Source code for conkit.io.psicov
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"""
Parser module specific to PSICOV predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.13.3"
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 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.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=(float(line[2]), float(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.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")
content = ""
for contact_map in contact_file:
for contact in contact_map:
line = "{} {} {} {} {:.6f}\n"
lb = int(contact.lower_bound) if float(contact.lower_bound).is_integer() else contact.lower_bound
ub = int(contact.upper_bound) if float(contact.upper_bound).is_integer() else contact.upper_bound
content += line.format(contact.res1_seq, contact.res2_seq, lb, ub, contact.raw_score)
f_handle.write(content)