allpy: 5091fef2ad88 lib/monomer.py

allpy

view lib/monomer.py @ 101:5091fef2ad88

lib::MonomerType operator== consider only one letter code align -- additional check of monomer equality fix bug with missing __ne__ where __eq__ present

author	boris <bnagaev@gmail.com>
date	Thu, 21 Oct 2010 00:39:57 +0400
parents	581c1f71c4ea
children	6479950a9ee3

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 """

13 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 # TO DISCUSS

36 def __eq__(self, other):

37 return self.code1 == other.code1

39 def __ne__(self, other):

40 return not self == other

43 class Monomer(object):

44 """

45 monomer_type -- link to monomer_type

46 pdb_residues -- dictionary like {Bio.PDB.Chain: Bio.PDB.Residue}

47 """

48 def __init__(self, monomer_type):

49 self.monomer_type = monomer_type

50 self.pdb_residue = []

52 def pdb_residue_add(self, pdb_chain, pdb_residue):

53 self.pdb_residue[pdb_chain] = pdb_residue

55 def __eq__(self, other):

56 return self.monomer_type == other.monomer_type

58 def __ne__(self, other):

59 return not self == other

61 class AminoAcidType(MonomerType):

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

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

64 if not is_modified:

65 index_code1_protein[self.code1] = self

67 @staticmethod

68 def from_code1(code1):

69 return index_code1_protein[code1.upper()]

70 def instance(self):

71 return AminoAcid(self)

74 class AminoAcid(Monomer):

75 """

76 Amino acid

77 """

78 pass

81 # prepare all aminoacids

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

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

85 if m_type == 'p':

86 aat = AminoAcidType(name, code1, code3, is_modified)