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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/shape-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:41:43 -0400
parents 31f5b5421a02
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0:31f5b5421a02 1:d7ecb50b2b66
1 <tool id="ctb_shapeit" name="Shape alignment" version="1.0.1.0"> 1 <tool id="ctb_shapeit" name="Shape alignment" version="1.0.1.0">
2 <description>Against a database of molecules (shape-it)</description> 2 <description>against a database of molecules (shape-it)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.1">shape_it</requirement> 4 <requirement type="package" version="1.0.1">shape_it</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"> 6 <command detect_errors="aggressive">
7 <![CDATA[ 7 <![CDATA[
29 && 29 &&
30 mv ./result.${database.ext} '$output' 30 mv ./result.${database.ext} '$output'
31 ]]> 31 ]]>
32 </command> 32 </command>
33 <inputs> 33 <inputs>
34 <param name="reference" type="data" format='sdf,mol,mol2' label="Refrence molecule (with 3D coordinates)" /> 34 <param name="reference" type="data" format='sdf,mol,mol2' label="Reference molecule (with 3D coordinates)" />
35 <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (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." 36 <param name="cutoff" type="float" value="0.0" label="Cutoff"
37 help="The scoring function is defined by the scoring scheme."> 37 help="Only molecules with a score higher than the cutoff are reported; the scoring function is defined by the scoring scheme.">
38 <validator type="in_range" min="0.0" /> 38 <validator type="in_range" min="0.0" />
39 </param> 39 </param>
40 <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' 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."/> 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"/> 42 <param name='best' type='integer' value='0' label='Number of best-scoring molecules to report' help="The N best scoring molecules are reported; 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" /> 43 <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a tab-delimited text file with the molecule scores' checked="false" />
44 <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" /> 44 <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='Do not write reference molecule into the output files' checked="false" />
45 <param name='scoreonly' type='boolean' truevalue='--scoreOnly' falsevalue='' 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" /> 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"> 47 <param name='rankBy' type='select' format='text' label="Scoring scheme">
48 <option value='TANIMOTO'>Tanimoto</option> 48 <option value='TANIMOTO'>Tanimoto</option>
49 <option value='TVERSKY_REF'>TVERSKY_REF</option> 49 <option value='TVERSKY_REF'>TVERSKY_REF</option>
50 <option value='TVERSKY_DB'>TVERSKY_DB</option> 50 <option value='TVERSKY_DB'>TVERSKY_DB</option>
51 </param> 51 </param>
52 </inputs> 52 </inputs>
74 .. class:: infomark 74 .. class:: infomark
75 75
76 **What this tool does** 76 **What this tool does**
77 77
78 Shape-it_ is a tool that aligns a reference molecule against a set of database 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. 79 molecules using the shape of the molecules as the alignment criterion.
80 It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup. 80 It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as was introduced by Grant and Pickup.
81 81
82 The program expects one reference molecule with 82 The program expects one reference molecule with
83 its three-dimensional coordinates and one database files containing one 83 its three-dimensional coordinates and one database files containing one
84 or more molecules in three dimensions. The results are either the alignment 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 85 of all database molecules and their respective scores or the N best
93 .. class:: infomark 93 .. class:: infomark
94 94
95 **Input** 95 **Input**
96 96
97 97
98 | - `formates recognized by OpenBabel`_ 98 `3D formats recognized by OpenBabel`_ - either SDF, MOL, or MOL2
99 99
100 .. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats 100 .. _3D formats recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats
101 101
102 * Example:: 102 * Example (SDF)::
103 103
104 - database 104 - database
105 27 28 0 0 0 0 0 0 0999 V2000 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 0 106 -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 0 107 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
191 191
192 .. class:: infomark 192 .. class:: infomark
193 193
194 **Output** 194 **Output**
195 195
196 The output file contains first the reference molecule, followed by the molecules
197 aligned to the reference molecule. If the 'Number of best-scoring molecules' option
198 is set only the top-best scoring molecules will be reported in the output file,
199 otherwise all molecules are written to the output file.
200
196 * Example:: 201 * Example::
197 202
198 27 28 0 0 0 0 0 0 0 0999 V2000 203 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 0 204 -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 0 205 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
234 5 18 1 0 0 0 0 239 5 18 1 0 0 0 0
235 5 19 1 0 0 0 0 240 5 19 1 0 0 0 0
236 6 8 2 0 0 0 0 241 6 8 2 0 0 0 0
237 ...... 242 ......
238 243
244 In addition, if the option to output scores is selected, a tabular file will be created.
245 Each line represents a molecule from the database, with columns describing the volumes
246 of the reference and database molecules, overlap volumes, and Shape-it scores produced
247 by the three scoring schemes.
248
249 * Example::
250
251 dbName refName Shape-it::Tanimoto Shape-it::Tversky_Ref Shape-it::Tversky_Db overlap refVolume dbVolume
252 3033 3037 0.562 0.754 0.688 128.56 169.59 187.87
253
239 254
240 ]]> 255 ]]>
241 </help> 256 </help>
242 <citations> 257 <citations>
243 <citation type="doi">10.1021/j100011a016</citation> 258 <citation type="doi">10.1021/j100011a016</citation>