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

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author bgruening
date Thu, 15 Aug 2013 03:34:00 -0400
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1 <tool id="ctb_alignit" name="Pharmacophore Alignment" version="0.1">
2 <description>and Optimization (Align-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 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 2>&#38;1
55 </command>
56 <inputs>
57 <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be used to screen"/>
58 <param name="reference" type="data" format='mol,mol2,sdf,smi,phar' label="Reference Molecule"/>
59
60 <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment">
61 <option value='AROM' selected="true">aromatic rings</option>
62 <option value='HDON' selected="true">hydrogen bond donors</option>
63 <option value='HACC' selected="true">hydrogen bond acceptors</option>
64 <option value='LIPO' selected="true">lipophilic spots</option>
65 <option value='CHARGE' selected="true">charge centers</option>
66 </param>
67
68
69 <param name="epsilon" type="float" value="0.5" label='Change the tolerance for points to be matched in the alignment phase' 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='' label='No normal information is included during the alignment' help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/>
74 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/>
75 <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue='' label='Add exclusion spheres into the optimization process instead of processing them afterwards' help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." />
76 <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' label='No translational or rotational optimization will be performed' help=""/>
77
78 <!--
79 <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format">
80 <option value='smi'>SMILES</option>
81 <option value='inchi'>InChI</option>
82 <option value='sdf'>SD file</option>
83 </param>
84 -->
85
86 <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files" help="This value should be between 0 and 1.">
87 <validator type="in_range" min="0" max="1" />
88 </param>
89 <param name="best" type="integer" value="0" label="With this option only a limited number of best scoring structures are written to the files" help="0 means this option is deactivated">
90 <validator type="in_range" min="0"/>
91 </param>
92
93 <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
94 <option value='TANIMOTO'>Tanimoto</option>
95 <option value='TVERSKY_REF'>TVERSKY_REF</option>
96 <option value='TVERSKY_DB'>TVERSKY_DB</option>
97 </param>
98
99 </inputs>
100 <outputs>
101 <data name="aligned_pharmacophores" format="phar" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
102 <!--<data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)">
103 <change_format>
104 <when input="oformat" value="inchi" format="inchi"/>
105 <when input="oformat" value="sdf" format="sdf"/>
106 </change_format>
107 </data>-->
108 <data name="score_result_file" format="tabular" label="${tool.name} on ${on_string} (scores)"/>
109 </outputs>
110 <tests>
111 <test>
112 </test>
113 </tests>
114 <help>
115
116 .. class:: infomark
117
118 **What this tool does**
119
120 Align-it_ is a tool to align molecules according to their pharmacophores.
121 A pharmacophore is an abstract concept based on the specific interactions
122 observed in drug-receptor interactions: hydrogen bonding,
123 charge transfer, electrostatic and hydrophobic interactions.
124 Molecular modeling and/or screening based on pharmacophore similarities
125 has been proven to be an important and useful method in drug discovery.
126
127 The functionality of Align-it_ consists mainly of two parts.
128 The first functionality is the generation of pharmacophores from molecules
129 (use the tool **Pharmacophore generation** if you want to store these for further use).
130 Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting
131 score is calculated from the volume overlap resulting of the alignments.
132
133 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
134
135 -----
136
137 .. class:: infomark
138
139 **Input**
140
141 * Example::
142
143 - database
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
177 - cutoff : 0.0
178
179 -----
180
181 .. class:: infomark
182
183 **Output**
184
185 The format of the output file is shown in the table below:
186
187 +--------+-----------------------------------------------------------------------+
188 | Column | Content |
189 +========+=======================================================================+
190 | 1 | Id of the reference structure |
191 +--------+-----------------------------------------------------------------------+
192 | 2 | Maximum volume of the reference structure |
193 +--------+-----------------------------------------------------------------------+
194 | 3 | Id of the database structure |
195 +--------+-----------------------------------------------------------------------+
196 | 4 | Maximum volume of the database structure |
197 +--------+-----------------------------------------------------------------------+
198 | 5 | Maximum volume overlap of the two structures |
199 +--------+-----------------------------------------------------------------------+
200 | 6 | Overlap between pharmacophore and exclusion spheres in the reference |
201 +--------+-----------------------------------------------------------------------+
202 | 7 | Corrected volume overlap between database pharmacophore and reference |
203 +--------+-----------------------------------------------------------------------+
204 | 8 | Number of pharmacophore points in the processed pharmacophore |
205 +--------+-----------------------------------------------------------------------+
206 | 9 | TANIMOTO score |
207 +--------+-----------------------------------------------------------------------+
208 | 10 | TVERSKY_REF score |
209 +--------+-----------------------------------------------------------------------+
210 | 11 | TVERSKY_DB score |
211 +--------+-----------------------------------------------------------------------+
212
213
214 * Example::
215
216 - aligned Pharmacophores
217
218 3033
219 HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0
220 HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0
221 HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827
222 HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616
223 HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767
224 $$$$
225
226 -----
227
228 .. class:: infomark
229
230 **Cite**
231
232 `Silicos-it`_ - align-it
233
234 .. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
235
236
237 </help>
238 </tool>