# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1374244127 -7200
# Node ID b4eaf75cac77b60dde1f05e56cdfb26cd0fde0cf
# Parent  47d2bf6919081343955b0ecde25c797315c8b085
ChemicalToolBoX update.

diff -r 47d2bf691908 -r b4eaf75cac77 force_pre-commit_hook_temp_file
diff -r 47d2bf691908 -r b4eaf75cac77 simsearch.xml
--- 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>