Mercurial > repos > bgruening > autodock_vina
diff prepare_receptor.xml @ 0:8bc060fcf41a 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 16:48:38 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_receptor.xml Fri Jun 03 16:48:38 2016 -0400 @@ -0,0 +1,92 @@ +<tool id="prepare_receptor" name="Prepare receptor" version="0.1.0"> + <description>- Tool to prepare receptor for Autodock Vina</description> + <requirements> + <requirement type="package" version="1.5.6">mgltools</requirement> + </requirements> + <stdio> + <exit_code range="1" /> + </stdio> + <command><![CDATA[ + ln -s $receptor ./receptor.pdb && prepare_receptor4.py -r ./receptor.pdb -o "$file_output" -v -U nphs_lps -A hydrogens + ]]></command> + <inputs> + <param type="data" name="receptor" format="pdb" help="Select a pdb file." /> + </inputs> + <outputs> + <data name="file_output" format="pdbqt" label="#echo os.path.splitext (str($receptor.name))[0]#.pdbqt" /> + </outputs> + <tests> + <test> + <param name="receptor" value="3u1i_for_DM.pdb"/> + <output name="file_output" file="3u1i_for_DM.pdbqt"/> + </test> + </tests> + <help><![CDATA[ + ** What it does? ** + + This tool uses the MGLTools programming packages to convert a pdb molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking. + + ** input ** + + It's required at least one pdb dataset in history, what is informed in ligand field, for use the tool. The pdb molecule file looks like the following example: + + ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 C + ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 O + ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 C + ATOM 4 1HH3 ACE A 49 6.747 -5.942 7.510 1.00 0.00 H + ATOM 5 2HH3 ACE A 49 5.492 -5.996 8.739 1.00 0.00 H + ATOM 6 3HH3 ACE A 49 5.518 -4.686 7.568 1.00 0.00 H + ATOM 7 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 N + ATOM 8 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 C + ATOM 9 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 C + ATOM 10 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 O + ATOM 11 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 C + ATOM 12 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 C + ATOM 13 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 O + ATOM 14 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 O1- + ATOM 15 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 N + ATOM 16 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 C + ATOM 17 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 C + ATOM 18 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 O + ATOM 19 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 C + ATOM 20 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 C + ATOM 21 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 C + ATOM 22 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 C + ATOM 23 N THR A 52 10.527 -5.061 16.117 1.00 55.68 N + ATOM 24 CA THR A 52 10.525 -4.607 17.507 1.00 55.35 C + ATOM 25 C THR A 52 11.729 -5.165 18.262 1.00 53.35 C + ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 O + ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 C + + ** output ** + + The output is a pdbqt molecule file converted from a pdb molecule file. The pdbqt molecule file looks like the following example: + + ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 0.214 C + ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 -0.274 OA + ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 0.117 C + ATOM 4 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 -0.348 N + ATOM 5 HN ASP A 50 6.246 -5.360 11.009 1.00 0.00 0.163 HD + ATOM 6 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 0.186 C + ATOM 7 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 0.241 C + ATOM 8 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 -0.271 OA + ATOM 9 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 0.147 C + ATOM 10 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 0.175 C + ATOM 11 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 -0.648 OA + ATOM 12 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 -0.648 OA + ATOM 13 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 -0.346 N + ATOM 14 HN LEU A 51 10.177 -3.384 12.264 1.00 0.00 0.163 HD + ATOM 15 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 0.177 C + ATOM 16 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 0.241 C + ATOM 17 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 -0.271 OA + ATOM 18 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 0.038 C + ATOM 19 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 -0.020 C + ATOM 20 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 0.009 C + ATOM 21 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 0.009 C + ATOM 22 N THR A 52 10.527 -5.061 16.117 1.00 55.68 -0.344 N + ATOM 23 HN THR A 52 10.475 -6.064 15.941 1.00 0.00 0.163 HD + ]]></help> + <citations> + <citation type="doi">10.1002/jcc.21334</citation> + </citations> +</tool> \ No newline at end of file