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comparison qed/silicos_qed.xml @ 0:bb92d30b4f52 draft

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author bgruening
date Thu, 15 Aug 2013 03:34:00 -0400
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1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1">
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="1.0.1">silicos_it</requirement>
6 <requirement type="package" version="2012_12_1">rdkit</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement>
8 </requirements>
9 <command interpreter="python">
10 qed.py -i "${infile}"
11 --method "${method}"
12 --iformat ${infile.ext}
13 -o "${outfile}" $header 2>&#38;1
14 </command>
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>
22 <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" />
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 **What this tool does**
52
53 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` ).
54
55 -----
56
57 .. class:: warningmark
58
59 **HINT**
60
61 - All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item.
62
63 - QED\ :sub:`w,max` using the set of weights that give maximal information content
64
65 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
66
67 - QED\ :sub:`w,u` with all weights as unity, hence unweighted.
68
69 -----
70
71 .. class:: infomark
72
73 **Input**
74
75
76 | - `SD-Format`_
77 | - `SMILES Format`_
78
79 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
80 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
81
82 -----
83
84 .. class:: infomark
85
86 **Output**
87
88 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
89 | MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 |
90 +========+=======+=====+=====+========+======+======+========+=======+================+=====+
91 | 286.34 | 1.092 | 6 | 3 | 101.88 | 4 | 2 | 1 | 0.737 | Abacavir | 0 |
92 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
93 | 181.21 | 0.481 | 4 | 2 | 83.47 | 5 | 0 | 2 | 0.487 | Acamprosate | 0 |
94 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
95 | 336.43 | 2.365 | 5 | 3 | 87.66 | 11 | 1 | 1 | 0.540 | Acebutolol | 0 |
96 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
97 | 151.16 | 1.351 | 2 | 2 | 49.33 | 2 | 1 | 1 | 0.633 | Acetaminophen | 0 |
98 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
99 | 222.25 | 0.225 | 5 | 2 | 115.04 | 3 | 1 | 1 | 0.727 | Acetazolamide | 0 |
100 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
101 | 324.40 | 3.291 | 4 | 2 | 92.34 | 6 | 1 | 1 | 0.772 | Acetohexamide | 0 |
102 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
103 | 411.57 | 3.492 | 6 | 1 | 47.02 | 7 | 2 | 1 | 0.688 | Acetophenazine | 0 |
104 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
105 | 329.37 | 3.327 | 4 | 1 | 39.72 | 4 | 2 | 0 | 0.917 | Paroxetine | 0 |
106 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
107 | 270.21 | 3.146 | 3 | 1 | 55.13 | 4 | 2 | 0 | 0.915 | Leflunomide | 0 |
108 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
109
110 -----
111
112 .. class:: infomark
113
114 **Cite**
115
116 Bickerton et al. - `Quantifying the chemical beauty of drugs`_
117
118 .. _Quantifying the chemical beauty of drugs: http://www.nature.com/nchem/journal/v4/n2/full/nchem.1243.html
119
120 </help>
121 </tool>