allpy: 675b402094be lib/monomer.py

allpy

view lib/monomer.py @ 151:675b402094be

day commit -- a lot of changes fasta.py: universal save_fasta() determine_long_line -- for determine length of fasta sequence string in user input everywhere: standart long_line=60 --> 70 blocK.sequences_chains: returns sequences in order as in project added monomer pdb_secstr to store secondary structure pdb adding: some improvements and fixes fix in from_pdb_chain: use all peptides, not only first Sequence.pdb_files added to store information about pdb file for each chain dssp bindings to get secondary structure /sec_str -- tool to map secondary structure on each sequence of alignment

author	boris (netbook) <bnagaev@gmail.com>
date	Tue, 26 Oct 2010 00:40:36 +0400
parents	f7dead025719
children	ff68a1bef5eb

line source

1 #!/usr/bin/python

2 # -*- coding: utf-8 -*-

4 from allpy_data.AAdict import AAdict

5 import Bio.PDB

7 index_code3 = {}

8 index_code1_protein = {}

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

53 pdb_secstr -- dictionary like {Bio.PDB.Chain: 'Secondary structure'}

54 Code Secondary structure

55 H ??-helix

56 B Isolated ??-bridge residue

57 E Strand

58 G 3-10 helix

59 I ??-helix

60 T Turn

61 S Bend

62 - Other

63 """

64 def __init__(self, monomer_type):

65 self.type = monomer_type

66 self.pdb_residues = {}

67 self.pdb_secstr = {}

69 def pdb_residue_add(self, chain, residue):

70 self.pdb_residues[chain] = residue

72 def __eq__(self, other):

73 return self.type == other.type

75 def __ne__(self, other):

76 return not (self == other)

78 class AminoAcidType(MonomerType):

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

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

81 if not is_modified:

82 index_code1_protein[self.code1] = self

84 @staticmethod

85 def from_code1(code1):

86 return index_code1_protein[code1.upper()]

87 def instance(self):

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

89 return AminoAcid(self)

92 class AminoAcid(Monomer):

93 """ Amino acid """

94 pass

97 # prepare all aminoacids

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

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

101 if m_type == 'p':

102 AminoAcidType(name, code1, code3, is_modified)

103

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

105