allpy: allpy/pdb.py annotate

allpy

annotate allpy/pdb.py @ 247:c85e3a2c87d8

allpy: allpy_data --> allpy.data

author	boris <bnagaev@gmail.com>
date	Sat, 04 Dec 2010 00:08:12 +0300
parents	73f9779491ef
children	90a75f2fe7df

rev	line source
bnagaev@79	1 import re
bnagaev@79	2 from Bio.PDB import PDBParser
bnagaev@156	3
bnagaev@79	4 """ Functions to get pdb information from fasta id
bnagaev@147	5 and to generate fasta id from pdb information
bnagaev@138	6
bnagaev@138	7 pdb information: code, chain, model
bnagaev@138	8
bnagaev@138	9 TODO: same for local pdb files
bnagaev@138	10 """
bnagaev@138	11
bnagaev@138	12 # for pdb-codes
bnagaev@79	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}))?)?", re.I)
bnagaev@151	14
bnagaev@79	15 #~ # for files
bnagaev@138	16 #~ re2 = re.compile(r"(^)([^^]+\.(ent\|pdb))([^a-zA-Z0-9]([0-9A-Za-z ]?)([^a-zA-Z0-9]([0-9]{1,3}))?)?$")
bnagaev@138	17
bnagaev@79	18 def std_id(pdb_id, pdb_chain, pdb_model=None):
bnagaev@138	19 if pdb_model:
bnagaev@138	20 return "%s_%s_%s" % \
bnagaev@138	21 (pdb_id.lower().strip(), pdb_chain.upper().strip(), pdb_model)
bnagaev@138	22 else:
bnagaev@138	23 return "%s_%s" % \
bnagaev@138	24 (pdb_id.lower().strip(), pdb_chain.upper().strip())
bnagaev@138	25
bnagaev@83	26 def pdb_id_parse(ID):
bnagaev@138	27 match = re1.search(ID)
bnagaev@139	28 if not match:
bnagaev@138	29 return None
bnagaev@138	30 d = match.groupdict()
bnagaev@139	31 if 'chain' not in d or not d['chain']:
bnagaev@139	32 d['chain'] = ' '
bnagaev@139	33 if 'model' not in d or not d['model']:
bnagaev@139	34 d['model'] = 0
bnagaev@139	35 return d
bnagaev@139	36
bnagaev@83	37
bnagaev@156	38 def get_structure(file, name):
bnagaev@156	39 return PDBParser().get_structure(name, file)
bnagaev@157	40
bnagaev@156	41 #~ def std_id_parse(ID):
bnagaev@138	42 #~ """
bnagaev@138	43 #~ Parse standart ID to pdb_code, chain and model
bnagaev@138	44 #~ """
bnagaev@138	45 #~ if '.ent' in ID.lower() or '.pdb' in ID.lower():
bnagaev@138	46 #~ # it is file
bnagaev@138	47 #~ parseO = self.re2.search(ID) # files
bnagaev@138	48 #~ else:
bnagaev@138	49 #~ parseO = self.re1.search(ID.lower()) # pdb codes
bnagaev@138	50 #~ if not parseO:
bnagaev@138	51 #~ return None
bnagaev@138	52 #~ parse = parseO.groups()
bnagaev@138	53 #~ if len(parse) < 2:
bnagaev@138	54 #~ return None
bnagaev@138	55 #~ code = parse[1]
bnagaev@138	56 #~ chain = ''
bnagaev@138	57 #~ model = None
bnagaev@138	58 #~ if len(parse) >= 4:
bnagaev@138	59 #~ chain = parse[3]
bnagaev@138	60 #~ if chain:
bnagaev@138	61 #~ chain = chain.upper()
bnagaev@138	62 #~ if len(parse) >= 6:
bnagaev@138	63 #~ if parse[5]:
bnagaev@138	64 #~ model = parse[5]
bnagaev@138	65 #~ return code, chain, model
bnagaev@138	66
bnagaev@83	67