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comparison docking.xml @ 2:18dec59e29ae 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 16:49:49 -0400
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1:d9ee79230d31 2:18dec59e29ae
1 <tool id="docking" name="Docking" version="0.1.0">
2 <description>- Tool to running molecular docking with Autodock Vina</description>
3 <requirements>
4 <requirement type="package" version="1.1.2">autodock-vina</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1" />
8 </stdio>
9 <command><![CDATA[
10 vina --config "$box" --receptor "$receptor" --ligand "$ligand" --out "$file_output1" --log "$file_output2"
11 ]]></command>
12 <inputs>
13 <param type="data" name="box" format="txt" label="Box configuration: " help="Select a text file with the box configurations" />
14 <param type="data" name="receptor" format="pdbqt" label="Receptor: " help="Select a receptor pdbqt file" />
15 <param type="data" name="ligand" format="pdbqt" label="Ligand: " help="Select a ligand pdbqt file" />
16 </inputs>
17 <outputs>
18 <data name="file_output1" format="pdbqt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.pdbqt" />
19 <data name="file_output2" format="txt" label="#echo (os.path.splitext (str($ligand.name))[0]) + '_-_' + (os.path.splitext (str($receptor.name))[0])#.log" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="box" value="config_complexo_dm.txt"/>
24 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
25 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
26 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
27 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31 ** What it does? **
32
33 This tool performs molecular docking with Autodock Vina program.
34
35 ** inputs **
36
37 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:
38
39 size_x = 20.00
40 size_y = 18.40
41 size_z = 23.60
42 center_x = 70.92
43 center_y = 70.57
44 center_z = 36.86
45 num_modes = 9999
46 energy_range = 9999
47 exhaustiveness = 10
48 cpu = 4
49 seed = 1
50
51 Where the parameters size_x, size_y, size_z, center_x, center_y and center_z are coordinates of the binding site.
52 The parameters num_modes, energy_range, exhaustiveness, cpu and seed are autodock vina configurations to execute the algorithm.
53
54 The second input is a receptor file (pdbqt) what is a output of the prepare receptor tool.
55 The last input is a ligand file (pdbqt) what is a output of the prepare ligand tool.
56
57 ** outputs **
58
59 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:
60
61 MODEL 1
62 REMARK VINA RESULT: -0.0 0.000 0.000
63 REMARK 9 active torsions:
64 REMARK status: ('A' for Active; 'I' for Inactive)
65 REMARK 1 A between atoms: C_2 and O_3
66 REMARK 2 A between atoms: C_2 and C_14
67 REMARK 3 A between atoms: O_3 and C_4
68 REMARK 4 A between atoms: C_4 and C_5
69 REMARK 5 A between atoms: C_6 and C_8
70 REMARK 6 A between atoms: C_8 and C_9
71 REMARK 7 A between atoms: C_9 and C_10
72 REMARK 8 A between atoms: C_16 and O_17
73 REMARK 9 A between atoms: C_19 and O_20
74 ROOT
75 ATOM 1 O LIG d 1 72.801 71.157 37.352 0.00 0.00 -0.259 OA
76 ATOM 2 C LIG d 1 73.413 72.112 37.794 0.00 0.00 0.293 C
77 ENDROOT
78 BRANCH 2 3
79 ATOM 3 O LIG d 1 72.912 73.321 38.144 0.00 0.00 -0.314 OA
80 BRANCH 3 4
81 ATOM 4 C LIG d 1 71.868 73.332 39.120 0.00 0.00 0.206 C
82 BRANCH 4 5
83 ATOM 5 C LIG d 1 72.522 73.555 40.453 0.00 0.00 0.002 C
84 ATOM 6 C LIG d 1 72.762 72.629 41.405 0.00 0.00 -0.085 C
85 ATOM 7 C LIG d 1 72.390 71.176 41.274 0.00 0.00 0.043 C
86 BRANCH 6 8
87 ATOM 8 C LIG d 1 73.435 73.012 42.714 0.00 0.00 0.037 C
88 BRANCH 8 9
89 ATOM 9 C LIG d 1 74.184 74.348 42.631 0.00 0.00 0.031 C
90 BRANCH 9 10
91 ATOM 10 C LIG d 1 75.668 74.175 42.431 0.00 0.00 -0.024 C
92 ATOM 11 C LIG d 1 76.399 74.547 41.360 0.00 0.00 -0.091 C
93 ATOM 12 C LIG d 1 75.833 75.151 40.104 0.00 0.00 0.042 C
94 ATOM 13 C LIG d 1 77.897 74.373 41.339 0.00 0.00 0.042 C
95 ENDBRANCH 9 10
96 ENDBRANCH 8 9
97 ENDBRANCH 6 8
98 ENDBRANCH 4 5
99 ENDBRANCH 3 4
100 ENDBRANCH 2 3
101 BRANCH 2 14
102 ATOM 14 C LIG d 1 74.882 72.132 38.012 0.00 0.00 0.042 A
103 ATOM 15 C LIG d 1 75.732 72.845 37.153 0.00 0.00 0.057 A
104 ATOM 16 C LIG d 1 77.101 72.826 37.385 0.00 0.00 0.099 A
105 ATOM 17 C LIG d 1 77.623 72.116 38.462 0.00 0.00 0.098 A
106 ATOM 18 C LIG d 1 76.791 71.422 39.330 0.00 0.00 0.040 A
107 ATOM 19 C LIG d 1 75.412 71.432 39.110 0.00 0.00 0.020 A
108 BRANCH 16 20
109 ATOM 20 O LIG d 1 77.978 73.498 36.578 0.00 0.00 -0.358 OA
110 ATOM 21 HO LIG d 1 77.680 74.093 35.900 1.00 0.00 0.217 HD
111 ENDBRANCH 16 20
112 BRANCH 17 22
113 ATOM 22 O LIG d 1 78.971 72.100 38.675 0.00 0.00 -0.358 OA
114 ATOM 23 HO LIG d 1 79.541 71.651 38.060 1.00 0.00 0.217 HD
115 ENDBRANCH 17 22
116 ENDBRANCH 2 14
117 TORSDOF 9
118 ENDMDL
119
120 The last is a log file with the binding affinity scores, this file looks like the following example:
121
122 -----------------------------------------------------------------
123 If you used AutoDock Vina in your work, please cite:
124
125 O. Trott, A. J. Olson,
126 AutoDock Vina: improving the speed and accuracy of docking
127 with a new scoring function, efficient optimization and
128 multithreading, Journal of Computational Chemistry 31 (2010)
129 455-461
130
131 DOI 10.1002/jcc.21334
132
133 Please see http://vina.scripps.edu for more information.
134 ------------------------------------------------------------------
135
136 Reading input ... done.
137 Setting up the scoring function ... done.
138 Analyzing the binding site ... done.
139 Using random seed: 1899908181
140 Performing search ... done.
141 Refining results ... done.
142
143 mode | affinity | dist from best mode
144 | (kcal/mol) | rmsd l.b.| rmsd u.b.
145 -----+------------+----------+----------
146 1 -0.0 0.000 0.000
147 2 -0.0 2.046 2.443
148 3 -0.0 5.896 7.949
149 4 -0.0 2.518 3.100
150 5 -0.0 2.417 4.527
151 6 -0.0 5.686 7.689
152 7 -0.0 2.828 4.792
153 8 -0.0 5.547 7.086
154 9 -0.0 7.388 9.966
155 10 -0.0 7.877 11.352
156 11 -0.0 8.203 10.157
157 12 -0.0 5.163 7.653
158 13 -0.0 3.093 6.011
159 14 -0.0 7.998 11.146
160 15 -0.0 7.015 10.108
161 16 -0.0 8.795 11.682
162 17 -0.0 7.317 10.367
163 18 0.0 3.274 4.160
164 19 0.0 10.286 12.001
165 20 0.0 3.566 5.349
166 Writing output ... done.
167 ]]></help>
168 <citations>
169 <citation type="doi">10.1002/jcc.21334</citation>
170 </citations>
171 </tool>