Source code for conkit.io.epcmap

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"""
Parser module specific to EPC-Map predictions
"""

__author__ = "Felix Simkovic"
__date__ = "12 Dec 2016"
__version__ = "0.13.3"

from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile


class EPCMapParser(ContactFileParser):
    """Class to parse a EPC-Map contact prediction
    """

    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:`~conkit.core.contactfile.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

    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`

        Raises
        ------
        :exc:`RuntimeError`
           More than one contact map in the hierarchy

        """
        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}\n"
                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

        f_handle.write(content)