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"""
Parser module specific to MapPred 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, 4.5), (4.5, 5), (5, 5.5), (5.5, 6), (6, 6.5), (6.5, 7), (7, 7.5), (7.5, 8), (8, 8.5),
(8.5, 9), (9, 9.5), (9.5, 10), (10, 10.5), (10.5, 11), (11, 11.5), (11.5, 12), (12, 12.5), (12.5, 13),
(13, 13.5), (13.5, 14), (14, 14.5), (14.5, 15), (15, 15.5), (15.5, 16), (16, 16.5), (16.5, 17),
(17, 17.5), (17.5, 18), (18, 18.5), (18.5, 19), (19, 19.5), (19.5, 20), (20, np.inf))
[docs]class MapPredParser(DistanceFileParser):
"""Parser class for MapPred distance prediction file"""
[docs] def read(self, f_handle, f_id="mappred"):
"""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 = "mappred"
_map = Distogram("distogram_1")
hierarchy.add(_map)
for line in f_handle.readlines():
line = line.lstrip().rstrip().split()
if not line or len(line) != 36 or not line[0].isdigit() or not line[1].isdigit():
continue
res1_seq = int(line[0])
res2_seq = int(line[1])
distance_scores = tuple([float(p) for p in line[2:]])
_distance = Distance(res1_seq, res2_seq, distance_scores, DISTANCE_BINS)
_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 = "#REMARK MapPred 1.1\n#REMARK idx_i, idx_j, distance distribution of 34 bins\n#REMARK 34 bins " \
"consist of 32 normal bins (4-20A with a step of 0.5A) and two boundary bins ( [0,4) and [20, inf) " \
"), as follows: [0,4,4.5,5,5.5,6,6.5,7,7.5,8,8.5,9,9.5,10,10.5,11,11.5,12,12.5,13,13.5,14,14.5,15," \
"15.5,16,16.5,17,17.5,18,18.5,19,19.5,20,inf]\n"
line_template = "{} {}" + " {:.6f}" * 34 + "\n"
for distance in distogram:
distance.reshape_bins(DISTANCE_BINS)
content += line_template.format(distance.res1_seq, distance.res2_seq, *distance.distance_scores)
f_handle.write(content)
