Mercurial > repos > bgruening > silicos_it
comparison align-it/align-it.xml @ 0:bb92d30b4f52 draft
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author | bgruening |
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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>&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> |