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comparison qed/silicos_qed.xml @ 20:9d1a5ff8c04f

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Mon, 22 Jul 2013 17:29:07 +0200
parents fd84ab7af088
children
comparison
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19:588e3ff42c28 20:9d1a5ff8c04f
1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1"> 1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1">
2 <description>quantitative estimation (QED)</description> 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> 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0.0">silicos_it</requirement> 5 <requirement type="package" version="1.0.1">silicos_it</requirement>
6 <requirement type="package" version="2012_12_1">rdkit</requirement> 6 <requirement type="package" version="2012_12_1">rdkit</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement> 7 <requirement type="package" version="1.7.1">numpy</requirement>
8 </requirements> 8 </requirements>
9 <command interpreter="python"> 9 <command interpreter="python">
10 qed.py -i "${infile}" 10 qed.py -i "${infile}"
46 </tests> 46 </tests>
47 <help> 47 <help>
48 48
49 .. class:: infomark 49 .. class:: infomark
50 50
51 **TIP:** If your data is not in SD- or SMILES format, use the pencil icon on your dataset to convert your data 51 **What this tool does**
52 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` ).
53 54
54 ----- 55 -----
55 56
56 **Syntax** 57 .. class:: warningmark
57 58
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 **HINT**
59 These three flavors correspond to the three different QED measures that were described in the original publication:
60 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.
61 62
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 - QED\ :sub:`w,max` using the set of weights that give maximal information content
63 64
64 - **QEDw,max** using the set of weights that give maximal information content.: 65 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
65 66
66 - **QEDw,mo** using the mean weights of the optimal 1,000 weight combinations that give the highest information content. 67 - QED\ :sub:`w,u` with all weights as unity, hence unweighted.
67
68 - **QEDw,u** with all weights as unity, hence unweighted.
69
70 68
71 ----- 69 -----
72 70
73 **Example** 71 .. class:: infomark
74 72
75 - Input file:: 73 **Input**
76 74
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 75
80 - Result:: 76 | - `SD-Format`_
77 | - `SMILES Format`_
81 78
82 ====== ===== === === ====== ==== ==== ====== ===== ============== 79 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
83 MW ALOGP HBA HBD PSA ROTB AROM ALERTS QED NAME 80 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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 81
97 ----- 82 -----
98 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
99 113
100 **Cite** 114 **Cite**
101 115
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, 90-98 116 Bickerton et al. - `Quantifying the chemical beauty of drugs`_
103 117
104 http://dx.doi.org/10.1038/nchem.1243 118 .. _Quantifying the chemical beauty of drugs: http://www.nature.com/nchem/journal/v4/n2/full/nchem.1243.html
119
105 </help> 120 </help>
106 </tool> 121 </tool>