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comparison align-it_create_db.xml @ 0:1b8b6787dfbb draft

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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_create_db" name="Pharmacophore" version="0.1">
2 <description>generation (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 --dbType '${database.ext}'
10 --dbase '$database'
11 --pharmacophore '$pharmacophores'
12 $merge
13 $noHybrid
14 ]]>
15 </command>
16 <inputs>
17 <param name="database" type="data" format='mol,mol2,sdf,smi'
18 label="Defines the database of molecules that will be converted to pharmacophores" />
19 <param name='merge' type='boolean' truevalue='--merge' falsevalue=''
20 label='Merge pharmacophore points' />
21 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue=''
22 label='Disable the use of hybrid pharmacophore points'
23 help="Using this flag will increase the number of pharmacophore points."/>
24 </inputs>
25 <outputs>
26 <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="database" ftype="sdf" value="6mol.sdf"/>
31 <output name="pharmacophores" file="alignit_Create_Phar_DB_6mol.phar" />
32 </test>
33 </tests>
34 <help>
35 <![CDATA[
36
37 .. class:: infomark
38
39 **What this tool does**
40
41 Align-it_ is a tool to align molecules according to their pharmacophores.
42 A pharmacophore is an abstract concept based on the specific interactions
43 observed in drug-receptor interactions: hydrogen bonding,
44 charge transfer, electrostatic and hydrophobic interactions.
45 Molecular modeling and/or screening based on pharmacophore similarities
46 has been proven to be an important and useful method in drug discovery.
47
48 The functionality of Align-it_ consists mainly of two parts.
49 The first functionality is the generation of pharmacophores from molecules
50 (the function of this tool). Secondly, pairs of pharmacophores
51 can be aligned (use the tool **Pharmacophore Alignment**). The resulting
52 score is calculated from the volume overlap resulting of the alignments.
53
54 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
55
56 -----
57
58 .. class:: infomark
59
60 **Input**
61
62 * Example::
63
64 - database
65
66 30 31 0 0 0 0 0 0 0999 V2000
67 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
68 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
69 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
70 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
71 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
72 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
73 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
74 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
75 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
76 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
77 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
78 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
79 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
80 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
81 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
82 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
83 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
84 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
85 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
86 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
87 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
88 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
89 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
90 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
91 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
92 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
93 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
94 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
95 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
96 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
97
98 - cutoff : 0.0
99
100 -----
101
102 .. class:: infomark
103
104 **Output**
105
106 * Example::
107
108 - aligned Pharmacophores
109
110 3033
111 HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0
112 HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0
113 HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827
114 HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616
115 HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767
116 $$$$
117
118
119 ]]>
120 </help>
121 <citations>
122 <citation type="doi">10.1016/j.jmgm.2008.04.003</citation>
123 </citations>
124 </tool>