allpy
changeset 897:cae08a1f7517
structure: allow to load custom pdbs
Add new sequence name pattern to auto_pdb() method:
file:path:chain:model:resi_begin:resi_end
Like regular expression:
file(:path(:chain(:model(:resi_begin(:resi_end)?)?)?)?)?
close #124
| author | Boris Nagaev <bnagaev@gmail.com> |
|---|---|
| date | Wed, 05 Oct 2011 20:42:15 +0300 |
| parents | 6134ae1dfdae |
| children | 8454b8206bd8 |
| files | allpy/structure.py |
| diffstat | 1 files changed, 15 insertions(+), 3 deletions(-) [+] |
line diff
1.1 --- a/allpy/structure.py Fri Sep 23 14:10:25 2011 +0400 1.2 +++ b/allpy/structure.py Wed Oct 05 20:42:15 2011 +0300 1.3 @@ -27,11 +27,18 @@ 1.4 1.5 1.6 # for pdb-codes 1.7 +pdb_file_pattern = re.compile(r"^file:(?P<path>[^:]+)(:(?P<chain>[0-9a-z ])(:(?P<model>[0-9]{1,3})(:(?P<resi_begin>-?\d+)(:(?P<resi_end>-?\d+))?)?)?)?", re.I) 1.8 + 1.9 +# for pdb-codes 1.10 re1 = re.compile(r"(^|[^a-z0-9])(?P<code>[0-9][0-9a-z]{3})([^a-z0-9](?P<chain>[0-9a-z ]?)([^a-z0-9/](?P<model>[0-9]{1,3}))?)?(/(?P<resi_begin>-?\d+):(?P<resi_end>-?\d+))?", re.I) 1.11 1.12 def pdb_id_parse(ID): 1.13 - match = re1.search(ID) 1.14 + if ID.startswith('file:'): 1.15 + match = pdb_file_pattern.search(ID) 1.16 + else: 1.17 + match = re1.search(ID) 1.18 if not match: 1.19 + print 21 1.20 return None 1.21 d = match.groupdict() 1.22 if 'chain' not in d or not d['chain']: 1.23 @@ -226,12 +233,17 @@ 1.24 """ 1.25 match = pdb_id_parse(self.name) 1.26 assert match 1.27 - code = match['code'] 1.28 + if 'path' in match: 1.29 + code = 'path' 1.30 + pdb_file = open(match['path']) 1.31 + print match['path'] 1.32 + else: 1.33 + code = match['code'] 1.34 + pdb_file = pdb_getter(code) 1.35 chain = match['chain'] 1.36 model = match['model'] 1.37 resi_begin = resi_begin or match['resi_begin'] 1.38 resi_end = resi_end or match['resi_end'] 1.39 - pdb_file = pdb_getter(code) 1.40 self.set_pdb_chain(pdb_file, code, chain, model, xyz_only=xyz_only, 1.41 resi_begin=resi_begin, resi_end=resi_end) 1.42