view lib/monomer.py @ 103:16cb30a3b387
lib::project::column
| author |
boris <bnagaev@gmail.com> |
| date |
Thu, 21 Oct 2010 01:00:18 +0400 |
| parents |
5091fef2ad88 |
| children |
7a87d55efc17 |
line source
3 from allpy_data.AAdict import AAdict
7 index_code1_protein = {}
11 class MonomerType(object):
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
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
29 def from_code3(code3):
30 return index_code3[code3.upper()]
33 return index_name[name.capitalize()]
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):
45 monomer_type -- link to monomer_type
46 pdb_residues -- dictionary like {Bio.PDB.Chain: Bio.PDB.Residue}
48 def __init__(self, monomer_type):
49 self.monomer_type = monomer_type
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)
65 index_code1_protein[self.code1] = self
68 def from_code1(code1):
69 return index_code1_protein[code1.upper()]
71 return AminoAcid(self)
74 class AminoAcid(Monomer):
81 # prepare all aminoacids
83 for code3, data in AAdict.items():
84 code1, m_type, is_modified, none, name = data
86 aat = AminoAcidType(name, code1, code3, is_modified)
