allpy: a6d287f9c901 lib/monomer.py

allpy

view lib/monomer.py @ 129:a6d287f9c901

broken: lib::block::geometrical_cores returns list of blocks added new parameters to geometrical_core test passed

author	boris <bnagaev@gmail.com>
date	Sun, 24 Oct 2010 00:26:18 +0400
parents	7a87d55efc17
children	db9d116e979f

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 @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 """

49 type -- link to MonomerType object

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

51 """

52 def __init__(self, monomer_type):

53 self.type = monomer_type

54 self.pdb_residues = {}

56 def pdb_residue_add(self, chain, residue):

57 self.pdb_residues[chain] = residue

59 def __eq__(self, other):

60 return self.type == other.type

62 def __ne__(self, other):

63 return not (self == other)

65 class AminoAcidType(MonomerType):

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

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

68 if not is_modified:

69 index_code1_protein[self.code1] = self

71 @staticmethod

72 def from_code1(code1):

73 return index_code1_protein[code1.upper()]

74 def instance(self):

75 return AminoAcid(self)

78 class AminoAcid(Monomer):

79 """

80 Amino acid

81 """

82 pass

85 # prepare all aminoacids

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

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

89 if m_type == 'p':

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