view qed/silicos_qed.xml @ 1:54edf22c93c0

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<tool id="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="1.0.0">silicos_it</requirement>
  </requirements>
  <command interpreter="python">qed.py -i "${infile}" --method "${method}" -o "${outfile}" 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>
  </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

**TIP:** If your data is not in SD- or SMILES format, use the pencil icon on your dataset to convert your data


-----

**Syntax**

The QED function comes in three flavors, each differing in the relative weight that is imposed on the underlying molecular descriptors (see [1]).
These three flavors correspond to the three different QED measures that were described in the original publication:


- All invalid, blank and comment lines are skipped when performing computations.  The number of skipped lines is displayed in the resulting history item.

- **QEDw,max** using the set of weights that give maximal information content.:

- **QEDw,mo** using the mean weights of the optimal 1,000 weight combinations that give the highest information content.

- **QEDw,u** with all weights as unity, hence unweighted.


-----

**Example**

- Input file::

    - SD-Format (http://en.wikipedia.org/wiki/Chemical_table_file)
    - SMILES Format (http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification)

- Result::

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


-----


**Cite**

[1] Bickerton, G.R.; Paolini, G.V.; Besnard, J.; Muresan, S.; Hopkins, A.L. (2012) ‘Quantifying the chemical beauty of drugs’, Nature Chemistry, 4, 90-98

http://dx.doi.org/10.1038/nchem.1243
  </help>
</tool>