Source code for conkit.io.epcmap

# 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 EPC-Map predictions
"""

__author__ = "Felix Simkovic"
__date__ = "12 Dec 2016"
__version__ = "0.1"

import os

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 EPCMapParser(ContactFileParser):
    """Class to parse a EPC-Map contact prediction
    """
[docs]    def read(self, f_handle, f_id="epcmap"):
        """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)
        _map = ContactMap("map_1")
        hierarchy.add(_map)

        for line in f_handle:
            line = line.strip().split()

            if not line or line[0].isalpha():
                continue

            elif line[0].isdigit():
                _contact = Contact(int(line[0]), int(line[1]), float(line[4]),
                                   distance_bound=(float(line[2]), float(line[3])))
                _map.add(_contact)

        hierarchy.method = 'Contact map predicted using EPC-Map'

        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
           More than one contact map in the hierarchy

        """
        # Double check the type of hierarchy and reconstruct if necessary
        contact_file = self._reconstruct(hierarchy)

        if len(contact_file) > 1:
            raise RuntimeError('More than one contact map provided')

        content = ""

        for contact_map in contact_file:
            for contact in contact_map:
                line = "{res1_seq} {res2_seq} {lb} {ub} {raw_score:.6f}"
                lb = int(contact.lower_bound) if float(contact.lower_bound).is_integer() else contact.lower_bound
                ub = int(contact.upper_bound) if float(contact.upper_bound).is_integer() else contact.upper_bound
                line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq, raw_score=contact.raw_score,
                                   lb=lb, ub=ub)
                content += line + os.linesep

        f_handle.write(content)