Source code for conkit.io.aleigen

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"""
Parser module specific to al-eigen map files
"""

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 AleigenParser(ContactFileParser):
    """Class to parse a al-eigen map file
    """

[docs]    def read(self, f_handle, f_id="map_align"):
        """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 len(line) == 2 and line[0].isdigit() and line[1].isdigit():
                # Al-eigen has no score field so we assume score=0.5
                _contact = Contact(int(line[0]), int(line[1]), 0.5)
                _map.add(_contact)

        hierarchy.method = "Contact map compatible with Al-Eigen"

        return hierarchy

[docs]    def write(self, f_handle, hierarchy):
        """Write a contact file instance to a 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")
        cmap = contact_file.top_map
        content = "{}\n".format(cmap.highest_residue_number)
        line_template = "{} {}\n"
        for contact in cmap:
            content += line_template.format(contact.res1_seq, contact.res2_seq)
        f_handle.write(content)