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"""
Parser module specific to CASP-RR predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "1.0"
import collections
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
from conkit.core.sequence import Sequence
# Credits to Stefan Seemayer - bits taken from PyMOL-RR
RE_PRFMAT = re.compile(r'PFRMAT\s+(RR)\s*$')
RE_TARGET = re.compile(r'^TARGET\s+(.*?)\s*$')
RE_AUTHOR = re.compile(r'^AUTHOR\s+(.*?)\s*$')
RE_REMARK = re.compile(r'^REMARK\s+(.*?)\s*$')
RE_METHOD = re.compile(r'^METHOD\s+(.*?)\s*$')
RE_MODEL = re.compile(r'^MODEL\s+(\w+)\s*$')
RE_SEQ = re.compile(r'^([A-Za-z\-]+)$')
RE_SPLIT = re.compile(r'\s+')
RE_RES = re.compile(r'([A-Za-z]+)([0-9]+)')
RE_ENDMDL = re.compile(r'^ENDMDL\s*$')
RE_END = re.compile(r'^END\s*$')
# Intermediate storage structures
ModelTemplate = collections.namedtuple('Model', ['id', 'contacts', 'sequence'])
ContactTemplate = collections.namedtuple('Contact', ['res1_seq', 'res2_seq', 'lb', 'ub', 'raw_score',
'res1_chain', 'res2_chain', 'res1_altseq', 'res2_altseq'])
[docs]class CaspParser(ContactFileParser):
"""Parser class for CASP RR contact prediction file
"""
def __init__(self):
super(CaspParser, self).__init__()
[docs] def read(self, f_handle, f_id="casp"):
"""Read a contact file into a :obj:`conkit.core.ContactFile` instance
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`ContactFile <conkit.core.ContactFile>`
"""
lines = [l.strip() for l in f_handle.readlines()]
contact_file = ContactFile(f_id)
it = iter(lines)
while True:
try:
line = next(it)
except StopIteration:
break
if RE_PRFMAT.match(line):
continue
elif RE_TARGET.match(line):
contact_file.remark = RE_TARGET.match(line).group(1)
elif RE_AUTHOR.match(line):
contact_file.author = RE_AUTHOR.match(line).group(1)
elif RE_REMARK.match(line):
contact_file.remark = RE_REMARK.match(line).group(1)
elif RE_METHOD.match(line):
contact_file.method = RE_METHOD.match(line).group(1)
elif RE_MODEL.match(line):
contact_map = ContactMap(RE_MODEL.match(line).group(1))
seq_chunks = []
while True:
try:
line = next(it)
except StopIteration:
break
if not line:
break
if RE_ENDMDL.match(line):
break
elif RE_END.match(line):
break
elif RE_SEQ.match(line):
seq_chunks.append(line)
else:
res1_entry, res2_entry, lb, ub, raw_score = RE_SPLIT.split(line)
# Split in case we have chain in inter-molecular scenarios
res1_split = RE_RES.split(res1_entry)
if len(res1_split) == 1:
res1_chain, res1_seq = '', res1_split[0]
elif len(res1_split) == 4:
res1_chain, res1_seq = res1_split[1], res1_split[2]
res2_split = RE_RES.split(res2_entry)
if len(res2_split) == 1:
res2_chain, res2_seq = '', res2_split[0]
elif len(res2_split) == 4:
res2_chain, res2_seq = res2_split[1], res2_split[2]
contact = Contact(int(res1_seq), int(res2_seq), float(raw_score),
distance_bound=(float(lb), float(ub)))
contact.res1_chain = res1_chain
contact.res2_chain = res2_chain
contact.res1_altseq = int(res1_seq)
contact.res2_altseq = int(res2_seq)
contact_map.add(contact)
if seq_chunks:
seq = "".join(seq_chunks)
sequence = Sequence('seq_{0}'.format(contact_map.id), seq)
contact_map.sequence = sequence
contact_map.assign_sequence_register()
contact_file.add(contact_map)
elif RE_END.match(line):
break
else:
raise ValueError('Unrecognized line type. Please report this issue')
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>`
"""
# Double check the type of hierarchy and reconstruct if necessary
contact_file = self._reconstruct(hierarchy)
content = "PFRMAT RR" + os.linesep
if contact_file.target:
content += "TARGET {0}".format(contact_file.target) + os.linesep
if contact_file.author:
content += "AUTHOR {0}".format(contact_file.author) + os.linesep
if contact_file.remark:
for remark in contact_file.remark:
content += "REMARK {0}".format(remark) + os.linesep
if contact_file.method:
for method in contact_file.method:
content += "METHOD {0}".format(method) + os.linesep
for contact_map in contact_file:
content += "MODEL {0}".format(contact_map.id) + os.linesep
if isinstance(contact_map.sequence, Sequence):
sequence = contact_map.sequence
for i in range(0, sequence.seq_len, 50):
content += sequence.seq[i:i+50] + os.linesep
# Casp Roll format specifies raw scores to be in [0, 1]
if any(c.raw_score > 1.0 or c.raw_score < 0.0 for c in contact_map):
contact_map.rescale(inplace=True)
for contact in contact_map:
s = '{res1_chain: <}{res1_seq: <4} {res2_chain: <}{res2_seq:<4} {lb: <3} {ub: <3} {raw_score: <.6f}'
if contact.res1_chain == contact.res2_chain:
res1_chain = res2_chain = ""
else:
res1_chain = contact.res1_chain
res2_chain = contact.res2_chain
lb = int(contact.lower_bound) if float(contact.lower_bound).is_integer() else contact.lower_bound
ub = int(contact.upper_bound) if float(contact.upper_bound).is_integer() else contact.upper_bound
s = s.format(res1_chain=res1_chain, res1_seq=contact.res1_seq, res2_chain=res2_chain,
res2_seq=contact.res2_seq, lb=lb, ub=ub, raw_score=contact.raw_score)
content += s + os.linesep
content += "ENDMDL" + os.linesep
content += "END" + os.linesep
f_handle.write(content)
