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comparison align-it/align-it_create_db.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_create_db" name="Pharmacophore" version="0.1">
2 <description>generation (Align-it)</description>
3 <requirements>
4 <requirement type="package" version="1.0.0">silicos_it</requirement>
5 <requirement type="package" version="2.3.2">openbabel</requirement>
6 </requirements>
7 <command>
8 align-it
9 --dbType ${database.ext}
10 --dbase $database
11 --pharmacophore $pharmacophores
12 $merge
13 $noHybrid
14
15 2>&#38;1
16 </command>
17 <inputs>
18 <param name="database" type="data" format='mol,mol2,sdf,smi' label="Defines the database of molecules that will be converted to pharmacophores" />
19 <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' />
20 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/>
21 </inputs>
22 <outputs>
23 <data name="pharmacophores" format="phar" label="${tool.name} on ${on_string} (scores)"/>
24 </outputs>
25 <tests>
26 <test>
27 </test>
28 </tests>
29 <help>
30
31 .. class:: infomark
32
33 **What this tool does**
34
35 Align-it_ is a tool to align molecules according to their pharmacophores.
36 A pharmacophore is an abstract concept based on the specific interactions
37 observed in drug-receptor interactions: hydrogen bonding,
38 charge transfer, electrostatic and hydrophobic interactions.
39 Molecular modeling and/or screening based on pharmacophore similarities
40 has been proven to be an important and useful method in drug discovery.
41
42 The functionality of Align-it_ consists mainly of two parts.
43 The first functionality is the generation of pharmacophores from molecules
44 (the function of this tool). Secondly, pairs of pharmacophores
45 can be aligned (use the tool **Pharmacophore Alignment**). The resulting
46 score is calculated from the volume overlap resulting of the alignments.
47
48 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
49
50 -----
51
52 .. class:: infomark
53
54 **Input**
55
56 * Example::
57
58 - database
59
60 30 31 0 0 0 0 0 0 0999 V2000
61 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
62 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
63 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
64 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
65 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
66 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
67 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
68 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
69 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
70 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
71 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
72 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
73 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
74 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
75 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
76 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
77 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
78 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
79 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
80 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
81 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
82 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
83 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
84 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
85 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
86 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
87 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
88 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
89 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
90 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
91
92 - cutoff : 0.0
93
94 -----
95
96 .. class:: infomark
97
98 **Output**
99
100 * Example::
101
102 - aligned Pharmacophores
103
104 3033
105 HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0
106 HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0
107 HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827
108 HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616
109 HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767
110 $$$$
111
112 -----
113
114 .. class:: infomark
115
116 **Cite**
117
118 `Silicos-it`_ - align-it
119
120 .. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
121
122 </help>
123 </tool>