Mercurial > repos > bgruening > autodock_vina
diff docking.xml @ 2:18dec59e29ae draft
planemo upload for repository https://github.com/leobiscassi/galaxytools/tree/autodock_vina_tools/chemicaltoolbox/autodock_vina commit a349cb4673231f12344e418513a08691925565d9
| author | bgruening |
|---|---|
| date | Fri, 03 Jun 2016 16:49:49 -0400 |
| parents | |
| children | 65ffed035ca8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docking.xml Fri Jun 03 16:49:49 2016 -0400 @@ -0,0 +1,171 @@ +<tool id="docking" name="Docking" version="0.1.0"> + <description>- Tool to running molecular 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[ + vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2" + ]]></command> + <inputs> + <param type="data" name="box" format="txt" label="Box configuration: " help="Select a text file with the box configurations" /> + <param type="data" name="receptor" format="pdbqt" label="Receptor: " help="Select a receptor pdbqt file" /> + <param type="data" name="ligand" format="pdbqt" label="Ligand: " help="Select a ligand pdbqt file" /> + </inputs> + <outputs> + <data name="file_output1" format="pdbqt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.pdbqt" /> + <data name="file_output2" format="txt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.log" /> + </outputs> + <tests> + <test> + <param name="box" value="config_complexo_dm.txt"/> + <param name="receptor" value="3u1i_for_DM.pdbqt"/> + <param name="ligand" value="NuBBE_1_obabel_3D.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> + </tests> + <help><![CDATA[ + ** What it does? ** + + This tool performs molecular docking with Autodock Vina program. + + ** inputs ** + + Three inputs are required for use this tools. The first is a text file with the box configurations, this file looks like the following example: + + size_x = 20.00 + size_y = 18.40 + size_z = 23.60 + center_x = 70.92 + center_y = 70.57 + center_z = 36.86 + num_modes = 9999 + energy_range = 9999 + exhaustiveness = 10 + cpu = 4 + seed = 1 + + Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site. + The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm. + + The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool. + The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool. + + ** outputs ** + + Two outputs are generated by this tool. The first is a pdbqt file with the molecule structure resulting of the molecular docking, this file looks like 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 last is a log file with the binding affinity scores, this file looks like the following example: + + ----------------------------------------------------------------- + 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> \ No newline at end of file