Mercurial > repos > bgruening > confab
changeset 18:a396884f933a
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Fri, 19 Jul 2013 16:28:23 +0200 |
| parents | 6eb2a0358b9c |
| children | 5eeebd391cc2 |
| files | confab.xml force_pre-commit_hook_temp_file |
| diffstat | 1 files changed, 45 insertions(+), 25 deletions(-) [+] |
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--- a/confab.xml Sat Jun 01 20:03:28 2013 +0200 +++ b/confab.xml Fri Jul 19 16:28:23 2013 +0200 @@ -36,41 +36,52 @@ </tests> <help> +.. class:: infomark -**What it does** +**What this tool does** - confab is an application to systematically generate diverse low-energy conformers for molecules. +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/ ----- -**Example** +.. class:: infomark -* input: +**Input** -Dataset:: +* 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 + 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 + + ....... - - 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 + 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 -* output:: + 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 @@ -111,6 +122,15 @@ 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>