view modify/remove_protonation_state.xml @ 16:3d3e7c1d0f49

ChemicalToolBoX update.

<tool id="ctb_remove_protonation_state" name="Remove protonation state" version="0.1">
    <description>of every atom</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'>
    remove_protonation_state.py
        -i $infile
        -o $outfile
        --iformat "${infile.ext}"
        2>&#38;1
    </command>
    <inputs>
        <param name="infile" type="data" format="sdf,smi,mol,inchi" label="Molecule file" help="Dataset missing? See TIP below"/>
    </inputs>
    <outputs>
        <data format_source="infile" name="outfile" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>

.. class:: infomark

**What this tool does**

Removes the protonation state of every atom.

-----

.. class:: infomark

**Cite**

`Open Babel`_

.. _Open Babel: http://openbabel.org/wiki/Main_Page

    </help>
</tool>