allpy: 0c7f6117481b lib/monomer.py

allpy

view lib/monomer.py @ 153:0c7f6117481b

idea implemented: pdb and sec_str data moved from monomer to sequence

author	boris <bnagaev@gmail.com>
date	Tue, 26 Oct 2010 21:53:23 +0400
parents	ff68a1bef5eb
children	9b601bbb1fde

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_name = {}

11 class MonomerType(object):

12 """ Monomer type

14 name -- string like "Valine"

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

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

17 is_modified -- True of False

18 """

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

20 self.name = name.capitalize()

21 self.code1 = code1.upper()

22 self.code3 = code3.upper()

23 self.is_modified = bool(is_modified) # ugly

25 index_name[self.name] = self

26 index_code3[self.code3] = self

28 @staticmethod

29 def from_code3(code3):

30 return index_code3[code3.upper()]

31 @staticmethod

32 def from_name(name):

33 return index_name[name.capitalize()]

35 @staticmethod

36 def from_pdb_residue(pdb_residue):

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

39 # TO DISCUSS

40 def __eq__(self, other):

41 return self.code1 == other.code1

43 def __ne__(self, other):

44 return not (self == other)

47 class Monomer(object):

48 """ Monomer

50 type -- link to MonomerType object

52 Idea: move pdb_residues and pdb_secstr to Sequence object

53 """

54 def __init__(self, monomer_type):

55 self.type = monomer_type

57 def __eq__(self, other):

58 return self.type == other.type

60 def __ne__(self, other):

61 return not (self == other)

63 class AminoAcidType(MonomerType):

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

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

66 if not is_modified:

67 index_code1_protein[self.code1] = self

69 @staticmethod

70 def from_code1(code1):

71 return index_code1_protein[code1.upper()]

72 def instance(self):

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

74 return AminoAcid(self)

77 class AminoAcid(Monomer):

78 """ Amino acid """

79 pass

82 # prepare all aminoacids

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

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

86 if m_type == 'p':

87 AminoAcidType(name, code1, code3, is_modified)

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