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| author | bgruening |
|---|---|
| date | Tue, 07 May 2019 13:41:43 -0400 |
| parents | 31f5b5421a02 |
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<tool id="ctb_shapeit" name="Shape alignment" version="1.0.1.0"> <description>against a database of molecules (shape-it)</description> <requirements> <requirement type="package" version="1.0.1">shape_it</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ ln -s ${database} ./database.${database.ext} && ln -s ${reference} ./reference.${reference.ext} && shape-it --format ${database.ext} --dbase ./database.${database.ext} --reference ./reference.${reference.ext} --addIterations $addIterations #if int($best) > 0: --best $best #end if --cutoff $cutoff #if $scores: --scores $output_scores #end if --rankBy $rankBy $noref $scoreonly --out ./result.${database.ext} && mv ./result.${database.ext} '$output' ]]> </command> <inputs> <param name="reference" type="data" format='sdf,mol,mol2' label="Reference molecule (with 3D coordinates)" /> <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" /> <param name="cutoff" type="float" value="0.0" label="Cutoff" help="Only molecules with a score higher than the cutoff are reported; the scoring function is defined by the scoring scheme."> <validator type="in_range" min="0.0" /> </param> <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' help="The default value is set to 0, which refers to only a local gradient ascent."/> <param name='best' type='integer' value='0' label='Number of best-scoring molecules to report' help="The N best scoring molecules are reported; 0 means all molecules are reported"/> <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a tab-delimited text file with the molecule scores' checked="false" /> <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='Do not write reference molecule into the output files' checked="false" /> <param name='scoreonly' type='boolean' truevalue='--scoreOnly' falsevalue='' label='Only the volume overlap between the reference and the given pose is computed' checked="false" /> <param name='rankBy' type='select' format='text' label="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="output" format_source='database' /> <data name="output_scores" format="tabular"> <filter>scores is True</filter> </data> </outputs> <tests> <test> <param name="database" ftype='sdf' value="CID_3033.sdf" /> <param name="reference" ftype="sdf" value='CID_3037.sdf' /> <param name="cutoff" value="0.0" /> <param name='addIterations' value='0' /> <param name='best' value='0' /> <param name='scoreonly' value="true" /> <output name="output" ftype='sdf' file="shapeit_on_CID3033_and_CID3037.sdf" lines_diff="4" /> </test> </tests> <help> <![CDATA[ .. class:: infomark **What this tool does** Shape-it_ is a tool that aligns a reference molecule against a set of database molecules using the shape of the molecules as the alignment criterion. It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as was introduced by Grant and Pickup. The program expects one reference molecule with its three-dimensional coordinates and one database files containing one or more molecules in three dimensions. The results are either the alignment of all database molecules and their respective scores or the N best scoring molecules of the complete database. .. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016 .. _Shape-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/shape-it/1.0.1/shape-it.html ----- .. class:: infomark **Input** `3D formats recognized by OpenBabel`_ - either SDF, MOL, or MOL2 .. _3D formats recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats * Example (SDF):: - database 27 28 0 0 0 0 0 0 0999 V2000 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 15 1 0 0 0 0 3 8 1 0 0 0 0 3 26 1 0 0 0 0 4 9 1 0 0 0 0 4 27 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 ..... - reference 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 1 14 1 0 0 0 0 2 15 1 0 0 0 0 3 16 1 0 0 0 0 3 30 1 0 0 0 0 4 16 2 0 0 0 0 5 7 1 0 0 0 0 5 9 1 0 0 0 0 5 22 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 ...... - cutoff : 0.0 ----- .. class:: infomark **Output** The output file contains first the reference molecule, followed by the molecules aligned to the reference molecule. If the 'Number of best-scoring molecules' option is set only the top-best scoring molecules will be reported in the output file, otherwise all molecules are written to the output file. * Example:: 27 28 0 0 0 0 0 0 0 0999 V2000 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 15 1 0 0 0 0 3 8 1 0 0 0 0 3 26 1 0 0 0 0 4 9 1 0 0 0 0 4 27 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 5 18 1 0 0 0 0 5 19 1 0 0 0 0 6 8 2 0 0 0 0 ...... In addition, if the option to output scores is selected, a tabular file will be created. Each line represents a molecule from the database, with columns describing the volumes of the reference and database molecules, overlap volumes, and Shape-it scores produced by the three scoring schemes. * Example:: dbName refName Shape-it::Tanimoto Shape-it::Tversky_Ref Shape-it::Tversky_Db overlap refVolume dbVolume 3033 3037 0.562 0.754 0.688 128.56 169.59 187.87 ]]> </help> <citations> <citation type="doi">10.1021/j100011a016</citation> </citations> </tool>