from ._protein import Protein as OFProtein
from ._protein import from_pdb_string as protein_from_pdb_string
from ._protein import to_pdb as protein_to_pdb
from ._rigids import Rigid, Rotation
from ._tensor_utils import (
    batched_gather,
    permute_final_dims,
    masked_mean,
    tree_map,
    tensor_tree_map,
)
from ._residue_constants import make_atom14_dists_bounds
from ._data_pipeline import make_pdb_features
from ._data_transforms import (
    make_pseudo_beta,
    make_seq_mask,
    make_atom14_masks,
    make_atom14_masks_np,
    make_atom14_positions,
    make_all_atom_aatype,
    atom37_to_frames,
    get_chi_atom_indices,
    atom37_to_torsion_angles,
    get_backbone_frames,
    get_chi_angles,
)
from ._feats import atom14_to_atom37
from ._fape import (
    compute_fape,
    backbone_loss,
    sidechain_loss,
    make_default_alphafold_loss,
)
