Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/file/2b324332f6f7/allpy/_monomer.py
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Дата индексирования: Mon Feb 4 07:43:20 2013
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allpy: 2b324332f6f7 allpy/_monomer.py

allpy

view allpy/_monomer.py @ 253:2b324332f6f7

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Fixed ReST markup in allpy.data.codes
author Daniil Alexeyevsky <me.dendik@gmail.com>
date Mon, 13 Dec 2010 22:16:04 +0300
parents 9369dbad919d
children 994b1a44bfc3
line source
1 #!/usr/bin/python
2
3 import data.codes as table
4
5 class MonomerType(object):
6 """Class of monomer types.
7
8 Each MonomerType object represents a known monomer type, e.g. Valine,
9 and is referenced to by each instance of monomer in a given sequence.
10
11 - `name`: full name of monomer type
12 - `code1`: one-letter code
13 - `code3`: three-letter code
14 - `is_modified`: either of True or False
15
16 class atributes:
17 - `by_code1`: a mapping from one-letter code to MonomerType object
18 - `by_code3`: a mapping from three-letter code to MonomerType object
19 - `by_name`: a mapping from monomer name to MonomerType object
20 - `instance_type`: class of Monomer objects to use when creating new
21 objects; this must be redefined in descendent classes
22
23 All of the class attributes MUST be redefined when subclassing.
24 """
25
26 by_code1 = {}
27 by_code3 = {}
28 by_name = {}
29 instance_type = None
30
31 def __init__(self, name="", code1="", code3="", is_modified=False):
32 self.name = name.capitalize()
33 self.code1 = code1.upper()
34 self.code3 = code3.upper()
35 self.is_modified = bool(is_modified)
36 if not is_modified:
37 self.by_code1[self.code1] = self
38 self.by_code3[code3] = self
39 self.by_name[name] = self
40 # We duplicate distinguished long names into MonomerType itself,
41 # so that we can use MonomerType.from_code3 to create the relevant
42 # type of monomer.
43 MonomerType.by_code3[code3] = self
44 MonomerType.by_name[name] = self
45
46 @classmethod
47 def _initialize(cls, type_letter, codes=table.codes):
48 """Create all relevant instances of MonomerType.
49
50 `type_letter` is either of:
51 - 'p' for protein
52 - 'd' for DNA
53 - 'r' for RNA
54
55 `codes` is a table of monomer codes
56 """
57 for type, code1, is_modified, code3, name in codes:
58 if type == type_letter:
59 cls(name, code1, code3, is_modified)
60
61 @classmethod
62 def from_code1(cls, code1):
63 """Return monomer type by one-letter code."""
64 return cls.by_code1[code1.upper()]
65
66 @classmethod
67 def from_code3(cls, code3):
68 """Return monomer type by three-letter code."""
69 return cls.by_code3[code3.upper()]
70
71 @classmethod
72 def from_name(cls, name):
73 """Return monomer type by name."""
74 return cls.by_name[name.capitalize()]
75
76 def instance(self):
77 """Create a new monomer of given type."""
78 return self.instance_type(self)
79
80 def __eq__(self, other):
81 if hasattr(other, "type"):
82 return self is other.type
83 return self is other
84
85 class Monomer(object):
86 """Monomer object.
87
88 attributes:
89 - `type`: type of monomer (a MonomerType object)
90
91 class attribute `monomer_type` is MonomerType or either of it's subclasses,
92 it is used when creating new monomers. It MUST be redefined when subclassing Monomer.
93 """
94 monomer_type = MonomerType
95
96 def __init__(self, type):
97 self.type = type
98
99 @classmethod
100 def from_code1(cls, code1):
101 return cls(cls.monomer_type.by_code1[code1.upper()])
102
103 @classmethod
104 def from_code3(cls, code3):
105 return cls(cls.monomer_type.by_code3[code3.upper()])
106
107 @classmethod
108 def from_name(cls, name):
109 return cls(cls.monomer_type.by_name[name.capitalize()])
110
111 def __eq__(self, other):
112 if hasattr(other, "type"):
113 return self.type is other.type
114 return self.type is other
115
116 # vim: set ts=4 sts=4 sw=4 et: