Source code for conkit.io.ComsatIO
"""
Parser module specific to COMSAT 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
import re
RE_SPLIT = re.compile(r'\s+')
[docs]class ComsatParser(_ContactFileParser):
"""Class to parse a COMSAT contact file
"""
def __init__(self):
super(ComsatParser, self).__init__()
[docs] def read(self, f_handle, f_id="comsat"):
"""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`
"""
contact_file = ContactFile(f_id)
contact_map = ContactMap("map_1")
contact_file.add(contact_map)
for line in f_handle:
line = line.rstrip()
if not line:
continue
else:
res1_seq, res1, res2_seq, res2, _ = RE_SPLIT.split(line)
contact = Contact(
int(res1_seq),
int(res2_seq),
0.0
)
contact.res1 = res1
contact.res2 = res2
contact_map.add(contact)
contact_file.method = 'Contact map predicted using COMSAT'
return contact_file
[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}{sep}{res1}{sep}{res2_seq}{sep}{res2}{sep}Hx-Hx"
line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq,
res1=contact.res1, res2=contact.res2, sep="\t")
f_handle.write(line + os.linesep)
return