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