Mercurial > repos > bgruening > rdock_rbdock

comparison rbdock.xml @ 0:1a1600fde77a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdock commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:33:51 -0400
parents
children 5f291eef9ef3
comparison
equal deleted inserted replaced
-1:000000000000 0:1a1600fde77a
1 <tool id="rdock_rbdock" name="rDock docking" version="0.1">
2 <description>- perform protein-ligand docking with rDock</description>
3 <macros>
4 <import>rdock_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command><![CDATA[
8 ln -s '$active_site' receptor.as &&
9 ln -s '$receptor' receptor.mol2 &&
10 ln -s $receptor_prm receptor.prm &&
11 #if $name == 'Y':
12 sdmodify -f_REC '$ligands' > ligands.sdf &&
13 #else
14 ln -s '$ligands' ligands.sdf &&
15 #end if
16 rbdock -i ligands.sdf -r receptor.prm -p dock.prm -n $num -o output &&
17 sdsort -n -s -fSCORE output.sd |
18 #if $score and $score > 0:
19 sdfilter -f'\$SCORE <= $score' |
20 #end if
21 #if $nscore and $nscore > 0:
22 sdfilter -f'\$SCORE.norm <= $nscore' |
23 #end if
24 sdfilter -f'\$_COUNT <= $top' > '$output'
25 ]]></command>
26
27 <configfiles>
28 <configfile name="receptor_prm">RBT_PARAMETER_FILE_V1.00
29 RECEPTOR_FILE receptor.mol2
30 RECEPTOR_FLEX 3.0
31 </configfile>
32 </configfiles>
33
34 <inputs>
35 <param type="data" name="receptor" format="mol2" label="Receptor" help="Select a receptor (mol2 format)."/>
36 <param type="data" name="active_site" format="rdock_as" label="Active site" help="Active site file"/>
37 <param type="data" name="ligands" format="sdf" label="Ligands" help="Ligands in SDF format"/>
38 <param name="num" type="integer" value="10" label="Number of dockings" help="Number of poses to generate"/>
39 <param name="top" type="integer" value="1" label="Number of best poses" help="Number of best scoring poses to keep"/>
40 <param name="score" type="float" optional="true" label="Score filter"
41 help="Exclude poses with score greater than this value"/>
42 <param name="nscore" type="float" optional="true" label="Normalised score filter"
43 help="Exclude poses with normalised score greater than this value"/>
44 <param name="name" type="boolean" label="Generate name field" truevalue="Y" falsevalue="N" checked="false"
45 help="Generate the name field (first line) for cases where this is empty"/>
46 </inputs>
47 <outputs>
48 <data name="output" format="sdf" label="rDock on ${on_string}"/>
49 </outputs>
50 <tests>
51 <test>
52 <param name="receptor" value="receptor.mol2"/>
53 <param name="ligands" value="ligands_names.sdf"/>
54 <param name="active_site" value="receptor.as"/>
55 <param name="num" value="3"/>
56 <param name="top" value="1"/>
57 <param name="name" value="false"/>
58 <output name="output">
59 <assert_contents>
60 <has_text text="Rbt.Current_Directory"/>
61 </assert_contents>
62 </output>
63 </test>
64 <test>
65 <param name="receptor" value="receptor.mol2"/>
66 <param name="ligands" value="ligands_nonames.sdf"/>
67 <param name="active_site" value="receptor.as"/>
68 <param name="num" value="3"/>
69 <param name="top" value="1"/>
70 <param name="name" value="true"/>
71 <output name="output">
72 <assert_contents>
73 <has_text text="Rbt.Current_Directory"/>
74 </assert_contents>
75 </output>
76 </test>
77 <test>
78 <param name="receptor" value="receptor.mol2"/>
79 <param name="ligands" value="ligands_names.sdf"/>
80 <param name="active_site" value="receptor.as"/>
81 <param name="num" value="1"/>
82 <param name="score" value="10"/>
83 <param name="nscore" value="1"/>
84 <param name="name" value="false"/>
85 <output name="output">
86 <assert_contents>
87 <has_text text="Rbt.Current_Directory"/>
88 </assert_contents>
89 </output>
90 </test>
91 </tests>
92 <help><![CDATA[
93
94 .. class:: infomark
95
96 This tool performs protein-ligand docking using the rDock program.
97 See http://rdock.sourceforge.net/ for more details about rDock and associated programs.
98
99 -----
100
101 .. class:: infomark
102
103 **Inputs**
104
105 1. The protein receptor to dock into as a file in Mol2 format.
106 2. The active site definition as a file as generated by the rbcavity tool.
107 3. A set of ligands (collection or single file) to dock as a file in SDF format.
108 4. The number of docking poses to generate (integer).
109 5. The number of best scoring dockings to keep (integer).
110 6. The max score that is allowed. Poses with scores greater than this are excluded (float, optional).
111 7. The max normalised score (the score normalised by the number of heavy atoms) that is allowed.
112 Poses with normalised scores greater than this are excluded (float, optional).
113 8. Optionally generate the name field in the ligands SDF (this is the first line in the entry).
114 This field must be present and be unique for sorting and filtering to work. If your results contain only one record
115 then the name field is probably absent and must be generated.
116
117 You will need to perform some test dockings to establish suitable values for the score filters.
118 The score is a number with lower values being better. Values can be negative.
119
120 -----
121
122 .. class:: infomark
123
124 **Outputs**
125
126 An SDF file is produced as output. The binding affinity scores are contained within the SDF file.::
127
128 1-pyrimethamine
129 rDOCK(R) 3D
130 libRbt.so/2013.1/901 2013/11/27
131 21 22 0 0 0 0 0 0 0 0999 V2000
132 -5.1897 17.8912 17.9590 N 0 0 0 0 0 0
133 -3.9121 17.9973 18.3210 C 0 0 0 0 0 0
134 -3.2404 19.1465 18.3804 N 0 0 0 0 0 0
135 -3.8989 20.2829 18.0453 C 0 0 0 0 0 0
136 -5.2389 20.2802 17.6553 C 0 0 0 0 0 0
137 -5.8448 19.0235 17.6464 C 0 0 0 0 0 0
138 -5.9601 21.5065 17.2850 C 0 0 0 0 0 0
139 -6.2108 22.5074 18.2382 C 0 0 0 0 0 0
140 -6.8903 23.6771 17.8851 C 0 0 0 0 0 0
141 -7.3267 23.8556 16.5746 C 0 0 0 0 0 0
142 -7.0903 22.8744 15.6151 C 0 0 0 0 0 0
143 -6.4107 21.7051 15.9695 C 0 0 0 0 0 0
144 -3.2455 16.8582 18.6507 N 0 0 0 0 0 0
145 -7.1550 18.8446 17.2393 N 0 0 0 0 0 0
146 -8.1626 25.2957 16.1391 Cl 0 0 0 0 0 0
147 -2.9891 22.1828 19.5033 C 0 0 0 0 0 0
148 -3.1112 21.5771 18.1096 C 0 0 0 0 0 0
149 -2.2766 16.9101 18.9273 H 0 0 0 0 0 0
150 -3.7237 15.9703 18.6154 H 0 0 0 0 0 0
151 -7.8809 19.3992 17.6807 H 0 0 0 0 0 0
152 -7.4159 17.8951 16.9940 H 0 0 0 0 0 0
153 1 2 2 0 0 0
154 1 6 1 0 0 0
155 2 3 1 0 0 0
156 2 13 1 0 0 0
157 3 4 2 0 0 0
158 4 5 1 0 0 0
159 4 17 1 0 0 0
160 5 6 2 0 0 0
161 5 7 1 0 0 0
162 6 14 1 0 0 0
163 7 8 2 0 0 0
164 7 12 1 0 0 0
165 8 9 1 0 0 0
166 9 10 2 0 0 0
167 10 11 1 0 0 0
168 10 15 1 0 0 0
169 11 12 2 0 0 0
170 13 18 1 0 0 0
171 13 19 1 0 0 0
172 14 20 1 0 0 0
173 14 21 1 0 0 0
174 16 17 1 0 0 0
175 M END
176 > <CHROM.0>
177 -177.71086620,1.45027861,170.39044546,46.02877151,68.76956623,70.55425150
178
179 > <CHROM.1>
180 -81.34718191,-65.90186149,129.45748660,-5.61305786,21.23281353,17.50152835
181 0.96119776,0.49809360,-3.12917831
182
183 > <Rbt.Current_Directory>
184 /home/timbo/github/im/docking-validation/targets/dhfr/expts/vs-simple-rdock
185
186 > <Rbt.Executable>
187 rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $)
188
189 > <Rbt.Library>
190 libRbt.so (2013.1, Build901 2013/11/27)
191
192 > <Rbt.Parameter_File>
193 /rDock_2013.1/data/scripts/dock.prm
194
195 > <Rbt.Receptor>
196 receptor.prm
197
198 > <SCORE>
199 0.445364
200
201 > <SCORE.INTER>
202 8.4
203
204 > <SCORE.INTER.CONST>
205 1
206
207 > <SCORE.INTER.POLAR>
208 0
209
210 > <SCORE.INTER.REPUL>
211 0
212
213 > <SCORE.INTER.ROT>
214 3
215
216 > <SCORE.INTER.VDW>
217 0
218
219 > <SCORE.INTER.norm>
220 0.494118
221
222 > <SCORE.INTRA>
223 -1.38672
224
225 > <SCORE.INTRA.DIHEDRAL>
226 -0.818539
227
228 > <SCORE.INTRA.DIHEDRAL.0>
229 6.01924
230
231 > <SCORE.INTRA.POLAR>
232 0
233
234 > <SCORE.INTRA.POLAR.0>
235 0
236
237 > <SCORE.INTRA.REPUL>
238 0
239
240 > <SCORE.INTRA.REPUL.0>
241 0
242
243 > <SCORE.INTRA.VDW>
244 -0.977448
245
246 > <SCORE.INTRA.VDW.0>
247 -1.0079
248
249 > <SCORE.INTRA.norm>
250 -0.0815716
251
252 > <SCORE.RESTR>
253
254 > <SCORE.RESTR.norm>
255 0
256
257 > <SCORE.SYSTEM>
258 -6.56792
259
260 > <SCORE.SYSTEM.CONST>
261 0
262
263 > <SCORE.SYSTEM.DIHEDRAL>
264 1.50415
265
266 > <SCORE.SYSTEM.POLAR>
267 -2.3289
268
269 > <SCORE.SYSTEM.VDW>
270 0.59827
271
272 > <SCORE.SYSTEM.norm>
273 -0.386348
274
275 > <SCORE.heavy>
276 17
277
278 > <SCORE.norm>
279 0.0261979
280
281 $$$$
282
283 ]]></help>
284 <expand macro="citations"/>
285 </tool>