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"""
Parser module specific to CASP-RR predictions
"""
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "0.13.3"
import collections
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.ContactFile` instance
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`~conkit.core.contactfile.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_{}".format(contact_map.id), seq)
contact_map.sequence = sequence
contact_map.set_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:`~conkit.core.contactfile.ContactFile`, :obj:`~conkit.core.contactmap.ContactMap`
or :obj:`~conkit.core.contact.Contact`
"""
contact_file = self._reconstruct(hierarchy)
content = "PFRMAT RR\n"
if contact_file.target:
content += "TARGET {}\n".format(contact_file.target)
if contact_file.author:
content += "AUTHOR {}\n".format(contact_file.author)
if contact_file.remark:
for remark in contact_file.remark:
content += "REMARK {}\n".format(remark)
if contact_file.method:
for method in contact_file.method:
content += "METHOD {}\n".format(method)
for contact_map in contact_file:
content += "MODEL {}\n".format(contact_map.id)
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] + "\n"
# 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}\n"
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
content += "ENDMDL\n"
content += "END\n"
f_handle.write(content)
