source: orange-bioinformatics/docs/rst/reference/kegg.rst @ 1736:b3b664abcfdd

Revision 1736:b3b664abcfdd, 2.5 KB checked in by Ales Erjavec <ales.erjavec@…>, 13 months ago (diff)

Added sphinx rst documentation for obiKEGG.

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[1736]1============================================================
2KEGG - Kyoto Encyclopedia of Genes and Genomes (:mod:`kegg`)
3============================================================
4
5
6.. automodule:: Orange.bio.obiKEGG
7   :members:
8   :member-order: bysource
9
10DBEntry (:mod:`entry`)
11----------------------
12
13The :class:`~.entry.DBEntry` represents a DBGET databas entry.
14The individual KEGG Database interfaces below provide their own
15specialization for this base class.
16 
17.. autoclass:: Orange.bio.obiKEGG.entry.DBEntry
18   :members:
19   :member-order: bysource
20   :show-inheritance:
21
22
23KEGG Databases interface (:mod:`databases`)
24-------------------------------------------
25
26.. autoclass:: Orange.bio.obiKEGG.databases.DBDataBase
27   :members:
28   :member-order: bysource
29   :show-inheritance:
30
31
32.. autoclass:: Orange.bio.obiKEGG.databases.GenomeEntry
33   :members:
34   :member-order: bysource
35   :show-inheritance:
36
37
38.. autoclass:: Orange.bio.obiKEGG.databases.Genome
39   :members:
40   :member-order: bysource
41   :show-inheritance:
42
43
44.. autoclass:: Orange.bio.obiKEGG.databases.GeneEntry
45   :members:
46   :exclude-members:
47      alt_names
48   :member-order: bysource
49   :show-inheritance:
50
51.. autoclass:: Orange.bio.obiKEGG.databases.Genes
52   :members:
53   :member-order: bysource
54   :show-inheritance:
55
56
57.. autoclass:: Orange.bio.obiKEGG.databases.CompoundEntry
58   :members:
59   :member-order: bysource
60   :show-inheritance:
61
62.. autoclass:: Orange.bio.obiKEGG.databases.Compound
63   :members:
64   :member-order: bysource
65   :show-inheritance:
66
67
68.. autoclass:: Orange.bio.obiKEGG.databases.ReactionEntry
69   :members:
70   :member-order: bysource
71   :show-inheritance:
72
73.. autoclass:: Orange.bio.obiKEGG.databases.Reaction
74   :members:
75   :member-order: bysource
76   :show-inheritance:
77
78
79.. autoclass:: Orange.bio.obiKEGG.databases.EnzymeEntry
80   :members:
81   :member-order: bysource
82   :show-inheritance:
83
84.. autoclass:: Orange.bio.obiKEGG.databases.Enzyme
85   :members:
86   :member-order: bysource
87   :show-inheritance:
88
89
90.. autoclass:: Orange.bio.obiKEGG.databases.PathwayEntry
91   :members:
92   :member-order: bysource
93   :show-inheritance:
94
95
96.. autoclass:: Orange.bio.obiKEGG.databases.Pathway
97   :members:
98   :member-order: bysource
99   :show-inheritance:
100
101
102KEGG Pathway (:mod:`pathway`)
103-----------------------------
104
105.. autoclass:: Orange.bio.obiKEGG.pathway.Pathway
106   :members:
107   :exclude-members:
108      entrys
109   :member-order: bysource
110   :show-inheritance:
111
112
113Utilities
114---------
115
116.. autoclass:: Orange.bio.obiKEGG.entry.parser.DBGETEntryParser
117   :members:
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