Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | V | W _ __init__() (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) 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) 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) add_base_pairing_interactions() (in module graphein.rna.edges) 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) add_bond_type() (in module graphein.molecule.features.edges.bonds) add_cation_pi_interactions() (in module graphein.protein.edges.distance) 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_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) 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_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) add_pseudoknots() (in module graphein.rna.edges) add_regnetwork_edges() (in module graphein.grn.edges) add_ring_status() (in module graphein.protein.edges.atomic) 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_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_vector_to_plot() (in module graphein.protein.visualisation) aggregate_graph_feature_over_chains() (in module graphein.protein.features.utils) 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) 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) 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) AROMATIC_RESIS (in module graphein.protein.resi_atoms) 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) assign_node_id_to_dataframe() (in module graphein.protein.graphs) asteroid_plot() (in module graphein.protein.visualisation) atom_type_one_hot() (in module graphein.molecule.features.nodes.atom_type) atomic_mass() (in module graphein.molecule.features.nodes.atom_type) 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_ATOMS (in module graphein.protein.resi_atoms) BASE_AMINO_ACIDS (in module graphein.protein.resi_atoms) BASE_ATOMS (in module graphein.molecule.atoms) 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] 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) BOND_ORDERS (in module graphein.protein.resi_atoms) bond_stereo() (in module graphein.molecule.features.edges.bonds) BOND_TYPES (in module graphein.protein.resi_atoms) 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) CARBOHYDRATE_CODES (in module graphein.protein.resi_atoms) CARBOHYDRATE_NAMES (in module graphein.protein.resi_atoms) CATION_PI_RESIS (in module graphein.protein.resi_atoms) CATION_RESIS (in module graphein.protein.resi_atoms) check_base_pairing_type() (in module graphein.rna.edges) check_for_pymol_installation() (in module graphein.protein.meshes) 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) COFACTOR_CODE_NAME_MAPPING (in module graphein.protein.resi_atoms) COFACTOR_CODES (in module graphein.protein.resi_atoms) COFACTOR_NAMES (in module graphein.protein.resi_atoms) 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_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_grn_graph() (in module graphein.grn.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_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.protein.graphs) construct_rna_graph() (in module graphein.rna.graphs) convert_graph_dict_feat_to_series() (in module graphein.protein.features.utils) convert_structure_to_centroids() (in module graphein.protein.graphs) convert_verts_and_face_to_mesh() (in module graphein.protein.meshes) COVALENT_RADII (in module graphein.protein.resi_atoms) create_mesh() (in module graphein.protein.meshes) D DEFAULT_BOND_STATE (in module graphein.protein.resi_atoms) degree() (in module graphein.molecule.features.nodes.atom_type) deprotonate_structure() (in module graphein.protein.graphs) dipeptide_composition() (in module graphein.protein.features.sequence.propy) 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) DISULFIDE_RESIS (in module graphein.protein.resi_atoms) download_alphafold_structure() (in module graphein.protein.utils) download_pdb() (in module graphein.protein.utils) E edge_data_equal() (in module graphein.testing.utils) edges_equal() (in module graphein.testing.utils) esm_residue_embedding() (in module graphein.protein.features.sequence.embeddings), [1] esm_sequence_embedding() (in module graphein.protein.features.sequence.embeddings), [1] 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_k_hop_subgraph() (in module graphein.protein.subgraphs) extract_subgraph() (in module graphein.protein.subgraphs) extract_subgraph_by_bond_type() (in module graphein.protein.subgraphs) extract_subgraph_by_sequence_position() (in module graphein.protein.subgraphs) extract_subgraph_from_atom_types() (in module graphein.protein.subgraphs) extract_subgraph_from_chains() (in module graphein.protein.subgraphs) extract_subgraph_from_node_list() (in module graphein.protein.subgraphs) extract_subgraph_from_point() (in module graphein.protein.subgraphs) extract_subgraph_from_residue_types() (in module graphein.protein.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_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) formal_charge() (in module graphein.molecule.features.nodes.atom_type) format_adjacency() (in module graphein.utils.utils) function_constructor() (in module graphein.utils.config_parser) G generate_adjacency_tensor() (in module graphein.utils.utils) generate_feature_dataframe() (in module graphein.utils.utils) get_contacts_df() (in module graphein.protein.edges.intramolecular) get_edge_trace() (in module graphein.ppi.visualisation) get_edges_by_bond_type() (in module graphein.protein.edges.distance) 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_name_from_filename() (in module graphein.protein.utils) get_ring_atoms() (in module graphein.protein.edges.distance) get_ring_centroids() (in module graphein.protein.edges.distance) GetContactsConfig (class in graphein.protein.config) GRANTHAM_CHEMICAL_DISTANCE_MATRIX (in module graphein.protein.resi_atoms) 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.molecule.atoms 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.visualisation 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.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 graphein.protein.subgraphs module graphein.protein.utils module graphein.protein.visualisation module graphein.rna.constants module graphein.rna.edges module graphein.rna.graphs 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 graphs_isomorphic() (in module graphein.testing.utils) GRNGraphConfig (class in graphein.grn.config) H 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) hydrogen_bond_donor() (in module graphein.protein.features.nodes.amino_acid) HYDROGEN_BOND_DONORS (in module graphein.protein.resi_atoms) hydrophobic() (in module graphein.protein.edges.intramolecular) HYDROPHOBIC_RESIS (in module graphein.protein.resi_atoms) I identify_bond_type_from_mapping() (in module graphein.protein.edges.atomic) implicit_valence() (in module graphein.molecule.features.nodes.atom_type) import_message() (in module graphein.utils.utils) initialise_graph_with_metadata() (in module graphein.molecule.graphs) (in module graphein.protein.graphs) IONIC_RESIS (in module graphein.protein.resi_atoms) is_aromatic() (in module graphein.molecule.features.nodes.atom_type) 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) is_tool() (in module graphein.protein.utils) ISOELECTRIC_POINTS (in module graphein.protein.resi_atoms) ISOELECTRIC_POINTS_STD (in module graphein.protein.resi_atoms) L 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 MAX_NEIGHBOURS (in module graphein.protein.resi_atoms) meiler_embedding() (in module graphein.protein.features.nodes.amino_acid) module graphein.grn.config graphein.grn.edges graphein.grn.features.node_features graphein.grn.graphs graphein.grn.parse_regnetwork graphein.grn.parse_trrust graphein.molecule.atoms 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.visualisation 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.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 graphein.protein.subgraphs graphein.protein.utils graphein.protein.visualisation graphein.rna.constants graphein.rna.edges graphein.rna.graphs 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) MOLECULAR_WEIGHTS_STD (in module graphein.protein.resi_atoms) MoleculeGraphConfig (class in graphein.molecule.config) N NEG_AA (in module graphein.protein.resi_atoms) node_coords() (in module graphein.protein.edges.distance) nodes_equal() (in module graphein.testing.utils) NON_STANDARD_AMINO_ACID_MAPPING_3_TO_1 (in module graphein.protein.resi_atoms) NON_STANDARD_AMINO_ACIDS (in module graphein.protein.resi_atoms) NON_STANDARD_RESI_NAMES (in module graphein.protein.resi_atoms) NON_STANDARD_RESIS_NAME (in module graphein.protein.resi_atoms) NON_STANDARD_RESIS_PARENT (in module graphein.protein.resi_atoms) normalize_and_center_mesh_vertices() (in module graphein.protein.meshes) num_explicit_h() (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_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) 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) pi_stacking() (in module graphein.protein.edges.intramolecular) ping() (in module graphein.utils.utils) 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_distance_landscape() (in module graphein.protein.visualisation) plot_distance_matrix() (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) 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) POS_AA (in module graphein.protein.resi_atoms) PPIGraphConfig (class in graphein.ppi.config) process_dataframe() (in module graphein.protein.graphs) process_dssp_df() (in module graphein.protein.features.nodes.dssp) protein_letters_3to1_all_caps() (in module graphein.utils.utils) ProteinGraphConfig (class in graphein.protein.config) ProteinGraphConfigurationError 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) R RDKIT_MOL_DESCRIPTORS (in module graphein.molecule.atoms) read_contacts_file() (in module graphein.protein.edges.intramolecular) read_pdb_to_dataframe() (in module graphein.protein.graphs) RegNetwork_df() (in module graphein.grn.parse_regnetwork) RegNetworkConfig (class in graphein.grn.config) remove_insertions() (in module graphein.protein.graphs) RESI_NAMES (in module graphein.protein.resi_atoms) RESI_THREE_TO_1 (in module graphein.protein.resi_atoms) RESIDUE_ATOM_BOND_STATE (in module graphein.protein.resi_atoms) RNA_BASE_COLORS (in module graphein.rna.constants) RNA_BASES (in module graphein.rna.constants) 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) 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) SCHNEIDER_WREDE_DISTMAT (in module graphein.protein.resi_atoms) 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) SIMPLE_DOTBRACKET_NOTATION (in module graphein.rna.constants) SS_BOND_TYPES (in module graphein.rna.constants) STANDARD_AMINO_ACIDS (in module graphein.protein.resi_atoms) STANDARD_RESI_NAMES (in module graphein.protein.resi_atoms) 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) SULPHUR_RESIS (in module graphein.protein.resi_atoms) SUPPORTED_DOTBRACKET_NOTATION (in module graphein.rna.constants) SUPPORTED_PSEUDOKNOT_NOTATION (in module graphein.rna.constants) T t_stacking() (in module graphein.protein.edges.intramolecular) three_to_one_with_mods() (in module graphein.protein.utils) 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) 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 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) W WOBBLE_BASE_PAIRINGS (in module graphein.rna.constants)