"""
Parser module specific to FreeContact predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Oct 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
import re
RE_SPLIT = re.compile(r'\s+')
[docs]class FreeContactParser(_ContactFileParser):
"""Class to parse a FreeContact contact file
"""
def __init__(self):
super(FreeContactParser, self).__init__()
[docs] def read(self, f_handle, f_id="freecontact"):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`ContactFile <conkit.core.ContactFile>`
"""
hierarchy = ContactFile(f_id)
contact_map = ContactMap("map_1")
hierarchy.add(contact_map)
for line in f_handle:
line = line.rstrip()
if not line:
continue
else:
res1_seq, res1, res2_seq, res2, raw_score, _ = RE_SPLIT.split(line)
contact = Contact(
int(res1_seq),
int(res2_seq),
float(raw_score)
)
contact.res1 = res1
contact.res2 = res2
contact_map.add(contact)
hierarchy.method = 'Contact map predicted using FreeContact'
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:`ContactFile <conkit.core.ContactFile>`, :obj:`ContactMap <conkit.core.ContactMap>`
or :obj:`Contact <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} {res1} {res2_seq} {res2} {raw_score} 0"
line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq,
res1=contact.res1, res2=contact.res2, raw_score=contact.raw_score)
f_handle.write(line + os.linesep)
return