Source code for conkit.io.membrain
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"""
Parser module specific to ComsatIO predictions
"""
__author__ = "Felix Simkovic"
__date__ = "12 Oct 2016"
__version__ = "0.1"
import os
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
RE_HEADER = re.compile(r'^Helix\s+Position\s+Residue\s+Helix\s+Position\s+Residue\s+Probability$')
RE_SPLIT = re.compile(r'\s+')
[docs]class MemBrainParser(ContactFileParser):
"""Class to parse a MemBrain contact file
"""
def __init__(self):
super(MemBrainParser, self).__init__()
[docs] def read(self, f_handle, f_id="membrain"):
"""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
if RE_HEADER.match(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 MemBrain'
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')
content = ""
for contact_map in contact_file:
content += 'Helix Position Residue Helix Position Residue Probability' + os.linesep
for contact in contact_map:
line = "Hx {res1_seq: <7} {res1: <7} Hx {res2_seq: <7} {res2: <7} {raw_score: <.6f}"
line = line.format(res1_seq=contact.res1_seq, res2_seq=contact.res2_seq,
res1=contact.res1, res2=contact.res2, raw_score=contact.raw_score)
content += line + os.linesep
f_handle.write(content)