view modify/ob_addh.xml @ 22:b4ba90dcfde0 default tip

ChemicalToolBoX update.

<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>