Mercurial > repos > bgruening > silicos_it
view align-it/align-it.xml @ 11:c904022ce8e2
updates to silicos-it
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Mon, 27 May 2013 14:34:37 +0200 |
| parents | 6e6b05e75a3f |
| children | 62897185a803 |
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<tool id="ctb_alignit" name="Pharmacophore Alignment"> <description>and Optimization (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 #if str($database.ext).strip() == 'phar': --dbType PHAR #else: --dbType MOL #end if --dbase $database --reference $reference #if str($reference.ext).strip() == 'phar': --refType PHAR #else: --refType MOL #end if ####################################### #### output options ####################################### --pharmacophore $aligned_pharmacophores ##--out $aligned_structures ##--outType $oformat #if float( str($cutoff) ) > 0: --cutOff $cutoff #end if #if int( str($best) ) > 0: --best $best #end if --rankBy $rankBy --scores $score_result_file ####################################### #### Options ####################################### #set $fgroups_combined = str( $fgroups ).strip() --funcGroup $fgroups_combined --epsilon $epsilon $merge $noNormal $noHybrid $scoreOnly $withExclusion 2>&1 </command> <inputs> <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be used to screen"/> <param name="reference" type="data" format='mol,mol2,sdf,smi,phar' label="Reference Molecule"/> <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment"> <option value='AROM' selected="true">aromatic rings</option> <option value='HDON' selected="true">hydrogen bond donors</option> <option value='HACC' selected="true">hydrogen bond acceptors</option> <option value='LIPO' selected="true">lipophilic spots</option> <option value='CHARGE' selected="true">charge centers</option> </param> <param name="epsilon" type="float" value="0.5" label='Change the tolerance for points to be matched in the alignment phase' help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned."> <validator type="in_range" min="0" max="1" /> </param> <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' /> <param name='noNormal' type='boolean' truevalue='--noNormal' falsevalue='' label='No normal information is included during the alignment' help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/> <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."/> <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue='' label='Add exclusion spheres into the optimization process instead of processing them afterwards' help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." /> <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' label='No translational or rotational optimization will be performed' help=""/> <!-- <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format"> <option value='smi'>SMILES</option> <option value='inchi'>InChI</option> <option value='sdf'>SD file</option> </param> --> <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files" help="This value should be between 0 and 1."> <validator type="in_range" min="0" max="1" /> </param> <param name="best" type="integer" value="0" label="With this option only a limited number of best scoring structures are written to the files" help="0 means this option is deactivated"> <validator type="in_range" min="0"/> </param> <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme"> <option value='TANIMOTO'>Tanimoto</option> <option value='TVERSKY_REF'>TVERSKY_REF</option> <option value='TVERSKY_DB'>TVERSKY_DB</option> </param> </inputs> <outputs> <data name="aligned_pharmacophores" format="phar" label="${tool.name} on ${on_string} (aligned pharmacophores)"/> <!--<data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)"> <change_format> <when input="oformat" value="inchi" format="inchi"/> <when input="oformat" value="sdf" format="sdf"/> </change_format> </data>--> <data name="score_result_file" format="tabular" label="${tool.name} on ${on_string} (scores)"/> </outputs> <tests> <test> </test> </tests> <help> **What it does** Align-it_ is a tool to align molecules according their pharmacophores. 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 based on pharmacophore similarities have proven to be an important and useful method in drug discovery. The functionality of Align-it_ consists mainly of two parts. The first functionality consists of the **generation of pharmacophores from molecules** (use the tool *Pharmacophore generation* if you want to store these for later use). Second, pairs of pharmacophores can be aligned and the resulting score is calculated from the volume overlap resulting from the alignments. .. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html ----- **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 $$$$ The format of this scores output file is as follows: ====== ===================================================================== Column Content ====== ===================================================================== 1 Id of the reference structure 2 Maximum volume of the reference structure 3 Id of the database structure 4 Maximum volume of the database structure 5 Maximum volume overlap of the two structures 6 Overlap between pharmacophore and exclusion spheres in the reference 7 Corrected volume overlap between database pharmacophore and reference 8 Number of pharmacophore points in the processed pharmacophore 9 TANIMOTO score 10 TVERSKY_REF score 11 TVERSKY_DB score ====== ===================================================================== </help> </tool>