allpy: 3d40d7b9a123 lib/monomer.py

allpy

view lib/monomer.py @ 98:3d40d7b9a123

lib::project::muscle_align project::save_fasta sequence::operator== fixes test -- alignment done

author	boris <bnagaev@gmail.com>
date	Wed, 20 Oct 2010 23:33:29 +0400
parents	c0689204093e
children	5091fef2ad88

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()]

37 # TODO -- create all MonomerTypes

40 class Monomer(object):

41 """

42 monomer_type -- link to monomer_type

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

44 """

45 def __init__(self, monomer_type):

46 self.monomer_type = monomer_type

47 self.pdb_residue = []

49 def pdb_residue_add(self, pdb_chain, pdb_residue):

50 self.pdb_residue[pdb_chain] = pdb_residue

52 def __eq__(self, other):

53 return self.monomer_type == other.monomer_type

57 class AminoAcidType(MonomerType):

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

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

60 if not is_modified:

61 index_code1_protein[self.code1] = self

63 @staticmethod

64 def from_code1(code1):

65 return index_code1_protein[code1.upper()]

66 def instance(self):

67 return AminoAcid(self)

70 class AminoAcid(Monomer):

71 """

72 Amino acid

73 """

74 pass

77 # prepare all aminoacids

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

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

81 if m_type == 'p':

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