"""
Parser module specific to BCL::Contact predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Dec 2016"
__version__ = "0.1"
from conkit.core import Contact
from conkit.core import ContactMap
from conkit.core import ContactFile
from conkit.io._ParserIO import _ContactFileParser
import re
RE_SPLIT = re.compile(r'\s+')
[docs]class BCLContactParser(_ContactFileParser):
"""Class to parse a BCL::Contact contact file
"""
def __init__(self):
super(BCLContactParser, self).__init__()
[docs] def read(self, f_handle, f_id="bclcontact"):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`ContactFile <conkit.core.ContactFile>`
"""
hierarchy = ContactFile(f_id)
contact_map = ContactMap("map_1")
hierarchy.add(contact_map)
for line in f_handle:
line = line.rstrip()
if not line:
continue
else:
res1_seq, res1, res2_seq, res2, _, _, _, _, _, raw_score = RE_SPLIT.split(line)
contact = Contact(
int(res1_seq),
int(res2_seq),
float(raw_score)
)
contact.res1 = res1
contact.res2 = res2
contact_map.add(contact)
hierarchy.method = 'Contact map predicted using BCL::Contact'
return hierarchy
[docs] def write(self, f_handle, hierarchy):
"""Write a contact file instance to to file
Parameters
----------
f_handle
Open file handle [write permissions]
hierarchy : :obj:`ContactFile <conkit.core.ContactFile>`, :obj:`ContactMap <conkit.core.ContactMap>`
or :obj:`Contact <conkit.core.Contact>`
Raises
------
RuntimeError
Not available
"""
raise RuntimeError("Not available")