esm/esmfold/v1/pretrained.py

# Copyright (c) Meta Platforms, Inc. and affiliates.

# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.

from pathlib import Path

import torch

from esm.esmfold.v1.esmfold import ESMFold


def _load_model(model_name):
    if model_name.endswith(".pt"):  # local, treat as filepath
        model_path = Path(model_name)
        model_data = torch.load(str(model_path), map_location="cpu")
    else:  # load from hub
        url = f"https://dl.fbaipublicfiles.com/fair-esm/models/{model_name}.pt"
        model_data = torch.hub.load_state_dict_from_url(url, progress=False, map_location="cpu")

    cfg = model_data["cfg"]["model"]
    model_state = model_data["model"]
    model = ESMFold(esmfold_config=cfg)

    expected_keys = set(model.state_dict().keys())
    found_keys = set(model_state.keys())

    missing_essential_keys = []
    for missing_key in expected_keys - found_keys:
        if not missing_key.startswith("esm."):
            missing_essential_keys.append(missing_key)

    if missing_essential_keys:
        raise RuntimeError(f"Keys '{', '.join(missing_essential_keys)}' are missing.")

    model.load_state_dict(model_state, strict=False)

    return model


def esmfold_v0():
    """
    ESMFold v0 model with 3B ESM-2, 48 folding blocks.
    This version was used for the paper (Lin et al, 2022). It was trained
    on all PDB chains until 2020-05, to ensure temporal holdout with CASP14
    and the CAMEO validation and test set reported there.
    """
    return _load_model("esmfold_3B_v0")


def esmfold_v1():
    """
    ESMFold v1 model using 3B ESM-2, 48 folding blocks.
    ESMFold provides fast high accuracy atomic level structure prediction
    directly from the individual sequence of a protein. ESMFold uses the ESM2
    protein language model to extract meaningful representations from the
    protein sequence.
    """
    return _load_model("esmfold_3B_v1")


def esmfold_structure_module_only_8M():
    """
    ESMFold baseline model using 8M ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 500K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_8M")


def esmfold_structure_module_only_8M_270K():
    """
    ESMFold baseline model using 8M ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 270K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_8M_270K")


def esmfold_structure_module_only_35M():
    """
    ESMFold baseline model using 35M ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 500K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_35M")


def esmfold_structure_module_only_35M_270K():
    """
    ESMFold baseline model using 35M ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 270K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_35M_270K")


def esmfold_structure_module_only_150M():
    """
    ESMFold baseline model using 150M ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 500K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_150M")


def esmfold_structure_module_only_150M_270K():
    """
    ESMFold baseline model using 150M ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 270K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_150M_270K")


def esmfold_structure_module_only_650M():
    """
    ESMFold baseline model using 650M ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 500K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_650M")


def esmfold_structure_module_only_650M_270K():
    """
    ESMFold baseline model using 650M ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 270K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_650M_270K")


def esmfold_structure_module_only_3B():
    """
    ESMFold baseline model using 3B ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 500K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_3B")


def esmfold_structure_module_only_3B_270K():
    """
    ESMFold baseline model using 3B ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 270K updates.
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_3B_270K")


def esmfold_structure_module_only_15B():
    """
    ESMFold baseline model using 15B ESM-2, 0 folding blocks.
    ESM-2 here is trained out to 270K updates.
    The 15B parameter ESM-2 was not trained out to 500K updates
    This is a model designed to test the capabilities of the language model
    when ablated for number of parameters in the language model.
    See table S1 in (Lin et al, 2022).
    """
    return _load_model("esmfold_structure_module_only_15B")