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"""
Parser module specific to CASP-RR MODE 2 distance predictions
"""
import numpy as np
from conkit.io._parser import DistanceFileParser
from conkit.core.distance import Distance
from conkit.core.distogram import Distogram
from conkit.core.distancefile import DistanceFile
DISTANCE_BINS = ((0, 4), (4, 6), (6, 8), (8, 10), (10, 12), (12, 14), (14, 16), (16, 18), (18, 20), (20, np.inf))
[docs]class CaspMode2Parser(DistanceFileParser):
"""Parser class for CASP RR MODE 2 distance prediction file"""
[docs] def read(self, f_handle, f_id="casp2"):
"""Read a distance prediction file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`~conkit.core.distancefile.DistanceFile`
"""
hierarchy = DistanceFile(f_id)
hierarchy.original_file_format = "caspmode2"
_map = Distogram("distogram_1")
hierarchy.add(_map)
for line in f_handle.readlines():
line = line.lstrip().rstrip().split()
if not line or len(line) != 13 or not line[0].isdigit() or not line[1].isdigit():
continue
res1_seq = int(line[0])
res2_seq = int(line[1])
raw_score = float(line[2])
distance_scores = tuple([float(p) for p in line[3:]])
_distance = Distance(res1_seq, res2_seq, distance_scores, DISTANCE_BINS, raw_score=raw_score)
_map.add(_distance)
return hierarchy
[docs] def write(self, f_handle, hierarchy):
"""Write a distance prediction file instance to a file
Parameters
----------
f_handle
Open file handle [write permissions]
hierarchy : :obj:`~conkit.core.distancefile.DistanceFile`, :obj:`~conkit.core.distogram.Distogram`
or :obj:`~conkit.core.distance.Distance`
Raises
------
:exc:`RuntimeError`
More than one contact map in the hierarchy
"""
distancefile = self._reconstruct(hierarchy)
if len(distancefile) > 1:
raise RuntimeError("More than one distogram provided")
distogram = distancefile.top_map
content = "PFRMAT RR\nRMODE 2\n"
line_template = "{} {} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f} {:.6f}\n"
for distance in distogram:
distance.reshape_bins(DISTANCE_BINS)
content += line_template.format(distance.res1_seq, distance.res2_seq,
distance.raw_score, *distance.distance_scores)
f_handle.write(content)
