allpy: 7de42d758354 allpy/markups.py

allpy

view allpy/markups.py @ 836:7de42d758354

Added deprecation warnings to the deprecated functions.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Tue, 19 Jul 2011 14:40:22 +0400
parents	4f896db3531d
children	077e5e18a600

line source

1 import base

3 by_name = {}

4 """A dictionary of default markup name -> markup class."""

6 def update(*args):

7 """Update `by_name` dictionary.

9 If any arguments are given, add them to markups namespace beforehands.

10 """

11 # Add user classes if necessary

12 for markup_class in args:

13 class_name = markup_class.__name__

14 assert class_name not in globals(), "SameNamed markup already exists!"

15 globals()[class_name] = markup_class

16 # Update `by_name` dictonary

17 global by_name

18 by_name = {}

19 for markup_class in globals().values():

20 if hasattr(markup_class, 'name') and hasattr(markup_class, 'kind'):

21 fullname = markup_class.kind, markup_class.name

22 assert fullname not in by_name, "Samenamed markup already exists!"

23 by_name[fullname] = markup_class

25 class IntMarkupMixin(base.Markup):

27 @classmethod

28 def from_record(cls, container, record, name=None):

29 assert record['io_class'] == 'IntMarkup'

30 result = container.add_markup(name, markup_class=cls)

31 separator = record.get('separator', ',')

32 values = record['markup'].split(separator)

33 assert len(values) == len(result.sorted_keys())

34 for key, value in zip(result.sorted_keys(), values):

35 if value:

36 result[key] = int(value)

37 return result

39 def to_record(self):

40 values = self.sorted_values(default='', map=str)

41 return {'markup': ','.join(values), 'io_class': 'IntMarkup'}

43 class SequenceNumberMarkup(base.SequenceMarkup):

45 name = 'number'

47 def refresh(self):

48 for number, monomer in enumerate(self.sequence, 1):

49 monomer.number = number

51 class SequenceIndexMarkup(base.SequenceMarkup):

53 name = 'index'

55 def refresh(self):

56 for index, monomer in enumerate(self.sequence):

57 monomer.index = index

59 class AlignmentNumberMarkup(base.AlignmentMarkup):

61 name = 'number'

63 def refresh(self):

64 for number, column in enumerate(self.alignment.columns, 1):

65 self[column] = number

67 class AlignmentIndexMarkup(base.AlignmentMarkup):

69 name = 'index'

71 def refresh(self):

72 for index, column in enumerate(self.alignment.columns):

73 self[column] = index

75 class SequenceCaseMarkup(base.SequenceMarkup):

77 name = 'case'

79 def refresh(self):

80 for monomer in self.sequence:

81 if monomer.input_code1.isupper():

82 monomer.case = 'upper'

83 elif monomer.input_code1.islower():

84 monomer.case = 'lower'

86 @classmethod

87 def from_record(cls, container, record, name=None):

88 assert record['io_class'] == 'SequenceCaseMarkup'

89 result = container.add_markup(name, markup_class=cls)

90 markup = record['markup']

91 assert markup[0] == markup[-1] == "'"

92 markup = markup[1:-1]

93 assert len(markup) == len(result.sequence)

94 for monomer, mark in zip(result.sequence, markup):

95 assert monomer.code1 == mark.upper()

96 if mark.isupper():

97 monomer.case = 'upper'

98 if mark.islower():

99 monomer.case = 'lower'

100 return result

101

102 def to_record(self):

103 markup = ''

104 for monomer in self.sequence:

105 case = self.get(monomer)

106 if case == 'upper':

107 markup += monomer.code1.upper()

108 elif case == 'lower':

109 markup += monomer.code1.lower()

110 return {'markup': "'%s'" % markup, 'io_class': 'SequenceCaseMarkup'}

111

112 class SequencePdbResiMarkup(base.SequenceMarkup, IntMarkupMixin):

113 name = 'pdb_resi'

114

115 def from_pdb(self):

116 for monomer in self.sequence:

117 try:

118 monomer.pdb_resi = monomer.pdb_residue.id[1]

119 except Exception:

120 pass

121

122 def add_pdb(self, download_pdb=None, xyz_only=False):

123 import structure

124 if download_pdb is None:

125 download_pdb = structure.cached_download_pdb

126

127 match = structure.pdb_id_parse(self.sequence.name)

128 code, model , chain = match['code'], match['model'], match['chain']

129 pdb_file = download_pdb(code)

130 pdb_structure = structure.get_structure(pdb_file, self.sequence.name)

131 pdb_chain = pdb_structure[0][chain]

132 if not xyz_only:

133 self.sequence.pdb_chain = pdb_chain

134 for monomer in self.sequence:

135 if monomer in self:

136 pdb_residue = pdb_chain[' ', monomer.pdb_resi, ' ']

137 monomer.ca_xyz = pdb_residue['CA'].get_vector()

138 if not xyz_only:

139 monomer.pdb_residue = pdb_residue

140

141 # This MUST be the last statement in this module.

142 update()

143

144 # vim: set ts=4 sts=4 sw=4 et: