LICENSE
README.md
pyproject.toml
src/rnaglib.egg-info/PKG-INFO
src/rnaglib.egg-info/SOURCES.txt
src/rnaglib.egg-info/dependency_links.txt
src/rnaglib.egg-info/entry_points.txt
src/rnaglib.egg-info/requires.txt
src/rnaglib.egg-info/top_level.txt
src/rnaglib/algorithms/__init__.py
src/rnaglib/algorithms/graph_algos.py
src/rnaglib/algorithms/graphlet_hash.py
src/rnaglib/algorithms/node_sim.py
src/rnaglib/algorithms/rna_ged_nx.py
src/rnaglib/bin/__init__.py
src/rnaglib/bin/rnaglib_download.py
src/rnaglib/bin/rnaglib_index.py
src/rnaglib/bin/rnaglib_prepare_data.py
src/rnaglib/bin/rnaglib_tokenize.py
src/rnaglib/config/__init__.py
src/rnaglib/config/build_iso_mat.py
src/rnaglib/config/feature_encoders.py
src/rnaglib/config/generate_modifications_cache.py
src/rnaglib/config/graph_keys.py
src/rnaglib/config/ligands.py
src/rnaglib/config/modifications.py
src/rnaglib/config/rna_smiles.txt
src/rnaglib/config/cache/__init__.py
src/rnaglib/config/cache/modifications_cache.json
src/rnaglib/data/__init__.py
src/rnaglib/data_loading/__init__.py
src/rnaglib/data_loading/create_dataset.py
src/rnaglib/data_loading/get_statistics.py
src/rnaglib/data_loading/graph_index_NR.json
src/rnaglib/data_loading/rna.py
src/rnaglib/data_loading/rna_dataset.py
src/rnaglib/data_loading/rna_loader.py
src/rnaglib/data_loading/test.py
src/rnaglib/dataset_transforms/__init__.py
src/rnaglib/dataset_transforms/cd_hit.py
src/rnaglib/dataset_transforms/distance_computer.py
src/rnaglib/dataset_transforms/linear_optimisation.py
src/rnaglib/dataset_transforms/redundancy_remover.py
src/rnaglib/dataset_transforms/similarity_splitter.py
src/rnaglib/dataset_transforms/splitters.py
src/rnaglib/dataset_transforms/splitting_utils.py
src/rnaglib/dataset_transforms/structure_distance_computer.py
src/rnaglib/drawing/__init__.py
src/rnaglib/drawing/rna_draw.py
src/rnaglib/drawing/rna_layout.py
src/rnaglib/encoders/__init__.py
src/rnaglib/encoders/encoders.py
src/rnaglib/examples/__init__.py
src/rnaglib/examples/rnaglib_first.py
src/rnaglib/learning/__init__.py
src/rnaglib/learning/gvp.py
src/rnaglib/learning/learn.py
src/rnaglib/learning/learning_utils.py
src/rnaglib/learning/models.py
src/rnaglib/learning/task_models.py
src/rnaglib/prepare_data/__init__.py
src/rnaglib/prepare_data/annotations.py
src/rnaglib/prepare_data/chopper.py
src/rnaglib/prepare_data/describe_datasets.py
src/rnaglib/prepare_data/dssr_2_graphs.py
src/rnaglib/prepare_data/filters.py
src/rnaglib/prepare_data/fr3d_2_graphs.py
src/rnaglib/prepare_data/hash_check.py
src/rnaglib/prepare_data/khop_annotate.py
src/rnaglib/prepare_data/main.py
src/rnaglib/prepare_data/retrieve_structures.py
src/rnaglib/prepare_data/test.py
src/rnaglib/prepare_data/tests/clean_graphs.py
src/rnaglib/prepare_data/tests/interfaces.py
src/rnaglib/prepare_data/tests/is_dna.py
src/rnaglib/prepare_data/tests/subset_graphs.py
src/rnaglib/tasks/__init__.py
src/rnaglib/tasks/task.py
src/rnaglib/tasks/RNA_CM/chemical_modification.py
src/rnaglib/tasks/RNA_CM/demo.py
src/rnaglib/tasks/RNA_GO/demo.py
src/rnaglib/tasks/RNA_GO/rna_go.py
src/rnaglib/tasks/RNA_IF/benchmark_demo.py
src/rnaglib/tasks/RNA_IF/demo.py
src/rnaglib/tasks/RNA_IF/inverse_folding.py
src/rnaglib/tasks/RNA_IF/data/das_split.pt
src/rnaglib/tasks/RNA_IF/data/downloader.py
src/rnaglib/tasks/RNA_IF/data/gRNAde_metadata.csv
src/rnaglib/tasks/RNA_Ligand/demo.py
src/rnaglib/tasks/RNA_Ligand/ligand_identity.py
src/rnaglib/tasks/RNA_Ligand/prepare_data.py
src/rnaglib/tasks/RNA_Prot/demo.py
src/rnaglib/tasks/RNA_Prot/protein_binding_site.py
src/rnaglib/tasks/RNA_Site/benchmark_demo.py
src/rnaglib/tasks/RNA_Site/binding_site.py
src/rnaglib/tasks/RNA_Site/demo.py
src/rnaglib/tasks/RNA_Site/experiments/run.py
src/rnaglib/tasks/RNA_VS/build_data.py
src/rnaglib/tasks/RNA_VS/data.py
src/rnaglib/tasks/RNA_VS/demo.py
src/rnaglib/tasks/RNA_VS/evaluate.py
src/rnaglib/tasks/RNA_VS/ligands.py
src/rnaglib/tasks/RNA_VS/model.py
src/rnaglib/tasks/RNA_VS/task.py
src/rnaglib/tasks/data/das_split.pt
src/rnaglib/tasks/data/gRNAde_metadata.csv
src/rnaglib/tasks/data/gmsm_dataset.csv
src/rnaglib/tasks/depr/IF_gRNAde_model.py
src/rnaglib/tasks/depr/binding_site.py
src/rnaglib/tasks/depr/inverse_folding.py
src/rnaglib/tasks/experiments/RBP_Node/run.py
src/rnaglib/tasks/experiments/RNA_CM/run.py
src/rnaglib/tasks/experiments/RNA_Site/run.py
src/rnaglib/tasks/experiments/depr/benchmark_binding_site_model.py
src/rnaglib/tasks/experiments/depr/benchmark_binding_site_model_embeddings.py
src/rnaglib/tasks/experiments/depr/benchmark_chemical_modification_model.py
src/rnaglib/tasks/experiments/depr/benchmark_chemical_modification_model_embeddings.py
src/rnaglib/tasks/experiments/depr/benchmark_protein_site_model.py
src/rnaglib/tasks/experiments/depr/benchmark_protein_site_model_embeddings.py
src/rnaglib/tasks/models/benchmark_binding_site_model.py
src/rnaglib/tasks/models/binding_site_model.py
src/rnaglib/tasks/models/chemical_modification_model.py
src/rnaglib/tasks/models/protein_binding_site_model.py
src/rnaglib/transforms/__init__.py
src/rnaglib/transforms/transform.py
src/rnaglib/transforms/annotate/__init__.py
src/rnaglib/transforms/annotate/binding_sites.py
src/rnaglib/transforms/annotate/cif_metadata.py
src/rnaglib/transforms/annotate/dummy.py
src/rnaglib/transforms/annotate/from_dict.py
src/rnaglib/transforms/annotate/names.py
src/rnaglib/transforms/annotate/rbp.py
src/rnaglib/transforms/annotate/rfam.py
src/rnaglib/transforms/annotate/rnafm.py
src/rnaglib/transforms/annotate/small_molecule.py
src/rnaglib/transforms/annotate/ss.py
src/rnaglib/transforms/featurize/__init__.py
src/rnaglib/transforms/featurize/features.py
src/rnaglib/transforms/filter/__init__.py
src/rnaglib/transforms/filter/filters.py
src/rnaglib/transforms/partition/__init__.py
src/rnaglib/transforms/partition/chain.py
src/rnaglib/transforms/partition/connected_component.py
src/rnaglib/transforms/partition/from_dict.py
src/rnaglib/transforms/represent/__init__.py
src/rnaglib/transforms/represent/graph.py
src/rnaglib/transforms/represent/point_cloud.py
src/rnaglib/transforms/represent/representation.py
src/rnaglib/transforms/represent/rings.py
src/rnaglib/transforms/represent/sequence.py
src/rnaglib/transforms/represent/voxel.py
src/rnaglib/utils/__init__.py
src/rnaglib/utils/graph_io.py
src/rnaglib/utils/misc.py
src/rnaglib/utils/rfam_utils.py
src/rnaglib/utils/task_utils.py
src/rnaglib/utils/wrappers.py
tests/test_data_loading.py
tests/test_features_computer.py
tests/test_prepare_data.py
tests/test_representations.py
tests/test_splitters.py
tests/test_tasks.py
tests/test_transforms.py
tests/test_utils.py