LICENSE
README.md
pyproject.toml
src/rnaglib/__init__.py
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/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/graph_keys.py
src/rnaglib/config/ligands.py
src/rnaglib/config/rna_smiles.txt
src/rnaglib/data/__init__.py
src/rnaglib/data_loading/__init__.py
src/rnaglib/data_loading/create_dataset.py
src/rnaglib/data_loading/features.py
src/rnaglib/data_loading/get_statistics.py
src/rnaglib/data_loading/graph_index_NR.json
src/rnaglib/data_loading/rna_dataset.py
src/rnaglib/data_loading/rna_loader.py
src/rnaglib/data_loading/test.py
src/rnaglib/drawing/__init__.py
src/rnaglib/drawing/rna_draw.py
src/rnaglib/drawing/rna_layout.py
src/rnaglib/examples/__init__.py
src/rnaglib/examples/rnaglib_first.py
src/rnaglib/ged/__init__.py
src/rnaglib/ged/ged_nx.py
src/rnaglib/ged/rna_ged_nx.py
src/rnaglib/kernels/__init__.py
src/rnaglib/kernels/node_sim.py
src/rnaglib/learning/__init__.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/representations/__init__.py
src/rnaglib/representations/graph.py
src/rnaglib/representations/point_cloud.py
src/rnaglib/representations/representation.py
src/rnaglib/representations/rings.py
src/rnaglib/representations/voxel.py
src/rnaglib/splitters/__init__.py
src/rnaglib/splitters/similarity_splitter.py
src/rnaglib/splitters/splitters.py
src/rnaglib/splitters/splitting_utils.py
src/rnaglib/tasks/__init__.py
src/rnaglib/tasks/task.py
src/rnaglib/tasks/RBP_Node/__init__.py
src/rnaglib/tasks/RBP_Node/demo.py
src/rnaglib/tasks/RBP_Node/protein_binding_site.py
src/rnaglib/tasks/RNA_CM/__init__.py
src/rnaglib/tasks/RNA_CM/chemical_modification.py
src/rnaglib/tasks/RNA_CM/demo.py
src/rnaglib/tasks/RNA_Family/__init__.py
src/rnaglib/tasks/RNA_Family/demo.py
src/rnaglib/tasks/RNA_Family/rfam.py
src/rnaglib/tasks/RNA_IF/__init__.py
src/rnaglib/tasks/RNA_IF/benchmark_demo.py
src/rnaglib/tasks/RNA_IF/demo.py
src/rnaglib/tasks/RNA_IF/gRNAde.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/__init__.py
src/rnaglib/tasks/RNA_Ligand/demo.py
src/rnaglib/tasks/RNA_Ligand/ligand_identity.py
src/rnaglib/tasks/RNA_Ligand/data/gmsm_dataset.csv
src/rnaglib/tasks/RNA_Site/__init__.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/__init__.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/filters.py
src/rnaglib/transforms/rnafm.py
src/rnaglib/transforms/transform.py
src/rnaglib/utils/__init__.py
src/rnaglib/utils/feature_maps.py
src/rnaglib/utils/graph_io.py
src/rnaglib/utils/graph_utils.py
src/rnaglib/utils/graphlet_hash.py
src/rnaglib/utils/misc.py
src/rnaglib/utils/task_utils.py
src/rnaglib/utils/wrappers.py
tests/test_data_loading.py
tests/test_features_computer.py
tests/test_representations.py
tests/test_splitters.py
tests/test_tasks.py
tests/test_transforms.py