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comparison shape-it/shape-it.xml @ 0:bb92d30b4f52 draft

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date Thu, 15 Aug 2013 03:34:00 -0400
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1 <tool id="ctb_shapeit" name="Shape alignment" version="0.1">
2 <description>against a database of molecules (Shape-it)</description>
3 <requirements>
4 <requirement type="package" version="1.0.1">silicos_it</requirement>
5 <requirement type="package" version="2.3.2">openbabel</requirement>
6 </requirements>
7 <command >
8 shape-it
9 --format ${database.ext}
10 --dbase $database
11 --reference $reference
12 --addIterations $addIterations
13 #if int($best) > 0:
14 --best $best
15 #end if
16 --cutoff $cutoff
17 #if $scores == 'yes':
18 --scores $output_scores
19 #end if
20 --rankBy $rankBy
21 $noref
22 --out $output 2>&#38;1
23 </command>
24 <inputs>
25 <param name="reference" type="data" format='sdf,mol,mol2' label="Refrence molecule (with 3D coordinates)" />
26 <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" />
27 <param name="cutoff" type="float" value="0.0" label="Only molecules with a score higher than the cutoff are reported." help="The scoring function is defined by the scoring scheme.">
28 <validator type="in_range" min="0.0" />
29 </param>
30 <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' help="The default value is set to 0, which refers to only a local gradient ascent."/>
31 <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' help="0 means all molecules are reported"/>
32 <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a Tab-delimited text file with the scores of molecules' checked="false" />
33 <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" />
34 <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
35 <option value='TANIMOTO'>Tanimoto</option>
36 <option value='TVERSKY_REF'>TVERSKY_REF</option>
37 <option value='TVERSKY_DB'>TVERSKY_DB</option>
38 </param>
39 </inputs>
40 <outputs>
41 <data name="output" format_source='database' />
42 <data name="output_scores" format="tabular">
43 <filter>scores == "yes"</filter>
44 </data>
45 </outputs>
46 <tests>
47 <test>
48 <param name="database" ftype='sdf' value="CID_3033.sdf" />
49 <param name="reference" type="sdf" value='CID_3037.sdf' />
50 <param name="cutoff" value="0.0" />
51 <param name='addIterations' value='0' />
52 <param name='best' value='0' />
53 <output name="output" ftype='sdf' file="shapeit_on_CID3033_and_CID3037.sdf" />
54 </test>
55 </tests>
56 <help>
57
58
59 .. class:: infomark
60
61 **What this tool does**
62
63 Shape-it_ is a tool that aligns a reference molecule against a set of database
64 molecules using the shape of the molecules as the align criterion.
65 It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup.
66
67 The program expects one reference molecule with
68 its three-dimensional coordinates and one database files containing one
69 or more molecules in three dimensions. The results are either the alignment
70 of all database molecules and their respective scores or the N best
71 scoring molecules of the complete database.
72
73 .. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016
74 .. _Shape-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html
75
76 -----
77
78 .. class:: infomark
79
80 **Input**
81
82
83 | - `formates recognized by OpenBabel`_
84
85 .. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats
86
87 * Example::
88
89 - database
90 27 28 0 0 0 0 0 0 0999 V2000
91 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
92 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
93 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
94 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
95 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
96 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
97 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
98 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
99 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
100 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
101 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
102 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
103 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
104 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
105 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
106 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
107 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
108 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
109 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
110 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
111 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
112 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
113 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
114 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
115 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
116 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
117 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
118 1 14 1 0 0 0 0
119 2 15 1 0 0 0 0
120 3 8 1 0 0 0 0
121 3 26 1 0 0 0 0
122 4 9 1 0 0 0 0
123 4 27 1 0 0 0 0
124 5 6 1 0 0 0 0
125 5 7 1 0 0 0 0
126 .....
127
128 - reference
129
130 30 31 0 0 0 0 0 0 0999 V2000
131 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
132 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
133 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
134 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
135 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
136 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
137 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
138 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
139 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
140 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
141 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
142 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
143 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
144 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
145 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
146 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
147 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
148 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
149 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
150 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
151 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
152 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
153 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
154 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
155 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
156 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
157 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
158 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
159 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
160 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
161 1 14 1 0 0 0 0
162 2 15 1 0 0 0 0
163 3 16 1 0 0 0 0
164 3 30 1 0 0 0 0
165 4 16 2 0 0 0 0
166 5 7 1 0 0 0 0
167 5 9 1 0 0 0 0
168 5 22 1 0 0 0 0
169 6 7 1 0 0 0 0
170 6 8 1 0 0 0 0
171 ......
172
173 - cutoff : 0.0
174
175 -----
176
177 .. class:: infomark
178
179 **Output**
180
181 * Example::
182
183 27 28 0 0 0 0 0 0 0 0999 V2000
184 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
185 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
186 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
187 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
188 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
189 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
190 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
191 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
192 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
193 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
194 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
195 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
196 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
197 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
198 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
199 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
200 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
201 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
202 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
203 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
204 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
205 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
206 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
207 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
208 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
209 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
210 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
211 1 14 1 0 0 0 0
212 2 15 1 0 0 0 0
213 3 8 1 0 0 0 0
214 3 26 1 0 0 0 0
215 4 9 1 0 0 0 0
216 4 27 1 0 0 0 0
217 5 6 1 0 0 0 0
218 5 7 1 0 0 0 0
219 5 18 1 0 0 0 0
220 5 19 1 0 0 0 0
221 6 8 2 0 0 0 0
222 ......
223
224 -----
225
226 .. class:: infomark
227
228 **Cite**
229
230 `Silicos-it`_ - shape-it
231
232 .. _Silicos-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html
233
234
235 </help>
236 </tool>