source: orange-bioinformatics/docs/rst/reference/kegg.rst @ 1980:e8f5310fa033

Revision 1980:e8f5310fa033, 2.5 KB checked in by markotoplak, 8 weeks ago (diff)

Moved obiKEGG.

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