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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
author bgruening
date Mon, 22 May 2017 03:02:39 -0400
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1 <tool id="ctb_alignit" name="Pharmacophore Alignment" version="1.0.3.1">
2 <description>and Optimization (Align-it)</description>
3 <requirements>
4 <requirement type="package" version="1.0.3">align_it</requirement>
5 </requirements>
6 <command detect_errors="aggressive">
7 <![CDATA[
8 align-it
9 #if str($database.ext).strip() == 'phar':
10 --dbType PHAR
11 #else:
12 --dbType '${database.ext}'
13 #end if
14 --dbase "$database"
15
16 --reference "$reference"
17 #if str($reference.ext).strip() == 'phar':
18 --refType PHAR
19 #else:
20 --refType ${reference.ext}
21 #end if
22 #######################################
23 #### output options
24 #######################################
25 --pharmacophore $aligned_pharmacophores
26
27
28 --out '$aligned_structures'
29 --outType $oformat
30
31 #if float( str($cutoff) ) > 0:
32 --cutOff $cutoff
33 #end if
34 #if int( str($best) ) > 0:
35 --best $best
36 #end if
37 --rankBy $rankBy
38 --scores '$score_result_file'
39
40 #######################################
41 #### Options
42 #######################################
43
44 #set $fgroups_combined = str( $fgroups ).strip()
45 --funcGroup $fgroups_combined
46
47 --epsilon $epsilon
48 $merge
49 $noNormal
50 $noHybrid
51 $scoreOnly
52 $withExclusion
53 ]]>
54 </command>
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"/>
57 <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference Molecule"/>
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">
60 <option value='AROM' selected="true">aromatic rings</option>
61 <option value='HDON' selected="true">hydrogen bond donors</option>
62 <option value='HACC' selected="true">hydrogen bond acceptors</option>
63 <option value='LIPO' selected="true">lipophilic spots</option>
64 <option value='CHARGE' selected="true">charge centers</option>
65 </param>
66
67
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.">
70 <validator type="in_range" min="0" max="1" />
71 </param>
72 <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' />
73 <param name='noNormal' type='boolean' truevalue='--noNormal' falsevalue=''
74 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 <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 <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue=''
79 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." />
81 <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue=''
82 label='No translational or rotational optimization will be performed' help=""/>
83
84 <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>
86 <option value='inchi'>InChI</option>
87 <option value='sdf'>SD file</option>
88 </param>
89
90 <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.">
92 <validator type="in_range" min="0" max="1" />
93 </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"
95 help="0 means this option is deactivated">
96 <validator type="in_range" min="0"/>
97 </param>
98
99 <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
100 <option value='TANIMOTO'>Tanimoto</option>
101 <option value='TVERSKY_REF'>TVERSKY_REF</option>
102 <option value='TVERSKY_DB'>TVERSKY_DB</option>
103 </param>
104
105 </inputs>
106 <outputs>
107 <data name="aligned_pharmacophores" format="txt" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
108 <data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)">
109 <change_format>
110 <when input="oformat" value="inchi" format="inchi"/>
111 <when input="oformat" value="sdf" format="sdf"/>
112 </change_format>
113 </data>
114 <data name="score_result_file" format="tabular" label="${tool.name} on ${on_string} (scores)"/>
115 </outputs>
116 <tests>
117 <test>
118 <param name="database" ftype="sdf" value="CID_2244.sdf"/>
119 <param name="reference" ftype="sdf" value="CID_2244.sdf"/>
120 <param name="oformat" value="sdf"/>
121 <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" />
122 <output name="aligned_structures" file="align-it_Search_on_CID2244.sdf" lines_diff="2" />
123 <output name="score_result_file" file="aliginit_scores.tabular.tabular" />
124 </test>
125 </tests>
126 <help>
127 <![CDATA[
128
129 .. class:: infomark
130
131 **What this tool does**
132
133 Align-it_ is a tool to align molecules according to their pharmacophores.
134 A pharmacophore is an abstract concept based on the specific interactions
135 observed in drug-receptor interactions: hydrogen bonding,
136 charge transfer, electrostatic and hydrophobic interactions.
137 Molecular modeling and/or screening based on pharmacophore similarities
138 has been proven to be an important and useful method in drug discovery.
139
140 The functionality of Align-it_ consists mainly of two parts.
141 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).
143 Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting
144 score is calculated from the volume overlap resulting of the alignments.
145
146 .. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html
147
148 -----
149
150 .. class:: infomark
151
152 **Input**
153
154 * Example::
155
156 - database
157
158 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
160 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
161 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
162 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
163 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
164 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
165 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
166 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
167 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
168 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
169 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
170 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
171 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
172 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
173 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
174 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
175 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
176 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
177 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
178 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
179 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
180 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
181 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
182 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
183 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
184 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
185 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
186 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
187 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
188 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
189
190 - cutoff : 0.0
191
192 -----
193
194 .. class:: infomark
195
196 **Output**
197
198 The format of the output file is shown in the table below:
199
200 +--------+-----------------------------------------------------------------------+
201 | Column | Content |
202 +========+=======================================================================+
203 | 1 | Id of the reference structure |
204 +--------+-----------------------------------------------------------------------+
205 | 2 | Maximum volume of the reference structure |
206 +--------+-----------------------------------------------------------------------+
207 | 3 | Id of the database structure |
208 +--------+-----------------------------------------------------------------------+
209 | 4 | Maximum volume of the database structure |
210 +--------+-----------------------------------------------------------------------+
211 | 5 | Maximum volume overlap of the two structures |
212 +--------+-----------------------------------------------------------------------+
213 | 6 | Overlap between pharmacophore and exclusion spheres in the reference |
214 +--------+-----------------------------------------------------------------------+
215 | 7 | Corrected volume overlap between database pharmacophore and reference |
216 +--------+-----------------------------------------------------------------------+
217 | 8 | Number of pharmacophore points in the processed pharmacophore |
218 +--------+-----------------------------------------------------------------------+
219 | 9 | TANIMOTO score |
220 +--------+-----------------------------------------------------------------------+
221 | 10 | TVERSKY_REF score |
222 +--------+-----------------------------------------------------------------------+
223 | 11 | TVERSKY_DB score |
224 +--------+-----------------------------------------------------------------------+
225
226
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 ]]>
241 </help>
242 <citations>
243 <citation type="doi">10.1016/j.jmgm.2008.04.003</citation>
244 </citations>
245 </tool>