biotite 1.5.0__cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/structure/alphabet/pb.py

@@ -0,0 +1,170 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+Conversion of structures into the *Protein Blocks* structural alphabet.
+"""
+
+__name__ = "biotite.structure.alphabet"
+__author__ = "Patrick Kunzmann"
+__all__ = ["ProteinBlocksSequence", "to_protein_blocks"]
+
+import numpy as np
+from biotite.sequence.alphabet import LetterAlphabet
+from biotite.sequence.sequence import Sequence
+from biotite.structure.chains import get_chain_starts
+from biotite.structure.geometry import dihedral_backbone
+
+# PB reference angles, adapted from PBxplore
+PB_ANGLES = np.array(
+    [
+        [41.14,    75.53,   13.92,  -99.80,  131.88,  -96.27, 122.08,  -99.68],
+        [108.24,  -90.12,  119.54,  -92.21,  -18.06, -128.93, 147.04,  -99.90],
+        [-11.61, -105.66,   94.81, -106.09,  133.56, -106.93, 135.97, -100.63],
+        [141.98, -112.79,  132.20, -114.79,  140.11, -111.05, 139.54, -103.16],
+        [133.25, -112.37,  137.64, -108.13,  133.00,  -87.30, 120.54,   77.40],
+        [116.40, -105.53,  129.32,  -96.68,  140.72,  -74.19, -26.65,  -94.51],
+        [0.40,    -81.83,    4.91, -100.59,   85.50,  -71.65, 130.78,   84.98],
+        [119.14, -102.58,  130.83,  -67.91,  121.55,   76.25,  -2.95,  -90.88],
+        [130.68,  -56.92,  119.26,   77.85,   10.42,  -99.43, 141.40,  -98.01],
+        [114.32, -121.47,  118.14,   82.88, -150.05,  -83.81,  23.35,  -85.82],
+        [117.16,  -95.41,  140.40,  -59.35,  -29.23,  -72.39, -25.08,  -76.16],
+        [139.20,  -55.96,  -32.70,  -68.51,  -26.09,  -74.44, -22.60,  -71.74],
+        [-39.62,  -64.73,  -39.52,  -65.54,  -38.88,  -66.89, -37.76,  -70.19],
+        [-35.34,  -65.03,  -38.12,  -66.34,  -29.51,  -89.10,  -2.91,   77.90],
+        [-45.29,  -67.44,  -27.72,  -87.27,    5.13,   77.49,  30.71,  -93.23],
+        [-27.09,  -86.14,    0.30,   59.85,   21.51,  -96.30, 132.67,  -92.91],
+    ]
+)  # fmt: skip
+
+
+class ProteinBlocksSequence(Sequence):
+    """
+    Representation of a structure in the *Protein Blocks* structural alphabet.
+    :footcite:`Brevern2000`
+
+    Parameters
+    ----------
+    sequence : iterable object, optional
+        The *Protein Blocks* sequence.
+        This may either be a list or a string.
+        May take upper or lower case letters.
+        By default the sequence is empty.
+
+    See Also
+    --------
+    to_protein_blocks : Create *Protein Blocks* sequences from a structure.
+
+    References
+    ----------
+
+    .. footbibliography::
+    """
+
+    alphabet = LetterAlphabet("abcdefghijklmnopz")
+    undefined_symbol = "z"
+
+    def __init__(self, sequence=""):
+        if isinstance(sequence, str):
+            sequence = sequence.lower()
+        else:
+            sequence = [symbol.upper() for symbol in sequence]
+        super().__init__(sequence)
+
+    def get_alphabet(self):
+        return ProteinBlocksSequence.alphabet
+
+    def remove_undefined(self):
+        """
+        Remove undefined symbols from the sequence.
+
+        Returns
+        -------
+        filtered_sequence : ProteinBlocksSequence
+            The sequence without undefined symbols.
+        """
+        undefined_code = ProteinBlocksSequence.alphabet.encode(
+            ProteinBlocksSequence.undefined_symbol
+        )
+        filtered_code = self.code[self.code != undefined_code]
+        filtered_sequence = ProteinBlocksSequence()
+        filtered_sequence.code = filtered_code
+        return filtered_sequence
+
+
+def to_protein_blocks(atoms):
+    """
+    Encode each chain in the given structure to the *Protein Blocks* structural
+    alphabet.
+    :footcite:`Brevern2000`
+
+    Parameters
+    ----------
+    atoms : AtomArray
+        The atom array to encode.
+        May contain multiple chains.
+
+    Returns
+    -------
+    sequences : list of Sequence, length=n
+        The encoded *Protein Blocks* sequence for each peptide chain in the structure.
+    chain_start_indices : ndarray, shape=(n,), dtype=int
+        The atom index where each chain starts.
+
+    References
+    ----------
+
+    .. footbibliography::
+
+    Examples
+    --------
+
+    >>> sequences, chain_starts = to_protein_blocks(atom_array)
+    >>> print(sequences[0])
+    zzmmmmmnopjmnopacdzz
+    """
+    sequences = []
+    chain_start_indices = get_chain_starts(atoms, add_exclusive_stop=True)
+    for i in range(len(chain_start_indices) - 1):
+        start = chain_start_indices[i]
+        stop = chain_start_indices[i + 1]
+        chain = atoms[start:stop]
+        sequences.append(_to_protein_blocks(chain))
+    return sequences, chain_start_indices[:-1]
+
+
+def _to_protein_blocks(chain):
+    undefined_code = ProteinBlocksSequence.alphabet.encode(
+        ProteinBlocksSequence.undefined_symbol
+    )
+
+    phi, psi, _ = dihedral_backbone(chain)
+
+    pb_angles = np.full((len(phi), 8), np.nan)
+    pb_angles[2:-2, 0] = psi[:-4]
+    pb_angles[2:-2, 1] = phi[1:-3]
+    pb_angles[2:-2, 2] = psi[1:-3]
+    pb_angles[2:-2, 3] = phi[2:-2]
+    pb_angles[2:-2, 4] = psi[2:-2]
+    pb_angles[2:-2, 5] = phi[3:-1]
+    pb_angles[2:-2, 6] = psi[3:-1]
+    pb_angles[2:-2, 7] = phi[4:]
+    pb_angles = np.rad2deg(pb_angles)
+
+    # Angle RMSD of all reference angles with all actual angles
+    rmsda = np.sum(
+        ((PB_ANGLES[:, np.newaxis] - pb_angles[np.newaxis, :] + 180) % 360 - 180) ** 2,
+        axis=-1,
+    )
+    # Where RMSDA is NaN, (missing atoms/residues or chain ends) set symbol to unknown
+    pb_seq_code = np.full(len(pb_angles), undefined_code, dtype=np.uint8)
+    pb_available_mask = ~np.isnan(rmsda).any(axis=0)
+    # Chose PB, where the RMSDA to the reference angle is lowest
+    # Due to the definition of Biotite symbol codes
+    # the index of the chosen PB is directly the symbol code
+    pb_seq_code[pb_available_mask] = np.argmin(rmsda[:, pb_available_mask], axis=0)
+    # Put the array of symbol codes into actual sequence objects
+    pb_sequence = ProteinBlocksSequence()
+    pb_sequence.code = pb_seq_code
+    return pb_sequence

biotite/structure/alphabet/unkerasify.py

@@ -0,0 +1,128 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+Parser for extracting weights from Keras files.
+
+Adapted from `moof2k/kerasify <https://github.com/moof2k/kerasify>`_.
+"""
+
+__name__ = "biotite.structure.alphabet"
+__author__ = "Martin Larralde"
+__all__ = ["load_kerasify"]
+
+import enum
+import functools
+import itertools
+import struct
+import numpy as np
+from biotite.structure.alphabet.layers import DenseLayer, Layer
+
+
+class LayerType(enum.IntEnum):
+    DENSE = 1
+    CONVOLUTION2D = 2
+    FLATTEN = 3
+    ELU = 4
+    ACTIVATION = 5
+    MAXPOOLING2D = 6
+    LSTM = 7
+    EMBEDDING = 8
+
+
+class ActivationType(enum.IntEnum):
+    LINEAR = 1
+    RELU = 2
+    SOFTPLUS = 3
+    SIGMOID = 4
+    TANH = 5
+    HARD_SIGMOID = 6
+
+
+class KerasifyParser:
+    """
+    An incomplete parser for model files serialized with `kerasify`.
+
+    Parameters
+    ----------
+    file : file-like
+        The ``.kerasify`` file to parse.
+
+    Notes
+    -----
+    Only dense layers are supported, since the ``foldseek`` VQ-VAE model
+    is only using 3 dense layers.
+    """
+
+    def __init__(self, file) -> None:
+        self.file = file
+        self.buffer = bytearray(1024)
+        (self.n_layers,) = self._get("I")
+
+    def read(self):
+        if self.n_layers == 0:
+            return None
+
+        self.n_layers -= 1
+        layer_type = LayerType(self._get("I")[0])
+        if layer_type == LayerType.DENSE:
+            (w0,) = self._get("I")
+            (w1,) = self._get("I")
+            (b0,) = self._get("I")
+            weights = (
+                np.frombuffer(self._read(f"={w0 * w1}f"), dtype="f4")
+                .reshape(w0, w1)
+                .copy()
+            )
+            biases = np.frombuffer(self._read(f"={b0}f"), dtype="f4").copy()
+            activation = ActivationType(self._get("I")[0])
+            if activation not in (ActivationType.LINEAR, ActivationType.RELU):
+                raise NotImplementedError(
+                    f"Unsupported activation type: {activation!r}"
+                )
+            return DenseLayer(weights, biases, activation == ActivationType.RELU)
+        else:
+            raise NotImplementedError(f"Unsupported layer type: {layer_type!r}")
+
+    def __iter__(self):
+        return self
+
+    def __next__(self) -> Layer:
+        layer = self.read()
+        if layer is None:
+            raise StopIteration
+        return layer
+
+    def _read(self, format: str) -> memoryview:
+        n = struct.calcsize(format)
+        if len(self.buffer) < n:
+            self.buffer.extend(
+                itertools.islice(itertools.repeat(0), n - len(self.buffer))
+            )
+        v = memoryview(self.buffer)[:n]
+        self.file.readinto(v)  # type: ignore
+        return v
+
+    def _get(self, format: str):
+        v = self._read(format)
+        return struct.unpack(format, v)
+
+
+@functools.cache
+def load_kerasify(file_path):
+    """
+    Load the the model layers from a ``.kerasify`` file.
+
+    Parameters
+    ----------
+    file_path : str
+        The path to the ``.kerasify`` file.
+
+    Returns
+    -------
+    layers : tuple of Layer
+        The model layers.
+    """
+    with open(file_path, "rb") as file:
+        return tuple(KerasifyParser(file))