Mercurial > repos > bgruening > shape_it

comparison shape-it.xml @ 0:31f5b5421a02 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/silicos-it/shape-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
author bgruening
date Mon, 22 May 2017 03:02:57 -0400
parents
children d7ecb50b2b66
comparison
equal deleted inserted replaced
-1:000000000000 0:31f5b5421a02
1 <tool id="ctb_shapeit" name="Shape alignment" version="1.0.1.0">
2 <description>Against a database of molecules (shape-it)</description>
3 <requirements>
4 <requirement type="package" version="1.0.1">shape_it</requirement>
5 </requirements>
6 <command detect_errors="aggressive">
7 <![CDATA[
8
9 ln -s ${database} ./database.${database.ext} &&
10 ln -s ${reference} ./reference.${reference.ext} &&
11
12 shape-it
13 --format ${database.ext}
14 --dbase ./database.${database.ext}
15 --reference ./reference.${reference.ext}
16 --addIterations $addIterations
17 #if int($best) > 0:
18 --best $best
19 #end if
20 --cutoff $cutoff
21 #if $scores:
22 --scores $output_scores
23 #end if
24 --rankBy $rankBy
25 $noref
26 $scoreonly
27 --out ./result.${database.ext}
28
29 &&
30 mv ./result.${database.ext} '$output'
31 ]]>
32 </command>
33 <inputs>
34 <param name="reference" type="data" format='sdf,mol,mol2' label="Refrence molecule (with 3D coordinates)" />
35 <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" />
36 <param name="cutoff" type="float" value="0.0" label="Only molecules with a score higher than the cutoff are reported."
37 help="The scoring function is defined by the scoring scheme.">
38 <validator type="in_range" min="0.0" />
39 </param>
40 <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure'
41 help="The default value is set to 0, which refers to only a local gradient ascent."/>
42 <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' help="0 means all molecules are reported"/>
43 <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a Tab-delimited text file with the scores of molecules' checked="false" />
44 <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" />
45 <param name='scoreonly' type='boolean' truevalue='--scoreOnly' falsevalue=''
46 label='Only the volume overlap between the reference and the given pose is computed' checked="false" />
47 <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
48 <option value='TANIMOTO'>Tanimoto</option>
49 <option value='TVERSKY_REF'>TVERSKY_REF</option>
50 <option value='TVERSKY_DB'>TVERSKY_DB</option>
51 </param>
52 </inputs>
53 <outputs>
54 <data name="output" format_source='database' />
55 <data name="output_scores" format="tabular">
56 <filter>scores is True</filter>
57 </data>
58 </outputs>
59 <tests>
60 <test>
61 <param name="database" ftype='sdf' value="CID_3033.sdf" />
62 <param name="reference" ftype="sdf" value='CID_3037.sdf' />
63 <param name="cutoff" value="0.0" />
64 <param name='addIterations' value='0' />
65 <param name='best' value='0' />
66 <param name='scoreonly' value="true" />
67 <output name="output" ftype='sdf' file="shapeit_on_CID3033_and_CID3037.sdf" lines_diff="4" />
68 </test>
69 </tests>
70 <help>
71 <![CDATA[
72
73
74 .. class:: infomark
75
76 **What this tool does**
77
78 Shape-it_ is a tool that aligns a reference molecule against a set of database
79 molecules using the shape of the molecules as the align criterion.
80 It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup.
81
82 The program expects one reference molecule with
83 its three-dimensional coordinates and one database files containing one
84 or more molecules in three dimensions. The results are either the alignment
85 of all database molecules and their respective scores or the N best
86 scoring molecules of the complete database.
87
88 .. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016
89 .. _Shape-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/shape-it/1.0.1/shape-it.html
90
91 -----
92
93 .. class:: infomark
94
95 **Input**
96
97
98 | - `formates recognized by OpenBabel`_
99
100 .. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats
101
102 * Example::
103
104 - database
105 27 28 0 0 0 0 0 0 0999 V2000
106 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
107 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
108 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
109 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
110 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
111 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
112 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
113 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
114 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
115 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
116 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
117 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
118 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
119 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
120 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
121 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
122 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
123 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
124 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
125 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
126 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
127 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
128 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
129 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
130 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
131 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
132 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
133 1 14 1 0 0 0 0
134 2 15 1 0 0 0 0
135 3 8 1 0 0 0 0
136 3 26 1 0 0 0 0
137 4 9 1 0 0 0 0
138 4 27 1 0 0 0 0
139 5 6 1 0 0 0 0
140 5 7 1 0 0 0 0
141 .....
142
143 - reference
144
145 30 31 0 0 0 0 0 0 0999 V2000
146 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
147 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
148 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
149 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
150 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
151 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
152 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
153 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
154 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
155 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
156 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
157 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
158 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
159 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
160 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
161 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
162 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
163 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
164 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
165 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
166 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
167 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
168 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
169 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
170 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
171 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
172 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
173 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
174 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
175 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
176 1 14 1 0 0 0 0
177 2 15 1 0 0 0 0
178 3 16 1 0 0 0 0
179 3 30 1 0 0 0 0
180 4 16 2 0 0 0 0
181 5 7 1 0 0 0 0
182 5 9 1 0 0 0 0
183 5 22 1 0 0 0 0
184 6 7 1 0 0 0 0
185 6 8 1 0 0 0 0
186 ......
187
188 - cutoff : 0.0
189
190 -----
191
192 .. class:: infomark
193
194 **Output**
195
196 * Example::
197
198 27 28 0 0 0 0 0 0 0 0999 V2000
199 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
200 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
201 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
202 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
203 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
204 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
205 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
206 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
207 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
208 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
209 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
210 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
211 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
212 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
213 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
214 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
215 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
216 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
217 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
218 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
219 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
220 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
221 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
222 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
223 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
224 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
225 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
226 1 14 1 0 0 0 0
227 2 15 1 0 0 0 0
228 3 8 1 0 0 0 0
229 3 26 1 0 0 0 0
230 4 9 1 0 0 0 0
231 4 27 1 0 0 0 0
232 5 6 1 0 0 0 0
233 5 7 1 0 0 0 0
234 5 18 1 0 0 0 0
235 5 19 1 0 0 0 0
236 6 8 2 0 0 0 0
237 ......
238
239
240 ]]>
241 </help>
242 <citations>
243 <citation type="doi">10.1021/j100011a016</citation>
244 </citations>
245 </tool>