diff modify/ob_addh.xml @ 16:3d3e7c1d0f49

ChemicalToolBoX update.

--- a/modify/ob_addh.xml	Sat Jun 01 20:02:50 2013 +0200
+++ b/modify/ob_addh.xml	Fri Jul 19 16:27:52 2013 +0200
@@ -32,31 +32,54 @@
 
 .. class:: infomark
 
-**What does this tool do?**
+**What this tool does**
+
+Parses a molecular file and adds hydrogen atoms at a user-defined pH value.
 
-  This tool parses a molecular file and adds hydrogen atoms at a certain pH value.
+* Protocol::
+
+	1. The hydrogen atoms included in the input molecule are deleted.
+	2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
 
 -----
 
 .. class:: infomark
 
-**Protocol:**
+**Input**
 
-  **1.** The hydrogen atoms included in the input molecule are deleted.
+3D format files are required, e.g. SDF_
+
+.. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
 
-  **2.** Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
+-----
+
+.. class:: warningmark
 
-  **Hint:** to avoid possible crashes, only molecules with >5 heavy atoms are parsed.
+**Hint** 
+
+To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
 
 -----
 
 .. class:: infomark
 
-  **Output:** the output format is the same as the input format. 3D format files are required for this tool.
+**Output** 
+
+Same output format as the input format.
 
 -----
 
-**This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5.
+.. class:: infomark
+
+**Cite**
+
+`Open Babel`_
+
+.. _Open Babel: http://openbabel.org/wiki/Main_Page
+
+N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
+
+.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
 
     </help>
 </tool>