allpy: allpy/pdb.py annotate

allpy

annotate allpy/pdb.py @ 268:3d61ade3a5e5

Regenerated Sphinx autodocs cleaner.

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Wed, 15 Dec 2010 02:13:30 +0300
parents	deae8240d396
children	4e6e85851133

rev	line source
bnagaev@147	1 """ Functions to get pdb information from fasta id
bnagaev@138	2 and to generate fasta id from pdb information
bnagaev@138	3
bnagaev@138	4 pdb information: code, chain, model
bnagaev@138	5
bnagaev@138	6 TODO: same for local pdb files
bnagaev@138	7 """
bnagaev@138	8
bnagaev@248	9 import re
bnagaev@248	10 from Bio.PDB import PDBParser
bnagaev@248	11
bnagaev@248	12
bnagaev@79	13 # for pdb-codes
bnagaev@151	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)
bnagaev@79	15
bnagaev@138	16 #~ # for files
bnagaev@138	17 #~ re2 = re.compile(r"(^)([^^]+\.(ent\|pdb))([^a-zA-Z0-9]([0-9A-Za-z ]?)([^a-zA-Z0-9]([0-9]{1,3}))?)?$")
bnagaev@79	18
bnagaev@138	19 def std_id(pdb_id, pdb_chain, pdb_model=None):
bnagaev@138	20 if pdb_model:
bnagaev@138	21 return "%s_%s_%s" % \
bnagaev@138	22 (pdb_id.lower().strip(), pdb_chain.upper().strip(), pdb_model)
bnagaev@138	23 else:
bnagaev@138	24 return "%s_%s" % \
bnagaev@138	25 (pdb_id.lower().strip(), pdb_chain.upper().strip())
bnagaev@83	26
bnagaev@138	27 def pdb_id_parse(ID):
bnagaev@139	28 match = re1.search(ID)
bnagaev@138	29 if not match:
bnagaev@138	30 return None
bnagaev@139	31 d = match.groupdict()
bnagaev@139	32 if 'chain' not in d or not d['chain']:
bnagaev@139	33 d['chain'] = ' '
bnagaev@139	34 if 'model' not in d or not d['model']:
bnagaev@139	35 d['model'] = 0
bnagaev@139	36 return d
bnagaev@83	37
bnagaev@156	38
bnagaev@156	39 def get_structure(file, name):
bnagaev@157	40 return PDBParser().get_structure(name, file)
bnagaev@156	41
bnagaev@138	42 #~ def std_id_parse(ID):
bnagaev@138	43 #~ """
bnagaev@138	44 #~ Parse standart ID to pdb_code, chain and model
bnagaev@138	45 #~ """
bnagaev@138	46 #~ if '.ent' in ID.lower() or '.pdb' in ID.lower():
bnagaev@138	47 #~ # it is file
bnagaev@138	48 #~ parseO = self.re2.search(ID) # files
bnagaev@138	49 #~ else:
bnagaev@138	50 #~ parseO = self.re1.search(ID.lower()) # pdb codes
bnagaev@138	51 #~ if not parseO:
bnagaev@138	52 #~ return None
bnagaev@138	53 #~ parse = parseO.groups()
bnagaev@138	54 #~ if len(parse) < 2:
bnagaev@138	55 #~ return None
bnagaev@138	56 #~ code = parse[1]
bnagaev@138	57 #~ chain = ''
bnagaev@138	58 #~ model = None
bnagaev@138	59 #~ if len(parse) >= 4:
bnagaev@138	60 #~ chain = parse[3]
bnagaev@138	61 #~ if chain:
bnagaev@138	62 #~ chain = chain.upper()
bnagaev@138	63 #~ if len(parse) >= 6:
bnagaev@138	64 #~ if parse[5]:
bnagaev@138	65 #~ model = parse[5]
bnagaev@138	66 #~ return code, chain, model
bnagaev@83	67