Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | V | W _ __init__() (graphein.ml.conversion.GraphFormatConvertor method) (graphein.ml.datasets.foldcomp_dataset.FoldCompDataset method) (graphein.ml.datasets.foldcomp_dataset.FoldCompLightningDataModule method) (graphein.ml.datasets.torch_geometric_dataset.InMemoryProteinGraphDataset method) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset method) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphListDataset method) (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) (graphein.protein.utils.ProteinGraphConfigurationError method) A aa_dipeptide_composition() (in module graphein.protein.features.sequence.propy) AA_RING_ATOMS (in module graphein.protein.resi_atoms), [1] aa_spectrum() (in module graphein.protein.features.sequence.propy) aaindex1() (in module graphein.protein.features.nodes.aaindex) add_all_dotbracket_edges() (in module graphein.rna.edges.base_pairing) add_aromatic_interactions() (in module graphein.protein.edges.distance) add_aromatic_sulphur_interactions() (in module graphein.protein.edges.distance) add_atom_bonds() (in module graphein.molecule.edges.atomic) add_atomic_edges() (in module graphein.protein.edges.atomic) (in module graphein.rna.edges.atomic) add_atomic_radii() (in module graphein.rna.features.atom) add_backbone_carbonyl_carbonyl_interactions() (in module graphein.protein.edges.distance) add_base_pairing_interactions() (in module graphein.rna.edges.base_pairing) add_beta_carbon_vector() (in module graphein.protein.features.nodes.geometry) add_biogrid_edges() (in module graphein.ppi.edges) add_biogrid_metadata() (in module graphein.ppi.graph_metadata) add_bond_order() (in module graphein.protein.edges.atomic) (in module graphein.rna.edges.atomic) add_bond_type() (in module graphein.molecule.features.edges.bonds) add_bond_type_one_hot() (in module graphein.molecule.features.edges.bonds) add_cation_pi_interactions() (in module graphein.protein.edges.distance) add_center_of_mol() (in module graphein.molecule.features.graph.molecule) add_chembl_metadata() (in module graphein.molecule.chembl) add_contacts_edge() (in module graphein.protein.edges.intramolecular) add_delaunay_triangulation() (in module graphein.protein.edges.distance) add_distance_threshold() (in module graphein.molecule.edges.distance) (in module graphein.protein.edges.distance) add_distance_to_edges() (in module graphein.protein.edges.distance) add_distance_window() (in module graphein.protein.edges.distance) add_disulfide_interactions() (in module graphein.protein.edges.distance) add_dssp_df() (in module graphein.protein.features.nodes.dssp) add_dssp_feature() (in module graphein.protein.features.nodes.dssp) add_fully_connected_edges() (in module graphein.molecule.edges.distance) (in module graphein.protein.edges.distance) add_hydrogen_bond_interactions() (in module graphein.protein.edges.distance) add_hydrophobic_interactions() (in module graphein.protein.edges.distance) add_interacting_genes() (in module graphein.grn.edges) add_interacting_proteins() (in module graphein.ppi.edges) add_interacting_resis() (in module graphein.protein.edges.distance) add_ionic_interactions() (in module graphein.protein.edges.distance) add_k_nn_edges() (in module graphein.molecule.edges.distance) (in module graphein.protein.edges.distance) add_labels_to_graph() (in module graphein.ml.utils) add_nodes_to_graph() (in module graphein.molecule.graphs) (in module graphein.protein.graphs) add_peptide_bonds() (in module graphein.protein.edges.distance) add_phosphodiester_bonds() (in module graphein.rna.edges.base_pairing) add_pi_stacking_interactions() (in module graphein.protein.edges.distance) add_positional_encoding() (in module graphein.protein.features.sequence.sequence) add_pseudoknots() (in module graphein.rna.edges.base_pairing) add_radius_of_gyration() (in module graphein.protein.features.graph.structure) add_regnetwork_edges() (in module graphein.grn.edges) add_ring_status() (in module graphein.protein.edges.atomic) (in module graphein.rna.edges.atomic) add_salt_bridges() (in module graphein.protein.edges.distance) add_sequence_distance_edges() (in module graphein.protein.edges.distance) add_sequence_neighbour_vector() (in module graphein.protein.features.nodes.geometry) add_sequence_to_nodes() (in module graphein.grn.features.node_features) (in module graphein.ppi.features.node_features) add_shape_moments() (in module graphein.molecule.features.graph.molecule) add_sidechain_vector() (in module graphein.protein.features.nodes.geometry) add_string_biogrid_metadata() (in module graphein.ppi.graph_metadata) add_string_edges() (in module graphein.ppi.edges) add_string_metadata() (in module graphein.ppi.graph_metadata) add_trrust_edges() (in module graphein.grn.edges) add_vdw_clashes() (in module graphein.protein.edges.distance) add_vdw_interactions() (in module graphein.protein.edges.distance) add_vector_to_plot() (in module graphein.protein.visualisation) add_virtual_beta_carbon_vector() (in module graphein.protein.features.nodes.geometry) adjacency_matrix_power() (in module graphein.ml.diffusion) aggregate_graph_feature_over_chains() (in module graphein.protein.features.utils) align_to() (graphein.protein.tensor.data.Protein method) ALL_BOND_TYPES (in module graphein.molecule.atoms) ALL_BOND_TYPES_TO_CHANNEL (in module graphein.molecule.atoms) all_composition_descriptors() (in module graphein.protein.features.sequence.propy) all_ctd_descriptors() (in module graphein.protein.features.sequence.propy) all_distribution_descriptors() (in module graphein.protein.features.sequence.propy) ALL_STEREO_TO_CHANNEL (in module graphein.molecule.atoms) ALL_STEREO_TYPES (in module graphein.molecule.atoms) all_transition_descriptors() (in module graphein.protein.features.sequence.propy) ALLOWED_BOND_TYPE_TO_CHANNEL (in module graphein.molecule.atoms) ALLOWED_BOND_TYPES (in module graphein.molecule.atoms) ALLOWED_DEGREES (in module graphein.molecule.atoms) ALLOWED_HYBRIDIZATIONS (in module graphein.molecule.atoms) ALLOWED_NUM_H (in module graphein.molecule.atoms) ALLOWED_VALENCES (in module graphein.molecule.atoms) alpha() (graphein.protein.tensor.data.Protein method) (in module graphein.protein.tensor.angles) alpha_carbon() (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) AltLocsOpts (in module graphein.protein.config) amino_acid_composition() (in module graphein.protein.features.sequence.propy) amino_acid_one_hot() (in module graphein.protein.features.nodes.amino_acid) AMINO_ACIDS (in module graphein.protein.resi_atoms), [1] angle_to_unit_circle() (in module graphein.protein.tensor.angles) annotate_edge_metadata() (in module graphein.utils.utils) annotate_graph_metadata() (in module graphein.utils.utils) annotate_node_features() (in module graphein.utils.utils) annotate_node_metadata() (in module graphein.utils.utils) apply_structural_noise() (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) (in module graphein.protein.tensor.geometry) apply_to() (graphein.protein.tensor.data.ProteinBatch method) AROMATIC_RESIS (in module graphein.protein.resi_atoms), [1] asa() (in module graphein.protein.features.nodes.dssp) assign_bond_states_to_dataframe() (in module graphein.protein.edges.atomic) assign_covalent_radii_to_dataframe() (in module graphein.protein.edges.atomic) asteroid_plot() (in module graphein.protein.visualisation) async_setup() (graphein.ml.datasets.foldcomp_dataset.FoldCompDataset method) ATOM_NUMBERING (in module graphein.protein.resi_atoms), [1] ATOM_NUMBERING_MODIFIED (in module graphein.protein.resi_atoms), [1] atom_type_one_hot() (in module graphein.molecule.features.nodes.atom_type) atomic_mass() (in module graphein.molecule.features.nodes.atom_type) ATOMIC_MASSES (in module graphein.protein.resi_atoms), [1] AtomTensor (class in graphein.protein.tensor.types) autocorrelation_geary_all() (in module graphein.protein.features.sequence.propy) autocorrelation_geary_av_flexibility() (in module graphein.protein.features.sequence.propy) autocorrelation_geary_free_energy() (in module graphein.protein.features.sequence.propy) autocorrelation_geary_hydrophobicity() (in module graphein.protein.features.sequence.propy) autocorrelation_geary_mutability() (in module graphein.protein.features.sequence.propy) autocorrelation_geary_polarizability() (in module graphein.protein.features.sequence.propy) autocorrelation_geary_residue_asa() (in module graphein.protein.features.sequence.propy) autocorrelation_geary_residue_vol() (in module graphein.protein.features.sequence.propy) autocorrelation_geary_steric() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_all() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_av_flexibility() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_free_energy() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_hydrophobicity() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_mutability() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_polarizability() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_residue_asa() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_residue_vol() (in module graphein.protein.features.sequence.propy) autocorrelation_moran_steric() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_all() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_av_flexibility() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_free_energy() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_hydrophobicity() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_mutability() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_polarizability() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_residue_asa() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_residue_vol() (in module graphein.protein.features.sequence.propy) autocorrelation_normalized_moreau_broto_steric() (in module graphein.protein.features.sequence.propy) autocorrelation_total() (in module graphein.protein.features.sequence.propy) B backbone() (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) BACKBONE_ATOMS (in module graphein.protein.resi_atoms), [1] backbone_frames() (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) BackboneFrameTensor (class in graphein.protein.tensor.types) BackboneTensor (class in graphein.protein.tensor.types) BASE_AMINO_ACIDS (in module graphein.protein.resi_atoms), [1] BASE_ATOMS (in module graphein.molecule.atoms) batch_get_smiles_from_zinc() (in module graphein.molecule.zinc) batch_get_zinc_id_from_smiles() (in module graphein.molecule.zinc) BB_BUILD_INFO (in module graphein.protein.resi_atoms), [1] BIOGRID_df() (in module graphein.ppi.parse_biogrid) BioGridConfig (class in graphein.ppi.config) biovec_sequence_embedding() (in module graphein.protein.features.sequence.embeddings), [1] blast() (in module graphein.ml.clustering) bond_is_aromatic() (in module graphein.molecule.features.edges.bonds) bond_is_conjugated() (in module graphein.molecule.features.edges.bonds) bond_is_in_ring() (in module graphein.molecule.features.edges.bonds) bond_is_in_ring_size() (in module graphein.molecule.features.edges.bonds) BOND_LENGTHS (in module graphein.protein.resi_atoms), [1] BOND_ORDERS (in module graphein.protein.resi_atoms), [1] bond_stereo() (in module graphein.molecule.features.edges.bonds) BOND_TYPES (in module graphein.protein.resi_atoms), [1] BpRNAConfig (class in graphein.rna.config) build_fasta_file_from_mapping() (in module graphein.ml.clustering) C calculate_centroid_positions() (in module graphein.protein.graphs) CANONICAL_BASE_PAIRINGS (in module graphein.rna.constants) CARBOHYDRATE_CODE_NAME_MAPPING (in module graphein.protein.resi_atoms), [1] CARBOHYDRATE_CODES (in module graphein.protein.resi_atoms), [1] CARBOHYDRATE_NAMES (in module graphein.protein.resi_atoms), [1] cast_pdb_column_to_type() (in module graphein.protein.utils) CATION_PI_RESIS (in module graphein.protein.resi_atoms), [1] CATION_RESIS (in module graphein.protein.resi_atoms), [1] center_protein() (in module graphein.protein.tensor.geometry) check_base_pairing_type() (in module graphein.rna.edges.base_pairing) check_for_pymol_installation() (in module graphein.protein.meshes) CHI_ANGLES_ATOMS (in module graphein.protein.resi_atoms), [1] chiral_tag() (in module graphein.molecule.features.nodes.atom_type) CHIRAL_TYPE (in module graphein.molecule.atoms) CHIRAL_TYPE_TO_CHANNEL (in module graphein.molecule.atoms) clustering_from_pairs() (in module graphein.ml.clustering) coarsen_sidechain() (in module graphein.protein.tensor.representation) COFACTOR_CODE_NAME_MAPPING (in module graphein.protein.resi_atoms), [1] COFACTOR_CODES (in module graphein.protein.resi_atoms), [1] COFACTOR_NAMES (in module graphein.protein.resi_atoms), [1] colour_edges() (in module graphein.protein.visualisation) colour_nodes() (in module graphein.protein.visualisation) compare_approximate() (in module graphein.testing.utils) compare_exact() (in module graphein.testing.utils) composition_charge() (in module graphein.protein.features.sequence.propy) composition_descriptor() (in module graphein.protein.features.sequence.propy) composition_hydrophobicity() (in module graphein.protein.features.sequence.propy) composition_normalized_vdwv() (in module graphein.protein.features.sequence.propy) composition_polarity() (in module graphein.protein.features.sequence.propy) composition_polarizability() (in module graphein.protein.features.sequence.propy) composition_secondary_str() (in module graphein.protein.features.sequence.propy) composition_solvent_accessibility() (in module graphein.protein.features.sequence.propy) compute_angle() (in module graphein.protein.edges.distance) compute_chain_graph() (in module graphein.protein.graphs) compute_distmat() (in module graphein.molecule.edges.distance) (in module graphein.protein.edges.distance) compute_edges() (in module graphein.protein.graphs) (in module graphein.utils.utils) compute_esm_embedding() (in module graphein.protein.features.sequence.embeddings), [1] compute_fragment_graphs() (in module graphein.molecule.graphs) compute_grn_graph() (in module graphein.grn.graphs) compute_line_graph() (in module graphein.protein.graphs) compute_ppi_graph() (in module graphein.ppi.graphs) compute_propy_feature() (in module graphein.protein.features.sequence.propy) compute_rgroup_dataframe() (in module graphein.protein.utils) compute_ring_normal() (in module graphein.protein.edges.distance) compute_secondary_structure_graph() (in module graphein.protein.graphs) compute_weighted_graph_from_multigraph() (in module graphein.protein.graphs) config_constructor() (in module graphein.utils.config_parser) configure_pymol_session() (in module graphein.protein.meshes) construct_graph() (in module graphein.molecule.graphs) (in module graphein.protein.graphs) construct_graphs_mp() (in module graphein.molecule.graphs) (in module graphein.protein.graphs) construct_rna_graph_2d() (in module graphein.rna.graphs) construct_rna_graph_3d() (in module graphein.rna.graphs) convert_dgl_to_nx() (graphein.ml.conversion.GraphFormatConvertor static method) convert_graph_dict_feat_to_series() (in module graphein.protein.features.utils) convert_nx_to_dgl() (graphein.ml.conversion.GraphFormatConvertor method) convert_nx_to_nx() (graphein.ml.conversion.GraphFormatConvertor static method) convert_nx_to_pyg() (graphein.ml.conversion.GraphFormatConvertor method) convert_pyg_to_nx() (graphein.ml.conversion.GraphFormatConvertor static method) convert_structure_to_centroids() (in module graphein.protein.graphs) convert_verts_and_face_to_mesh() (in module graphein.protein.meshes) CoordTensor (class in graphein.protein.tensor.types) COVALENT_RADII (in module graphein.protein.resi_atoms), [1] create_mesh() (in module graphein.protein.meshes) create_pairs_for_clustering() (in module graphein.ml.clustering) CRYST1_PLACEHOLDER (in module graphein.protein.features.nodes.dssp) D DEFAULT_BOND_STATE (in module graphein.protein.resi_atoms), [1] degree() (in module graphein.molecule.features.nodes.atom_type) deprecated() (in module graphein.utils.utils) deprotonate_structure() (in module graphein.protein.graphs) dihedral_to_point_fixed() (in module graphein.protein.tensor.pnerf) dihedral_to_point_variable() (in module graphein.protein.tensor.pnerf) dihedrals() (graphein.protein.tensor.data.Protein method) dihedrals_to_rad() (in module graphein.protein.tensor.angles) DihedralTensor (class in graphein.protein.tensor.types) dipeptide_composition() (in module graphein.protein.features.sequence.propy) dist_mat_to_coords() (in module graphein.protein.tensor.reconstruction) distribution_charge() (in module graphein.protein.features.sequence.propy) distribution_descriptor() (in module graphein.protein.features.sequence.propy) distribution_hydrophobicity() (in module graphein.protein.features.sequence.propy) distribution_normalized_vdwv() (in module graphein.protein.features.sequence.propy) distribution_polarity() (in module graphein.protein.features.sequence.propy) distribution_polarizability() (in module graphein.protein.features.sequence.propy) distribution_secondary_str() (in module graphein.protein.features.sequence.propy) distribution_solvent_accessibility() (in module graphein.protein.features.sequence.propy) DISULFIDE_ATOMS (in module graphein.protein.resi_atoms), [1] DISULFIDE_RESIS (in module graphein.protein.resi_atoms), [1] download() (graphein.ml.datasets.foldcomp_dataset.FoldCompDataset method) (graphein.ml.datasets.torch_geometric_dataset.InMemoryProteinGraphDataset method) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset method) download_alphafold_structure() (in module graphein.protein.utils) download_bp_rna_1m() (in module graphein.rna.utils) download_pdb() (in module graphein.protein.utils) download_pdb_multiprocessing() (in module graphein.protein.utils) DSSP_COLS (in module graphein.protein.features.nodes.dssp) DSSP_SS (in module graphein.protein.features.nodes.dssp) DSSPConfig (class in graphein.protein.config) E edge_data_equal() (in module graphein.testing.utils) edge_distances() (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) edges() (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) edges_equal() (in module graphein.testing.utils) ELEMENT_SYMBOL_MAP (in module graphein.protein.resi_atoms), [1] esm_residue_embedding() (in module graphein.protein.features.sequence.embeddings), [1] esm_sequence_embedding() (in module graphein.protein.features.sequence.embeddings), [1] esmfold() (in module graphein.protein.utils) expasy_protein_scale() (in module graphein.protein.features.nodes.amino_acid) explicit_valence() (in module graphein.molecule.features.nodes.atom_type) EXTENDED_ATOMS (in module graphein.molecule.atoms) extract_chains_to_file() (in module graphein.protein.utils) extract_interface_subgraph() (in module graphein.protein.subgraphs) extract_k_hop_subgraph() (in module graphein.protein.subgraphs) (in module graphein.rna.subgraphs) extract_subgraph() (in module graphein.protein.subgraphs) extract_subgraph_by_bond_type() (in module graphein.protein.subgraphs) (in module graphein.rna.subgraphs) extract_subgraph_by_sequence_position() (in module graphein.protein.subgraphs) (in module graphein.rna.subgraphs) extract_subgraph_from_atom_types() (in module graphein.protein.subgraphs) (in module graphein.rna.subgraphs) extract_subgraph_from_backbone() (in module graphein.rna.subgraphs) extract_subgraph_from_bases() (in module graphein.rna.subgraphs) extract_subgraph_from_chains() (in module graphein.protein.subgraphs) (in module graphein.rna.subgraphs) extract_subgraph_from_node_list() (in module graphein.protein.subgraphs) (in module graphein.rna.subgraphs) extract_subgraph_from_phosphoric_acid() (in module graphein.rna.subgraphs) extract_subgraph_from_point() (in module graphein.protein.subgraphs) (in module graphein.rna.subgraphs) extract_subgraph_from_residue_types() (in module graphein.protein.subgraphs) (in module graphein.rna.subgraphs) extract_subgraph_from_ribose() (in module graphein.rna.subgraphs) extract_subgraph_from_secondary_structure() (in module graphein.protein.subgraphs) extract_surface_subgraph() (in module graphein.protein.subgraphs) F fetch_AAIndex() (in module graphein.protein.features.nodes.aaindex) filter_BIOGRID() (in module graphein.ppi.parse_biogrid) filter_dataframe() (in module graphein.protein.utils) (in module graphein.utils.utils) filter_distmat() (in module graphein.protein.edges.distance) filter_hetatms() (in module graphein.protein.graphs) filter_RegNetwork() (in module graphein.grn.parse_regnetwork) filter_STRING() (in module graphein.ppi.parse_stringdb) filter_TRRUST() (in module graphein.grn.parse_trrust) FOLDCOMP_DATABASE_TYPES (in module graphein.ml.datasets.foldcomp_dataset) FoldCompDataset (class in graphein.ml.datasets.foldcomp_dataset) FoldCompLightningDataModule (class in graphein.ml.datasets.foldcomp_dataset) formal_charge() (in module graphein.molecule.features.nodes.atom_type) format_adjacency() (in module graphein.utils.utils) from_data() (graphein.protein.tensor.data.Protein method) from_dataframe() (graphein.protein.tensor.data.Protein method) full_atom_coords() (graphein.protein.tensor.data.Protein method) function_constructor() (in module graphein.utils.config_parser) G generate_3d() (in module graphein.molecule.graphs) generate_adjacency_tensor() (in module graphein.utils.utils) generate_feature_dataframe() (in module graphein.utils.utils) generate_random_sets() (in module graphein.ml.clustering) get() (graphein.ml.datasets.foldcomp_dataset.FoldCompDataset method) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset method) get_atom_indices() (in module graphein.protein.tensor.sequence) get_backbone() (in module graphein.protein.tensor.representation) get_backbone_bond_angles() (in module graphein.protein.tensor.angles) get_backbone_bond_lengths() (in module graphein.protein.tensor.angles) get_backbone_frames() (in module graphein.protein.tensor.representation) get_c_alpha() (in module graphein.protein.tensor.representation) get_center() (in module graphein.protein.tensor.geometry) get_chembl_id_from_smiles() (in module graphein.molecule.chembl) get_chembl_metadata() (in module graphein.molecule.chembl) get_contacts_df() (in module graphein.protein.edges.intramolecular) get_coords() (in module graphein.molecule.graphs) get_edge_trace() (in module graphein.ppi.visualisation) get_edges_by_bond_type() (in module graphein.protein.edges.distance) get_full_atom_coords() (in module graphein.protein.tensor.representation) get_ideal_backbone_coords() (in module graphein.protein.tensor.reconstruction) get_interacting_atoms() (in module graphein.molecule.edges.distance) (in module graphein.protein.edges.distance) get_loader() (in module graphein.utils.config_parser) get_node_trace() (in module graphein.ppi.visualisation) get_obj_file() (in module graphein.protein.meshes) get_obsolete_mapping() (in module graphein.protein.utils) get_protein() (graphein.protein.tensor.data.ProteinBatch method) get_protein_length() (in module graphein.protein.tensor.io) get_protein_name_from_filename() (in module graphein.protein.utils) get_random_batch() (in module graphein.protein.tensor.data) get_random_protein() (in module graphein.protein.tensor.data) get_residue_id() (in module graphein.protein.tensor.sequence) get_ring_atoms() (in module graphein.protein.edges.distance) get_ring_centroids() (in module graphein.protein.edges.distance) get_ring_normals() (in module graphein.protein.edges.distance) get_seq_records() (in module graphein.ml.clustering) get_sequence() (in module graphein.protein.tensor.sequence) get_sinusoid_encoding_table() (in module graphein.protein.features.sequence.sequence) get_smiles_from_chembl() (in module graphein.molecule.chembl) get_smiles_from_zinc() (in module graphein.molecule.zinc) get_zinc_id_from_smile() (in module graphein.molecule.zinc) GetContactsConfig (class in graphein.protein.config) GRANTHAM_CHEMICAL_DISTANCE_MATRIX (in module graphein.protein.resi_atoms), [1] GranularityOpts (in module graphein.protein.config) graph_summary() (in module graphein.protein.analysis) GraphAtoms (in module graphein.molecule.config) (in module graphein.protein.config) graphein.grn.config module graphein.grn.edges module graphein.grn.features.node_features module graphein.grn.graphs module graphein.grn.parse_regnetwork module graphein.grn.parse_trrust module graphein.ml.clustering module graphein.ml.conversion module graphein.ml.datasets.foldcomp_dataset module graphein.ml.datasets.torch_geometric_dataset module graphein.ml.diffusion module graphein.ml.utils module graphein.molecule.atoms module graphein.molecule.chembl module graphein.molecule.config module graphein.molecule.edges.atomic module graphein.molecule.edges.distance module graphein.molecule.features.edges.bonds module graphein.molecule.features.graph.molecule module graphein.molecule.features.nodes.atom_type module graphein.molecule.graphs module graphein.molecule.utils module graphein.molecule.visualisation module graphein.molecule.zinc module graphein.ppi.config module graphein.ppi.edges module graphein.ppi.features.node_features module graphein.ppi.graph_metadata module graphein.ppi.graphs module graphein.ppi.parse_biogrid module graphein.ppi.parse_stringdb module graphein.ppi.visualisation module graphein.protein.analysis module graphein.protein.config module graphein.protein.edges.atomic module graphein.protein.edges.distance module graphein.protein.edges.intramolecular module graphein.protein.features.graph.structure module graphein.protein.features.nodes.aaindex module graphein.protein.features.nodes.amino_acid module graphein.protein.features.nodes.dssp module graphein.protein.features.nodes.geometry module graphein.protein.features.sequence.embeddings module, [1] graphein.protein.features.sequence.propy module graphein.protein.features.sequence.sequence module graphein.protein.features.utils module graphein.protein.graphs module graphein.protein.meshes module graphein.protein.resi_atoms module, [1] graphein.protein.subgraphs module graphein.protein.tensor.angles module graphein.protein.tensor.data module graphein.protein.tensor.geometry module graphein.protein.tensor.io module graphein.protein.tensor.plot module graphein.protein.tensor.pnerf module graphein.protein.tensor.reconstruction module graphein.protein.tensor.representation module graphein.protein.tensor.sequence module graphein.protein.tensor.testing module graphein.protein.tensor.types module graphein.protein.utils module graphein.protein.visualisation module graphein.rna.config module graphein.rna.constants module graphein.rna.edges.atomic module graphein.rna.edges.base_pairing module graphein.rna.edges.distance module graphein.rna.features.atom module graphein.rna.graphs module graphein.rna.subgraphs module graphein.rna.utils module graphein.rna.visualisation module graphein.testing.utils module graphein.utils.config module graphein.utils.config_parser module graphein.utils.pymol.compat module graphein.utils.pymol.core module graphein.utils.utils module GraphFormatConvertor (class in graphein.ml.conversion) graphs_isomorphic() (in module graphein.testing.utils) GRNGraphConfig (class in graphein.grn.config) H has_complete_backbone() (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) (in module graphein.protein.tensor.testing) has_complete_residue() (in module graphein.protein.tensor.testing) has_nan() (in module graphein.protein.tensor.testing) hybridization() (in module graphein.molecule.features.nodes.atom_type) hydrogen_bond() (in module graphein.protein.edges.intramolecular) hydrogen_bond_acceptor() (in module graphein.protein.features.nodes.amino_acid) HYDROGEN_BOND_ACCEPTORS (in module graphein.protein.resi_atoms), [1] hydrogen_bond_donor() (in module graphein.protein.features.nodes.amino_acid) HYDROGEN_BOND_DONORS (in module graphein.protein.resi_atoms), [1] hydrophobic() (in module graphein.protein.edges.intramolecular) HYDROPHOBIC_RESIS (in module graphein.protein.resi_atoms), [1] I IDEAL_BB_BOND_ANGLES (in module graphein.protein.resi_atoms), [1] IDEAL_BB_BOND_LENGTHS (in module graphein.protein.resi_atoms), [1] idealize_backbone() (graphein.protein.tensor.data.Protein method) (in module graphein.protein.tensor.geometry) identify_bond_type_from_mapping() (in module graphein.protein.edges.atomic) identity_matrix() (in module graphein.ml.diffusion) implicit_valence() (in module graphein.molecule.features.nodes.atom_type) infer_residue_types() (in module graphein.protein.tensor.sequence) initialise_graph_with_metadata() (in module graphein.molecule.graphs) (in module graphein.protein.graphs) InMemoryProteinGraphDataset (class in graphein.ml.datasets.torch_geometric_dataset) inverse_distance_matrix() (in module graphein.ml.diffusion) IONIC_RESIS (in module graphein.protein.resi_atoms), [1] is_aromatic() (in module graphein.molecule.features.nodes.atom_type) is_complete() (graphein.protein.tensor.data.Protein method) is_complete_structure() (in module graphein.protein.tensor.testing) is_isotope() (in module graphein.molecule.features.nodes.atom_type) is_ring() (in module graphein.molecule.features.nodes.atom_type) is_ring_size() (in module graphein.molecule.features.nodes.atom_type) ISOELECTRIC_POINTS (in module graphein.protein.resi_atoms), [1] ISOELECTRIC_POINTS_STD (in module graphein.protein.resi_atoms), [1] K kabsch() (in module graphein.protein.tensor.geometry) kappa() (graphein.protein.tensor.data.Protein method) (in module graphein.protein.tensor.angles) L label_node_id() (in module graphein.protein.graphs) len() (graphein.ml.datasets.foldcomp_dataset.FoldCompDataset method) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset method) load_expasy_scales() (in module graphein.protein.features.nodes.amino_acid) load_meiler_embeddings() (in module graphein.protein.features.nodes.amino_acid) load_RegNetwork_interactions() (in module graphein.grn.parse_regnetwork) load_RegNetwork_regulation_types() (in module graphein.grn.parse_regnetwork) load_TRRUST() (in module graphein.grn.parse_trrust) M matrix_to_quaternion() (in module graphein.protein.tensor.geometry) MAX_NEIGHBOURS (in module graphein.protein.resi_atoms), [1] meiler_embedding() (in module graphein.protein.features.nodes.amino_acid) model_config (graphein.grn.config.GRNGraphConfig attribute) (graphein.grn.config.RegNetworkConfig attribute) (graphein.grn.config.TRRUSTConfig attribute) (graphein.molecule.config.MoleculeGraphConfig attribute) (graphein.ppi.config.BioGridConfig attribute) (graphein.ppi.config.PPIGraphConfig attribute) (graphein.ppi.config.STRINGConfig attribute) (graphein.protein.config.DSSPConfig attribute) (graphein.protein.config.GetContactsConfig attribute) (graphein.protein.config.ProteinGraphConfig attribute) (graphein.protein.config.ProteinMeshConfig attribute) (graphein.rna.config.BpRNAConfig attribute) (graphein.rna.config.RNAGraphConfig attribute) module graphein.grn.config graphein.grn.edges graphein.grn.features.node_features graphein.grn.graphs graphein.grn.parse_regnetwork graphein.grn.parse_trrust graphein.ml.clustering graphein.ml.conversion graphein.ml.datasets.foldcomp_dataset graphein.ml.datasets.torch_geometric_dataset graphein.ml.diffusion graphein.ml.utils graphein.molecule.atoms graphein.molecule.chembl graphein.molecule.config graphein.molecule.edges.atomic graphein.molecule.edges.distance graphein.molecule.features.edges.bonds graphein.molecule.features.graph.molecule graphein.molecule.features.nodes.atom_type graphein.molecule.graphs graphein.molecule.utils graphein.molecule.visualisation graphein.molecule.zinc graphein.ppi.config graphein.ppi.edges graphein.ppi.features.node_features graphein.ppi.graph_metadata graphein.ppi.graphs graphein.ppi.parse_biogrid graphein.ppi.parse_stringdb graphein.ppi.visualisation graphein.protein.analysis graphein.protein.config graphein.protein.edges.atomic graphein.protein.edges.distance graphein.protein.edges.intramolecular graphein.protein.features.graph.structure graphein.protein.features.nodes.aaindex graphein.protein.features.nodes.amino_acid graphein.protein.features.nodes.dssp graphein.protein.features.nodes.geometry graphein.protein.features.sequence.embeddings, [1] graphein.protein.features.sequence.propy graphein.protein.features.sequence.sequence graphein.protein.features.utils graphein.protein.graphs graphein.protein.meshes graphein.protein.resi_atoms, [1] graphein.protein.subgraphs graphein.protein.tensor.angles graphein.protein.tensor.data graphein.protein.tensor.geometry graphein.protein.tensor.io graphein.protein.tensor.plot graphein.protein.tensor.pnerf graphein.protein.tensor.reconstruction graphein.protein.tensor.representation graphein.protein.tensor.sequence graphein.protein.tensor.testing graphein.protein.tensor.types graphein.protein.utils graphein.protein.visualisation graphein.rna.config graphein.rna.constants graphein.rna.edges.atomic graphein.rna.edges.base_pairing graphein.rna.edges.distance graphein.rna.features.atom graphein.rna.graphs graphein.rna.subgraphs graphein.rna.utils graphein.rna.visualisation graphein.testing.utils graphein.utils.config graphein.utils.config_parser graphein.utils.pymol.compat graphein.utils.pymol.core graphein.utils.utils mol_descriptors() (in module graphein.molecule.features.graph.molecule) MOLECULAR_WEIGHTS (in module graphein.protein.resi_atoms), [1] MOLECULAR_WEIGHTS_STD (in module graphein.protein.resi_atoms), [1] MoleculeGraphConfig (class in graphein.molecule.config) N NEG_AA (in module graphein.protein.resi_atoms), [1] node_coords() (in module graphein.protein.edges.distance) nodes_equal() (in module graphein.testing.utils) NON_STANDARD_AMINO_ACID_MAPPING_1_TO_3 (in module graphein.protein.resi_atoms), [1] NON_STANDARD_AMINO_ACID_MAPPING_3_TO_1 (in module graphein.protein.resi_atoms), [1] NON_STANDARD_AMINO_ACIDS (in module graphein.protein.resi_atoms), [1] NON_STANDARD_RESI_NAMES (in module graphein.protein.resi_atoms), [1] NON_STANDARD_RESIS_NAME (in module graphein.protein.resi_atoms), [1] NON_STANDARD_RESIS_PARENT (in module graphein.protein.resi_atoms), [1] normalize_and_center_mesh_vertices() (in module graphein.protein.meshes) num_explicit_h() (in module graphein.molecule.features.nodes.atom_type) num_heavy_atoms() (in module graphein.molecule.features.nodes.atom_type) num_implicit_h() (in module graphein.molecule.features.nodes.atom_type) num_radical_electrons() (in module graphein.molecule.features.nodes.atom_type) number_groups_of_runs() (in module graphein.protein.graphs) O onek_encoding_unk() (in module graphein.utils.utils) P params_BIOGRID() (in module graphein.ppi.parse_biogrid) params_STRING() (in module graphein.ppi.parse_stringdb) parse_aggregation_type() (in module graphein.utils.utils) parse_BIOGRID() (in module graphein.ppi.parse_biogrid) parse_config() (in module graphein.utils.config_parser) parse_dssp_df() (in module graphein.protein.features.nodes.dssp) parse_kwargs_from_config() (in module graphein.grn.graphs) (in module graphein.ppi.graphs) parse_pymol_commands() (in module graphein.protein.meshes) parse_RegNetwork() (in module graphein.grn.parse_regnetwork) parse_STRING() (in module graphein.ppi.parse_stringdb) parse_TRRUST() (in module graphein.grn.parse_trrust) partial_functions_equal() (in module graphein.utils.config) PartialMatchOperator (class in graphein.utils.config) PathMatchOperator (class in graphein.utils.config) pdb_charge_to_numeric() (in module graphein.protein.utils) PDB_DOWNLOAD_SOURCES (in module graphein.protein.utils) peptide_bonds() (in module graphein.protein.edges.intramolecular) phi() (in module graphein.protein.features.nodes.dssp) pi_cation() (in module graphein.protein.edges.intramolecular) PI_RESIS (in module graphein.protein.resi_atoms), [1] pi_stacking() (in module graphein.protein.edges.intramolecular) ping() (in module graphein.utils.utils) place_fourth_atom() (in module graphein.protein.tensor.reconstruction) place_o_coords() (in module graphein.protein.tensor.reconstruction) plot_chord_diagram() (in module graphein.protein.visualisation) plot_degree_by_residue_type() (in module graphein.protein.analysis) plot_degree_distribution() (in module graphein.protein.analysis) plot_dihedrals() (in module graphein.protein.tensor.plot) plot_distance_landscape() (in module graphein.protein.visualisation) plot_distance_matrix() (graphein.protein.tensor.data.Protein method) (in module graphein.protein.tensor.plot) (in module graphein.protein.visualisation) plot_edge_type_distribution() (in module graphein.protein.analysis) plot_graph_metric_property_correlation() (in module graphein.protein.analysis) plot_molecular_graph() (in module graphein.molecule.visualisation) plot_pointcloud() (in module graphein.protein.visualisation) plot_ppi_graph() (in module graphein.ppi.visualisation) plot_protein_structure_graph() (in module graphein.protein.visualisation) plot_residue_composition() (in module graphein.protein.analysis) plot_rna_graph() (in module graphein.rna.visualisation) plot_structure() (graphein.protein.tensor.data.Protein method) (in module graphein.protein.tensor.plot) plotly_molecular_graph() (in module graphein.molecule.visualisation) plotly_ppi_graph() (in module graphein.ppi.visualisation) plotly_protein_structure_graph() (in module graphein.protein.visualisation) point_to_coordinate() (in module graphein.protein.tensor.pnerf) POS_AA (in module graphein.protein.resi_atoms), [1] PositionTensor (class in graphein.protein.tensor.types) PPIGraphConfig (class in graphein.ppi.config) process() (graphein.ml.datasets.foldcomp_dataset.FoldCompDataset method) (graphein.ml.datasets.torch_geometric_dataset.InMemoryProteinGraphDataset method) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset method) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphListDataset method) process_blast_results() (in module graphein.ml.clustering) process_dataframe() (in module graphein.protein.graphs) processed_file_names (graphein.ml.datasets.foldcomp_dataset.FoldCompDataset property) (graphein.ml.datasets.torch_geometric_dataset.InMemoryProteinGraphDataset property) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset property) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphListDataset property) Protein (class in graphein.protein.tensor.data) protein_apply() (graphein.protein.tensor.data.ProteinBatch method) PROTEIN_ATOMS (in module graphein.protein.resi_atoms), [1] protein_df_to_chain_tensor() (in module graphein.protein.tensor.io) protein_df_to_tensor() (in module graphein.protein.tensor.io) protein_letters_3to1_all_caps() (in module graphein.utils.utils) protein_to_pyg() (in module graphein.protein.tensor.io) ProteinBatch (class in graphein.protein.tensor.data) ProteinGraphConfig (class in graphein.protein.config) ProteinGraphConfigurationError ProteinGraphDataset (class in graphein.ml.datasets.torch_geometric_dataset) ProteinGraphListDataset (class in graphein.ml.datasets.torch_geometric_dataset) ProteinMeshConfig (class in graphein.protein.config) PSEUDOKNOT_CLOSING_SYMBOLS (in module graphein.rna.constants) PSEUDOKNOT_OPENING_SYMBOLS (in module graphein.rna.constants) psi() (in module graphein.protein.features.nodes.dssp) Q quasi_sequence_order() (in module graphein.protein.features.sequence.propy) quaternion_to_matrix() (in module graphein.protein.tensor.geometry) QuaternionTensor (class in graphein.protein.tensor.types) R radius_of_gyration() (in module graphein.protein.features.graph.structure) random_atom_tensor() (in module graphein.protein.tensor.testing) random_coord_tensor() (in module graphein.protein.tensor.testing) raw_file_names (graphein.ml.datasets.foldcomp_dataset.FoldCompDataset property) (graphein.ml.datasets.torch_geometric_dataset.InMemoryProteinGraphDataset property) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset property) RDKIT_MOL_DESCRIPTORS (in module graphein.molecule.atoms) read_contacts_file() (in module graphein.protein.edges.intramolecular) read_dbn_file() (in module graphein.rna.utils) read_fasta() (in module graphein.protein.utils) read_pdb_to_dataframe() (in module graphein.protein.graphs) reconstruct_dihedrals() (in module graphein.protein.tensor.pnerf) RegNetwork_df() (in module graphein.grn.parse_regnetwork) RegNetworkConfig (class in graphein.grn.config) remove_alt_locs() (in module graphein.protein.graphs) remove_insertions() (in module graphein.protein.graphs) RESI_NAMES (in module graphein.protein.resi_atoms), [1] RESI_THREE_TO_1 (in module graphein.protein.resi_atoms), [1] RESIDUE_ATOM_BOND_STATE (in module graphein.protein.resi_atoms), [1] residue_type_tensor() (in module graphein.protein.tensor.sequence) ResidueFrameTensor (class in graphein.protein.tensor.types) ResidueTensor (class in graphein.protein.tensor.types) RING_NORMAL_ATOMS (in module graphein.protein.resi_atoms), [1] RNA_ATOM_BOND_STATE (in module graphein.rna.constants) RNA_ATOMIC_RADII (in module graphein.rna.constants) RNA_ATOMS (in module graphein.rna.constants) RNA_BASE_COLORS (in module graphein.rna.constants) RNA_BASES (in module graphein.rna.constants) RNAGraphConfig (class in graphein.rna.config) RotationMatrix (class in graphein.protein.tensor.types) RotationMatrix2D (class in graphein.protein.tensor.types) RotationMatrix3D (class in graphein.protein.tensor.types) rsa() (in module graphein.protein.features.nodes.dssp) run_get_contacts() (in module graphein.protein.edges.intramolecular) run_pymol_commands() (in module graphein.protein.meshes) S salt_bridge() (in module graphein.protein.edges.intramolecular) SALT_BRIDGE_ANIONS (in module graphein.protein.resi_atoms), [1] SALT_BRIDGE_ATOMS (in module graphein.protein.resi_atoms), [1] SALT_BRIDGE_CATIONS (in module graphein.protein.resi_atoms), [1] SALT_BRIDGE_RESIDUES (in module graphein.protein.resi_atoms), [1] save() (graphein.protein.tensor.data.Protein method) (graphein.protein.tensor.data.ProteinBatch method) save_graph_to_pdb() (in module graphein.protein.utils) save_pdb_df_to_pdb() (in module graphein.protein.utils) save_rgroup_df_to_pdb() (in module graphein.protein.utils) SC_BUILD_INFO (in module graphein.protein.resi_atoms), [1] SCHNEIDER_WREDE_DISTMAT (in module graphein.protein.resi_atoms), [1] secondary_structure() (in module graphein.protein.features.nodes.dssp) select_chains() (in module graphein.protein.graphs) sequence_order_coupling_number_total() (in module graphein.protein.features.sequence.propy) sequence_positions() (in module graphein.protein.utils) setup() (graphein.ml.datasets.foldcomp_dataset.FoldCompLightningDataModule method) sidechain_torsion() (graphein.protein.tensor.data.Protein method) (in module graphein.protein.tensor.angles) SIMPLE_DOTBRACKET_NOTATION (in module graphein.rna.constants) sn_nerf() (in module graphein.protein.tensor.pnerf) sort_dataframe() (in module graphein.protein.graphs) SS_BOND_TYPES (in module graphein.rna.constants) STANDARD_AMINO_ACID_MAPPING_1_TO_3 (in module graphein.protein.resi_atoms), [1] STANDARD_AMINO_ACID_MAPPING_3_TO_1 (in module graphein.protein.resi_atoms), [1] STANDARD_AMINO_ACIDS (in module graphein.protein.resi_atoms), [1] STANDARD_RESI_NAMES (in module graphein.protein.resi_atoms), [1] STANDARD_RESIDUE_ATOMS (in module graphein.protein.resi_atoms), [1] standardise_BIOGRID() (in module graphein.ppi.parse_biogrid) standardise_RegNetwork() (in module graphein.grn.parse_regnetwork) standardise_STRING() (in module graphein.ppi.parse_stringdb) standardise_TRRUST() (in module graphein.grn.parse_trrust) STRING_df() (in module graphein.ppi.parse_stringdb) STRINGConfig (class in graphein.ppi.config) subset_structure_to_atom_type() (in module graphein.protein.graphs) subset_structure_to_rna() (in module graphein.protein.graphs) SULPHUR_RESIS (in module graphein.protein.resi_atoms), [1] SUPPORTED_DOTBRACKET_NOTATION (in module graphein.rna.constants) SUPPORTED_FORMATS (in module graphein.ml.conversion) SUPPORTED_PSEUDOKNOT_NOTATION (in module graphein.rna.constants) SUPPORTED_VERBOSITY (in module graphein.ml.conversion) T t_stacking() (in module graphein.protein.edges.intramolecular) test_dataloader() (graphein.ml.datasets.foldcomp_dataset.FoldCompLightningDataModule method) test_dataset() (graphein.ml.datasets.foldcomp_dataset.FoldCompLightningDataModule method) three_to_one_with_mods() (in module graphein.protein.utils) to_ang() (in module graphein.protein.tensor.angles) to_batch() (graphein.protein.tensor.data.ProteinBatch method) to_data() (graphein.protein.tensor.data.Protein method) to_dataframe() (graphein.protein.tensor.data.Protein method) (in module graphein.protein.tensor.io) to_pdb() (graphein.protein.tensor.data.Protein method) (in module graphein.protein.tensor.io) to_protein() (in module graphein.protein.tensor.data) to_protein_list() (graphein.protein.tensor.data.ProteinBatch method) to_protein_mp() (in module graphein.protein.tensor.data) torsion_to_rad() (in module graphein.protein.tensor.angles) TorsionTensor (class in graphein.protein.tensor.types) total_degree() (in module graphein.molecule.features.nodes.atom_type) total_num_h() (in module graphein.molecule.features.nodes.atom_type) total_valence() (in module graphein.molecule.features.nodes.atom_type) train_and_test_from_fasta() (in module graphein.ml.clustering) train_dataloader() (graphein.ml.datasets.foldcomp_dataset.FoldCompLightningDataModule method) train_dataset() (graphein.ml.datasets.foldcomp_dataset.FoldCompLightningDataModule method) transform_pdbs() (graphein.ml.datasets.torch_geometric_dataset.InMemoryProteinGraphDataset method) (graphein.ml.datasets.torch_geometric_dataset.ProteinGraphDataset method) transition_charge() (in module graphein.protein.features.sequence.propy) transition_descriptor() (in module graphein.protein.features.sequence.propy) transition_hydrophobicity() (in module graphein.protein.features.sequence.propy) transition_normalized_vdwv() (in module graphein.protein.features.sequence.propy) transition_polarity() (in module graphein.protein.features.sequence.propy) transition_polarizability() (in module graphein.protein.features.sequence.propy) transition_secondary_str() (in module graphein.protein.features.sequence.propy) transition_solvent_accessibility() (in module graphein.protein.features.sequence.propy) TRRUST_df() (in module graphein.grn.parse_trrust) TRRUSTConfig (class in graphein.grn.config) V val_dataloader() (graphein.ml.datasets.foldcomp_dataset.FoldCompLightningDataModule method) val_dataset() (graphein.ml.datasets.foldcomp_dataset.FoldCompLightningDataModule method) VALID_BASE_PAIRINGS (in module graphein.rna.constants) validate_dotbracket() (in module graphein.rna.graphs) validate_lengths() (in module graphein.rna.graphs) validate_rna_sequence() (in module graphein.rna.graphs) van_der_waals() (in module graphein.protein.edges.intramolecular) VDW_RADII (in module graphein.protein.resi_atoms), [1] VECTOR_FEATURE_NAMES (in module graphein.protein.features.nodes.geometry) W WOBBLE_BASE_PAIRINGS (in module graphein.rna.constants)