Mercurial > repos > bgruening > align_it
changeset 1:10c0df29e6d1 draft
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 13:41:07 -0400 |
parents | 1b8b6787dfbb |
children | 06d9381593a4 |
files | align-it.xml align-it_create_db.xml |
diffstat | 2 files changed, 44 insertions(+), 33 deletions(-) [+] |
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--- a/align-it.xml Mon May 22 03:02:39 2017 -0400 +++ b/align-it.xml Tue May 07 13:41:07 2019 -0400 @@ -1,5 +1,5 @@ -<tool id="ctb_alignit" name="Pharmacophore Alignment" version="1.0.3.1"> - <description>and Optimization (Align-it)</description> +<tool id="ctb_alignit" name="Pharmacophore alignment" version="1.0.3.1"> + <description>and optimization (Align-it)</description> <requirements> <requirement type="package" version="1.0.3">align_it</requirement> </requirements> @@ -54,9 +54,9 @@ </command> <inputs> <param name="database" type="data" format='mol,mol2,sdf,smi,txt' label="Defines the database of molecules that will be used to screen"/> - <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference Molecule"/> + <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference molecule"/> - <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment"> + <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups to be used in the alignment"> <option value='AROM' selected="true">aromatic rings</option> <option value='HDON' selected="true">hydrogen bond donors</option> <option value='HACC' selected="true">hydrogen bond acceptors</option> @@ -69,30 +69,33 @@ help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned."> <validator type="in_range" min="0" max="1" /> </param> - <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' /> + <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' + help='Reduces computational time by merging neighboring pharmacophore points of the same type'/> <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."/> + help="Using this flag makes the pharmacophore models less specific, but also less conformation-dependent."/> <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."/> + label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points, providing a more + specific description of the molecule."/> <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." /> + help="When this flag is set, the exclusion spheres also have an impact on the alignment optimization procedure, + rather than merely used to calculate the score at the end." /> <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' - label='No translational or rotational optimization will be performed' help=""/> + label='Skip translational and rotational optimization prior to alignment' help=""/> <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format"> <option value='smi'>SMILES</option> <option value='inchi'>InChI</option> - <option value='sdf'>SD file</option> + <option value='sdf'>SDF</option> </param> <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."> <validator type="in_range" min="0" max="1" /> </param> - <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"> + <param name="best" type="integer" value="0" label="Maximum number of best scoring structures to write to the files" + help="With this option the number of best scoring structures written to the files is limited. 0 means this option is deactivated"> <validator type="in_range" min="0"/> </param> @@ -140,8 +143,10 @@ The functionality of Align-it_ consists mainly of two parts. The first functionality is the generation of pharmacophores from molecules (use the tool **Pharmacophore generation** if you want to store these for further use). -Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting -score is calculated from the volume overlap resulting of the alignments. +Secondly, the similarity between pairs of pharmacophores can be +quantified. For this purpose, the pharmacophores need +to be aligned in three-dimensional space and the overlap volume of the +alignments calculated. .. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html @@ -151,7 +156,11 @@ **Input** -* Example:: +Upload a file containing molecular representations in MOL, MOL2, SMILES or +SDF format; alternatively, if you have already calculated the pharmacophores, +upload the .phar file containing them. + +* Example (SDF):: - database @@ -224,19 +233,6 @@ +--------+-----------------------------------------------------------------------+ -* Example:: - - - aligned Pharmacophores - - 3033 - HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0 - HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0 - HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827 - HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616 - HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767 - $$$$ - - ]]> </help> <citations>
--- 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