Mercurial > repos > bgruening > silicos_it
annotate qed/silicos_qed.xml @ 9:6e6b05e75a3f
several updates to the silics-it repository
| author | Björn Grüning <bjoern.gruening@gmail.com> |
|---|---|
| date | Sun, 26 May 2013 16:50:00 +0200 |
| parents | 147814e45209 |
| children | fd84ab7af088 |
| rev | line source |
|---|---|
| 1 | 1 <tool id="silicos_qed" name="Drug-likeness" version="0.1"> |
| 0 | 2 <description>quantitative estimation (QED)</description> |
| 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="1.0.0">silicos_it</requirement> | |
| 8 | 6 <requirement type="package" version="2012_12_1">rdkit</requirement> |
| 7 <requirement type="package" version="1.7.1">numpy</requirement> | |
| 0 | 8 </requirements> |
|
9
6e6b05e75a3f
several updates to the silics-it repository
Björn Grüning <bjoern.gruening@gmail.com>
parents:
8
diff
changeset
|
9 <command interpreter="python"> |
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6e6b05e75a3f
several updates to the silics-it repository
Björn Grüning <bjoern.gruening@gmail.com>
parents:
8
diff
changeset
|
10 qed.py -i "${infile}" |
|
6e6b05e75a3f
several updates to the silics-it repository
Björn Grüning <bjoern.gruening@gmail.com>
parents:
8
diff
changeset
|
11 --method "${method}" |
|
6e6b05e75a3f
several updates to the silics-it repository
Björn Grüning <bjoern.gruening@gmail.com>
parents:
8
diff
changeset
|
12 --iformat ${infile.ext} |
|
6e6b05e75a3f
several updates to the silics-it repository
Björn Grüning <bjoern.gruening@gmail.com>
parents:
8
diff
changeset
|
13 -o "${outfile}" $header 2>&1 |
|
6e6b05e75a3f
several updates to the silics-it repository
Björn Grüning <bjoern.gruening@gmail.com>
parents:
8
diff
changeset
|
14 </command> |
| 0 | 15 <inputs> |
| 16 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/> | |
| 17 <param name="method" type="select" label="Method"> | |
| 18 <option value="max">Max weight (QEDw,max)</option> | |
| 19 <option value="mean">Mean weight (QEDw,mo)</option> | |
| 20 <option value="unweighted">unweighted (QEDw,u)</option> | |
| 21 </param> | |
| 5 | 22 <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" /> |
| 0 | 23 </inputs> |
| 24 <outputs> | |
| 25 <data format="tabular" name="outfile" /> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <!-- | |
| 29 Test a tabular input with the first line being a comment without a # character to start | |
| 30 --> | |
| 31 <test> | |
| 32 <param name="infile" value="qed_test.smi"/> | |
| 33 <param name="method" value="max"/> | |
| 34 <output name="outfile" file="qed_test_max.tab"/> | |
| 35 </test> | |
| 36 <test> | |
| 37 <param name="infile" value="qed_test.smi"/> | |
| 38 <param name="method" value="mean"/> | |
| 39 <output name="outfile" file="qed_test_mean.tab"/> | |
| 40 </test> | |
| 41 <test> | |
| 42 <param name="infile" value="qed_test.smi"/> | |
| 43 <param name="method" value="unweighted"/> | |
| 44 <output name="outfile" file="qed_test_unweighted.tab"/> | |
| 45 </test> | |
| 46 </tests> | |
| 47 <help> | |
| 48 | |
| 49 .. class:: infomark | |
| 50 | |
| 51 **TIP:** If your data is not in SD- or SMILES format, use the pencil icon on your dataset to convert your data | |
| 52 | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 **Syntax** | |
| 57 | |
| 58 The QED function comes in three flavors, each differing in the relative weight that is imposed on the underlying molecular descriptors (see [1]). | |
| 59 These three flavors correspond to the three different QED measures that were described in the original publication: | |
| 60 | |
| 61 | |
| 62 - All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item. | |
| 63 | |
| 64 - **QEDw,max** using the set of weights that give maximal information content.: | |
| 65 | |
| 66 - **QEDw,mo** using the mean weights of the optimal 1,000 weight combinations that give the highest information content. | |
| 67 | |
| 68 - **QEDw,u** with all weights as unity, hence unweighted. | |
| 69 | |
| 70 | |
| 71 ----- | |
| 72 | |
| 73 **Example** | |
| 74 | |
| 75 - Input file:: | |
| 76 | |
| 77 - SD-Format (http://en.wikipedia.org/wiki/Chemical_table_file) | |
| 78 - SMILES Format (http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification) | |
| 79 | |
| 80 - Result:: | |
| 81 | |
| 82 ====== ===== === === ====== ==== ==== ====== ===== ============== | |
| 83 MW ALOGP HBA HBD PSA ROTB AROM ALERTS QED NAME | |
| 84 ------ ----- --- --- ------ ---- ---- ------ ----- -------------- | |
| 85 286.34 1.092 6 3 101.88 4 2 1 0.737 Abacavir | |
| 86 181.21 0.481 4 2 83.47 5 0 2 0.487 Acamprosate | |
| 87 336.43 2.365 5 3 87.66 11 1 1 0.540 Acebutolol | |
| 88 151.16 1.351 2 2 49.33 2 1 1 0.633 Acetaminophen | |
| 89 222.25 0.225 5 2 115.04 3 1 1 0.727 Acetazolamide | |
| 90 324.40 3.291 4 2 92.34 6 1 1 0.772 Acetohexamide | |
| 91 411.57 3.492 6 1 47.02 7 2 1 0.688 Acetophenazine | |
| 92 329.37 3.327 4 1 39.72 4 2 0 0.917 Paroxetine | |
| 93 270.21 3.146 3 1 55.13 4 2 0 0.915 Leflunomide | |
| 94 ====== ===== === === ====== ==== ==== ====== ===== ============== | |
| 95 | |
| 96 | |
| 97 ----- | |
| 98 | |
| 99 | |
| 100 **Cite** | |
| 101 | |
| 102 [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 | |
| 103 | |
| 104 http://dx.doi.org/10.1038/nchem.1243 | |
| 105 </help> | |
| 106 </tool> |