Source code for conkit.io.ncont

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"""
Parser module specific to ncont contact comparison
"""

__author__ = "Felix Simkovic"
__date__ = "16 Nov 2017"
__version__ = "0.1"

import re
import warnings

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_hit_part = "\/\d+\/([A-Za-z])\/\s*(\d+)\(([A-Z]{3})\)\.\s+\/\s*[A-Z]+\s+\[\s*[A-Z]\]:\s+"
RE_CONTACT = re.compile(_re_hit_part + _re_hit_part + "(\d+\.\d+)\s*")


[docs]class NcontParser(ContactFileParser):
    """Class to parse a Ncont contact file
    """

    def __init__(self):
        super(NcontParser, self).__init__()

[docs]    def read(self, f_handle, f_id="ncont"):
        """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.strip()

            if RE_CONTACT.match(line):
                matches = RE_CONTACT.match(line)
                res1_seq = int(matches.group(2))
                res2_seq = int(matches.group(5))
                lb = ub = float(matches.group(7))

                if (res1_seq, res2_seq) in contact_map:
                    msg = "This parser cannot handle multiple atoms of the same residue. " \
                          "If your contact map contains such entries, only the first will be stored!"
                    warnings.warn(msg)
                    continue

                contact = Contact(res1_seq, res2_seq, 1.0,
                                  distance_bound=(lb, ub))
                contact.res1_chain = matches.group(1)
                contact.res2_chain = matches.group(4)
                contact.res1 = matches.group(3)
                contact.res2 = matches.group(6)
                contact_map.add(contact)

        contact_file.method = 'Contact map generated using Ncont'
        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 Ncont 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")