allpy: d60f272dc921 allpy/markups.py

allpy

view allpy/markups.py @ 842:d60f272dc921

blocks3d/wt: suggest better filenames for downloading If input alignment provided, name of input alignment file is concatenated with ".html" and used as name of output file. Otherwise "blocks3d.html" name is used

author	boris (kodomo) <bnagaev@gmail.com>
date	Wed, 20 Jul 2011 02:38:59 +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: