view ob_spectrophore_search.xml @ 16:5b8d2f65f288 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

<tool id="openbabel_spectrophore_search" name="Spectrophores search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>- similarity search based on 1D chemical features</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">1</token>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.19.1">numpy</requirement>
    </expand>
    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/ob_spectrophore_search.py'
      --target '$target'
      --library '$library'
      --output '$outfile'
      --column $column
]]>
    </command>
    <inputs>
        <param name="target" type="data" format="sdf"
            label="Target molecule in SDF format (it must contain Spectrophores stored as meta-data)"/>
        <param name="library" type="data" format="tabular"
            label="Tabular file with pre-computed Spectrophores in one column"/>
        <param name="column" label="Specify the column number containing the Spectrophores descriptors"
            type="data_column" data_ref="library" accept_default="true" />
    </inputs>
    <outputs>
        <data format="tabular" name="outfile"/>
    </outputs>
    <tests>
        <test>
            <param name="target" ftype="sdf" value="CID2244_with_spectrophore.sdf"/>
            <param name="library" value="lib.tabular" />
            <param name="column" value="8" />
            <output name="outfile" ftype="tabular" file="ob_spectrophore_search.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What does this tool do?**

This tool computes the Euclidean distance between the |Spectrophores (TM)| descriptors of the target to each molecule stored in the library.

|Spectrophores (TM)| search
		|Spectrophores (TM)| is a screening technology by Silicos_ which converts three-dimensional molecular property data into one-dimensional spectra. Typical characteristics that can be converted include electrostatic potentials, molecular shape, lipophilicity, hardness and softness potentials. The computation is independent of the position and orientation of a molecule and allows easy comparison of |Spectrophores (TM)| of different molecules.

		Molecules with similar three-dimensional properties and shape, and therefore also similar biological activities, always have similar |Spectrophores (TM)|. As a result this technique is a very powerful tool to investigate the similarity of molecules and can be applied as a screening tool for molecular databases, virtual screening, and database characterisations.

*Advantages:*

- |Spectrophores (TM)| can realistically compute ligand-protein interactions based on aforementioned molecular descriptors
- |Spectrophores (TM)| can be applied in both a ligand- or target-based setting
- |Spectrophores (TM)| can distinguish, if needed, between the different enantiomers of stereo-selective compounds
- |Spectrophores (TM)| can be computed rapidly


-----

.. class:: warningmark

**Hint:** this tool is useful to select compounds with similar chemical features to a target, but accounting for the discovery of diverse scaffolds. This is in contrast to the results expected in a similarity search based on atom connectivity.

-----

.. class:: infomark

**Input**

The target molecule must be a SD formatted file with the |Spectrophores (TM)| descriptors stored as metadata. Such files can be generated using the *Compute physico-chemical properties* tool.

-----

.. class:: infomark

**Output**

The library of compounds is a tabular file with one line per compound. One column contains the |Spectrophores (TM)| descriptors.

-----

.. class:: infomark

**Cite**

N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_

Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel.

.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
.. _Silicos: https://open-babel.readthedocs.io/en/latest/Fingerprints/spectrophore.html
.. |Spectrophores (TM)| unicode:: Spectrophores U+2122

]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1186/1752-153X-2-5</citation>
    </expand>
</tool>