allpy: 4e4d53155e42 allpy/markups.py

allpy

view allpy/markups.py @ 814:4e4d53155e42

structure: fix filtering by model in save_pdb method of SequenceMixin * add accept_model method to MySelect class * move class code after code defining model to use closure * use is instead of Equal-to operator for chains and models in MySelect * create helper variables chain and model

author	boris (kodomo) <bnagaev@gmail.com>
date	Fri, 15 Jul 2011 02:56:28 +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: