Mercurial > repos > bgruening > silicos_it
changeset 10:c5a538ec7b43
delete obsolete file
| author | Björn Grüning <bjoern.gruening@gmail.com> |
|---|---|
| date | Sun, 26 May 2013 16:50:31 +0200 |
| parents | 6e6b05e75a3f |
| children | c904022ce8e2 fd688cfd7566 |
| files | align-it/alignit_create_db.xml |
| diffstat | 1 files changed, 0 insertions(+), 91 deletions(-) [+] |
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--- a/align-it/alignit_create_db.xml Sun May 26 16:50:00 2013 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,91 +0,0 @@ -<tool id="ctb_alignit_create_db" name="Pharmacophore"> - <description>database building (Align-it)</description> - <requirements> - <requirement type="package" version="1.0.0">silicos_it</requirement> - <requirement type="package" version="2.3.2">openbabel</requirement> - </requirements> - <command > - align-it --format ${database.ext} -d $database -p $Pharmacophores --dbType MOL 2>&1 - </command> - <inputs> - <param name="database" type="data" format='sdf,mol,mol2,inchi,smi' label="database"/> - </inputs> - <outputs> - <data name="Pharmacophores" format="phar" /> - </outputs> - <tests> - <test> - <param name="database" ftype='sdf' value='6mol.sdf'/> - <data name="Pharmacophores" ftype="phar" file='alignit_create_db_on_6mol.phar' /> - </test> - </tests> - <help> - -**What it does** - -Pharao is an acronym for Pharmacophore Alignment and Optimization. A -pharmacophore is an abstract concept based on the specific interactions -that have been observed in drug-receptor interactions: hydrogen bonding, -charge transfer, electrostatic and hydrophobic interactions. Molecular -modeling and/or screening using pharmacophores have proven to be an -important and useful method in drug discovery. - - ------ - -**Example** - -* input:: - - - 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 - -* output:: - - - 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> -</tool>