allpy: 2c0391cca127 allpy/markups.py

allpy

view allpy/markups.py @ 815:2c0391cca127

structure: fix model saving (workaround) Biopython seems to set MODEL record always to 1. (Maybe it is not biopython but our error.) Instead of changing model field of biopython model, generate MODEL and ENDMDL records manually. Biopython's MODEL record is skipped using StringIO.

author	boris (kodomo) <bnagaev@gmail.com>
date	Fri, 15 Jul 2011 03:03:39 +0400
parents	52ce523138d5
children	91e73fb1ac79

line source

1 import base

3 class IntMarkupMixin(base.Markup):

5 @classmethod

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

7 assert record['io-class'] == 'IntMarkup'

8 result = cls(container, name=name)

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

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

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

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

13 if value:

14 result[key] = int(value)

15 return result

17 def to_record(self):

18 def fmt(value):

19 if value is None:

20 return ""

21 return str(value)

22 values = [fmt(self.get(key)) for key in self.sorted_keys()]

23 return {'markup': ','.join(values), 'io-class': 'IntMarkup'}

25 class SequenceNumberMarkup(base.SequenceMarkup):

27 name = 'number'

29 def refresh(self):

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

31 monomer.number = number

33 class SequenceIndexMarkup(base.SequenceMarkup):

35 name = 'index'

37 def refresh(self):

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

39 monomer.index = index

41 class AlignmentNumberMarkup(base.AlignmentMarkup):

43 name = 'number'

45 def refresh(self):

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

47 self[column] = number

49 class AlignmentIndexMarkup(base.AlignmentMarkup):

51 name = 'index'

53 def refresh(self):

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

55 self[column] = index

57 class SequenceCaseMarkup(base.SequenceMarkup):

59 name = 'case'

61 def refresh(self):

62 for monomer in self.sequence:

63 if monomer.input_code1.isupper():

64 monomer.case = 'upper'

65 elif monomer.input_code1.islower():

66 monomer.case = 'lower'

68 @classmethod

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

70 assert record['io-class'] == 'SequenceCaseMarkup'

71 result = cls(container, name=name)

72 markup = record['markup']

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

74 markup = markup[1:-1]

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

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

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

78 if mark.isupper():

79 monomer.case = 'upper'

80 if mark.islower():

81 monomer.case = 'lower'

82 return result

84 def to_record(self):

85 markup = ''

86 for monomer in self.sequence:

87 case = self.get(monomer)

88 if case == 'upper':

89 markup += monomer.code1.upper()

90 elif case == 'lower':

91 markup += monomer.code1.lower()

92 return {'markup': "'%s'" % markup, 'io-class': 'SequenceCaseMarkup'}

94 class SequencePdbResiMarkup(base.SequenceMarkup, IntMarkupMixin):

95 name = 'pdb_resi'

97 def from_pdb(self):

98 for monomer in self.sequence:

99 try:

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

101 except Exception:

102 pass

103

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

105 import structure

106 if download_pdb is None:

107 download_pdb = structure.cached_download_pdb

108

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

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

111 pdb_file = download_pdb(code)

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

113 pdb_chain = pdb_structure[0][chain]

114 if not xyz_only:

115 self.sequence.pdb_chain = pdb_chain

116 for monomer in self.sequence:

117 if monomer in self:

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

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

120 if not xyz_only:

121 monomer.pdb_residue = pdb_residue

122

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