| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.2.3+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/1.1.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.3.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.2.1 |
| toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.2.0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.1.0 |
| docking |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| vina | 1.2.3 | package |
| python | 3.9 | package |
| openbabel | 3.1.1 | package |
| parallel | 20211022 | package |
| Additional information about this tool |
#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
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
receptor: protein.pdbqt ligands: input_ligands.sdf config_params|box: box.txt |
protein.pdbqt input_ligands.sdf box.txt |
|
| Test-2 |
receptor: protein.pdbqt ligands: input_ligand.pdbqt config_params|box: box.txt |
protein.pdbqt input_ligand.pdbqt box.txt |
|
| Test-3 |
receptor: protein.pdbqt ligands: input_ligand.pdbqt config_params|box: box.txt settings|scoring: vinardo settings|num_modes: 20 settings|min_rmsd: 0.5 settings|energy_range: 5 |
protein.pdbqt input_ligand.pdbqt box.txt |
|
| Test-4 |
receptor: protein.pdbqt ligands: input_ligand.pdbqt config_params|center_x: 36.454 config_params|center_y: -43.608000000000004 config_params|center_z: 75.176 config_params|size_x: 18.768 config_params|size_y: 10.205999999999996 config_params|size_z: 15.521999999999991 config_params|exh: 10 config_params|seed|seed_value: 8 config_params|seed|seed: True config_params|config_params: vals |
protein.pdbqt input_ligand.pdbqt |
|
| Test-5 |
receptor: protein_rigid.pdbqt ligands: input_ligands.sdf flex: protein_flex.pdbqt config_params|center_x: 15.2 config_params|center_y: 53.9 config_params|center_z: 16.9 config_params|size_x: 20 config_params|size_y: 20 config_params|size_z: 20 config_params|exh: 10 config_params|seed|seed_value: 8 config_params|seed|seed: True config_params|config_params: vals output: pdbqt |
protein_rigid.pdbqt input_ligands.sdf protein_flex.pdbqt |