Mercurial > repos > bgruening > autodock_vina

comparison prepare_receptor.xml @ 0:8bc060fcf41a draft

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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
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-1:000000000000 0:8bc060fcf41a
1 <tool id="prepare_receptor" name="Prepare receptor" version="0.1.0">
2 <description>- Tool to prepare receptor for Autodock Vina</description>
3 <requirements>
4 <requirement type="package" version="1.5.6">mgltools</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1" />
8 </stdio>
9 <command><![CDATA[
10 ln -s $receptor ./receptor.pdb && prepare_receptor4.py -r ./receptor.pdb -o "$file_output" -v -U nphs_lps -A hydrogens
11 ]]></command>
12 <inputs>
13 <param type="data" name="receptor" format="pdb" help="Select a pdb file." />
14 </inputs>
15 <outputs>
16 <data name="file_output" format="pdbqt" label="#echo os.path.splitext (str($receptor.name))[0]#.pdbqt" />
17 </outputs>
18 <tests>
19 <test>
20 <param name="receptor" value="3u1i_for_DM.pdb"/>
21 <output name="file_output" file="3u1i_for_DM.pdbqt"/>
22 </test>
23 </tests>
24 <help><![CDATA[
25 ** What it does? **
26
27 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.
28
29 ** input **
30
31 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:
32
33 ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 C
34 ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 O
35 ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 C
36 ATOM 4 1HH3 ACE A 49 6.747 -5.942 7.510 1.00 0.00 H
37 ATOM 5 2HH3 ACE A 49 5.492 -5.996 8.739 1.00 0.00 H
38 ATOM 6 3HH3 ACE A 49 5.518 -4.686 7.568 1.00 0.00 H
39 ATOM 7 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 N
40 ATOM 8 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 C
41 ATOM 9 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 C
42 ATOM 10 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 O
43 ATOM 11 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 C
44 ATOM 12 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 C
45 ATOM 13 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 O
46 ATOM 14 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 O1-
47 ATOM 15 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 N
48 ATOM 16 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 C
49 ATOM 17 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 C
50 ATOM 18 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 O
51 ATOM 19 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 C
52 ATOM 20 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 C
53 ATOM 21 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 C
54 ATOM 22 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 C
55 ATOM 23 N THR A 52 10.527 -5.061 16.117 1.00 55.68 N
56 ATOM 24 CA THR A 52 10.525 -4.607 17.507 1.00 55.35 C
57 ATOM 25 C THR A 52 11.729 -5.165 18.262 1.00 53.35 C
58 ATOM 26 O THR A 52 12.413 -6.076 17.786 1.00 52.40 O
59 ATOM 27 CB THR A 52 9.185 -4.964 18.195 1.00 56.95 C
60
61 ** output **
62
63 The output is a pdbqt molecule file converted from a pdb molecule file. The pdbqt molecule file looks like the following example:
64
65 ATOM 1 C ACE A 49 7.007 -4.529 9.096 1.00 0.00 0.214 C
66 ATOM 2 O ACE A 49 7.822 -3.710 8.650 1.00 0.00 -0.274 OA
67 ATOM 3 CH3 ACE A 49 6.132 -5.342 8.166 1.00 0.00 0.117 C
68 ATOM 4 N ASP A 50 6.886 -4.713 10.549 1.00 65.94 -0.348 N
69 ATOM 5 HN ASP A 50 6.246 -5.360 11.009 1.00 0.00 0.163 HD
70 ATOM 6 CA ASP A 50 7.845 -3.806 11.248 1.00 64.98 0.186 C
71 ATOM 7 C ASP A 50 8.508 -4.537 12.430 1.00 62.63 0.241 C
72 ATOM 8 O ASP A 50 7.898 -5.423 13.032 1.00 63.05 -0.271 OA
73 ATOM 9 CB ASP A 50 7.146 -2.511 11.685 1.00 66.87 0.147 C
74 ATOM 10 CG ASP A 50 8.017 -1.267 11.465 1.00 68.22 0.175 C
75 ATOM 11 OD1 ASP A 50 9.140 -1.204 12.030 1.00 67.77 -0.648 OA
76 ATOM 12 OD2 ASP A 50 7.570 -0.351 10.729 1.00 69.97 -0.648 OA
77 ATOM 13 N LEU A 51 9.760 -4.189 12.730 1.00 60.07 -0.346 N
78 ATOM 14 HN LEU A 51 10.177 -3.384 12.264 1.00 0.00 0.163 HD
79 ATOM 15 CA LEU A 51 10.551 -4.934 13.712 1.00 57.24 0.177 C
80 ATOM 16 C LEU A 51 10.592 -4.245 15.069 1.00 56.84 0.241 C
81 ATOM 17 O LEU A 51 10.689 -3.020 15.157 1.00 57.09 -0.271 OA
82 ATOM 18 CB LEU A 51 11.979 -5.179 13.205 1.00 55.78 0.038 C
83 ATOM 19 CG LEU A 51 12.250 -6.074 11.987 1.00 54.47 -0.020 C
84 ATOM 20 CD1 LEU A 51 13.717 -6.000 11.623 1.00 52.72 0.009 C
85 ATOM 21 CD2 LEU A 51 11.857 -7.523 12.233 1.00 53.53 0.009 C
86 ATOM 22 N THR A 52 10.527 -5.061 16.117 1.00 55.68 -0.344 N
87 ATOM 23 HN THR A 52 10.475 -6.064 15.941 1.00 0.00 0.163 HD
88 ]]></help>
89 <citations>
90 <citation type="doi">10.1002/jcc.21334</citation>
91 </citations>
92 </tool>