allpy: 32b9f4fadd35 lib/allpy

allpy

view lib/allpy_pdb.py @ 138:32b9f4fadd35

allpy_pdb: new fasta id parsing function broken: remove class Pdb

author	boris <bnagaev@gmail.com>
date	Sun, 24 Oct 2010 17:29:59 +0400
parents	ea3113da42ca
children	57c923c2e333

line source

1 import re

3 """

4 Functions to get pdb information from fasta id

5 and to generate fasta id from pdb information

7 pdb information: code, chain, model

9 TODO: same for local pdb files

10 """

12 # for pdb-codes

13 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}))?)?($|[^a-z0-9])")

15 #~ # for files

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

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

19 if pdb_model:

20 return "%s_%s_%s" % \

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

22 else:

23 return "%s_%s" % \

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

26 def pdb_id_parse(ID):

27 match = re1.search(ID, re.I)

28 if not match:

29 return None

30 return match.groupdict()

33 #~ def std_id_parse(ID):

34 #~ """

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

36 #~ """

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

38 #~ # it is file

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

40 #~ else:

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

42 #~ if not parseO:

43 #~ return None

44 #~ parse = parseO.groups()

45 #~ if len(parse) < 2:

46 #~ return None

47 #~ code = parse[1]

48 #~ chain = ''

49 #~ model = None

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

51 #~ chain = parse[3]

52 #~ if chain:

53 #~ chain = chain.upper()

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

55 #~ if parse[5]:

56 #~ model = parse[5]

57 #~ return code, chain, model