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comparison align-it_create_db.xml @ 1:9825e7be61df draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:29:20 -0400
parents c021d69c8e2e
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0:c021d69c8e2e 1:9825e7be61df
15 </command> 15 </command>
16 <inputs> 16 <inputs>
17 <param name="database" type="data" format='mol,mol2,sdf,smi' 17 <param name="database" type="data" format='mol,mol2,sdf,smi'
18 label="Defines the database of molecules that will be converted to pharmacophores" /> 18 label="Defines the database of molecules that will be converted to pharmacophores" />
19 <param name='merge' type='boolean' truevalue='--merge' falsevalue='' 19 <param name='merge' type='boolean' truevalue='--merge' falsevalue=''
20 label='Merge pharmacophore points' /> 20 label='Merge pharmacophore points'
21 help='Reduces computational time by merging neighboring pharmacophore points of the same type'/>
21 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' 22 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue=''
22 label='Disable the use of hybrid pharmacophore points' 23 label='Disable the use of hybrid pharmacophore points'
23 help="Using this flag will increase the number of pharmacophore points."/> 24 help="Using this flag will increase the number of pharmacophore points, providing a more
25 specific description of the molecule"/>
24 </inputs> 26 </inputs>
25 <outputs> 27 <outputs>
26 <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/> 28 <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/>
27 </outputs> 29 </outputs>
28 <tests> 30 <tests>
39 **What this tool does** 41 **What this tool does**
40 42
41 Align-it_ is a tool to align molecules according to their pharmacophores. 43 Align-it_ is a tool to align molecules according to their pharmacophores.
42 A pharmacophore is an abstract concept based on the specific interactions 44 A pharmacophore is an abstract concept based on the specific interactions
43 observed in drug-receptor interactions: hydrogen bonding, 45 observed in drug-receptor interactions: hydrogen bonding,
44 charge transfer, electrostatic and hydrophobic interactions. 46 charge transfer, electrostatic and hydrophobic interactions. Each pharmacophore
47 contains multiple lines, representing so-called pharmacophore
48 points, each of which corresponds to a functional group of the molecule.
45 Molecular modeling and/or screening based on pharmacophore similarities 49 Molecular modeling and/or screening based on pharmacophore similarities
46 has been proven to be an important and useful method in drug discovery. 50 has been proven to be an important and useful method in drug discovery.
47 51
48 The functionality of Align-it_ consists mainly of two parts. 52 The functionality of Align-it_ consists mainly of two parts.
49 The first functionality is the generation of pharmacophores from molecules 53 The first functionality is the generation of pharmacophores from molecules
50 (the function of this tool). Secondly, pairs of pharmacophores 54 (the function of this tool). Secondly, pairs of pharmacophores
51 can be aligned (use the tool **Pharmacophore Alignment**). The resulting 55 can be aligned (use the tool **Pharmacophore Alignment**). The resulting
52 score is calculated from the volume overlap resulting of the alignments. 56 score is calculated from the volume overlap resulting of the alignments.
53 57
54 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html 58 .. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html
55 59
56 ----- 60 -----
57 61
58 .. class:: infomark 62 .. class:: infomark
59 63
60 **Input** 64 **Input**
61 65
62 * Example:: 66 Upload a file containing molecular representations in MOL, MOL2, SMILES or
67 SDF format.
68
69 * Example (SDF)::
63 70
64 - database 71 - database
65 72
66 30 31 0 0 0 0 0 0 0999 V2000 73 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 74 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
101 108
102 .. class:: infomark 109 .. class:: infomark
103 110
104 **Output** 111 **Output**
105 112
113 A series of lines for each molecule, each describing a pharmocophore point
114 (functional group) of the molecules. The first column specifies a functional
115 type (e.g. HACC is a hydrogen bond acceptor; HYBL is a aromatic, lipophilic
116 region). Subsequent columns specify the position of the center in three-dimensional
117 space; see the documentation_ for more details.
118
119 .. _documentation: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html
120
106 * Example:: 121 * Example::
107 122
108 - aligned Pharmacophores 123 - aligned Pharmacophores
109 124
110 3033 125 3033