Mercurial > repos > bgruening > align_it
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| author | bgruening |
|---|---|
| date | Mon, 22 May 2017 03:02:39 -0400 |
| parents | |
| children | 10c0df29e6d1 |
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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 $noHybrid ]]> </command> <inputs> <param name="database" type="data" format='mol,mol2,sdf,smi' label="Defines the database of molecules that will be converted to pharmacophores" /> <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' /> <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/> </inputs> <outputs> <data name="pharmacophores" format="txt" label="${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. 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://www.silicos-it.com/software/align-it/1.0.3/align-it.html ----- .. class:: infomark **Input** * Example:: - 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** * 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>