Mercurial > repos > bgruening > confab
view confab.xml @ 20:df8c4f142ae3
ChemicalToolBoX update.
author | Bjoern Gruening <bjoern.gruening@gmail.com> |
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date | Tue, 23 Jul 2013 14:53:58 +0200 |
parents | a396884f933a |
children | ff23947232d0 |
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<tool id="ctb_confab" name="Conformer calculation" version="0.1"> <description>for molecules (confab)</description> <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism> <requirements> <requirement type="package" version="1.0.1">confab</requirement> </requirements> <command> confab -i ${infile.ext} -o sdf -r $RMSD -e $energy -c $conformers $first_conformer $infile $outfile 2>&1 </command> <inputs> <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/> <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' /> <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' /> <param name='conformers' type='integer' value='100' label='Max number of conformers to test' /> <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' /> </inputs> <outputs> <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/> </outputs> <tests> <test> <param name="infile" value='CID_3033.sdf' ftype='sdf' /> <param name='RMSD' value='0.5' /> <param name='energy' value='50.0' /> <param name='conformers' value='100000' /> <param name='first_conformer' value='-a' /> <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' /> </test> </tests> <help> .. class:: infomark **What this tool does** Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers. .. _Confab: https://code.google.com/p/confab/ ----- .. class:: infomark **Input** * Example:: 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0 ....... 1 2 1 0 0 0 0 1 11 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 RMSD cutoff (in Angstrom) 0.5 Energy cutoff (in kcal/mol) 50.0 Max number of conformers to test 100000 Include the input conformation as the first conformer False ----- .. class:: infomark **Output** * Example:: 23 26 0 0 0 0 0 0 0 0999 V2000 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0 :: 1 2 1 0 0 0 0 1 11 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 6 11 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 6 0 0 0 10 9 1 1 0 0 0 ----- .. class:: infomark **Cite** Confab_ .. _Confab: https://code.google.com/p/confab/ </help> </tool>