Mercurial > repos > bgruening > simsearch
changeset 15:b4eaf75cac77
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Fri, 19 Jul 2013 16:28:47 +0200 |
| parents | 47d2bf691908 |
| children | 987b62da416d |
| files | force_pre-commit_hook_temp_file simsearch.xml |
| diffstat | 1 files changed, 15 insertions(+), 10 deletions(-) [+] |
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--- a/simsearch.xml Sun Jun 02 19:54:51 2013 +0200 +++ b/simsearch.xml Fri Jul 19 16:28:47 2013 +0200 @@ -34,7 +34,7 @@ "${method_opts.query_opts.targets}" #else: ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that. - ## Furthermore OpenBabel is really picky with fileextensions. We need to specify every datatype. I did not find a solution to specify the query-filetype. + ## Furthermore OpenBabel is really picky with file extensions. We need to specify every datatype. I did not find a solution to specify the query-filetype. ## A workaround is to create a symlink with a proper file-extension. #import tempfile #set $temp_file = tempfile.NamedTemporaryFile() @@ -95,22 +95,27 @@ <help> -**What it does** +.. class:: infomark + +**What this tool does** -Similarity search of compounds using fingerprint data sets. Depending on the input either chemfp_ of `Open Babel`_ is used. +Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index. +.. _chemfp: http://chemfp.com/ +.. _FastSearch: http://openbabel.org/wiki/FastSearch -**References** +----- -Please reference the `Open Babel`_ or the chemfp_ project. +.. class:: infomark -N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_ -The Open Babel Package http://openbabel.sourceforge.net/ +**Cite** +| The chemfp_ project +| +| N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch and G R Hutchison - `Open Babel: An open chemical toolbox`_ -.. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33 -.. _chemfp: http://chemfp.com/ -.. _`Open Babel`: http://openbabel.org/ +.. _`Open Babel: An open chemical toolbox`: http://www.jcheminf.com/content/3/1/33 + </help> </tool>