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)