view strip-it/strip-it.xml @ 10:c5a538ec7b43

delete obsolete file

<tool id="stripit" name="Strip-it" version="1.0.0">
    <description> extracts predefined scaffolds from molecules</description>
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
        <requirement type="package" version="1.0.0">silicos_it</requirement>
    </requirements>
    <command>
        strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog 2>&#38;1
    </command>
    <inputs>
        <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
    </inputs>
    <outputs>
        <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="infile" type='sdf' value="CID_3037.sdf"/>
            <data name="output" type="tabular" file="Strip-it_on_CID3037.tabular" />
        </test>
    </tests>
    <help>

**What it does**

Strip-it is a program that extracts predefined scaffolds from organic
molecules

The program comes with a number of predefined molecular scaffolds for
extraction. These scaffolds include, amongst others

    - Molecular frameworks as originally described by Bemis and
      Murcko;1
    - Molecular frameworks and the reduced molecular frameworks as
      described by Ansgar Schuffenhauer and coworkers;2
    - Scaffold topologies as described by Sara Pollock and coworkers.3


http://silicos-it.com/software/strip-it/1.0.1/strip-it.html

-----

Example
-------

**input**

- `SDF Format`_
- `SMILES Format`_
- `MOL2 Format`_

.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES FORMAT: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
.. _MOL2 FORMAT: http://www.tripos.com/data/support/mol2.pdf


**output**

TODO:

    ====    ===========================    ====================    ====================    ===================    ==================    ==========    ==========    ==========
    NAME    MOLECULE                       RINGS_WITH_LINKERS_1    RINGS_WITH_LINKERS_2    MURCKO_1               MURCKO_2              OPREA_1       OPREA_2         OPREA_3
    ====    ===========================    ====================    ====================    ===================    ==================    ==========    ==========    ==========
    3037    Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl    c1ccc(cc1)Cc1ccccc1     c1ccc(cc1)Cc1ccccc1     C1CCC(CC1)CC1CCCCC1    C1CCC(CC1)C1CCCCC1    C1CC1C1CC1    C1CC1C1CC1    C1CC1C1CC1
    3037    Oc1ccc(cc1Cc1cc(Cl)ccc1O)Cl    c1ccc(cc1)Cc1ccccc1     c1ccc(cc1)Cc1ccccc1     C1CCC(CC1)CC1CCCCC1    C1CCC(CC1)C1CCCCC1    C1CC1C1CC1    C1CC1C1CC1    C1CC1C1CC1
    ====    ===========================    ====================    ====================    ===================    ==================    ==========    ==========    ==========

    </help>
</tool>