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comparison docking.xml @ 6:0ae768a0e5c0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a2f6034a691af458e3df662e36d7f05617982bdc
author bgruening
date Wed, 19 Jun 2019 06:43:41 -0400
parents c410ffcabf9d
children 7b2f205b3f68
comparison
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5:c410ffcabf9d 6:0ae768a0e5c0
1 <tool id="docking" name="Docking" version="0.2.0"> 1 <tool id="docking" name="Docking" version="0.2.1">
2 <description>tool to perform protein-ligand docking with Autodock Vina</description> 2 <description>tool to perform protein-ligand docking with Autodock Vina</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">autodock-vina</requirement> 4 <requirement type="package" version="1.1.2">autodock-vina</requirement>
5 <requirement type="package" version="2.4.1">openbabel</requirement>
5 </requirements> 6 </requirements>
6 <stdio> 7 <stdio>
7 <exit_code range="1" /> 8 <exit_code range="1" />
8 </stdio> 9 </stdio>
9 <command><![CDATA[ 10 <command><![CDATA[
18 --exhaustiveness '$config_params.exh' 19 --exhaustiveness '$config_params.exh'
19 --num_modes 9999 20 --num_modes 9999
20 --energy_range 9999 21 --energy_range 9999
21 --receptor '$receptor' 22 --receptor '$receptor'
22 --ligand '$ligand' 23 --ligand '$ligand'
23 --out '$file_output1' 24 --out './output1.dat'
24 --log '$file_output2' 25 --log './output2.dat'
25 --cpu \${GALAXY_SLOTS:-1} 26 --cpu \${GALAXY_SLOTS:-1}
26 #if $config_params.seed.seed == 'true': 27 #if $config_params.seed.seed == 'true':
27 --seed '$config_params.seed.seed_value' 28 --seed '$config_params.seed.seed_value'
28 #end if 29 #end if
29 #end if 30 #end if
30 #if $config_params.config_params == 'file': 31 #if $config_params.config_params == 'file':
31 vina 32 vina
32 --config '$config_params.box' 33 --config '$config_params.box'
33 --receptor '$receptor' 34 --receptor '$receptor'
34 --ligand '$ligand' 35 --ligand '$ligand'
35 --out '$file_output1' 36 --out './output1.dat'
36 --log '$file_output2' 37 --log './output2.dat'
37 --cpu \${GALAXY_SLOTS:-1} 38 --cpu \${GALAXY_SLOTS:-1}
38 39 #if $config_params.exh != "":
40 --exhaustiveness $config_params.exh
41 #end if
42 #end if
43 #if $output_format == 'sdf':
44 && python '$__tool_directory__/convert_pdbqt_to_sdf.py' './output1.dat' '$sdf_output'
45 #else
46 && mv ./output1.dat '$file_output1'
47 && mv ./output2.dat '$file_output2'
39 #end if 48 #end if
40 49
41 ]]></command> 50 ]]></command>
42 <inputs> 51 <inputs>
43 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool." /> 52 <param type="data" name="receptor" format="pdbqt" label="Receptor" help="Select a receptor (PDBQT format). This can be prepared using the receptor preparation tool." />
63 <when value="false"/> 72 <when value="false"/>
64 </conditional> 73 </conditional>
65 </when> 74 </when>
66 <when value="file"> 75 <when value="file">
67 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" /> 76 <param type="data" name="box" format="txt" label="Box configuration" help="Text file with the box configurations" />
77 <param type="integer" name="exh" label="Exhaustiveness" help="The number of poses to return from the docking job (optional, will override any value specified in the config file)" optional="true"/>
68 </when> 78 </when>
69 </conditional> 79 </conditional>
80 <param type="select" name="output_format" label="Output format" help="Select a format for the output files">
81 <option value="pdbqt" selected="true">PDBQT (and separate log file with binding scores)</option>
82 <option value="sdf">SDF</option>
83 </param>
70 </inputs> 84 </inputs>
71 <outputs> 85 <outputs>
72 <data name="file_output1" format="pdbqt" /> 86 <data name="file_output1" format="pdbqt">
73 <data name="file_output2" format="txt" /> 87 <filter>output_format == 'pdbqt'</filter>
88 </data>
89 <data name="file_output2" format="txt">
90 <filter>output_format == 'pdbqt'</filter>
91 </data>
92 <data name="sdf_output" format="sdf">
93 <filter>output_format == 'sdf'</filter>
94 </data>
74 </outputs> 95 </outputs>
75 <tests> 96 <tests>
76 <test> 97 <test expect_num_outputs="2">
77 <param name="receptor" value="3u1i_for_DM.pdbqt"/> 98 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
78 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/> 99 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
79 <param name="config_params" value="vals"/> 100 <param name="config_params" value="vals"/>
80 <param name="center_x" value="70.92" /> 101 <param name="center_x" value="70.92" />
81 <param name="center_y" value="70.57" /> 102 <param name="center_y" value="70.57" />
83 <param name="size_x" value="20.00" /> 104 <param name="size_x" value="20.00" />
84 <param name="size_y" value="18.40" /> 105 <param name="size_y" value="18.40" />
85 <param name="size_z" value="23.60" /> 106 <param name="size_z" value="23.60" />
86 <param name="seed" value="true" /> 107 <param name="seed" value="true" />
87 <param name="seed_value" value="1" /> 108 <param name="seed_value" value="1" />
88 <param name="exhaustivenesss" value="10" /> 109 <param name="exhaustiveness" value="10" />
110 <param name="output_format" value="pdbqt" />
89 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/> 111 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
90 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/> 112 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
91 </test> 113 </test>
92 <test> 114 <test expect_num_outputs="2">
93 <param name="receptor" value="3u1i_for_DM.pdbqt"/> 115 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
94 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/> 116 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
95 <param name="config_params" value="file"/> 117 <param name="config_params" value="file"/>
96 <param name="box" value="config_complexo_dm.txt"/> 118 <param name="box" value="config_complexo_dm.txt"/>
119 <param name="output_format" value="pdbqt" />
97 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/> 120 <output name="file_output1" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.pdbqt"/>
98 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/> 121 <output name="file_output2" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.log"/>
99 </test> 122 </test>
123 <test expect_num_outputs="1">
124 <param name="receptor" value="3u1i_for_DM.pdbqt"/>
125 <param name="ligand" value="NuBBE_1_obabel_3D.pdbqt"/>
126 <param name="config_params" value="file"/>
127 <param name="box" value="config_complexo_dm.txt"/>
128 <param name="output_format" value="sdf" />
129 <output name="sdf_output" file="NuBBE_1_obabel_3D_-_3u1i_for_DM.sdf" lines_diff="40"/>
130 </test>
100 </tests> 131 </tests>
101 <help><![CDATA[ 132 <help><![CDATA[
102 133
103 This tool performs protein-ligand docking using the Autodock Vina program. 134 This tool performs protein-ligand docking using the Autodock Vina program.
104 135
136 -----
137
138 .. class:: infomark
139
105 **Inputs** 140 **Inputs**
106 141
107 The first two inputs required are files (in the pdbqt format) describing the receptor and ligand respectively. These files are produced by the receptor and ligand preparation tools. 142 The first two inputs required are files (in the pdbqt format) describing the receptor and ligand respectively. These files are produced by the receptor and ligand preparation tools.
108 143
109 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be generated from the box parameter calculation file. 144 In addition, parameters for docking must be defined. The Cartesian coordinates of the center of the binding site should be provided, along with the size of the binding site along each dimension. Effectively, this defines a cuboidal volume in which docking is performed. Alternatively, a config file can be uploaded containing this information - such a file can be generated from the box parameter calculation file.
110 145
146 A format for the output should also be selected: the available options are PDBQT or SDF.
147
148 -----
149
150 .. class:: infomark
151
111 **Outputs** 152 **Outputs**
112 153
113 Two outputs are generated by this tool. The first is another pdbqt file containing the molecular structure resulting from docking, such as the following example:: 154 Either PDBQT or SDF may be selected as output.
155
156 **Option 1: SDF**
157
158 An SDF file is produced as output. The binding affinity scores are also contained within the SDF file.::
159
160 OpenBabel06171915303D
161
162 23 23 0 0 0 0 0 0 0 0999 V2000
163 66.9030 73.3450 36.0040 O 0 0 0 0 0 0 0 0 0 0 0 0
164 66.8190 73.2170 37.2120 C 0 0 0 0 0 0 0 0 0 0 0 0
165 66.0490 72.3370 37.8940 O 0 0 0 0 0 0 0 0 0 0 0 0
166 66.2290 70.9500 37.5970 C 0 0 0 0 0 0 0 0 0 0 0 0
167 67.2070 70.4140 38.6010 C 0 0 0 0 0 0 0 0 0 0 0 0
168 68.5140 70.1440 38.3980 C 0 0 0 0 0 0 0 0 0 0 0 0
169 69.2150 70.3400 37.0800 C 0 0 0 0 0 0 0 0 0 0 0 0
170 69.3810 69.5970 39.5210 C 0 0 0 0 0 0 0 0 0 0 0 0
171 68.7730 69.8280 40.9100 C 0 0 0 0 0 0 0 0 0 0 0 0
172 69.3750 71.0120 41.6220 C 0 0 0 0 0 0 0 0 0 0 0 0
173 68.7550 72.1570 41.9760 C 0 0 0 0 0 0 0 0 0 0 0 0
174 67.3280 72.4970 41.6430 C 0 0 0 0 0 0 0 0 0 0 0 0
175 69.4770 73.2270 42.7560 C 0 0 0 0 0 0 0 0 0 0 0 0
176 67.5570 74.0540 38.1920 C 0 0 0 0 0 0 0 0 0 0 0 0
177 66.9010 75.0480 38.9340 C 0 0 0 0 0 0 0 0 0 0 0 0
178 67.6300 75.8170 39.8300 C 0 0 0 0 0 0 0 0 0 0 0 0
179 68.9950 75.5990 39.9980 C 0 0 0 0 0 0 0 0 0 0 0 0
180 69.6510 74.6060 39.2850 C 0 0 0 0 0 0 0 0 0 0 0 0
181 68.9300 73.8240 38.3800 C 0 0 0 0 0 0 0 0 0 0 0 0
182 67.0450 76.8040 40.5760 O 0 0 0 0 0 0 0 0 0 0 0 0
183 67.5560 77.4980 40.9760 H 0 0 0 0 0 0 0 0 0 0 0 0
184 69.7010 76.3670 40.8780 O 0 0 0 0 0 0 0 0 0 0 0 0
185 69.2520 76.7930 41.5990 H 0 0 0 0 0 0 0 0 0 0 0 0
186 1 2 2 0 0 0 0
187 2 3 1 0 0 0 0
188 2 14 1 0 0 0 0
189 4 3 1 0 0 0 0
190 4 5 1 0 0 0 0
191 6 5 2 0 0 0 0
192 6 8 1 0 0 0 0
193 7 6 1 0 0 0 0
194 8 9 1 0 0 0 0
195 9 10 1 0 0 0 0
196 10 11 2 0 0 0 0
197 11 13 1 0 0 0 0
198 12 11 1 0 0 0 0
199 14 19 2 0 0 0 0
200 14 15 1 0 0 0 0
201 15 16 2 0 0 0 0
202 16 17 1 0 0 0 0
203 16 20 1 0 0 0 0
204 17 22 1 0 0 0 0
205 18 17 2 0 0 0 0
206 19 18 1 0 0 0 0
207 20 21 1 0 0 0 0
208 22 23 1 0 0 0 0
209 M END
210 > <MODEL>
211 1
212
213 > <REMARK>
214 VINA RESULT: 0.0 0.000 0.000
215 9 active torsions:
216 status: ('A' for Active; 'I' for Inactive)
217 1 A between atoms: C_2 and O_3
218 2 A between atoms: C_2 and C_14
219 3 A between atoms: O_3 and C_4
220 4 A between atoms: C_4 and C_5
221 5 A between atoms: C_6 and C_8
222 6 A between atoms: C_8 and C_9
223 7 A between atoms: C_9 and C_10
224 8 A between atoms: C_16 and O_17
225 9 A between atoms: C_19 and O_20
226
227 > <TORSDO>
228 F 9
229
230 > <SCORE>
231 0.0
232
233 > <RMSD_LB>
234 0.000
235
236 > <RMSD_UB>
237 0.000
238
239
240 **Option 2: PDBQT**
241
242 Two outputs are generated if PDBQT output is selected. The first is another pdbqt file containing the molecular structure resulting from docking, such as the following example::
114 243
115 MODEL 1 244 MODEL 1
116 REMARK VINA RESULT: -0.0 0.000 0.000 245 REMARK VINA RESULT: -0.0 0.000 0.000
117 REMARK 9 active torsions: 246 REMARK 9 active torsions:
118 REMARK status: ('A' for Active; 'I' for Inactive) 247 REMARK status: ('A' for Active; 'I' for Inactive)