view modify/ob_addh.xml @ 15:ec87a42dccec

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 does this tool do?**

  This tool parses a molecular file and adds hydrogen atoms at a certain pH value.

-----

.. class:: infomark

**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.

  **Hint:** to avoid possible crashes, only molecules with >5 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.

-----

**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.

    </help>
</tool>