Mercurial > repos > bgruening > align_it
diff align-it_create_db.xml @ 1:10c0df29e6d1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author | bgruening |
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date | Tue, 07 May 2019 13:41:07 -0400 |
parents | 1b8b6787dfbb |
children |
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--- a/align-it_create_db.xml Mon May 22 03:02:39 2017 -0400 +++ b/align-it_create_db.xml Tue May 07 13:41:07 2019 -0400 @@ -17,10 +17,12 @@ <param name="database" type="data" format='mol,mol2,sdf,smi' label="Defines the database of molecules that will be converted to pharmacophores" /> <param name='merge' type='boolean' truevalue='--merge' falsevalue='' - label='Merge pharmacophore points' /> + label='Merge pharmacophore points' + help='Reduces computational time by merging neighboring pharmacophore points of the same type'/> <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."/> + help="Using this flag will increase the number of pharmacophore points, providing a more + specific description of the molecule"/> </inputs> <outputs> <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/> @@ -41,7 +43,9 @@ Align-it_ is a tool to align molecules according to their pharmacophores. A pharmacophore is an abstract concept based on the specific interactions observed in drug-receptor interactions: hydrogen bonding, -charge transfer, electrostatic and hydrophobic interactions. +charge transfer, electrostatic and hydrophobic interactions. Each pharmacophore +contains multiple lines, representing so-called pharmacophore +points, each of which corresponds to a functional group of the molecule. Molecular modeling and/or screening based on pharmacophore similarities has been proven to be an important and useful method in drug discovery. @@ -51,7 +55,7 @@ can be aligned (use the tool **Pharmacophore Alignment**). The resulting score is calculated from the volume overlap resulting of the alignments. -.. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html +.. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html ----- @@ -59,7 +63,10 @@ **Input** -* Example:: +Upload a file containing molecular representations in MOL, MOL2, SMILES or +SDF format. + +* Example (SDF):: - database @@ -103,6 +110,14 @@ **Output** +A series of lines for each molecule, each describing a pharmocophore point +(functional group) of the molecules. The first column specifies a functional +type (e.g. HACC is a hydrogen bond acceptor; HYBL is a aromatic, lipophilic +region). Subsequent columns specify the position of the center in three-dimensional +space; see the documentation_ for more details. + +.. _documentation: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html + * Example:: - aligned Pharmacophores