diff modify/ob_addh.xml @ 0:527ecd2fc500 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/modify/ob_addh.xml	Thu Aug 15 03:25:06 2013 -0400
@@ -0,0 +1,85 @@
+<tool id="ctb_ob_addh" name="Add hydrogen atoms" version="1.0">
+    <description>at a certain pH value</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter="python">
+    ob_addh.py
+      -i "${infile}"
+      --iformat "${infile.ext}"
+      -o "${outfile}"
+      $polar
+      --pH "${pH_value}"
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/>
+        <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/>
+        <param name="pH_value" type="float" size="4" value="7.4" label="Specify pH value"/>
+    </inputs>
+    <outputs>
+        <data format_source="infile" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="CID_2244.can" ftype="smi" />
+            <param name="polar" value="--polar" />
+            <param name="pH_value" value="7.4" />
+            <output name="outfile" file="CID_2244_addh.can" ftype="can" />
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Parses a molecular file and adds hydrogen atoms at a user-defined 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
+
+**Input**
+
+3D format files are required, e.g. SDF_
+
+.. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
+
+-----
+
+.. class:: warningmark
+
+**Hint** 
+
+To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
+
+-----
+
+.. class:: infomark
+
+**Output** 
+
+Same output format as the input format.
+
+-----
+
+.. 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>