Source code for conkit.io.alphafold

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"""
Parser module specific to AF2 distance predictions
"""

import numpy as np
from scipy.special import softmax
from conkit.io._parser import BinaryDistanceFileParser
from conkit.core.distance import Distance
from conkit.core.distogram import Distogram
from conkit.core.distancefile import DistanceFile


class AlphaFold2Parser(BinaryDistanceFileParser):
    """Parser class for AF2 distance prediction file"""

    def read(self, f_handle, f_id="alphafold2"):
        """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 = "alphafold2"
        _map = Distogram("distogram_1")
        hierarchy.add(_map)

        prediction = np.load(f_handle, allow_pickle=True)
        predicted_distogram = prediction['distogram']
        probs = softmax(predicted_distogram['logits'], axis=-1)
        bin_edges = predicted_distogram['bin_edges']

        distance_bins = [(0, bin_edges[0])]
        distance_bins += [(bin_edges[idx], bin_edges[idx + 1]) for idx in range(len(bin_edges) - 1)]
        distance_bins.append((bin_edges[-1], np.inf))
        distance_bins = tuple(distance_bins)
        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

    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")