Mercurial > repos > bgruening > align_it
diff align-it_create_db.xml @ 0:1b8b6787dfbb draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
| author | bgruening |
|---|---|
| date | Mon, 22 May 2017 03:02:39 -0400 |
| parents | |
| children | 10c0df29e6d1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it_create_db.xml Mon May 22 03:02:39 2017 -0400 @@ -0,0 +1,124 @@ +<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>