allpy: 50633fcbbdc4 allpy/monomer.py

allpy

view allpy/monomer.py @ 192:50633fcbbdc4

Removed old implementation of geometrical_core. The proper place for obsolete implementations is either in history in the repository, or in separate branches, not in subdirectories within the current branch in the repository.

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Thu, 18 Nov 2010 21:42:16 +0300
parents	be4773230e65
children	346a6cd4fc1d

line source

1 #!/usr/bin/python

3 from allpy_data.AAdict import AAdict

4 import Bio.PDB

6 index_code3 = {}

7 index_code1_protein = {}

8 index_code1_nucleotide = {}

9 index_name = {}

12 class MonomerType(object):

13 """ Monomer type

15 name -- string like "Valine"

16 code1 -- one-letter code (in upper case)

17 code3 -- three-letter code (in upper case)

18 is_modified -- True of False

19 """

20 def __init__(self, name, code1, code3, is_modified=False):

21 self.name = name.capitalize()

22 self.code1 = code1.upper()

23 self.code3 = code3.upper()

24 self.is_modified = bool(is_modified) # ugly

26 index_name[self.name] = self

27 index_code3[self.code3] = self

29 @staticmethod

30 def from_code3(code3):

31 return index_code3[code3.upper()]

32 @staticmethod

33 def from_name(name):

34 return index_name[name.capitalize()]

36 @staticmethod

37 def from_pdb_residue(pdb_residue):

38 return MonomerType.from_code3(pdb_residue.get_resname())

40 # TO DISCUSS

41 def __eq__(self, other):

42 return self.code1 == other.code1

44 def __ne__(self, other):

45 return not (self == other)

48 class Monomer(object):

49 """ Monomer

51 type -- link to MonomerType object

52 """

53 def __init__(self, monomer_type):

54 self.type = monomer_type

56 def __eq__(self, other):

57 return self.type == other.type

59 def __ne__(self, other):

60 return not (self == other)

62 class AminoAcidType(MonomerType):

63 def __init__(self, name, code1, code3, is_modified=False):

64 MonomerType.__init__(self, name, code1, code3, is_modified)

65 if not is_modified:

66 index_code1_protein[self.code1] = self

68 @staticmethod

69 def from_code1(code1):

70 return index_code1_protein[code1.upper()]

71 def instance(self):

72 """ Returns new AminoAcid object of this type """

73 return AminoAcid(self)

75 class DNAType(MonomerType):

76 def __init__(self, name, code1, code3, is_modified=False):

77 MonomerType.__init__(self, name, code1, code3, is_modified)

78 if not is_modified:

79 index_code1_nucleotide[self.code1] = self

81 @staticmethod

82 def from_code1(code1):

83 return index_code1_nucleotide[code1.upper()]

84 def instance(self):

85 """ Returns new AminoAcid object of this type """

86 return DNA(self)

88 class AminoAcid(Monomer):

89 """ Amino acid """

90 pass

92 class DNA(Monomer):

93 """ Deoxyribonucleic acid """

94 pass

96 # prepare all aminoacids

98 for code3, data in AAdict.items():

99 code1, m_type, is_modified, none, name = data

100 if m_type == 'p':

101 AminoAcidType(name, code1, code3, is_modified)

102 if m_type == 'd':

103 DNAType(name, code1, code3, is_modified)

104 del code3, data, code1, m_type, is_modified, none, name

105