Mercurial > repos > bgruening > silicos_it
view shape-it/shape-it.xml @ 17:62897185a803
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Fri, 31 May 2013 22:32:15 +0200 |
| parents | 6e6b05e75a3f |
| children | 588e3ff42c28 |
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<tool id="shapeit" name="Shape alignment" version="0.1"> <description>against a database of molecules (Shape-it)</description> <requirements> <requirement type="package" version="1.0.0">silicos_it</requirement> <requirement type="package" version="2.3.2">openbabel</requirement> </requirements> <command > shape-it --format ${database.ext} --dbase $database --reference $reference --addIterations $addIterations --best $best --cutoff $cutoff #if $scores == 'yes': --scores $output_scores #end if --rankBy $rankBy $noref --out $output 2>&1 </command> <inputs> <param name="reference" type="data" format='sdf,mol,mol2,smi' label="Refrence molecule" /> <param name="database" type="data" format='sdf,mol,mol2' label="Database of Molecules (needs 3D coordinates)" /> <param name="cutoff" type="float" value="0.0"> <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' /> <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' /> <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a Tab-delimited text file with the scores of molecules' checked="false" /> <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" /> <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="output" format_source='database' /> <data name="output_scores" format="tabular"> <filter>scores == "yes"</filter> </data> </outputs> <tests> <test> <param name="database" ftype='sdf' value="CID_3033.sdf" /> <param name="reference" type="sdf" value='CID_3037.sdf' /> <param name="cutoff" value="0.0" /> <param name='addIterations' value='0' /> <param name='best' value='0' /> <output name="output" ftype='sdf' file="shapeit_on_CID3033_and_CID3037.sdf" /> </test> </tests> <help> **What it 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 align criterion. It is based on the use of Gaussian volumes as descriptor for molecular shape as it 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 from the complete database. .. _Shape-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html .. _`Grant and Pickup`: http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(19961115)17:14%3C1653::AID-JCC7%3E3.0.CO;2-K/abstract ----- **Example** * input:: - 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 * output:: 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 ...... </help> </tool>