Mercurial > repos > bgruening > align_it
view 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 |
|---|---|
| date | Tue, 07 May 2019 13:41:07 -0400 |
| parents | 1b8b6787dfbb |
| children |
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<tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1"> <description>generation (Align-it)</description> <requirements> <requirement type="package" version="1.0.3">align_it</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ align-it --dbType '${database.ext}' --dbase '$database' --pharmacophore '$pharmacophores' $merge $noHybrid ]]> </command> <inputs> <param name="database" type="data" format='mol,mol2,sdf,smi' label="Defines the database of molecules that will be converted to pharmacophores" /> <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' help='Reduces computational time by merging neighboring pharmacophore points of the same type'/> <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points, providing a more specific description of the molecule"/> </inputs> <outputs> <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/> </outputs> <tests> <test> <param name="database" ftype="sdf" value="6mol.sdf"/> <output name="pharmacophores" file="alignit_Create_Phar_DB_6mol.phar" /> </test> </tests> <help> <![CDATA[ .. class:: infomark **What this tool does** 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. 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. The functionality of Align-it_ consists mainly of two parts. The first functionality is the generation of pharmacophores from molecules (the function of this tool). Secondly, pairs of pharmacophores can be aligned (use the tool **Pharmacophore Alignment**). The resulting score is calculated from the volume overlap resulting of the alignments. .. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html ----- .. class:: infomark **Input** Upload a file containing molecular representations in MOL, MOL2, SMILES or SDF format. * Example (SDF):: - database 30 31 0 0 0 0 0 0 0999 V2000 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 - cutoff : 0.0 ----- .. class:: infomark **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 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> <citation type="doi">10.1016/j.jmgm.2008.04.003</citation> </citations> </tool>