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")