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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit e1bdd1a326072b9c6a318863aabcba2d9918f787 |
modified:
docking.xml |
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diff -r 65ffed035ca8 -r 3c8e86318a81 docking.xml --- a/docking.xml Sat Jun 04 12:36:59 2016 -0400 +++ b/docking.xml Mon Feb 12 04:23:13 2018 -0500 |
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b"@@ -28,142 +28,142 @@\n </test>\n </tests>\n <help><![CDATA[\n- ** What it does? **\n+**What it does?**\n \n- This tool performs molecular docking with Autodock Vina program.\n+This tool performs molecular docking with Autodock Vina program.\n \n- ** inputs **\n+**Inputs**\n \n- 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:\n+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::\n \n- size_x = 20.00\n- size_y = 18.40\n- size_z = 23.60\n- center_x = 70.92\n- center_y = 70.57\n- center_z = 36.86\n- num_modes = 9999\n- energy_range = 9999\n- exhaustiveness = 10\n- cpu = 4\n- seed = 1\n+ size_x = 20.00\n+ size_y = 18.40\n+ size_z = 23.60\n+ center_x = 70.92\n+ center_y = 70.57\n+ center_z = 36.86\n+ num_modes = 9999\n+ energy_range = 9999\n+ exhaustiveness = 10\n+ cpu = 4\n+ seed = 1\n \n- Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site. \n- The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.\n+Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site. \n+The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.\n \n- The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.\n- The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.\n+The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.\n+The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.\n \n- ** outputs **\n+**Outputs**\n \n- 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:\n+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::\n \n- MODEL 1\n- REMARK VINA RESULT: -0.0 0.000 0.000\n- REMARK 9 active torsions:\n- REMARK status: ('A' for Active; 'I' for Inactive)\n- REMARK 1 A between atoms: C_2 and O_3 \n- REMARK 2 A between atoms: C_2 and C_14 \n- REMARK 3 A between atoms: O_3 and C_4 \n- REMARK 4 A between atoms: C_4 and C_5 \n- REMARK 5 A between atoms: C_6 and C_8 \n- REMARK 6 A between atoms: C_8 and C_9 \n- REMARK 7 A between atoms: C_9 and C_10 \n- REMARK 8 A between atoms: C_16 and O_17 \n- REMARK 9 A between atoms: C_19 and O_20 \n- ROOT\n- ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA\n- ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C \n- ENDROOT\n- BRANCH 2 3\n- ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA\n- BRANCH 3 4\n- ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C \n- BRANCH 4 5\n- ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C \n- ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C \n- ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C \n- BRANCH 6 8\n- ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C \n- BRANCH 8 9\n- ATOM 9 C LIG d 1 74.184 "..b' \n- DOI 10.1002/jcc.21334 \n- \n- Please see http://vina.scripps.edu for more information. \n- ------------------------------------------------------------------\n+ -----------------------------------------------------------------\n+ If you used AutoDock Vina in your work, please cite: \n+ \n+ O. Trott, A. J. Olson, \n+ AutoDock Vina: improving the speed and accuracy of docking \n+ with a new scoring function, efficient optimization and \n+ multithreading, Journal of Computational Chemistry 31 (2010) \n+ 455-461 \n+ \n+ DOI 10.1002/jcc.21334 \n+ \n+ Please see http://vina.scripps.edu for more information. \n+ ------------------------------------------------------------------\n \n- Reading input ... done.\n- Setting up the scoring function ... done.\n- Analyzing the binding site ... done.\n- Using random seed: 1899908181\n- Performing search ... done.\n- Refining results ... done.\n+ Reading input ... done.\n+ Setting up the scoring function ... done.\n+ Analyzing the binding site ... done.\n+ Using random seed: 1899908181\n+ Performing search ... done.\n+ Refining results ... done.\n \n- mode | affinity | dist from best mode\n- | (kcal/mol) | rmsd l.b.| rmsd u.b.\n- -----+------------+----------+----------\n- 1 -0.0 0.000 0.000\n- 2 -0.0 2.046 2.443\n- 3 -0.0 5.896 7.949\n- 4 -0.0 2.518 3.100\n- 5 -0.0 2.417 4.527\n- 6 -0.0 5.686 7.689\n- 7 -0.0 2.828 4.792\n- 8 -0.0 5.547 7.086\n- 9 -0.0 7.388 9.966\n- 10 -0.0 7.877 11.352\n- 11 -0.0 8.203 10.157\n- 12 -0.0 5.163 7.653\n- 13 -0.0 3.093 6.011\n- 14 -0.0 7.998 11.146\n- 15 -0.0 7.015 10.108\n- 16 -0.0 8.795 11.682\n- 17 -0.0 7.317 10.367\n- 18 0.0 3.274 4.160\n- 19 0.0 10.286 12.001\n- 20 0.0 3.566 5.349\n- Writing output ... done.\n+ mode | affinity | dist from best mode\n+ | (kcal/mol) | rmsd l.b.| rmsd u.b.\n+ -----+------------+----------+----------\n+ 1 -0.0 0.000 0.000\n+ 2 -0.0 2.046 2.443\n+ 3 -0.0 5.896 7.949\n+ 4 -0.0 2.518 3.100\n+ 5 -0.0 2.417 4.527\n+ 6 -0.0 5.686 7.689\n+ 7 -0.0 2.828 4.792\n+ 8 -0.0 5.547 7.086\n+ 9 -0.0 7.388 9.966\n+ 10 -0.0 7.877 11.352\n+ 11 -0.0 8.203 10.157\n+ 12 -0.0 5.163 7.653\n+ 13 -0.0 3.093 6.011\n+ 14 -0.0 7.998 11.146\n+ 15 -0.0 7.015 10.108\n+ 16 -0.0 8.795 11.682\n+ 17 -0.0 7.317 10.367\n+ 18 0.0 3.274 4.160\n+ 19 0.0 10.286 12.001\n+ 20 0.0 3.566 5.349\n+ Writing output ... done.\n ]]></help>\n <citations>\n <citation type="doi">10.1002/jcc.21334</citation>\n' |