Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z _ __eq__() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method) __getitem__() (neurosnap.structure.Chain method) (neurosnap.structure.Structure method) (neurosnap.structure.structure.Chain method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) __hash__() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method) __init__() (neurosnap.algos.wolfpsort.wolfpsort.WoLFPSortPredictor method) (neurosnap.algos.wolfpsort.WoLFPSortPredictor method) (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) __iter__() (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) (neurosnap.structure.Chain method) (neurosnap.structure.Structure method) (neurosnap.structure.structure.Chain method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) __len__() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) __post_init__() (neurosnap.algos.evoef2.Atom method) __repr__() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) A a (neurosnap.algos.evoef2.Bond attribute) aap (neurosnap.algos.evoef2.AAppTable attribute) AAppTable (class in neurosnap.algos.evoef2) AARecord (class in neurosnap.constants) (class in neurosnap.constants.sequence) AARecordTable (class in neurosnap.constants) (class in neurosnap.constants.sequence) abr (neurosnap.constants.AARecord attribute) (neurosnap.constants.sequence.AARecord attribute) add_annotation() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) add_atom() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) add_atoms() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) add_bond() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) add_bonds() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) add_compound() (neurosnap.chemistry.landscape.GraphBuilder method) add_edge() (neurosnap.chemistry.landscape.GraphBuilder method) add_edges() (neurosnap.chemistry.landscape.GraphBuilder method) add_fragment() (neurosnap.chemistry.landscape.GraphBuilder method) add_hydrogens_with_pdb2pqr() (in module neurosnap.structure) (in module neurosnap.structure.prepare) add_interaction() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) add_interactions() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) add_scaffold() (neurosnap.chemistry.landscape.GraphBuilder method) add_terminal_capping_groups() (in module neurosnap.structure) (in module neurosnap.structure.prepare) adjacency() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) align() (in module neurosnap.structure) (in module neurosnap.structure.compare) align_mafft() (in module neurosnap.sequence.align) align_molecule_to_reference() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) alignment_coverage() (in module neurosnap.sequence.align) all_residues() (neurosnap.algos.evoef2.Structure method) analyze_interactions() (in module neurosnap.structure) (in module neurosnap.structure.interactions) angle_deg (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) animate_frames() (in module neurosnap.structure) (in module neurosnap.structure.rendering) animate_results() (in module neurosnap.algos.clusterprot) annotation_names (neurosnap.structure.Structure property) (neurosnap.structure.structure.Structure property) annotations (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute) append() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) apply_reversible_cut() (in module neurosnap.chemistry.landscape) assign_pqr() (in module neurosnap.algos.pdb2pqr) Atom (class in neurosnap.algos.evoef2) (class in neurosnap.structure) (class in neurosnap.structure.structure) atom (neurosnap.structure.confidence.PLDDTReport attribute) (neurosnap.structure.PLDDTReport attribute) atom_a (neurosnap.algos.evoef2.CharmmIC attribute) atom_b (neurosnap.algos.evoef2.CharmmIC attribute) atom_c (neurosnap.algos.evoef2.CharmmIC attribute) atom_count (neurosnap.structure.structure.StructureStack property) (neurosnap.structure.StructureStack property) atom_d (neurosnap.algos.evoef2.CharmmIC attribute) atom_index (neurosnap.structure.AtomReference attribute) (neurosnap.structure.interaction_report.AtomReference attribute) atom_index1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) atom_index2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) atom_indices() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method) atom_name (neurosnap.structure.Atom attribute) (neurosnap.structure.AtomReference attribute) (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.AtomReference attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.structure.Atom attribute) atom_name1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) atom_name2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) AtomParam (class in neurosnap.algos.evoef2) AtomReference (class in neurosnap.structure) (class in neurosnap.structure.interaction_report) atoms (neurosnap.algos.evoef2.Residue attribute) (neurosnap.algos.evoef2.ResidueTopology attribute) atoms() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method) attach_rgroup() (in module neurosnap.chemistry) (in module neurosnap.chemistry.landscape) average_path_length (neurosnap.chemistry.landscape.NetworkMetrics attribute) average_path_length() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) B b (neurosnap.algos.evoef2.Bond attribute) (neurosnap.log.c attribute) BASE_URL (neurosnap.api.NeurosnapAPI attribute) bins (neurosnap.algos.evoef2.DunbrackLibrary attribute) Bond (class in neurosnap.algos.evoef2) bond_type (neurosnap.algos.evoef2.Bond attribute) bonds (neurosnap.algos.evoef2.Residue attribute) (neurosnap.algos.evoef2.ResidueTopology attribute) BondType (class in neurosnap.structure) (class in neurosnap.structure.structure) br (neurosnap.log.c attribute) BRICS (neurosnap.chemistry.FragmentMethod attribute) (neurosnap.chemistry.landscape.FragmentMethod attribute) bridges (neurosnap.chemistry.landscape.IslandResult attribute) bucket_cap (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) build() (neurosnap.chemistry.landscape.GraphBuilder method) build_all() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) build_fragments() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) build_mutant() (in module neurosnap.algos.evoef2) build_mutants() (in module neurosnap.algos.evoef2) build_scaffolds() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) build_similarity_edges() (in module neurosnap.chemistry.landscape) build_similarity_graph() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) by_residue (neurosnap.algos.evoef2.DunbrackBin attribute) C c (class in neurosnap.log) (neurosnap.log.c attribute) ca_distance_matrix() (in module neurosnap.structure) (in module neurosnap.structure.analysis) calc_d0() (in module neurosnap.algos.ipsae) calc_d0_array() (in module neurosnap.algos.ipsae) calc_lddt() (in module neurosnap.algos.lddt) calculate_binding() (in module neurosnap.algos.evoef2) calculate_bsa() (in module neurosnap.structure) (in module neurosnap.structure.interface) calculate_center_of_mass() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) calculate_distance_matrix() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) (in module neurosnap.structure) (in module neurosnap.structure.analysis) calculate_geometric_center() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) calculate_hydrogen_bonds() (in module neurosnap.structure) (in module neurosnap.structure.interactions) calculate_interface_energy() (in module neurosnap.algos.evoef2) calculate_interface_hydrogen_bonding_residues() (in module neurosnap.structure) (in module neurosnap.structure.interactions) calculate_ipSAE() (in module neurosnap.algos.ipsae) calculate_pDockQ() (in module neurosnap.algos.pdockq) calculate_protein_volume() (in module neurosnap.structure) (in module neurosnap.structure.analysis) calculate_rmsd() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) (in module neurosnap.structure) (in module neurosnap.structure.compare) calculate_rog() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) calculate_stability() (in module neurosnap.algos.evoef2) calculate_surface_area() (in module neurosnap.structure) (in module neurosnap.structure.analysis) canonicalize_smiles() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) CCD (class in neurosnap.database) (class in neurosnap.database.ccd) center_at() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) center_id (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) central_nodes (neurosnap.chemistry.landscape.NetworkMetrics attribute) Chain (class in neurosnap.algos.evoef2) (class in neurosnap.structure) (class in neurosnap.structure.structure) chain (neurosnap.algos.evoef2.Atom attribute), [1] (neurosnap.algos.evoef2.Residue attribute) (neurosnap.structure.confidence.PLDDTReport attribute) (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.PLDDTReport attribute) chain1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) chain2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) chain_id (neurosnap.algos.evoef2.Mutation attribute), [1] (neurosnap.structure.Atom attribute) (neurosnap.structure.AtomReference attribute) (neurosnap.structure.Chain attribute), [1] (neurosnap.structure.interaction_report.AtomReference attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Chain attribute), [1] (neurosnap.structure.structure.Residue attribute), [1] chain_ids() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) chains (neurosnap.algos.evoef2.Structure attribute) chains() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) CharacterizationReport (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) characterize() (in module neurosnap.chemistry.landscape) (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) charge (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] CharmmIC (class in neurosnap.algos.evoef2) check_alignment_tool() (in module neurosnap.algos.kluster) chemical_coverage (neurosnap.chemistry.landscape.DiversityMetrics attribute) ChemicalGraph (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) ChemicalLandscape (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) chunk_size (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) cluster_projection() (in module neurosnap.algos.kluster) ClusterProt() (in module neurosnap.algos.clusterprot) code (neurosnap.constants.AARecord attribute) (neurosnap.constants.sequence.AARecord attribute) (neurosnap.database.CCD attribute), [1] (neurosnap.database.ccd.CCD attribute), [1] common_cores() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) component_size_distribution (neurosnap.chemistry.landscape.NetworkMetrics attribute) COMPOUND (neurosnap.chemistry.landscape.NodeType attribute) (neurosnap.chemistry.NodeType attribute) COMPOUND_FRAGMENT (neurosnap.chemistry.EdgeType attribute) (neurosnap.chemistry.landscape.EdgeType attribute) compound_ids (neurosnap.chemistry.ChemicalLandscape property) (neurosnap.chemistry.landscape.ChemicalLandscape property) compound_nodes (neurosnap.chemistry.landscape.IslandResult attribute) COMPOUND_SCAFFOLD (neurosnap.chemistry.EdgeType attribute) (neurosnap.chemistry.landscape.EdgeType attribute) COMPOUND_SIMILARITY (neurosnap.chemistry.EdgeType attribute) (neurosnap.chemistry.landscape.EdgeType attribute) compounds_per_scaffold (neurosnap.chemistry.landscape.DiversityMetrics attribute) compute_distance_matrix() (in module neurosnap.algos.kluster) compute_ec() (in module neurosnap.algos.ec_interface) compute_features() (in module neurosnap.algos.wolfpsort) (in module neurosnap.algos.wolfpsort.wolfpsort) (neurosnap.algos.wolfpsort.wolfpsort.WoLFPSortPredictor method) (neurosnap.algos.wolfpsort.WoLFPSortPredictor method) compute_features_dataframe() (in module neurosnap.algos.wolfpsort) (in module neurosnap.algos.wolfpsort.wolfpsort) (neurosnap.algos.wolfpsort.wolfpsort.WoLFPSortPredictor method) (neurosnap.algos.wolfpsort.WoLFPSortPredictor method) connected_components() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) consensus_sequence() (in module neurosnap.sequence.align) contiguous_ranges() (in module neurosnap.algos.ipsae) coord (neurosnap.structure.Atom property) (neurosnap.structure.structure.Atom property) coordination_centers_dataframe() (neurosnap.structure.interaction_report.InteractionReport method) (neurosnap.structure.InteractionReport method) coordination_number (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) CoordinationCenterRecord (class in neurosnap.structure) (class in neurosnap.structure.interaction_report) core_smiles (neurosnap.chemistry.landscape.RGroupDecompositionResult attribute) (neurosnap.chemistry.RGroupDecompositionResult attribute) count_edges() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) count_nodes() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) counts (neurosnap.chemistry.CharacterizationReport attribute) (neurosnap.chemistry.landscape.CharacterizationReport attribute) COVALENT (neurosnap.structure.BondType attribute) (neurosnap.structure.structure.BondType attribute) create_figure_plotly() (in module neurosnap.algos.clusterprot) CustomLogger (class in neurosnap.log) D decompose() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) decompose_molecules() (in module neurosnap.chemistry) (in module neurosnap.chemistry.landscape) degree_histogram (neurosnap.chemistry.landscape.NetworkMetrics attribute) degrees() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) delete_job_share() (neurosnap.api.NeurosnapAPI method) deletes (neurosnap.algos.evoef2.ResidueTopology attribute) delimiter (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) dense() (neurosnap.chemistry.landscape.FingerprintBlock method) density (neurosnap.chemistry.landscape.NetworkMetrics attribute) details (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) detect_coordination_centers() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) detect_interactions() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) detect_islands() (in module neurosnap.chemistry.landscape) deviations (neurosnap.algos.evoef2.DunbrackRotamer attribute) distance_a (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) distances_from() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) distribution (neurosnap.structure.confidence.PLDDTReport attribute) (neurosnap.structure.PLDDTReport attribute) DISULFIDE (neurosnap.structure.BondType attribute) (neurosnap.structure.structure.BondType attribute) diversity (neurosnap.chemistry.CharacterizationReport attribute) (neurosnap.chemistry.landscape.CharacterizationReport attribute) diversity_metrics() (in module neurosnap.chemistry.landscape) DiversityMetrics (class in neurosnap.chemistry.landscape) donor_atom_indices (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) donor_elements (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) DunbrackBin (class in neurosnap.algos.evoef2) DunbrackLibrary (class in neurosnap.algos.evoef2) DunbrackRotamer (class in neurosnap.algos.evoef2) E edge_type_counts (neurosnap.chemistry.landscape.NetworkMetrics attribute) edges_of_type() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) EdgeType (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) eef1_free_dg (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] eef1_lambda (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] eef1_volume (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] element (neurosnap.algos.evoef2.AtomParam attribute) (neurosnap.algos.evoef2.AtomParam property) (neurosnap.structure.Atom attribute) (neurosnap.structure.AtomReference attribute) (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.AtomReference attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.structure.Atom attribute) element1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) element2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) empty_like() (neurosnap.structure.Structure class method) (neurosnap.structure.structure.Structure class method) entities (neurosnap.structure.Structure property) (neurosnap.structure.structure.Structure property) entity (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) entity1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) entity2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) enumerate() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) enumerate_core() (in module neurosnap.chemistry) (in module neurosnap.chemistry.landscape) epsilon (neurosnap.algos.evoef2.AtomParam attribute), [1] evidence (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) exact_below (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) export_graphml() (in module neurosnap.chemistry.landscape) (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) export_json() (in module neurosnap.chemistry.landscape) (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) extract_interchain_metrics() (in module neurosnap.algos.ipsae) extract_minimum_interchain_metrics() (in module neurosnap.algos.ipsae) extract_non_biopolymers() (in module neurosnap.structure) (in module neurosnap.structure.analysis) F failures (neurosnap.chemistry.ChemicalLandscape property) (neurosnap.chemistry.landscape.ChemicalLandscape property) fetch_accessions() (in module neurosnap.database) (in module neurosnap.database.uniprot) fetch_uniprot() (in module neurosnap.database) (in module neurosnap.database.uniprot) filter() (neurosnap.structure.interaction_report.InteractionReport method) (neurosnap.structure.InteractionReport method) find_contacts() (in module neurosnap.structure) (in module neurosnap.structure.interface) find_disulfide_bonds() (in module neurosnap.structure) (in module neurosnap.structure.interactions) find_hydrophobic_residues() (in module neurosnap.structure) (in module neurosnap.structure.interactions) find_interface_contacts() (in module neurosnap.structure) (in module neurosnap.structure.interface) find_interface_residues() (in module neurosnap.structure) (in module neurosnap.structure.interface) find_LCS() (in module neurosnap.chemistry) (in module neurosnap.chemistry.conformers) find_non_interface_hydrophobic_patches() (in module neurosnap.structure) (in module neurosnap.structure.interface) find_salt_bridges() (in module neurosnap.structure) (in module neurosnap.structure.interactions) FingerprintBlock (class in neurosnap.chemistry.landscape) FingerprintConfig (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) fingerprints (neurosnap.chemistry.ChemicalLandscape property) (neurosnap.chemistry.landscape.ChemicalLandscape property) (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) first() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) fix_nucleic_termini() (in module neurosnap.structure) (in module neurosnap.structure.filters) flatten_chirality (neurosnap.chemistry.landscape.ScaffoldConfig attribute) (neurosnap.chemistry.ScaffoldConfig attribute) foldseek_search() (in module neurosnap.database) (in module neurosnap.database.foldseek) format() (neurosnap.log.CustomLogger method) FRAGMENT (neurosnap.chemistry.landscape.NodeType attribute) (neurosnap.chemistry.NodeType attribute) fragment_coverage (neurosnap.chemistry.landscape.DiversityMetrics attribute) fragment_cut_bonds() (in module neurosnap.chemistry.landscape) fragment_entropy (neurosnap.chemistry.landscape.DiversityMetrics attribute) fragment_entropy_normalized (neurosnap.chemistry.landscape.DiversityMetrics attribute) fragment_library() (in module neurosnap.chemistry.landscape) fragment_molecule() (in module neurosnap.chemistry.landscape) FRAGMENT_SHARED (neurosnap.chemistry.EdgeType attribute) (neurosnap.chemistry.landscape.EdgeType attribute) FragmentConfig (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) FragmentMethod (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) FragmentResult (class in neurosnap.chemistry.landscape) fragments (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) from_dict() (neurosnap.chemistry.ChemicalGraph class method) (neurosnap.chemistry.landscape.ChemicalGraph class method) (neurosnap.chemistry.landscape.LandscapeConfig class method) (neurosnap.chemistry.landscape.ReverseFragmentRecord class method) (neurosnap.chemistry.LandscapeConfig class method) (neurosnap.chemistry.ReverseFragmentRecord class method) from_ensemble() (neurosnap.structure.structure.StructureStack class method) (neurosnap.structure.StructureStack class method) from_store() (neurosnap.chemistry.ChemicalLandscape class method) (neurosnap.chemistry.landscape.ChemicalLandscape class method) frontier (neurosnap.chemistry.CharacterizationReport attribute) (neurosnap.chemistry.landscape.CharacterizationReport attribute) frontier_scaffolds() (in module neurosnap.chemistry.landscape) G g (neurosnap.log.c attribute) generate() (in module neurosnap.chemistry) (in module neurosnap.chemistry.conformers) geometry (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) geometry_deviation_deg (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) get_atom() (neurosnap.algos.evoef2.Residue method) get_backbone() (in module neurosnap.structure) (in module neurosnap.structure.analysis) get_by_abr() (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) get_by_code() (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) get_by_name() (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) get_canonical_record() (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) get_ccd() (in module neurosnap.database) (in module neurosnap.database.ccd) get_ccd_canonical_aa() (in module neurosnap.database) (in module neurosnap.database.ccd) get_ccd_entries() (in module neurosnap.database) (in module neurosnap.database.ccd) get_job_data() (neurosnap.api.NeurosnapAPI method) get_job_file() (neurosnap.api.NeurosnapAPI method) get_job_status() (neurosnap.api.NeurosnapAPI method) get_jobs() (neurosnap.api.NeurosnapAPI method) get_mol_center() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) get_pipeline() (neurosnap.api.NeurosnapAPI method) get_raw_contacts() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) get_reverse_complement() (in module neurosnap.sequence.nucleotide) get_services() (neurosnap.api.NeurosnapAPI method) get_standard_record() (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) get_team_info() (neurosnap.api.NeurosnapAPI method) get_team_jobs() (neurosnap.api.NeurosnapAPI method) get_weights() (in module neurosnap.algos.evoef2_lib.weights) graph (neurosnap.chemistry.ChemicalLandscape property) (neurosnap.chemistry.landscape.ChemicalLandscape property) GraphBuilder (class in neurosnap.chemistry.landscape) grey (neurosnap.log.c attribute) H has_hydrogens() (in module neurosnap.structure) (in module neurosnap.structure.prepare) hb_b2 (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] hb_d_or_b (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] hb_h_or_a (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] hetero (neurosnap.structure.Atom attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Residue attribute), [1] hybrid (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] HYDROGEN_BOND (neurosnap.structure.InteractionType attribute) (neurosnap.structure.structure.InteractionType attribute) I ic_param (neurosnap.algos.evoef2.CharmmIC attribute) ics (neurosnap.algos.evoef2.ResidueTopology attribute) id_column (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) include_generic (neurosnap.chemistry.landscape.ScaffoldConfig attribute) (neurosnap.chemistry.ScaffoldConfig attribute) init_pairdict_array() (in module neurosnap.algos.ipsae) init_pairdict_scalar() (in module neurosnap.algos.ipsae) init_pairdict_set() (in module neurosnap.algos.ipsae) input_scale (neurosnap.structure.confidence.PLDDTReport attribute) (neurosnap.structure.PLDDTReport attribute) ins_code (neurosnap.structure.Atom attribute) (neurosnap.structure.AtomReference attribute) (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.AtomReference attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Residue attribute), [1] ins_code1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) ins_code2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) interaction_id (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) interaction_type (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) InteractionEntity (class in neurosnap.structure) (class in neurosnap.structure.interaction_report) InteractionRecord (class in neurosnap.structure) (class in neurosnap.structure.interaction_report) InteractionReport (class in neurosnap.structure) (class in neurosnap.structure.interaction_report) InteractionType (class in neurosnap.structure) (class in neurosnap.structure.structure) IONIC (neurosnap.structure.InteractionType attribute) (neurosnap.structure.structure.InteractionType attribute) is_bb (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] is_h (neurosnap.algos.evoef2.Atom attribute) is_hbond_a (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam property) is_hbond_h (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam property) is_in_hbond (neurosnap.algos.evoef2.Atom attribute), [1] is_nucleic (neurosnap.algos.evoef2.Residue attribute) is_protein (neurosnap.algos.evoef2.Chain attribute) (neurosnap.algos.evoef2.Residue attribute) is_xyz_valid (neurosnap.algos.evoef2.Atom attribute), [1] island_of() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) IslandResult (class in neurosnap.chemistry.landscape) islands (neurosnap.chemistry.CharacterizationReport attribute) (neurosnap.chemistry.landscape.CharacterizationReport attribute) (neurosnap.chemistry.landscape.IslandResult attribute) isoelectric_point() (in module neurosnap.sequence.protein) items() (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) K k (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) keep_only_first_fragment (neurosnap.chemistry.landscape.ScaffoldConfig attribute) (neurosnap.chemistry.ScaffoldConfig attribute) key() (neurosnap.structure.Residue method) (neurosnap.structure.structure.Residue method) L label() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) labels (neurosnap.chemistry.landscape.IslandResult attribute) LandscapeConfig (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) largest_component_fraction (neurosnap.chemistry.landscape.NetworkMetrics attribute) largest_component_size (neurosnap.chemistry.landscape.NetworkMetrics attribute) largest_fragment() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) limit (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) LINKER (neurosnap.chemistry.FragmentMethod attribute) (neurosnap.chemistry.landscape.FragmentMethod attribute) load() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) load_aapropensity() (in module neurosnap.algos.evoef2) load_atom_params() (in module neurosnap.algos.evoef2) load_dunbrack() (in module neurosnap.algos.evoef2) load_landscape() (in module neurosnap.chemistry.landscape) load_ramachandran() (in module neurosnap.algos.evoef2) load_topology() (in module neurosnap.algos.evoef2) log_format_basic (neurosnap.log.CustomLogger attribute) log_format_detailed (neurosnap.log.CustomLogger attribute) louvain_local_moving() (in module neurosnap.chemistry.landscape) M max_candidate_pairs (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) max_degree (neurosnap.chemistry.landscape.NetworkMetrics attribute) max_fragments_per_molecule (neurosnap.chemistry.FragmentConfig attribute) (neurosnap.chemistry.landscape.FragmentConfig attribute) max_level (neurosnap.chemistry.landscape.ScaffoldConfig attribute) (neurosnap.chemistry.ScaffoldConfig attribute) max_nodes_per_molecule (neurosnap.chemistry.landscape.ScaffoldConfig attribute) (neurosnap.chemistry.ScaffoldConfig attribute) max_rotatable_cuts (neurosnap.chemistry.FragmentConfig attribute) (neurosnap.chemistry.landscape.FragmentConfig attribute) mean_degree (neurosnap.chemistry.landscape.NetworkMetrics attribute) median_degree (neurosnap.chemistry.landscape.NetworkMetrics attribute) merge() (neurosnap.chemistry.landscape.FragmentResult class method) (neurosnap.chemistry.landscape.ScaffoldNetworkResult class method) metadata (neurosnap.chemistry.CharacterizationReport attribute) (neurosnap.chemistry.landscape.CharacterizationReport attribute) (neurosnap.structure.confidence.PLDDTReport attribute) (neurosnap.structure.PLDDTReport attribute) metal_atom_index (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) METAL_COORDINATION (neurosnap.structure.BondType attribute) (neurosnap.structure.structure.BondType attribute) METAL_DONOR_ELEMENTS (in module neurosnap.structure.interaction_rules) method (neurosnap.chemistry.landscape.IslandResult attribute) metric (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) min_fragment_atoms (neurosnap.chemistry.FragmentConfig attribute) (neurosnap.chemistry.landscape.FragmentConfig attribute) minhash_signatures() (in module neurosnap.chemistry.landscape) minimize() (in module neurosnap.algos.amber_relax) (in module neurosnap.chemistry) (in module neurosnap.chemistry.conformers) missing_residue_ids() (neurosnap.structure.Chain method) (neurosnap.structure.structure.Chain method) model_id (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) models() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) modularity (neurosnap.chemistry.landscape.IslandResult attribute) module neurosnap neurosnap.algos neurosnap.algos.alphafold neurosnap.algos.amber_relax neurosnap.algos.clusterprot neurosnap.algos.ec_interface neurosnap.algos.evoef2 neurosnap.algos.evoef2_lib neurosnap.algos.evoef2_lib.constants neurosnap.algos.evoef2_lib.weights neurosnap.algos.ipsae neurosnap.algos.kluster neurosnap.algos.lddt neurosnap.algos.pdb2pqr neurosnap.algos.pdockq neurosnap.algos.wolfpsort neurosnap.algos.wolfpsort.wolfpsort neurosnap.api neurosnap.chemistry neurosnap.chemistry.conformers neurosnap.chemistry.geometry neurosnap.chemistry.landscape neurosnap.chemistry.smiles neurosnap.constants neurosnap.constants.api neurosnap.constants.chemistry neurosnap.constants.sequence neurosnap.constants.structure neurosnap.database neurosnap.database.blast neurosnap.database.ccd neurosnap.database.foldseek neurosnap.database.uniprot neurosnap.io neurosnap.io.mmcif neurosnap.io.pdb neurosnap.io.pqr neurosnap.io.sdf neurosnap.log neurosnap.sequence neurosnap.sequence.align neurosnap.sequence.nucleotide neurosnap.sequence.protein neurosnap.structure neurosnap.structure.analysis neurosnap.structure.compare neurosnap.structure.confidence neurosnap.structure.filters neurosnap.structure.interaction_report neurosnap.structure.interaction_rules neurosnap.structure.interactions neurosnap.structure.interface neurosnap.structure.prepare neurosnap.structure.rendering neurosnap.structure.selectors neurosnap.structure.structure molecular_weight() (in module neurosnap.sequence.protein) morgan_packed() (in module neurosnap.chemistry.landscape) move_ligand_to_center() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) murcko_smiles() (in module neurosnap.chemistry.landscape) Mutation (class in neurosnap.algos.evoef2) mutual_only (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) N n_bands (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) n_bits (neurosnap.chemistry.FingerprintConfig attribute) (neurosnap.chemistry.landscape.FingerprintConfig attribute) n_bridges (neurosnap.chemistry.landscape.IslandResult property) n_cb_in_8a (neurosnap.algos.evoef2.Residue attribute) n_components (neurosnap.chemistry.landscape.NetworkMetrics attribute) n_compounds (neurosnap.chemistry.landscape.DiversityMetrics attribute) n_cuts (neurosnap.chemistry.landscape.ReverseFragmentRecord property) (neurosnap.chemistry.ReverseFragmentRecord property) n_edges (neurosnap.chemistry.ChemicalGraph property) (neurosnap.chemistry.landscape.ChemicalGraph property) (neurosnap.chemistry.landscape.NetworkMetrics attribute) n_failed (neurosnap.chemistry.landscape.RGroupDecompositionResult attribute) (neurosnap.chemistry.RGroupDecompositionResult attribute) n_fragments (neurosnap.chemistry.landscape.DiversityMetrics attribute) (neurosnap.chemistry.landscape.FragmentResult property) n_hierarchy_edges (neurosnap.chemistry.landscape.ScaffoldNetworkResult property) n_islands (neurosnap.chemistry.landscape.IslandResult property) n_mols (neurosnap.chemistry.landscape.FingerprintBlock property) n_murcko_scaffolds (neurosnap.chemistry.landscape.DiversityMetrics attribute) n_nodes (neurosnap.chemistry.ChemicalGraph property) (neurosnap.chemistry.landscape.ChemicalGraph property) (neurosnap.chemistry.landscape.NetworkMetrics attribute) n_permutations (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) n_populated_scaffolds (neurosnap.chemistry.landscape.DiversityMetrics attribute) n_scaffold_nodes (neurosnap.chemistry.landscape.DiversityMetrics attribute) n_scaffolds (neurosnap.chemistry.landscape.ScaffoldNetworkResult property) n_singletons (neurosnap.chemistry.landscape.NetworkMetrics attribute) n_words (neurosnap.chemistry.FingerprintConfig property) (neurosnap.chemistry.landscape.FingerprintBlock property) (neurosnap.chemistry.landscape.FingerprintConfig property) na_torsions (neurosnap.algos.evoef2.Residue attribute) name (neurosnap.algos.evoef2.Atom attribute), [1] (neurosnap.algos.evoef2.AtomParam attribute), [1] (neurosnap.algos.evoef2.Chain attribute) (neurosnap.algos.evoef2.Residue attribute) (neurosnap.algos.evoef2.ResidueTopology attribute) (neurosnap.constants.AARecord attribute) (neurosnap.constants.sequence.AARecord attribute) (neurosnap.database.CCD attribute), [1] (neurosnap.database.ccd.CCD attribute), [1] neighborhood() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) neighbors() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalLandscape method) net_charge() (in module neurosnap.sequence.protein) network (neurosnap.chemistry.CharacterizationReport attribute) (neurosnap.chemistry.landscape.CharacterizationReport attribute) network_metrics() (in module neurosnap.chemistry.landscape) NetworkMetrics (class in neurosnap.chemistry.landscape) neurosnap module neurosnap.algos module neurosnap.algos.alphafold module neurosnap.algos.amber_relax module neurosnap.algos.clusterprot module neurosnap.algos.ec_interface module neurosnap.algos.evoef2 module neurosnap.algos.evoef2_lib module neurosnap.algos.evoef2_lib.constants module neurosnap.algos.evoef2_lib.weights module neurosnap.algos.ipsae module neurosnap.algos.kluster module neurosnap.algos.lddt module neurosnap.algos.pdb2pqr module neurosnap.algos.pdockq module neurosnap.algos.wolfpsort module neurosnap.algos.wolfpsort.wolfpsort module neurosnap.api module neurosnap.chemistry module neurosnap.chemistry.conformers module neurosnap.chemistry.geometry module neurosnap.chemistry.landscape module neurosnap.chemistry.smiles module neurosnap.constants module neurosnap.constants.api module neurosnap.constants.chemistry module neurosnap.constants.sequence module neurosnap.constants.structure module neurosnap.database module neurosnap.database.blast module neurosnap.database.ccd module neurosnap.database.foldseek module neurosnap.database.uniprot module neurosnap.io module neurosnap.io.mmcif module neurosnap.io.pdb module neurosnap.io.pqr module neurosnap.io.sdf module neurosnap.log module neurosnap.sequence module neurosnap.sequence.align module neurosnap.sequence.nucleotide module neurosnap.sequence.protein module neurosnap.structure module neurosnap.structure.analysis module neurosnap.structure.compare module neurosnap.structure.confidence module neurosnap.structure.filters module neurosnap.structure.interaction_report module neurosnap.structure.interaction_rules module neurosnap.structure.interactions module neurosnap.structure.interface module neurosnap.structure.prepare module neurosnap.structure.rendering module neurosnap.structure.selectors module neurosnap.structure.structure module NeurosnapAPI (class in neurosnap.api) neutralize_molecule() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) node_id_of_compound() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) node_id_of_smiles() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) node_of() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) node_type_counts (neurosnap.chemistry.landscape.NetworkMetrics attribute) nodes_of_type() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) NodeType (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) num_atoms (neurosnap.structure.Structure property) (neurosnap.structure.structure.Structure property) O o (neurosnap.log.c attribute) onbits_csr() (neurosnap.chemistry.landscape.FingerprintBlock method) optimize_hydrogens_with_pdb2pqr() (in module neurosnap.structure) (in module neurosnap.structure.prepare) OTHER (neurosnap.structure.BondType attribute) (neurosnap.structure.structure.BondType attribute) OTHER_NONCOVALENT (neurosnap.structure.InteractionType attribute) (neurosnap.structure.structure.InteractionType attribute) P p (neurosnap.log.c attribute) pad_seqs() (in module neurosnap.sequence.align) pagerank() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) param (neurosnap.algos.evoef2.Atom attribute), [1] parse_chain_pairs() (in module neurosnap.algos.ec_interface) parse_mmcif() (in module neurosnap.io.mmcif) parse_pdb() (in module neurosnap.io.pdb) parse_sdf() (in module neurosnap.io.sdf) patches (neurosnap.algos.evoef2.Residue attribute) path_between() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) path_length_exact (neurosnap.chemistry.landscape.NetworkMetrics attribute) path_sample_pairs (neurosnap.chemistry.landscape.NetworkMetrics attribute) phipsi (neurosnap.algos.evoef2.Residue attribute) PLDDTReport (class in neurosnap.structure) (class in neurosnap.structure.confidence) plot() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) polarity (neurosnap.algos.evoef2.Atom attribute) (neurosnap.algos.evoef2.AtomParam attribute), [1] popcount_rows() (in module neurosnap.chemistry.landscape) popcount_words() (in module neurosnap.chemistry.landscape) pos (neurosnap.algos.evoef2.Atom attribute), [1] (neurosnap.algos.evoef2.Residue attribute) position (neurosnap.algos.evoef2.Mutation attribute), [1] positions (neurosnap.chemistry.landscape.RGroupDecompositionResult property) (neurosnap.chemistry.RGroupDecompositionResult property) predict() (neurosnap.algos.wolfpsort.wolfpsort.WoLFPSortPredictor method) (neurosnap.algos.wolfpsort.WoLFPSortPredictor method) predict_dataframe() (neurosnap.algos.wolfpsort.wolfpsort.WoLFPSortPredictor method) (neurosnap.algos.wolfpsort.WoLFPSortPredictor method) predict_localization() (in module neurosnap.algos.wolfpsort) (in module neurosnap.algos.wolfpsort.wolfpsort) probability (neurosnap.algos.evoef2.DunbrackRotamer attribute) ptm_func() (in module neurosnap.algos.ipsae) R r (neurosnap.log.c attribute) radii (neurosnap.chemistry.FingerprintConfig attribute) (neurosnap.chemistry.landscape.FingerprintConfig attribute) radius (neurosnap.algos.evoef2.AtomParam attribute), [1] rama (neurosnap.algos.evoef2.RamaTable attribute) RamaTable (class in neurosnap.algos.evoef2) read_msa() (in module neurosnap.sequence.align) reassemble() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) reassemble_fragments() (in module neurosnap.chemistry) (in module neurosnap.chemistry.landscape) rebuild_missing_atoms() (in module neurosnap.algos.evoef2) reduce_dimensions() (in module neurosnap.algos.kluster) remove_altlocs_and_duplicate_atoms() (in module neurosnap.structure) (in module neurosnap.structure.prepare) remove_annotation() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) remove_atoms() (in module neurosnap.structure) (in module neurosnap.structure.filters) remove_chains() (in module neurosnap.structure) (in module neurosnap.structure.filters) remove_model() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) remove_non_biopolymers() (in module neurosnap.structure) (in module neurosnap.structure.filters) remove_nucleotides() (in module neurosnap.structure) (in module neurosnap.structure.filters) remove_residues() (in module neurosnap.structure.filters) remove_salts() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) remove_waters() (in module neurosnap.structure) (in module neurosnap.structure.filters) render_pseudo3D() (in module neurosnap.structure) (in module neurosnap.structure.rendering) render_structure_pseudo3D() (in module neurosnap.structure) (in module neurosnap.structure.rendering) renumber() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) report (neurosnap.chemistry.ChemicalLandscape property) (neurosnap.chemistry.landscape.ChemicalLandscape property) res (neurosnap.algos.evoef2.Atom attribute), [1] res_id (neurosnap.structure.Atom attribute) (neurosnap.structure.AtomReference attribute) (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.AtomReference attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Residue attribute), [1] res_id1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) res_id2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) res_name (neurosnap.structure.Atom attribute) (neurosnap.structure.AtomReference attribute) (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.AtomReference attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.Residue attribute), [1] (neurosnap.structure.structure.Atom attribute) (neurosnap.structure.structure.Residue attribute), [1] res_name1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) res_name2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) Residue (class in neurosnap.algos.evoef2) (class in neurosnap.structure) (class in neurosnap.structure.structure) residue (neurosnap.structure.confidence.PLDDTReport attribute) (neurosnap.structure.PLDDTReport attribute) residues (neurosnap.algos.evoef2.Chain attribute) residues() (neurosnap.structure.Chain method) (neurosnap.structure.structure.Chain method) ResidueTopology (class in neurosnap.algos.evoef2) resolution (neurosnap.chemistry.landscape.IslandResult attribute) ReverseFragmentRecord (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) reversible (neurosnap.chemistry.FragmentConfig attribute) (neurosnap.chemistry.landscape.FragmentConfig attribute) reversible_fragment_record() (in module neurosnap.chemistry) (in module neurosnap.chemistry.landscape) RGroupDecompositionResult (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) rgroups_at() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) role1 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) role2 (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) ROTATABLE_BOND (neurosnap.chemistry.FragmentMethod attribute) (neurosnap.chemistry.landscape.FragmentMethod attribute) rows (neurosnap.chemistry.landscape.RGroupDecompositionResult attribute) (neurosnap.chemistry.RGroupDecompositionResult attribute) rule_set (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) rule_version (neurosnap.structure.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.CoordinationCenterRecord attribute) (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) run_alignment() (in module neurosnap.algos.kluster) run_blast() (in module neurosnap.database) (in module neurosnap.database.blast) run_mmseqs2() (in module neurosnap.sequence.align) run_mmseqs2_modes() (in module neurosnap.sequence.align) run_phmmer() (in module neurosnap.sequence.align) run_phmmer_mafft() (in module neurosnap.sequence.align) S SALT_BRIDGE (neurosnap.structure.InteractionType attribute) (neurosnap.structure.structure.InteractionType attribute) sanitize_aa_seq() (in module neurosnap.sequence.protein) save() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) save_cif() (in module neurosnap.io.mmcif) (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) save_landscape() (in module neurosnap.chemistry.landscape) save_pdb() (in module neurosnap.io.pdb) (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) save_pqr() (in module neurosnap.io.pqr) save_sdf() (in module neurosnap.io.sdf) SCAFFOLD (neurosnap.chemistry.landscape.NodeType attribute) (neurosnap.chemistry.NodeType attribute) scaffold_entropy (neurosnap.chemistry.landscape.DiversityMetrics attribute) scaffold_entropy_normalized (neurosnap.chemistry.landscape.DiversityMetrics attribute) scaffold_gini (neurosnap.chemistry.landscape.DiversityMetrics attribute) SCAFFOLD_HIERARCHY (neurosnap.chemistry.EdgeType attribute) (neurosnap.chemistry.landscape.EdgeType attribute) scaffold_levels (neurosnap.chemistry.landscape.DiversityMetrics attribute) scaffold_network() (in module neurosnap.chemistry.landscape) scaffold_redundancy (neurosnap.chemistry.landscape.DiversityMetrics attribute) ScaffoldConfig (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) ScaffoldNetworkResult (class in neurosnap.chemistry.landscape) scaffolds (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) score_af2m_binding() (in module neurosnap.algos.alphafold) sdf_to_smiles() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) seed (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) select() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) select_residues() (in module neurosnap.structure) (in module neurosnap.structure.selectors) seqid() (in module neurosnap.sequence.align) sequence() (neurosnap.structure.Chain method) (neurosnap.structure.structure.Chain method) set_frequency() (neurosnap.chemistry.landscape.GraphBuilder method) set_job_note() (neurosnap.api.NeurosnapAPI method) set_job_share() (neurosnap.api.NeurosnapAPI method) shannon_entropy() (in module neurosnap.chemistry.landscape) shared_fragment_edges() (in module neurosnap.chemistry.landscape) shared_links_per_fragment (neurosnap.chemistry.FragmentConfig attribute) (neurosnap.chemistry.landscape.FragmentConfig attribute) shortest_path() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) similarity (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) SimilarityConfig (class in neurosnap.chemistry) (class in neurosnap.chemistry.landscape) singleton_scaffold_fraction (neurosnap.chemistry.landscape.DiversityMetrics attribute) smiles (neurosnap.chemistry.ChemicalLandscape property) (neurosnap.chemistry.landscape.ChemicalLandscape property) (neurosnap.database.CCD attribute), [1] (neurosnap.database.ccd.CCD attribute), [1] smiles_canonical() (neurosnap.database.CCD method) (neurosnap.database.ccd.CCD method) smiles_column (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) smiles_to_sdf() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) source (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) split_interleaved_fastq() (in module neurosnap.sequence.nucleotide) standard_equiv_abr (neurosnap.constants.AARecord attribute) (neurosnap.constants.sequence.AARecord attribute) standardize_molecule() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) stream_chunks() (in module neurosnap.chemistry.landscape) strip_attachments (neurosnap.chemistry.landscape.ScaffoldConfig attribute) (neurosnap.chemistry.ScaffoldConfig attribute) strip_hydrogens() (in module neurosnap.structure) (in module neurosnap.structure.prepare) Structure (class in neurosnap.algos.evoef2) (class in neurosnap.structure) (class in neurosnap.structure.structure) StructureEnsemble (class in neurosnap.structure) (class in neurosnap.structure.structure) StructureStack (class in neurosnap.structure) (class in neurosnap.structure.structure) submit_job() (neurosnap.api.NeurosnapAPI method) summarize_plddt() (in module neurosnap.structure) (in module neurosnap.structure.confidence) summary() (neurosnap.chemistry.CharacterizationReport method) (neurosnap.chemistry.landscape.CharacterizationReport method) swap_rgroup() (neurosnap.chemistry.ChemicalLandscape method) (neurosnap.chemistry.landscape.ChemicalLandscape method) T target_residue (neurosnap.algos.evoef2.Mutation attribute), [1] threshold (neurosnap.chemistry.landscape.SimilarityConfig attribute) (neurosnap.chemistry.SimilarityConfig attribute) to_csv() (neurosnap.structure.interaction_report.InteractionReport method) (neurosnap.structure.InteractionReport method) to_dataframe() (neurosnap.structure.interaction_report.InteractionReport method) (neurosnap.structure.InteractionReport method) (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureEnsemble method) (neurosnap.structure.StructureStack method) to_dict() (neurosnap.chemistry.CharacterizationReport method) (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.CharacterizationReport method) (neurosnap.chemistry.landscape.ChemicalGraph method) (neurosnap.chemistry.landscape.DiversityMetrics method) (neurosnap.chemistry.landscape.IslandResult method) (neurosnap.chemistry.landscape.LandscapeConfig method) (neurosnap.chemistry.landscape.NetworkMetrics method) (neurosnap.chemistry.landscape.ReverseFragmentRecord method) (neurosnap.chemistry.landscape.RGroupDecompositionResult method) (neurosnap.chemistry.LandscapeConfig method) (neurosnap.chemistry.ReverseFragmentRecord method) (neurosnap.chemistry.RGroupDecompositionResult method) to_ensemble() (neurosnap.structure.structure.StructureStack method) (neurosnap.structure.StructureStack method) to_json() (neurosnap.structure.interaction_report.InteractionReport method) (neurosnap.structure.InteractionReport method) to_mol() (neurosnap.database.CCD method) (neurosnap.database.ccd.CCD method) to_stack() (neurosnap.structure.structure.StructureEnsemble method) (neurosnap.structure.StructureEnsemble method) top_fragments (neurosnap.chemistry.landscape.DiversityMetrics attribute) top_scaffolds (neurosnap.chemistry.landscape.DiversityMetrics attribute) torsion_proper (neurosnap.algos.evoef2.CharmmIC attribute) torsions (neurosnap.algos.evoef2.DunbrackRotamer attribute) translate() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) translate_molecule() (in module neurosnap.chemistry) (in module neurosnap.chemistry.geometry) type (neurosnap.algos.evoef2.AtomParam attribute), [1] (neurosnap.database.CCD attribute), [1] (neurosnap.database.ccd.CCD attribute), [1] U UNKNOWN (neurosnap.chemistry.FragmentMethod attribute) (neurosnap.chemistry.landscape.FragmentMethod attribute) use_brics (neurosnap.chemistry.FragmentConfig attribute) (neurosnap.chemistry.landscape.FragmentConfig attribute) use_chirality (neurosnap.chemistry.FingerprintConfig attribute) (neurosnap.chemistry.landscape.FingerprintConfig attribute) use_features (neurosnap.chemistry.FingerprintConfig attribute) (neurosnap.chemistry.landscape.FingerprintConfig attribute) use_linkers (neurosnap.chemistry.FragmentConfig attribute) (neurosnap.chemistry.landscape.FragmentConfig attribute) use_rotatable_bonds (neurosnap.chemistry.FragmentConfig attribute) (neurosnap.chemistry.landscape.FragmentConfig attribute) V VALID_ORGANISMS (neurosnap.algos.wolfpsort.wolfpsort.WoLFPSortPredictor attribute) (neurosnap.algos.wolfpsort.WoLFPSortPredictor attribute) validate_entities() (neurosnap.structure.Structure method) (neurosnap.structure.structure.Structure method) validate_smiles() (in module neurosnap.chemistry) (in module neurosnap.chemistry.smiles) values() (neurosnap.constants.AARecordTable method) (neurosnap.constants.sequence.AARecordTable method) vdw_epsilon (neurosnap.algos.evoef2.Atom attribute) vdw_gap_a (neurosnap.structure.interaction_report.InteractionRecord attribute) (neurosnap.structure.InteractionRecord attribute) vdw_radius (neurosnap.algos.evoef2.Atom attribute) visualize_projection() (in module neurosnap.algos.kluster) visualize_projection_interactive() (in module neurosnap.algos.kluster) W wait_job_status() (neurosnap.api.NeurosnapAPI method) weighted_adjacency() (neurosnap.chemistry.ChemicalGraph method) (neurosnap.chemistry.landscape.ChemicalGraph method) WoLFPSortPredictor (class in neurosnap.algos.wolfpsort) (class in neurosnap.algos.wolfpsort.wolfpsort) workers (neurosnap.chemistry.landscape.LandscapeConfig attribute) (neurosnap.chemistry.LandscapeConfig attribute) write_msa() (in module neurosnap.sequence.align) write_single_chain_pdb() (in module neurosnap.algos.ec_interface) X x (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute) xtorsions (neurosnap.algos.evoef2.Residue attribute) xyz (neurosnap.algos.evoef2.Atom attribute), [1] Y y (neurosnap.log.c attribute) (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute) Z z (neurosnap.structure.Atom attribute) (neurosnap.structure.structure.Atom attribute)