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"""
Parser module specific to rosetta NPZ distance predictions
"""
import numpy as np
from conkit.io._parser import BinaryDistanceFileParser
from conkit.core.distance import Distance
from conkit.core.distogram import Distogram
from conkit.core.distancefile import DistanceFile
DISTANCE_BINS = ((0, 2), (2, 2.5), (2.5, 3), (3, 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 RosettaNpzParser(BinaryDistanceFileParser):
"""Parser class for rosetta NPZ distance prediction file"""
[docs] def read(self, f_handle, f_id="rosettanpz"):
"""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 = "rosettanpz"
_map = Distogram("distogram_1")
hierarchy.add(_map)
prediction = np.load(f_handle, allow_pickle=True)
probs = prediction['dist']
# Bin #0 corresponds with d>20A & bins #1 ~ #36 correspond with 2A<d<20A in increments of 0.5A
probs = probs[:, :, [x for x in range(1, 37)] + [0]]
L = probs.shape[0]
for i in range(L):
for j in range(i, L):
_distance = Distance(i + 1, j + 1, tuple(probs[i, j, :].tolist()), DISTANCE_BINS)
_map.add(_distance)
return hierarchy
[docs] def write(self, f_handle, hierarchy):
"""Write a distance file instance to a file
Raises
------
:exc:`NotImplementedError`
Write function not available
"""
raise NotImplementedError("Write function not available yet")
