Source code for conkit.io.PsicovIO
"""
Parser module specific to PSICOV predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 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
[docs]class PsicovParser(_ContactFileParser):
"""Class to parse a PSICOV contact prediction
"""
[docs] def read(self, f_handle, f_id="psicov"):
"""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`
"""
hierarchy = ContactFile(f_id)
_map = ContactMap("map_1")
hierarchy.add(_map)
for line in f_handle:
line = line.strip().split()
if not line or line[0].isalpha():
continue
elif line[0].isdigit():
_contact = Contact(int(line[0]), int(line[1]), float(line[4]),
distance_bound=(int(line[2]), int(line[3])))
_map.add(_contact)
hierarchy.method = 'Contact map predicted using PSICOV'
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:`conkit.core.ContactFile`, :obj:`conkit.core.ContactMap` or :obj:`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:
for contact in contact_map:
line = "{res1_seq} {res2_seq} {lb} {ub} {raw_score:.6f}"
line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq, raw_score=contact.raw_score,
lb=contact.distance_bound[0], ub=contact.distance_bound[1])
f_handle.write(line + os.linesep)
return