Mercurial > repos > bgruening > silicos_it
diff align-it/align-it.xml @ 0:bb92d30b4f52 draft
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| author | bgruening |
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| date | Thu, 15 Aug 2013 03:34:00 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align-it/align-it.xml Thu Aug 15 03:34:00 2013 -0400 @@ -0,0 +1,238 @@ +<tool id="ctb_alignit" name="Pharmacophore Alignment" version="0.1"> + <description>and Optimization (Align-it)</description> + <requirements> + <requirement type="package" version="1.0.1">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 ${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 + + 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> + +.. 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, pairs of pharmacophores can be aligned (the function of this tool). 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** + +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 | ++--------+-----------------------------------------------------------------------+ + + +* 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 + $$$$ + +----- + +.. class:: infomark + +**Cite** + +`Silicos-it`_ - align-it + +.. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html + + + </help> +</tool>