Mercurial > repos > bgruening > align_it
comparison 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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| -1:000000000000 | 0:1b8b6787dfbb |
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| 1 <tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1"> | |
| 2 <description>generation (Align-it)</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.3">align_it</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="aggressive"> | |
| 7 <![CDATA[ | |
| 8 align-it | |
| 9 --dbType '${database.ext}' | |
| 10 --dbase '$database' | |
| 11 --pharmacophore '$pharmacophores' | |
| 12 $merge | |
| 13 $noHybrid | |
| 14 ]]> | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param name="database" type="data" format='mol,mol2,sdf,smi' | |
| 18 label="Defines the database of molecules that will be converted to pharmacophores" /> | |
| 19 <param name='merge' type='boolean' truevalue='--merge' falsevalue='' | |
| 20 label='Merge pharmacophore points' /> | |
| 21 <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' | |
| 22 label='Disable the use of hybrid pharmacophore points' | |
| 23 help="Using this flag will increase the number of pharmacophore points."/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="database" ftype="sdf" value="6mol.sdf"/> | |
| 31 <output name="pharmacophores" file="alignit_Create_Phar_DB_6mol.phar" /> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help> | |
| 35 <![CDATA[ | |
| 36 | |
| 37 .. class:: infomark | |
| 38 | |
| 39 **What this tool does** | |
| 40 | |
| 41 Align-it_ is a tool to align molecules according to their pharmacophores. | |
| 42 A pharmacophore is an abstract concept based on the specific interactions | |
| 43 observed in drug-receptor interactions: hydrogen bonding, | |
| 44 charge transfer, electrostatic and hydrophobic interactions. | |
| 45 Molecular modeling and/or screening based on pharmacophore similarities | |
| 46 has been proven to be an important and useful method in drug discovery. | |
| 47 | |
| 48 The functionality of Align-it_ consists mainly of two parts. | |
| 49 The first functionality is the generation of pharmacophores from molecules | |
| 50 (the function of this tool). Secondly, pairs of pharmacophores | |
| 51 can be aligned (use the tool **Pharmacophore Alignment**). The resulting | |
| 52 score is calculated from the volume overlap resulting of the alignments. | |
| 53 | |
| 54 .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html | |
| 55 | |
| 56 ----- | |
| 57 | |
| 58 .. class:: infomark | |
| 59 | |
| 60 **Input** | |
| 61 | |
| 62 * Example:: | |
| 63 | |
| 64 - database | |
| 65 | |
| 66 30 31 0 0 0 0 0 0 0999 V2000 | |
| 67 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 68 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 69 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 70 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 71 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 72 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 73 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 74 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 75 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 76 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 77 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 78 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 79 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 80 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 81 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 82 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 83 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 84 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 85 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 86 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 87 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 88 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 89 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 90 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 91 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 92 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 93 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 94 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 95 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 96 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 97 | |
| 98 - cutoff : 0.0 | |
| 99 | |
| 100 ----- | |
| 101 | |
| 102 .. class:: infomark | |
| 103 | |
| 104 **Output** | |
| 105 | |
| 106 * Example:: | |
| 107 | |
| 108 - aligned Pharmacophores | |
| 109 | |
| 110 3033 | |
| 111 HYBL -1.98494 1.9958 0.532089 0.7 0 0 0 0 | |
| 112 HYBL 3.52122 -0.309347 0.122783 0.7 0 0 0 0 | |
| 113 HYBH -3.262 -2.9284 -1.0647 1 1 -3.5666 -3.7035 -1.61827 | |
| 114 HDON 0.2679 -0.2051 -0.399 1 1 -0.076102 -0.981133 -0.927616 | |
| 115 HACC -2.7906 -1.9108 0.9092 1 1 -2.74368 -1.94015 1.90767 | |
| 116 $$$$ | |
| 117 | |
| 118 | |
| 119 ]]> | |
| 120 </help> | |
| 121 <citations> | |
| 122 <citation type="doi">10.1016/j.jmgm.2008.04.003</citation> | |
| 123 </citations> | |
| 124 </tool> |