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r"""Biological Embeddings (:mod:`skbio.embedding`)
=================================================
.. currentmodule:: skbio.embedding
This module provides support for storing embeddings for biological objects, such
as protein embeddings outputted from protein language models (pLMs).
Embedding types
---------------
.. autosummary::
:toctree: generated/
Embedding
SequenceEmbedding
ProteinEmbedding
Embedding vector types
----------------------
.. autosummary::
:toctree: generated/
SequenceVector
ProteinVector
Embedding vector utilities
--------------------------
.. autosummary::
:toctree: generated/
embed_vec_to_numpy
embed_vec_to_distances
embed_vec_to_ordination
embed_vec_to_dataframe
"""
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# ----------------------------------------------------------------------------
from ._embedding import (
Embedding,
SequenceEmbedding,
EmbeddingVector,
SequenceVector,
embed_vec_to_numpy,
embed_vec_to_distances,
embed_vec_to_ordination,
embed_vec_to_dataframe,
)
from ._protein import ProteinEmbedding, ProteinVector, example_protein_embedding
__all__ = [
"Embedding",
"SequenceEmbedding",
"EmbeddingVector",
"SequenceVector",
"embed_vec_to_numpy",
"embed_vec_to_distances",
"embed_vec_to_ordination",
"embed_vec_to_dataframe",
"ProteinEmbedding",
"ProteinVector",
"example_protein_embedding",
]
|
