view silicos_qed.xml @ 1:ab73abead7fa draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit ed9b6859de648aa5f7cde483732f5df20aaff90e

<tool id="ctb_silicos_qed" name="Drug-likeness" version="0.2">
    <description>quantitative estimation (QED)</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="2019.03.1">rdkit</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
    python '$__tool_directory__/qed.py'
        -i '${infile}'
        --method '${method}'
        --iformat ${infile.ext}
        -o '${outfile}'
        $header
]]>
    </command>
    <inputs>
        <param format="smi,sdf" name="infile" type="data" label="Molecule data in SDF or SMILES format" help="Dataset missing? See TIP below"/>
        <param name="method" type="select" label="Method" help="Method for weighting features">
            <option value="max">Max weight (QEDw,max)</option>
            <option value="mean">Mean weight (QEDw,mo)</option>
            <option value="unweighted">Unweighted (QEDw,u)</option>
        </param>
        <param name="header" type="boolean" label="Include the descriptor names as header" truevalue="--header" falsevalue="" checked="false" />
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" />
    </outputs>
    <tests>
        <!--
        Test a tabular input with the first line being a comment without a # character to start
        -->
        <test>
          <param name="infile" value="qed_test.smi" ftype="smi"/>
          <param name="method" value="max"/>
          <param name="header" value="True"/>
          <output name="outfile" file="qed_test_max.tab" ftype="tabular"/>
        </test>
        <test>
          <param name="infile" value="qed_test.smi" ftype="smi"/>
          <param name="method" value="mean"/>
          <param name="header" value="True"/>
          <output name="outfile" file="qed_test_mean.tab" ftype="tabular"/>
        </test>
        <test>
          <param name="infile" value="qed_test.smi" ftype="smi" />
          <param name="method" value="unweighted"/>
          <param name="header" value="True"/>
          <output name="outfile" file="qed_test_unweighted.tab" ftype="tabular" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

Estimates the drug-likeness of molecules, based on eight commonly used molecular
properties, and reports a score between 0 (all properties unfavourable) to 1 (all
properties favourable). Two possible methods to weight the features are available
(QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\), as well as an option to leave features
unweighted (QED\ :sub:`w,u`).

The eight properties used are: molecular weight (MW), octanol–water partition 
coefficient (ALOGP), number of hydrogen bond donors (HBDs), number of hydrogen
bond acceptors (HBAs), molecular polar surface area (PSA), number of rotatable
bonds (ROTBs), number of aromatic rings (AROMs) and number of structural alerts
(ALERTS).

-----

.. class:: warningmark

**Hint**

All invalid, blank and comment lines are skipped when performing computations. The
number of skipped lines is displayed in the resulting history item. The method refers
to a set of weights that can be applied to the features. These are derived in the
`original paper`_ describing QED.


- QED\ :sub:`w,max` using the set of weights that give maximal information content

- QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content

- QED\ :sub:`w,u` with all weights as unity i.e. unweighted.

.. _original paper: https://www.nature.com/articles/nchem.1243

-----

.. class:: infomark

**Input**


| - `SDF format`_
| - `SMILES format`_

.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
.. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification

-----

.. class:: infomark

**Output**

A table listing the values of the eight features, the QED score, the name of the
molecule, and the number of Lipinski rules which the molecule obeys. 

+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
|   MW   | ALOGP | HBA | HBD |   PSA  | ROTB | AROM | ALERTS |  QED  |      NAME      | Ro5 |
+========+=======+=====+=====+========+======+======+========+=======+================+=====+
| 286.34 | 1.092 |  6  |  3  | 101.88 |   4  |   2  |    1   | 0.737 | Abacavir       |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
| 181.21 | 0.481 |  4  |  2  |  83.47 |   5  |   0  |    2   | 0.487 | Acamprosate    |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
| 336.43 | 2.365 |  5  |  3  |  87.66 |  11  |   1  |    1   | 0.540 | Acebutolol     |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
| 151.16 | 1.351 |  2  |  2  |  49.33 |   2  |   1  |    1   | 0.633 | Acetaminophen  |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
| 222.25 | 0.225 |  5  |  2  | 115.04 |   3  |   1  |    1   | 0.727 | Acetazolamide  |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
| 324.40 | 3.291 |  4  |  2  |  92.34 |   6  |   1  |    1   | 0.772 | Acetohexamide  |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
| 411.57 | 3.492 |  6  |  1  |  47.02 |   7  |   2  |    1   | 0.688 | Acetophenazine |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
| 329.37 | 3.327 |  4  |  1  |  39.72 |   4  |   2  |    0   | 0.917 | Paroxetine     |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
| 270.21 | 3.146 |  3  |  1  |  55.13 |   4  |   2  |    0   | 0.915 | Leflunomide    |  0  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+



]]>
    </help>
    <citations>
        <citation type="doi">10.1038/nchem.1243</citation>
    </citations>
</tool>