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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit 00844534f9a2ffdf41fb9d5186d9a1e574c302d2"
| author | bgruening |
|---|---|
| date | Fri, 10 Sep 2021 08:08:30 +0000 |
| parents | 9825e7be61df |
| children |
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<tool id="ctb_alignit" name="Pharmacophore alignment" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>and optimization (Align-it)</description> <macros> <token name="@TOOL_VERSION@">1.0.4</token> <token name="@GALAXY_VERSION@">0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">align_it</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ align-it #if str($database.ext).strip() == 'phar': --dbType PHAR #else: --dbType '${database.ext}' #end if --dbase "$database" --reference "$reference" #if str($reference.ext).strip() == 'phar': --refType PHAR #else: --refType ${reference.ext} #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 ]]> </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 to be 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' help='Reduces computational time by merging neighboring pharmacophore points of the same type'/> <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, providing a more specific description of the molecule."/> <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 also have an impact on the alignment optimization procedure, rather than merely used to calculate the score at the end." /> <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue='' label='Skip translational and rotational optimization prior to alignment' 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'>SDF</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="Maximum number of best scoring structures to write to the files" help="With this option the number of best scoring structures written to the files is limited. 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> <param name="database" ftype="sdf" value="CID_2244.sdf"/> <param name="reference" ftype="sdf" value="CID_2244.sdf"/> <param name="oformat" value="sdf"/> <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" ftype="phar" /> <output name="aligned_structures" file="align-it_Search_on_CID2244.sdf" lines_diff="2" /> <output name="score_result_file" file="aliginit_scores.tabular.tabular" /> </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 (use the tool **Pharmacophore generation** if you want to store these for further use). Secondly, the similarity between pairs of pharmacophores can be quantified. For this purpose, the pharmacophores need to be aligned in three-dimensional space and the overlap volume of the alignments calculated. .. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html ----- .. class:: infomark **Input** Upload a file containing molecular representations in MOL, MOL2, SMILES or SDF format; alternatively, if you have already calculated the pharmacophores, upload the .phar file containing them. * Example (SDF):: - 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** The format of the output file is shown in the table below: +--------+-----------------------------------------------------------------------+ | 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> <citations> <citation type="doi">10.1016/j.jmgm.2008.04.003</citation> </citations> </tool>