ML# Core Modules# Common Utilities as_list() generate_example_id() parse_example_id() Enums 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 Parsers Dataset Parsers Base Parser Custom Metadata Parsers Default Metadata Parsers Preprocessing Core Preprocessing Functions Constants Utilities Preprocessing Utilities Clustering Utilities FASTA Utilities Structure Utilities 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() ESM Transforms 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
