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multimolecule/pipelines/README.zh.md
multimolecule/pipelines/__init__.py
multimolecule/pipelines/mean_ribosome_load.py
multimolecule/pipelines/methylation.py
multimolecule/pipelines/polyadenylation.py
multimolecule/pipelines/regulatory.py
multimolecule/pipelines/rna_secondary_structure.py
multimolecule/pipelines/splicing.py
multimolecule/runner/README.md
multimolecule/runner/README.zh.md
multimolecule/runner/__init__.py
multimolecule/runner/config.py
multimolecule/runner/registry.py
multimolecule/runner/runner.py
multimolecule/tasks/__init__.py
multimolecule/tasks/task.py
multimolecule/tokenisers/README.md
multimolecule/tokenisers/README.zh.md
multimolecule/tokenisers/__init__.py
multimolecule/tokenisers/alphabet.py
multimolecule/tokenisers/tokenization_utils.py
multimolecule/tokenisers/utils.py
multimolecule/tokenisers/dna/ALPHABET.md
multimolecule/tokenisers/dna/README.md
multimolecule/tokenisers/dna/__init__.py
multimolecule/tokenisers/dna/tokenization_dna.py
multimolecule/tokenisers/dna/utils.py
multimolecule/tokenisers/dot_bracket/ALPHABET.md
multimolecule/tokenisers/dot_bracket/README.md
multimolecule/tokenisers/dot_bracket/__init__.py
multimolecule/tokenisers/dot_bracket/tokenization_db.py
multimolecule/tokenisers/dot_bracket/utils.py
multimolecule/tokenisers/protein/ALPHABET.md
multimolecule/tokenisers/protein/README.md
multimolecule/tokenisers/protein/__init__.py
multimolecule/tokenisers/protein/tokenization_protein.py
multimolecule/tokenisers/protein/utils.py
multimolecule/tokenisers/rna/ALPHABET.md
multimolecule/tokenisers/rna/README.md
multimolecule/tokenisers/rna/__init__.py
multimolecule/tokenisers/rna/tokenization_rna.py
multimolecule/tokenisers/rna/utils.py
multimolecule/utils/__init__.py
multimolecule/utils/environment.py
multimolecule/utils/rna/__init__.py
multimolecule/utils/rna/secondary_structure/__init__.py
multimolecule/utils/rna/secondary_structure/bprna.py
multimolecule/utils/rna/secondary_structure/noncanonical.py
multimolecule/utils/rna/secondary_structure/notations.py
multimolecule/utils/rna/secondary_structure/pairs.py
multimolecule/utils/rna/secondary_structure/pseudoknot.py
multimolecule/utils/rna/secondary_structure/topology.py
multimolecule/utils/rna/secondary_structure/types.py
multimolecule/utils/summary/__init__.py
multimolecule/utils/summary/flops.py
multimolecule/utils/summary/parameters.py
multimolecule/visualize/__init__.py
multimolecule/visualize/palettes.py
multimolecule/visualize/rna/__init__.py
multimolecule/visualize/rna/palettes.py
multimolecule/visualize/rna/secondary_structure/__init__.py
multimolecule/visualize/rna/secondary_structure/alignment.py
multimolecule/visualize/rna/secondary_structure/arc.py
multimolecule/visualize/rna/secondary_structure/circular.py
multimolecule/visualize/rna/secondary_structure/comparison.py
multimolecule/visualize/rna/secondary_structure/contact_map.py
multimolecule/visualize/rna/secondary_structure/layout.py
multimolecule/visualize/rna/secondary_structure/planar.py
multimolecule/visualize/rna/secondary_structure/probability.py
multimolecule/visualize/rna/secondary_structure/tracks.py
multimolecule/visualize/rna/secondary_structure/utils.py
tests/__init__.py
tests/data/test_dataset.py
tests/data/test_utils.py
tests/datasets/test_database.py
tests/examples/test_examples.py
tests/graph/test_matching.py
tests/graph/test_ops_spatial.py
tests/graph/test_topology.py
tests/io/test_fasta.py
tests/io/test_rna_secondary_structure.py
tests/metrics/rna/secondary_structure/conftest.py
tests/metrics/rna/secondary_structure/test_adjacency.py
tests/metrics/rna/secondary_structure/test_common.py
tests/metrics/rna/secondary_structure/test_exports.py
tests/metrics/rna/secondary_structure/test_functional.py
tests/metrics/rna/secondary_structure/test_graph.py
tests/metrics/rna/secondary_structure/test_loops.py
tests/metrics/rna/secondary_structure/test_metrics.py
tests/metrics/rna/secondary_structure/test_noncanonical.py
tests/metrics/rna/secondary_structure/test_pair.py
tests/metrics/rna/secondary_structure/test_paired.py
tests/metrics/rna/secondary_structure/test_pseudoknot.py
tests/metrics/rna/secondary_structure/test_stems.py
tests/metrics/rna/secondary_structure/test_topology.py
tests/metrics/rna/secondary_structure/utils.py
tests/modules/backbones/test_sequence.py
tests/modules/backbones/sequences/test_onehot.py
tests/modules/criterions/test_binary.py
tests/modules/criterions/test_criterion.py
tests/modules/criterions/test_multiclass.py
tests/modules/criterions/test_multilabel.py
tests/modules/criterions/test_regression.py
tests/modules/embeddings/test_rotary.py
tests/modules/embeddings/test_sinusoidal.py
tests/modules/heads/test_generic.py
tests/modules/layers/test_symmetric_convolutions.py
tests/modules/networks/test_resnet.py
tests/modules/networks/test_unet.py
tests/pipelines/test_mean_ribosome_load_pipeline.py
tests/pipelines/test_methylation_pipeline.py
tests/pipelines/test_polyadenylation_pipeline.py
tests/pipelines/test_regulatory_pipeline.py
tests/pipelines/test_rna_secondary_structure_pipeline.py
tests/pipelines/test_splicing_pipeline.py
tests/utils/test_summary.py
tests/utils/rna/secondary_structure/bprna_cases.py
tests/utils/rna/secondary_structure/conftest.py
tests/utils/rna/secondary_structure/test_bprna.py
tests/utils/rna/secondary_structure/test_noncanonical.py
tests/utils/rna/secondary_structure/test_notations.py
tests/utils/rna/secondary_structure/test_pairs.py
tests/utils/rna/secondary_structure/test_pseudoknot.py
tests/utils/rna/secondary_structure/test_topology.py
tests/utils/rna/secondary_structure/test_types.py
tests/visualize/rna/secondary_structure/__init__.py
tests/visualize/rna/secondary_structure/conftest.py
tests/visualize/rna/secondary_structure/test_comparison.py
tests/visualize/rna/secondary_structure/test_layout.py
tests/visualize/rna/secondary_structure/test_plots.py
tests/visualize/rna/secondary_structure/test_tracks.py