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"""
Parser module specific to bbcontacts predictions
"""
__author__ = "Felix Simkovic"
__date__ = "23 Jul 2018"
__version__ = "0.2"
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
[docs]class BbcontactsParser(ContactFileParser):
"""Class to parse a Bbcontacts contact file
"""
def __init__(self):
super(BbcontactsParser, self).__init__()
[docs] def read(self, f_handle, f_id="bbcontacts", del_one_two=False):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
del_one_two : bool
Remove one- & two-strand sheets
Returns
-------
:obj:`~conkit.core.contactfile.ContactFile`
"""
contact_file = ContactFile(f_id)
contact_map = ContactMap("map_1")
contact_file.add(contact_map)
previous = "first"
for line in f_handle:
line = line.strip()
if line and not line.startswith("#"):
_, _, _, raw_score, _, current, res2_seq, res1_seq = line.split()
if del_one_two and previous == "first" and current == "last":
contact_map.child_list.pop()
elif any(value == "NA" for value in [raw_score, res2_seq, res1_seq]):
pass
else:
contact = Contact(int(res1_seq), int(res2_seq), float(raw_score))
contact_map.add(contact)
previous = current
if del_one_two and previous == "first" and len(contact_map) > 0:
contact_map.child_list.pop()
contact_file.method = "Contact map predicted using Bbcontacts"
return contact_file
[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:`~conkit.core.contactfile.ContactFile`, :obj:`~conkit.core.contactmap.ContactMap`
or :obj:`~conkit.core.contact.Contact`
Note
----
Creating a :meth:`~conkit.io.bbcontacts.BbcontactsParser.write` method
would come with a lot of issues, such as the parallel/antiparallel
direction, scoring etc ... thus, this function is unvailable.
Raises
------
:exc:`NotImplementedError`
Write function not available
"""
raise NotImplementedError("Write function not available")