diff filter/ob_grep.xml @ 16:3d3e7c1d0f49

ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Fri, 19 Jul 2013 16:27:52 +0200
parents ec87a42dccec
children
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--- a/filter/ob_grep.xml	Sat Jun 01 20:02:50 2013 +0200
+++ b/filter/ob_grep.xml	Fri Jul 19 16:27:52 2013 +0200
@@ -48,28 +48,51 @@
     </test>
     </tests>
     <help>
-.. class:: warningmark
+
+.. class:: infomark
 
-**What it does**
+**What this tool does**
 
-The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files.
+Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
 
 
-.. _obgrep: http://openbabel.org/wiki/Obgrep
+.. _Obgrep: http://openbabel.org/wiki/Obgrep
 .. _here: http://openbabel.org/wiki/SMARTS
 
 -----
 
-**Output format**
+.. class:: infomark
+
+**Input**
+
+| - `SD-Format`_
+| - `SMILES Format`_
 
+.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
 
-**References**
+-----
+
+.. class:: infomark
+
+**Output**
 
-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/
+Same as input format.
+
+-----
+
+.. class:: infomark
+
+**Cite**
 
-.. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33
+N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
+
+.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
+
+`Open Babel`_
+
+.. _`Open Babel`: http://openbabel.org/wiki/Main_Page
 
     </help>
 </tool>