# BSD 3-Clause License
#
# Copyright (c) 2016-17, University of Liverpool
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# * Neither the name of the copyright holder nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""
Parser module specific to bbcontacts predictions
"""
__author__ = "Felix Simkovic"
__date__ = "26 Oct 2016"
__version__ = "0.1"
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
RE_COMMENT = re.compile(r'^#+.*$')
[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"):
"""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>`
"""
contact_file = ContactFile(f_id)
contact_map = ContactMap("map_1")
contact_file.add(contact_map)
for line in f_handle:
line = line.rstrip()
if not line:
continue
elif RE_COMMENT.match(line):
continue
else:
# bbcontacts reverse residue numbering so swap
_, _, _, raw_score, _, _, res2_seq, res1_seq = line.split()
if any(value == "NA" for value in [raw_score, res2_seq, res1_seq]):
continue
contact = Contact(int(res1_seq), int(res2_seq), float(raw_score))
contact_map.add(contact)
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:`ContactFile <conkit.core.ContactFile>`, :obj:`ContactMap <conkit.core.ContactMap>`
or :obj:`Contact <conkit.core.Contact>`
Notes
-----
Creating a :func`write` function for the Bbcontacts parser
would come with a lot of issues, such as the parallel/antiparallel
direction, scoring etc.
Thus, no :func:`write` method is available.
Raises
------
NotImplementedError
Write function not available
"""
raise NotImplementedError("Write function not available")