ML# Core Modules# Encoding Definitions AF2_ATOM14_ENCODING AF2_ATOM37_ENCODING AF3SequenceEncoding AF3_TOKENS RF2AA_ATOM36_ENCODING RF2AA_STANDARDIZED_TOKENS RF2AA_TOKEN_TO_STANDARD_TOKEN RF2_ATOM14_ENCODING RF2_ATOM23_ENCODING TokenEncoding UNKNOWN_ELEMENT_TOKEN Samplers DistributedMixedSampler FallbackSamplerWrapper LazyWeightedRandomSampler LoadBalancedDistributedSampler MixedSampler calculate_af3_example_weights() calculate_weights_by_inverse_cluster_size() calculate_weights_for_pdb_dataset_df() get_cluster_sizes() set_sampler_epoch() Data Processing Modules# Datasets Core Dataset Classes Functional Loaders Dataset Architecture and Migration Guide Pipelines AF3 Pipeline RF2AA Pipeline Transforms Core Transform Classes Utility Modules Submodules Diffusion Transforms BatchStructuresForDiffusionNoising SampleEDMNoise sample_noise_edm() sample_t_edm() DNA Transforms PadDNA base_pairs() generate_bform_dna() to_reverse_complement() Feature Aggregation Transforms MSA Transforms Utilities Debug Utilities Error Handling Geometry Utilities I/O Utilities Miscellaneous Utilities Nested Dictionary Utilities NumPy Utilities Random Number Generation Testing Utilities Timer Utilities Token Utilities
