allpy: 7c30000dd742 lib/allpy

allpy

view lib/allpy_pdb.py @ 85:7c30000dd742

wt: add resources files

author	boris <bnagaev@gmail.com>
date	Tue, 19 Oct 2010 17:54:14 +0400
parents
children	ea3113da42ca

line source

1 import re

3 # for pdb-codes

4 re1 = re.compile(r"(^|[^a-z0-9])([0-9][0-9a-z]{3})([^a-z0-9]([0-9a-z ]?)([^a-z0-9]([0-9]{1,3}))?)?($|[^a-z0-9])")

6 # for files

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

9 class Pdb(object):

10 """

11 """

12 @staticmethod

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

14 if pdb_model:

15 return "%s_%s_%s" % pdb_id.lower().strip(), pdb_chain.upper().strip(), pdb_model

16 else:

17 return "%s_%s" % pdb_id.lower().strip(), pdb_chain.upper().strip()

20 def std_id_parse(ID):

21 """

22 Parse standart ID to pdb_code, chain and model

23 """

24 if '.ent' in ID.lower() or '.pdb' in ID.lower():

25 # it is file

26 parseO = self.re2.search(ID) # files

27 else:

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

29 if not parseO:

30 return None

31 parse = parseO.groups()

32 if len(parse) < 2:

33 return None

34 code = parse[1]

35 chain = ''

36 model = None

37 if len(parse) >= 4:

38 chain = parse[3]

39 if chain:

40 chain = chain.upper()

41 if len(parse) >= 6:

42 if parse[5]:

43 model = parse[5]

44 return code, chain, model

51 #~ class Coordinates(object):

52 """

53 float x, y, z

55 Coordinates(x, y, z) -> Coordinates

56 Coordinates() -> new Coordinates

57 """