Source code for conkit.io.rosetta

# MIT License
#
# Copyright (c) 2017-18 Felix Simkovic
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__author__ = 'Felix Simkovic'
__date__ = '13 Aug 2018'
__version__ = '1.0'

from conkit.io._parser import ContactFileParser
from conkit.misc.distances import DynamicDistances
from conkit.misc.energyfunction import RosettaFunctionConstructs


[docs]class RosettaParser(ContactFileParser):
    """Implementation of a ROSETTA restraint file parser"""

[docs]    def read(self, f_handle, f_id='rosetta'):
        """Read a contact file into a :obj:`~conkit.core.contactfile.ContactFile` instance

        Parameters
        ----------
        f_handle
           Open file handle [read permissions]
        f_id : str, optional
           Unique contact file identifier

        Returns
        -------
        :obj:`~conkit.core.contactfile.ContactFile`

        Raises
        ------
        :exc:`NotImplementedError`

        """
        raise NotImplementedError

[docs]    def write(self, f_handle, hierarchy, efunc='FADE'):
        """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`
        efunc : str, optional
           The output format

        """
        if not hasattr(RosettaFunctionConstructs, efunc):
            raise ValueError('Unknown Rosetta energy function: {}'.format(efunc))
        contact_file = self._reconstruct(hierarchy)
        construct = getattr(RosettaFunctionConstructs, efunc).fget(RosettaFunctionConstructs)
        for contact in contact_file.top:
            contact_dict = contact._to_dict()
            contact_dict['atom1'] = 'CA' if contact.res1 == 'G' else 'CB'
            contact_dict['atom2'] = 'CA' if contact.res2 == 'G' else 'CB'
            contact_dict['energy_bonus'] = contact.weight * 15.00
            contact_dict['scalar_score'] = contact.scalar_score * contact.weight
            contact_dict['sigmoid_cutoff'] = DynamicDistances.cutoff(contact.res1, contact.res2)
            contact_dict['sigmoid_slope'] = 1.0 / DynamicDistances.percentile(contact.res1, contact.res2)
            f_handle.write(construct.format(**contact_dict) + '\n')