annotate qed/silicos_qed.xml @ 2:5f1d98674a21 draft default tip

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<tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1">
  <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="1.0.1">silicos_it</requirement>
    <requirement type="package" version="2012_12_1">rdkit</requirement>
    <requirement type="package" version="1.7.1">numpy</requirement>
  </requirements>
  <command interpreter="python">
    qed.py -i "${infile}" 
        --method "${method}" 
        --iformat ${infile.ext} 
        -o "${outfile}" $header 2>&#38;1
  </command>
  <inputs>
    <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/>
    <param name="method" type="select" label="Method">
      <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 name 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"/>
      <param name="method" value="max"/>
      <output name="outfile" file="qed_test_max.tab"/>
    </test>
    <test>
      <param name="infile" value="qed_test.smi"/>
      <param name="method" value="mean"/>
      <output name="outfile" file="qed_test_mean.tab"/>
    </test>
    <test>
      <param name="infile" value="qed_test.smi"/>
      <param name="method" value="unweighted"/>
      <output name="outfile" file="qed_test_unweighted.tab"/>
    </test>
  </tests>
  <help>

.. class:: infomark

**What this tool does**

Estimates the drug-likeness of molecules and reports a score. Comes with three applicable varieties (QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\ , QED\ :sub:`w,u` ).

-----

.. 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.

- 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, hence unweighted.

-----

.. class:: infomark

**Input**


| - `SD-Format`_
| - `SMILES Format`_

.. _SD-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**

+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
|   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  |
+--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+

-----

.. class:: infomark

**Cite**

Bickerton et al. - `Quantifying the chemical beauty of drugs`_

.. _Quantifying the chemical beauty of drugs: http://www.nature.com/nchem/journal/v4/n2/full/nchem.1243.html

  </help>
</tool>