allpy: cf24b0082aa0 allpy/pdb.py

allpy

view allpy/pdb.py @ 269:cf24b0082aa0

Fixed reference to module index in docs

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Wed, 15 Dec 2010 02:22:38 +0300
parents	deae8240d396
children	4e6e85851133

line source

1 """ Functions to get pdb information from fasta id

2 and to generate fasta id from pdb information

4 pdb information: code, chain, model

6 TODO: same for local pdb files

7 """

9 import re

10 from Bio.PDB import PDBParser

13 # for pdb-codes

14 re1 = re.compile(r"(^|[^a-z0-9])(?P<code>[0-9][0-9a-z]{3})([^a-z0-9](?P<chain>[0-9a-z ]?)(?P<model>[^a-z0-9]([0-9]{1,3}))?)?", re.I)

16 #~ # for files

17 #~ re2 = re.compile(r"(^)([^^]+\.(ent|pdb))([^a-zA-Z0-9]([0-9A-Za-z ]?)([^a-zA-Z0-9]([0-9]{1,3}))?)?$")

19 def std_id(pdb_id, pdb_chain, pdb_model=None):

20 if pdb_model:

21 return "%s_%s_%s" % \

22 (pdb_id.lower().strip(), pdb_chain.upper().strip(), pdb_model)

23 else:

24 return "%s_%s" % \

25 (pdb_id.lower().strip(), pdb_chain.upper().strip())

27 def pdb_id_parse(ID):

28 match = re1.search(ID)

29 if not match:

30 return None

31 d = match.groupdict()

32 if 'chain' not in d or not d['chain']:

33 d['chain'] = ' '

34 if 'model' not in d or not d['model']:

35 d['model'] = 0

36 return d

39 def get_structure(file, name):

40 return PDBParser().get_structure(name, file)

42 #~ def std_id_parse(ID):

43 #~ """

44 #~ Parse standart ID to pdb_code, chain and model

45 #~ """

46 #~ if '.ent' in ID.lower() or '.pdb' in ID.lower():

47 #~ # it is file

48 #~ parseO = self.re2.search(ID) # files

49 #~ else:

50 #~ parseO = self.re1.search(ID.lower()) # pdb codes

51 #~ if not parseO:

52 #~ return None

53 #~ parse = parseO.groups()

54 #~ if len(parse) < 2:

55 #~ return None

56 #~ code = parse[1]

57 #~ chain = ''

58 #~ model = None

59 #~ if len(parse) >= 4:

60 #~ chain = parse[3]

61 #~ if chain:

62 #~ chain = chain.upper()

63 #~ if len(parse) >= 6:

64 #~ if parse[5]:

65 #~ model = parse[5]

66 #~ return code, chain, model