Source code for conkit.io.plmdca
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"""
Parser module specific to plmDCA predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.1"
import os
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 PlmDCAParser(ContactFileParser):
"""Class to parse a plmDCA contact prediction
"""
def __init__(self):
super(PlmDCAParser, self).__init__()
[docs] def read(self, f_handle, f_id="plmdca"):
"""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>`
"""
contact_file = ContactFile(f_id)
contact_map = ContactMap("map_1")
contact_file.add(contact_map)
for line in f_handle:
line = line.strip()
if not line or line[0].isalpha():
continue
elif line[0].isdigit():
res1_seq, res2_seq, raw_score = line.split(',')
contact = Contact(int(res1_seq), int(res2_seq), float(raw_score))
contact_map.add(contact)
contact_file.method = 'Contact map predicted using plmDCA'
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:`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')
content = ""
for contact_map in contact_file:
for contact in contact_map:
line = "{res1_seq},{res2_seq},{raw_score:.6f}"
line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq, raw_score=contact.raw_score)
content += line + os.linesep
f_handle.write(content)