from alphafold3_pytorch.attention import (
    Attention,
    Attend,
    full_pairwise_repr_to_windowed
)

from alphafold3_pytorch.alphafold3 import (
    RelativePositionEncoding,
    SmoothLDDTLoss,
    WeightedRigidAlign,
    ExpressCoordinatesInFrame,
    ComputeAlignmentError,
    CentreRandomAugmentation,
    TemplateEmbedder,
    PreLayerNorm,
    AdaptiveLayerNorm,
    ConditionWrapper,
    OuterProductMean,
    MSAPairWeightedAveraging,
    TriangleMultiplication,
    AttentionPairBias,
    TriangleAttention,
    Transition,
    MSAModule,
    PairformerStack,
    DiffusionTransformer,
    DiffusionModule,
    ElucidatedAtomDiffusion,
    InputFeatureEmbedder,
    ConfidenceHead,
    DistogramHead,
    Alphafold3
)

from alphafold3_pytorch.inputs import (
    register_input_transform
)

from alphafold3_pytorch.trainer import (
    Trainer,
    DataLoader,
    AtomInput
)

from alphafold3_pytorch.configs import (
    Alphafold3Config,
    TrainerConfig,
    ConductorConfig,
    create_alphafold3_from_yaml,
    create_trainer_from_yaml,
    create_trainer_from_conductor_yaml
)

__all__ = [
    Attention,
    Attend,
    RelativePositionEncoding,
    SmoothLDDTLoss,
    WeightedRigidAlign,
    ExpressCoordinatesInFrame,
    ComputeAlignmentError,
    CentreRandomAugmentation,
    TemplateEmbedder,
    PreLayerNorm,
    AdaptiveLayerNorm,
    ConditionWrapper,
    OuterProductMean,
    MSAPairWeightedAveraging,
    TriangleMultiplication,
    AttentionPairBias,
    TriangleAttention,
    Transition,
    MSAModule,
    PairformerStack,
    DiffusionTransformer,
    DiffusionModule,
    ElucidatedAtomDiffusion,
    InputFeatureEmbedder,
    ConfidenceHead,
    DistogramHead,
    Alphafold3,
    Alphafold3Config,
    AtomInput,
    Trainer,
    TrainerConfig,
    ConductorConfig,
    create_alphafold3_from_yaml,
    create_trainer_from_yaml,
    create_trainer_from_conductor_yaml
]
