allpy: 7a87d55efc17 lib/allpy

allpy

view lib/allpy_pdb.py @ 104:7a87d55efc17

lib: renamed monomer_type to either type or monomer_kind where appropriate

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Thu, 21 Oct 2010 15:22:36 +0400
parents	65c3e3aad2e4
children	32b9f4fadd35

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" % \

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

17 else:

18 return "%s_%s" % \

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

22 def std_id_parse(ID):

23 """

24 Parse standart ID to pdb_code, chain and model

25 """

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

27 # it is file

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

29 else:

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

31 if not parseO:

32 return None

33 parse = parseO.groups()

34 if len(parse) < 2:

35 return None

36 code = parse[1]

37 chain = ''

38 model = None

39 if len(parse) >= 4:

40 chain = parse[3]

41 if chain:

42 chain = chain.upper()

43 if len(parse) >= 6:

44 if parse[5]:

45 model = parse[5]

46 return code, chain, model

53 #~ class Coordinates(object):

54 """

55 float x, y, z

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

58 Coordinates() -> new Coordinates

59 """