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comparison prepare_ligand.xml @ 1:d9ee79230d31 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 16:49:02 -0400
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0:8bc060fcf41a 1:d9ee79230d31
1 <tool id="prepare_ligand" name="Prepare ligand" version="0.1.0">
2 <description>- Tool to prepare ligand 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 $ligand ./ligand.mol2 && prepare_ligand4.py -l ./ligand.mol2 -v -o "$file_output" -U nphs_lps -A hydrogens
11 ]]></command>
12 <inputs>
13 <param type="data" name="ligand" format="mol2" label="Ligand: " help="Select a mol2 file." />
14 </inputs>
15 <outputs>
16 <data name="file_output" format="pdbqt" label="#echo os.path.splitext (str($ligand.name))[0]#.pdbqt" />
17 </outputs>
18 <tests>
19 <test>
20 <param name="ligand" value="NuBBE_1_obabel_3D.mol2"/>
21 <output name="file_output" file="NuBBE_1_obabel_3D.pdbqt"/>
22 </test>
23 </tests>
24 <help><![CDATA[
25 ** What it does? **
26
27 This tool uses the MGLTools programming packages to convert a mol2 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 mol2 dataset in history, what is informed in ligand field, for use the tool. The mol2 molecule file looks like the following example:
32
33 @<TRIPOS>MOLECULE
34 NuBBE_1
35 21 21 0 0 0
36 SMALL
37 GASTEIGER
38
39 @<TRIPOS>ATOM
40 1 O -0.9469 -0.4359 -3.2099 O.2 1 LIG1 -0.2449
41 2 C -1.2069 0.2449 -2.2351 C.2 1 LIG1 0.3396
42 3 O -1.9353 -0.1138 -1.1515 O.3 1 LIG1 -0.4570
43 4 C -2.3385 -1.4828 -1.0650 C.3 1 LIG1 0.1113
44 5 C -1.7447 -2.0319 0.2001 C.2 1 LIG1 -0.0480
45 6 C -0.5501 -2.6439 0.3381 C.2 1 LIG1 -0.0731
46 7 C 0.4046 -2.8855 -0.8015 C.3 1 LIG1 -0.0437
47 8 C -0.0862 -3.1529 1.6937 C.3 1 LIG1 -0.0285
48 9 C 0.7304 -2.1137 2.4728 C.3 1 LIG1 -0.0308
49 10 C 1.1870 -2.6184 3.8183 C.2 1 LIG1 -0.0850
50 11 C 2.3521 -3.2333 4.1099 C.2 1 LIG1 -0.0796
51 12 C 3.4007 -3.6048 3.0986 C.3 1 LIG1 -0.0440
52 13 C 2.6989 -3.6136 5.5272 C.3 1 LIG1 -0.0440
53 14 C -0.7776 1.6572 -2.0661 C.ar 1 LIG1 0.0627
54 15 C -0.6402 2.2240 -0.7903 C.ar 1 LIG1 -0.0026
55 16 C -0.2486 3.5509 -0.6768 C.ar 1 LIG1 0.1590
56 17 O -0.1045 4.1587 0.5397 O.3 1 LIG1 -0.5033
57 18 C 0.0124 4.3080 -1.8161 C.ar 1 LIG1 0.1583
58 19 O 0.3891 5.6141 -1.6913 O.3 1 LIG1 -0.5033
59 20 C -0.1020 3.7535 -3.0825 C.ar 1 LIG1 -0.0158
60 21 C -0.4936 2.4191 -3.2122 C.ar 1 LIG1 -0.0441
61 @<TRIPOS>BOND
62 1 1 2 2
63 2 2 3 1
64 3 3 4 1
65 4 4 5 1
66 5 5 6 2
67 6 6 7 1
68 7 6 8 1
69 8 8 9 1
70 9 9 10 1
71 10 10 11 2
72 11 11 12 1
73 12 11 13 1
74 13 2 14 1
75 14 14 15 ar
76 15 15 16 ar
77 16 16 17 1
78 17 16 18 ar
79 18 18 19 1
80 19 18 20 ar
81 20 20 21 ar
82 21 14 21 ar
83
84 ** output **
85
86 The output is a pdbqt molecule file converted from a mol2 molecule file. The pdbqt molecule file looks like the following example:
87
88 REMARK 9 active torsions:
89 REMARK status: ('A' for Active; 'I' for Inactive)
90 REMARK 1 A between atoms: C_2 and O_3
91 REMARK 2 A between atoms: C_2 and C_14
92 REMARK 3 A between atoms: O_3 and C_4
93 REMARK 4 A between atoms: C_4 and C_5
94 REMARK 5 A between atoms: C_6 and C_8
95 REMARK 6 A between atoms: C_8 and C_9
96 REMARK 7 A between atoms: C_9 and C_10
97 REMARK 8 A between atoms: C_16 and O_17
98 REMARK 9 A between atoms: C_19 and O_20
99 ROOT
100 ATOM 1 O LIG d 1 -0.947 -0.436 -3.210 0.00 0.00 -0.259 OA
101 ATOM 2 C LIG d 1 -1.207 0.245 -2.235 0.00 0.00 0.293 C
102 ENDROOT
103 BRANCH 2 3
104 ATOM 3 O LIG d 1 -1.935 -0.114 -1.151 0.00 0.00 -0.314 OA
105 BRANCH 3 4
106 ATOM 4 C LIG d 1 -2.338 -1.483 -1.065 0.00 0.00 0.206 C
107 BRANCH 4 5
108 ATOM 5 C LIG d 1 -1.745 -2.032 0.200 0.00 0.00 0.002 C
109 ATOM 6 C LIG d 1 -0.550 -2.644 0.338 0.00 0.00 -0.085 C
110 ATOM 7 C LIG d 1 0.405 -2.885 -0.801 0.00 0.00 0.043 C
111 BRANCH 6 8
112 ATOM 8 C LIG d 1 -0.086 -3.153 1.694 0.00 0.00 0.037 C
113 BRANCH 8 9
114 ATOM 9 C LIG d 1 0.730 -2.114 2.473 0.00 0.00 0.031 C
115 BRANCH 9 10
116 ATOM 10 C LIG d 1 1.187 -2.618 3.818 0.00 0.00 -0.024 C
117 ATOM 11 C LIG d 1 2.352 -3.233 4.110 0.00 0.00 -0.091 C
118 ATOM 12 C LIG d 1 3.401 -3.605 3.099 0.00 0.00 0.042 C
119 ATOM 13 C LIG d 1 2.699 -3.614 5.527 0.00 0.00 0.042 C
120 ENDBRANCH 9 10
121 ENDBRANCH 8 9
122 ENDBRANCH 6 8
123 ENDBRANCH 4 5
124 ENDBRANCH 3 4
125 ENDBRANCH 2 3
126 BRANCH 2 14
127 ATOM 14 C LIG d 1 -0.778 1.657 -2.066 0.00 0.00 0.042 A
128 ATOM 15 C LIG d 1 -0.640 2.224 -0.790 0.00 0.00 0.057 A
129 ATOM 16 C LIG d 1 -0.249 3.551 -0.677 0.00 0.00 0.099 A
130 ATOM 17 C LIG d 1 0.012 4.308 -1.816 0.00 0.00 0.098 A
131 ATOM 18 C LIG d 1 -0.102 3.753 -3.083 0.00 0.00 0.040 A
132 ATOM 19 C LIG d 1 -0.494 2.419 -3.212 0.00 0.00 0.020 A
133 BRANCH 16 20
134 ATOM 20 O LIG d 1 -0.104 4.159 0.540 0.00 0.00 -0.358 OA
135 ATOM 21 HO LIG d 1 0.164 5.067 0.617 1.00 0.00 0.217 HD
136 ENDBRANCH 16 20
137 BRANCH 17 22
138 ATOM 22 O LIG d 1 0.389 5.614 -1.691 0.00 0.00 -0.358 OA
139 ATOM 23 HO LIG d 1 0.567 6.131 -2.469 1.00 0.00 0.217 HD
140 ENDBRANCH 17 22
141 ENDBRANCH 2 14
142 TORSDOF 9
143
144 ]]></help>
145 <citations>
146 <citation type="doi">10.1002/jcc.21334</citation>
147 </citations>
148 </tool>