Mercurial > repos > bgruening > confab
diff confab.xml @ 0:4a73b5059c22 draft
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| author | bgruening |
|---|---|
| date | Thu, 15 Aug 2013 03:31:39 -0400 |
| parents | |
| children | 731ad135ddb4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confab.xml Thu Aug 15 03:31:39 2013 -0400 @@ -0,0 +1,138 @@ +<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>