Mercurial > repos > bgruening > autodock_vina
diff docking.xml @ 6:0ae768a0e5c0 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
| author | bgruening |
|---|---|
| date | Wed, 19 Jun 2019 06:43:41 -0400 |
| parents | c410ffcabf9d |
| children | 7b2f205b3f68 |
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--- a/docking.xml Tue May 07 13:31:43 2019 -0400 +++ b/docking.xml Wed Jun 19 06:43:41 2019 -0400 @@ -1,7 +1,8 @@ -<tool id="docking" name="Docking" version="0.2.0"> +<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" /> @@ -20,8 +21,8 @@ --energy_range 9999 --receptor '$receptor' --ligand '$ligand' - --out '$file_output1' - --log '$file_output2' + --out './output1.dat' + --log './output2.dat' --cpu \${GALAXY_SLOTS:-1} #if $config_params.seed.seed == 'true': --seed '$config_params.seed.seed_value' @@ -32,10 +33,18 @@ --config '$config_params.box' --receptor '$receptor' --ligand '$ligand' - --out '$file_output1' - --log '$file_output2' + --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> @@ -65,15 +74,27 @@ </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" /> - <data name="file_output2" format="txt" /> + <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> + <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"/> @@ -85,32 +106,140 @@ <param name="size_z" value="23.60" /> <param name="seed" value="true" /> <param name="seed_value" value="1" /> - <param name="exhaustivenesss" value="10" /> + <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> + <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** -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:: +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