}.pdbqt output/\${OUTNAME}.sdf #end if ' #if $output == "pdbqt": && mv *docked.pdbqt output/ #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. If the 'Flexible side chains' option is chosen, it should contain only the rigid part of the receptor." /> <param type="data" name="ligands" format="sdf,pdbqt" label="Ligands" help="Select ligands (SDF format with multiple ligands or PDBQT format with single ligand)." /> <param type="data" name="flex" format="pdbqt" optional="true" label="Flexible side chains" help="Part of the receptor which should be treated flexibly (PDBQT format)." /> <param name="ph_value" type="float" value="7.4" min="0" max="14" label="Specify pH value for ligand protonation" help="Only used if the input is a SD file."/> <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" optional="true" help="Exhaustiveness of global search (optional - if not specified a default of 8 is used)"/> <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" optional="true" help="Exhaustiveness of global search (optional - if not specified a default of 8 is used, if specified will override any value specified in the config file)"/> </when> </conditional> <section name="settings" title="Optional settings" expanded="true" help="All these settings can also be specified in the config file. Specifying them additionally here overrides the config file."> <param type="select" name="scoring" label="Scoring function" optional="true" help="Function to use for scoring the poses." value="vina"> <option value="vina">vina</option> <option value="ad4">ad4</option> <option value="vinardo">vinardo</option> </param> <param type="integer" name="num_modes" optional="true" label="Number of poses" help="Maximum number of binding poses to generate (default 9)" /> <param type="float" name="min_rmsd" optional="true" label="Minimum RMSD between output poses (default 1)" /> <param type="float" name="energy_range" optional="true" label="Energy range" help="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) (default 3)"/> </section> <param type="select" name="output" label="Output format" help="Format for the docking poses."> <option value="sdf" selected="true">SDF</option> <option value="pdbqt">PDBQT</option> </param> </inputs> <outputs> <collection name="sdf_outputs" type="list" label="Docked ligands for ${on_string}" > <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" /> <filter>output == "sdf"</filter> </collection> <collection name="pdbqt_outputs" type="list" label="Docked structures for ${on_string}" > <discover_datasets pattern="__name_and_ext__" directory="output" visible="false" /> <filter>output == "pdbqt"</filter> </collection> </outputs> <tests> <test> <param name="receptor" value="protein.pdbqt"/> <param name="ligands" value="input_ligands.sdf"/> <param name="box" value="box.txt"/> <output_collection name="sdf_outputs" type="list" count="5"> <!-- linesdiff because there is a time stamp for each of the 9 poses --> <element name="ligand1_docked" file="ligand1_docked.sdf" lines_diff="18"/> <element name="ligand2_docked" file="ligand2_docked.sdf" lines_diff="18"/> <!-- we check only the first 2 --> </output_collection> </test> <test> <param name="receptor" value="protein.pdbqt"/> <param name="ligands" value="input_ligand.pdbqt"/> <param name="box" value="box.txt"/> <output_collection name="sdf_outputs" type="list" count="1"> <element name="ligand1_docked" file="ligand_docked.sdf" lines_diff="18"/> </output_collection> </test> <!-- test with optional params --> <test> <param name="receptor" value="protein.pdbqt"/> <param name="ligands" value="input_ligand.pdbqt"/> <param name="box" value="box.txt"/> <param name="scoring" value="vinardo"/> <param name="energy_range" value="5"/> <param name="num_modes" value="20"/> <param name="min_rmsd" value="0.5"/> <output_collection name="sdf_outputs" type="list" count="1"> <element name="ligand1_docked" file="ligand_docked_opt.sdf" lines_diff="40"/> </output_collection> </test> <!-- TODO - this should be able to use the same output as the previous test but there is inconsistency in how the parameters are handled that needs to be resolved so we use a different output file to compare to. --> <test> <param name="receptor" value="protein.pdbqt"/> <param name="ligands" value="input_ligand.pdbqt"/> <param name="config_params" value="vals"/> <param name="center_x" value="36.454" /> <param name="center_y" value="-43.608000000000004" /> <param name="center_z" value="75.176" /> <param name="size_x" value="18.768" /> <param name="size_y" value="10.205999999999996" /> <param name="size_z" value="15.521999999999991" /> <param name="seed" value="true" /> <param name="seed_value" value="8" /> <param name="exh" value="10" /> <output_collection name="sdf_outputs" type="list" count="1"> <element name="ligand1_docked" file="ligand_params.sdf" lines_diff="18"/> </output_collection> </test> <!-- flexible docking --> <test> <param name="receptor" value="protein_rigid.pdbqt"/> <param name="flex" value="protein_flex.pdbqt"/> <param name="ligands" value="input_ligands.sdf"/> <param name="config_params" value="vals"/> <param name="center_x" value="15.2" /> <param name="center_y" value="53.9" /> <param name="center_z" value="16.9" /> <param name="size_x" value="20" /> <param name="size_y" value="20" /> <param name="size_z" value="20" /> <param name="seed" value="true" /> <param name="seed_value" value="8" /> <param name="exh" value="10" /> <param name="output" value="pdbqt"/> <output_collection name="pdbqt_outputs" type="list" count="5"> <element name="ligand1_docked" file="ligand1_docked_flex.pdbqt"/> <element name="ligand2_docked" file="ligand2_docked_flex.pdbqt"/> <!-- we check only the first 2 --> </output_collection> </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 describing the receptor (in the pdbqt format) and ligands (in SDF of PDBQT format) respectively. These files are produced by the receptor and ligand preparation tools. If using PDBQT format for the ligands only a single ligand can be specified. If using SDF you can include multiple ligands and those ligands are converted to individual PDBQT format files using openbabel as the first step of tool execution. You can specify the pH for protonation by openbabel VINA will dock each of the ligands in the SDF file sequentially. If there are a large number of ligands then first split them into a collection of smaller files e.g. using the splitter tool. This allows each split chunk of molecules to be docked as a separate task. The optimal size of the chunk will depend on the number of ligands and the capacity of the execution environment. 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. ----- .. class:: infomark **Outputs** SDF files are produced as output. There is one file for each ligand in the input. Each entry in the file is a docked pose for that ligand. The binding affinity scores are 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 ]]></help> <citations> <citation type="doi">10.1002/jcc.21334</citation> <citation type="doi">10.1021/acs.jcim.1c00203</citation> </citations> </tool>