Mercurial > repos > bgruening > align_it
comparison align-it.xml @ 1:10c0df29e6d1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author | bgruening |
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date | Tue, 07 May 2019 13:41:07 -0400 |
parents | 1b8b6787dfbb |
children | 06d9381593a4 |
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0:1b8b6787dfbb | 1:10c0df29e6d1 |
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1 <tool id="ctb_alignit" name="Pharmacophore Alignment" version="1.0.3.1"> | 1 <tool id="ctb_alignit" name="Pharmacophore alignment" version="1.0.3.1"> |
2 <description>and Optimization (Align-it)</description> | 2 <description>and optimization (Align-it)</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.0.3">align_it</requirement> | 4 <requirement type="package" version="1.0.3">align_it</requirement> |
5 </requirements> | 5 </requirements> |
6 <command detect_errors="aggressive"> | 6 <command detect_errors="aggressive"> |
7 <![CDATA[ | 7 <![CDATA[ |
52 $withExclusion | 52 $withExclusion |
53 ]]> | 53 ]]> |
54 </command> | 54 </command> |
55 <inputs> | 55 <inputs> |
56 <param name="database" type="data" format='mol,mol2,sdf,smi,txt' label="Defines the database of molecules that will be used to screen"/> | 56 <param name="database" type="data" format='mol,mol2,sdf,smi,txt' label="Defines the database of molecules that will be used to screen"/> |
57 <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference Molecule"/> | 57 <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference molecule"/> |
58 | 58 |
59 <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment"> | 59 <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups to be used in the alignment"> |
60 <option value='AROM' selected="true">aromatic rings</option> | 60 <option value='AROM' selected="true">aromatic rings</option> |
61 <option value='HDON' selected="true">hydrogen bond donors</option> | 61 <option value='HDON' selected="true">hydrogen bond donors</option> |
62 <option value='HACC' selected="true">hydrogen bond acceptors</option> | 62 <option value='HACC' selected="true">hydrogen bond acceptors</option> |
63 <option value='LIPO' selected="true">lipophilic spots</option> | 63 <option value='LIPO' selected="true">lipophilic spots</option> |
64 <option value='CHARGE' selected="true">charge centers</option> | 64 <option value='CHARGE' selected="true">charge centers</option> |
67 | 67 |
68 <param name="epsilon" type="float" value="0.5" label='Change the tolerance for points to be matched in the alignment phase' | 68 <param name="epsilon" type="float" value="0.5" label='Change the tolerance for points to be matched in the alignment phase' |
69 help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned."> | 69 help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned."> |
70 <validator type="in_range" min="0" max="1" /> | 70 <validator type="in_range" min="0" max="1" /> |
71 </param> | 71 </param> |
72 <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' /> | 72 <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' |
73 help='Reduces computational time by merging neighboring pharmacophore points of the same type'/> | |
73 <param name='noNormal' type='boolean' truevalue='--noNormal' falsevalue='' | 74 <param name='noNormal' type='boolean' truevalue='--noNormal' falsevalue='' |
74 label='No normal information is included during the alignment' | 75 label='No normal information is included during the alignment' |
75 help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/> | 76 help="Using this flag makes the pharmacophore models less specific, but also less conformation-dependent."/> |
76 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' | 77 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' |
77 label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/> | 78 label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points, providing a more |
79 specific description of the molecule."/> | |
78 <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue='' | 80 <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue='' |
79 label='Add exclusion spheres into the optimization process instead of processing them afterwards' | 81 label='Add exclusion spheres into the optimization process instead of processing them afterwards' |
80 help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." /> | 82 help="When this flag is set, the exclusion spheres also have an impact on the alignment optimization procedure, |
83 rather than merely used to calculate the score at the end." /> | |
81 <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' | 84 <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' |
82 label='No translational or rotational optimization will be performed' help=""/> | 85 label='Skip translational and rotational optimization prior to alignment' help=""/> |
83 | 86 |
84 <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format"> | 87 <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format"> |
85 <option value='smi'>SMILES</option> | 88 <option value='smi'>SMILES</option> |
86 <option value='inchi'>InChI</option> | 89 <option value='inchi'>InChI</option> |
87 <option value='sdf'>SD file</option> | 90 <option value='sdf'>SDF</option> |
88 </param> | 91 </param> |
89 | 92 |
90 <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files" | 93 <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files" |
91 help="This value should be between 0 and 1."> | 94 help="This value should be between 0 and 1."> |
92 <validator type="in_range" min="0" max="1" /> | 95 <validator type="in_range" min="0" max="1" /> |
93 </param> | 96 </param> |
94 <param name="best" type="integer" value="0" label="With this option only a limited number of best scoring structures are written to the files" | 97 <param name="best" type="integer" value="0" label="Maximum number of best scoring structures to write to the files" |
95 help="0 means this option is deactivated"> | 98 help="With this option the number of best scoring structures written to the files is limited. 0 means this option is deactivated"> |
96 <validator type="in_range" min="0"/> | 99 <validator type="in_range" min="0"/> |
97 </param> | 100 </param> |
98 | 101 |
99 <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme"> | 102 <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme"> |
100 <option value='TANIMOTO'>Tanimoto</option> | 103 <option value='TANIMOTO'>Tanimoto</option> |
138 has been proven to be an important and useful method in drug discovery. | 141 has been proven to be an important and useful method in drug discovery. |
139 | 142 |
140 The functionality of Align-it_ consists mainly of two parts. | 143 The functionality of Align-it_ consists mainly of two parts. |
141 The first functionality is the generation of pharmacophores from molecules | 144 The first functionality is the generation of pharmacophores from molecules |
142 (use the tool **Pharmacophore generation** if you want to store these for further use). | 145 (use the tool **Pharmacophore generation** if you want to store these for further use). |
143 Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting | 146 Secondly, the similarity between pairs of pharmacophores can be |
144 score is calculated from the volume overlap resulting of the alignments. | 147 quantified. For this purpose, the pharmacophores need |
148 to be aligned in three-dimensional space and the overlap volume of the | |
149 alignments calculated. | |
145 | 150 |
146 .. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html | 151 .. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html |
147 | 152 |
148 ----- | 153 ----- |
149 | 154 |
150 .. class:: infomark | 155 .. class:: infomark |
151 | 156 |
152 **Input** | 157 **Input** |
153 | 158 |
154 * Example:: | 159 Upload a file containing molecular representations in MOL, MOL2, SMILES or |
160 SDF format; alternatively, if you have already calculated the pharmacophores, | |
161 upload the .phar file containing them. | |
162 | |
163 * Example (SDF):: | |
155 | 164 |
156 - database | 165 - database |
157 | 166 |
158 30 31 0 0 0 0 0 0 0999 V2000 | 167 30 31 0 0 0 0 0 0 0999 V2000 |
159 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 | 168 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 |
222 +--------+-----------------------------------------------------------------------+ | 231 +--------+-----------------------------------------------------------------------+ |
223 | 11 | TVERSKY_DB score | | 232 | 11 | TVERSKY_DB score | |
224 +--------+-----------------------------------------------------------------------+ | 233 +--------+-----------------------------------------------------------------------+ |
225 | 234 |
226 | 235 |
227 * Example:: | |
228 | |
229 - aligned Pharmacophores | |
230 | |
231 3033 | |
232 HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0 | |
233 HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0 | |
234 HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827 | |
235 HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616 | |
236 HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767 | |
237 $$$$ | |
238 | |
239 | |
240 ]]> | 236 ]]> |
241 </help> | 237 </help> |
242 <citations> | 238 <citations> |
243 <citation type="doi">10.1016/j.jmgm.2008.04.003</citation> | 239 <citation type="doi">10.1016/j.jmgm.2008.04.003</citation> |
244 </citations> | 240 </citations> |