Source code for conkit.io.MemBrainIO

"""
Parser module specific to ComsatIO predictions
"""

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

from conkit.core import Contact
from conkit.core import ContactMap
from conkit.core import ContactFile
from conkit.io._ParserIO import _ContactFileParser

import os
import re

RE_HEADER = re.compile(r'^Helix\s+Position\s+Residue\s+Helix\s+Position\s+Residue\s+Probability$')
RE_SPLIT = re.compile(r'\s+')


[docs]class MemBrainParser(_ContactFileParser):
    """Class to parse a MemBrain contact file
    """
    def __init__(self):
        super(MemBrainParser, self).__init__()

[docs]    def read(self, f_handle, f_id="membrain"):
        """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)
        contact_map = ContactMap("map_1")
        hierarchy.add(contact_map)

        for line in f_handle:
            line = line.rstrip()

            if not line:
                continue

            if RE_HEADER.match(line):
                continue

            else:
                _, res1_seq, res1, _, res2_seq, res2, raw_score = RE_SPLIT.split(line)

                contact = Contact(
                    int(res1_seq),
                    int(res2_seq),
                    float(raw_score)
                )
                contact.res1 = res1
                contact.res2 = res2
                contact_map.add(contact)

        hierarchy.method = 'Contact map predicted using MemBrain'

        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')

        for contact_map in contact_file:
            f_handle.write('Helix   Position        Residue Helix   Position        Residue Probability' + os.linesep)
            for contact in contact_map:
                line = "Hx      {res1_seq: <7} {res1: <7} Hx      {res2_seq: <7} {res2: <7} {raw_score: <.6f}"
                line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq,
                                   res1=contact.res1, res2=contact.res2, raw_score=contact.raw_score)
                f_handle.write(line + os.linesep)

        return