Index

A

a (graph_tool.PropertyMap attribute) add_edge() (graph_tool.Graph method) add_edge_list() (graph_tool.Graph method) add_vertex() (graph_tool.Graph method) (graph_tool.inference.BlockState method) (graph_tool.inference.NestedBlockState method) adjacency() (in module graph_tool.spectral) all_circuits() (in module graph_tool.topology) all_edges() (graph_tool.Vertex method) all_neighbors() (graph_tool.Vertex method) all_paths() (in module graph_tool.topology) all_predecessors() (in module graph_tool.topology)

all_shortest_paths() (in module graph_tool.topology) angle_changed() (graph_tool.draw.GraphWidget method) apply_transform() (graph_tool.draw.GraphWidget method) arf_layout() (in module graph_tool.draw) asdict() (graph_tool.inference.BlockPairHist method) (graph_tool.inference.PartitionHist method) assortativity() (in module graph_tool.correlations) astar_iterator() (in module graph_tool.search) astar_search() (in module graph_tool.search) AStarVisitor (class in graph_tool.search) avg_combined_corr() (in module graph_tool.correlations) avg_neighbor_corr() (in module graph_tool.correlations) avg_neighbour_corr() (in module graph_tool.correlations)

B

back_edge() (graph_tool.search.DFSVisitor method) base (graph_tool.GraphView attribute) bellman_ford_search() (in module graph_tool.search) BellmanFordVisitor (class in graph_tool.search) bethe_entropy() (in module graph_tool.inference) betweenness() (in module graph_tool.centrality) bfs_iterator() (in module graph_tool.search) bfs_search() (in module graph_tool.search)

BFSVisitor (class in graph_tool.search) bisection_minimize() (in module graph_tool.inference) black_target() (graph_tool.search.AStarVisitor method) (graph_tool.search.BFSVisitor method) BlockPairHist (class in graph_tool.inference) BlockState (class in graph_tool.inference) boykov_kolmogorov_max_flow() (in module graph_tool.flow) button_press_event() (graph_tool.draw.GraphWidget method) button_release_event() (graph_tool.draw.GraphWidget method)

C

cairo_draw() (in module graph_tool.draw) central_point_dominance() (in module graph_tool.centrality) circular_graph() (in module graph_tool.generation) cleanup() (graph_tool.draw.GraphWidget method) clear() (graph_tool.Graph method) clear_edges() (graph_tool.Graph method) clear_filters() (graph_tool.Graph method) clear_vertex() (graph_tool.Graph method) closeness() (in module graph_tool.centrality) collect_edge_marginals() (graph_tool.inference.BlockState method) collect_partition_histogram() (graph_tool.inference.BlockState method) (graph_tool.inference.NestedBlockState method)

collect_vertex_marginals() (graph_tool.inference.BlockState method) combined_corr_hist() (in module graph_tool.correlations) complete_graph() (in module graph_tool.generation) condensation_graph() (in module graph_tool.generation) copy() (graph_tool.Graph method) (graph_tool.PropertyMap method) (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.NestedBlockState method) (graph_tool.inference.OverlapBlockState method) copy_property() (graph_tool.Graph method) corr_hist() (in module graph_tool.correlations)

D

data (in module graph_tool.collection) data_ptr() (graph_tool.PropertyMap method) degree_property_map() (graph_tool.Graph method) delete_level() (graph_tool.inference.NestedBlockState method) descriptions (in module graph_tool.collection) dfs_iterator() (in module graph_tool.search) dfs_search() (in module graph_tool.search) DFSVisitor (class in graph_tool.search) dijkstra_iterator() (in module graph_tool.search) dijkstra_search() (in module graph_tool.search) DijkstraVisitor (class in graph_tool.search) discover_vertex() (graph_tool.search.AStarVisitor method) (graph_tool.search.BFSVisitor method) (graph_tool.search.DFSVisitor method) (graph_tool.search.DijkstraVisitor method)

distance_histogram() (in module graph_tool.stats) dominator_tree() (in module graph_tool.topology) drag_gesture_begin() (graph_tool.draw.GraphWidget method) drag_gesture_end() (graph_tool.draw.GraphWidget method) drag_gesture_update() (graph_tool.draw.GraphWidget method) draw() (graph_tool.draw.GraphWidget method) (graph_tool.inference.BlockState method) (graph_tool.inference.EMBlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.NestedBlockState method) (graph_tool.inference.OverlapBlockState method) draw_hierarchy() (in module graph_tool.draw) duplicate_level() (graph_tool.inference.NestedBlockState method)

E

e_iter() (graph_tool.inference.EMBlockState method) Edge (class in graph_tool) edge() (graph_tool.Graph method) edge_average() (in module graph_tool.stats) edge_endpoint_property() (in module graph_tool) edge_hist() (in module graph_tool.stats) edge_index (graph_tool.Graph attribute) edge_index_range (graph_tool.Graph attribute) edge_minimized() (graph_tool.search.BellmanFordVisitor method) edge_not_minimized() (graph_tool.search.BellmanFordVisitor method) edge_not_relaxed() (graph_tool.search.AStarVisitor method) (graph_tool.search.BellmanFordVisitor method) (graph_tool.search.DijkstraVisitor method) edge_percolation() (in module graph_tool.topology) edge_properties (graph_tool.Graph attribute) edge_reciprocity() (in module graph_tool.topology) edge_relaxed() (graph_tool.search.AStarVisitor method) (graph_tool.search.BellmanFordVisitor method) (graph_tool.search.DijkstraVisitor method) edges() (graph_tool.Graph method)

edmonds_karp_max_flow() (in module graph_tool.flow) eigentrust() (in module graph_tool.centrality) eigenvector() (in module graph_tool.centrality) em_infer() (in module graph_tool.inference) EMBlockState (class in graph_tool.inference) entropy() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.NestedBlockState method) (graph_tool.inference.OverlapBlockState method) (graph_tool.inference.TemperingState method) ep (graph_tool.Graph attribute) examine_edge() (graph_tool.search.AStarVisitor method) (graph_tool.search.BFSVisitor method) (graph_tool.search.BellmanFordVisitor method) (graph_tool.search.DFSVisitor method) (graph_tool.search.DijkstraVisitor method) examine_vertex() (graph_tool.search.AStarVisitor method) (graph_tool.search.BFSVisitor method) (graph_tool.search.DijkstraVisitor method) exhaustive_sweep() (graph_tool.inference.BlockState method) extended_clustering() (in module graph_tool.clustering)

F

fa (graph_tool.PropertyMap attribute) find_edge() (in module graph_tool.util) find_edge_range() (in module graph_tool.util) find_new_level() (graph_tool.inference.NestedBlockState method) find_vertex() (in module graph_tool.util) find_vertex_range() (in module graph_tool.util)

finish_vertex() (graph_tool.search.AStarVisitor method) (graph_tool.search.BFSVisitor method) (graph_tool.search.DFSVisitor method) (graph_tool.search.DijkstraVisitor method) fit_to_window() (graph_tool.draw.GraphWidget method) forward_or_cross_edge() (graph_tool.search.DFSVisitor method) fruchterman_reingold_layout() (in module graph_tool.draw)

G

generate_sbm() (in module graph_tool.generation) geometric_graph() (in module graph_tool.generation) get_2d_array() (graph_tool.PropertyMap method) get_ak() (graph_tool.inference.EMBlockState method) get_allowed_energies() (graph_tool.inference.MulticanonicalState method) get_array() (graph_tool.PropertyMap method) get_B() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) get_bclabel() (graph_tool.inference.BlockState method) get_bg() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) get_block_edge_gradient() (in module graph_tool.inference) get_block_state() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) get_blocks() (graph_tool.inference.BlockState method) get_bpclabel() (graph_tool.inference.BlockState method) get_bs() (graph_tool.inference.NestedBlockState method) get_bstack() (graph_tool.inference.NestedBlockState method) get_clabel() (graph_tool.inference.NestedBlockState method) get_data_path() (in module graph_tool.collection) get_density() (graph_tool.inference.MulticanonicalState method) get_E() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) get_edge_blocks() (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) get_edge_filter() (graph_tool.Graph method) get_edges() (graph_tool.Graph method) get_edges_prob() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.NestedBlockState method) get_energies() (graph_tool.inference.MulticanonicalState method) get_er() (graph_tool.inference.BlockState method) get_ers() (graph_tool.inference.BlockState method) get_fast_edge_removal() (graph_tool.Graph method) get_fe() (graph_tool.inference.EMBlockState method) get_flatness() (graph_tool.inference.MulticanonicalState method) get_graph() (graph_tool.PropertyMap method) get_group_sizes() (graph_tool.inference.EMBlockState method) get_hierarchy_control_points() (in module graph_tool.draw) get_hierarchy_tree() (in module graph_tool.inference) get_hist() (graph_tool.inference.MulticanonicalState method) get_in_degrees() (graph_tool.Graph method) get_in_edges() (graph_tool.Graph method) get_in_neighbors() (graph_tool.Graph method) get_levels() (graph_tool.inference.NestedBlockState method) get_majority_blocks() (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) get_MAP() (graph_tool.inference.EMBlockState method) get_matrix() (graph_tool.inference.BlockState method) (graph_tool.inference.EMBlockState method)

get_move_prob() (graph_tool.inference.BlockState method) get_N() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) get_nonempty_B() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) get_nonoverlap_blocks() (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) get_nr() (graph_tool.inference.BlockState method) get_out_degrees() (graph_tool.Graph method) get_out_edges() (graph_tool.Graph method) get_out_neighbors() (graph_tool.Graph method) get_overlap_blocks() (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) get_perm_hist() (graph_tool.inference.MulticanonicalState method) get_posterior() (graph_tool.inference.MulticanonicalState method) get_range() (graph_tool.inference.MulticanonicalState method) get_rec_params() (graph_tool.inference.BlockState method) get_vertex_filter() (graph_tool.Graph method) get_vertex_marginals() (graph_tool.inference.EMBlockState method) get_vertices() (graph_tool.Graph method) gibbs_sweep() (graph_tool.inference.BlockState method) (graph_tool.inference.NestedBlockState method) (graph_tool.inference.TemperingState method) global_clustering() (in module graph_tool.clustering) gp (graph_tool.Graph attribute) Graph (class in graph_tool) graph_draw() (in module graph_tool.draw) graph_properties (graph_tool.Graph attribute) graph_tool (module) graph_tool.centrality (module) graph_tool.clustering (module) graph_tool.collection (module) graph_tool.correlations (module) graph_tool.draw (module) graph_tool.flow (module) graph_tool.generation (module) graph_tool.inference (module) graph_tool.search (module) graph_tool.spectral (module) graph_tool.stats (module) graph_tool.topology (module) graph_tool.util (module) graph_union() (in module graph_tool.generation) GraphView (class in graph_tool) graphviz_draw() (in module graph_tool.draw) GraphWidget (class in graph_tool.draw) GraphWindow (class in graph_tool.draw) gray_target() (graph_tool.search.BFSVisitor method) group_vector_property() (in module graph_tool)

H

half_edge_graph() (in module graph_tool.inference)

hierarchy_minimize() (in module graph_tool.inference) hits() (in module graph_tool.centrality)

I

in_degree() (graph_tool.Vertex method) in_neighbors() (graph_tool.Vertex method) incidence() (in module graph_tool.spectral) incident_edges_op() (in module graph_tool) infect_vertex_property() (in module graph_tool) init_picked() (graph_tool.draw.GraphWidget method) initialize_vertex() (graph_tool.search.AStarVisitor method) (graph_tool.search.BFSVisitor method) (graph_tool.search.DFSVisitor method) (graph_tool.search.DijkstraVisitor method)

interactive_window() (in module graph_tool.draw) is_bipartite() (in module graph_tool.topology) is_DAG() (in module graph_tool.topology) is_directed() (graph_tool.Graph method) is_planar() (in module graph_tool.topology) is_reversed() (graph_tool.Graph method) is_valid() (graph_tool.Edge method) (graph_tool.Vertex method) is_writable() (graph_tool.PropertyMap method) isomorphism() (in module graph_tool.topology)

K

katz() (in module graph_tool.centrality) kcore_decomposition() (in module graph_tool.topology) key_press_event() (graph_tool.draw.GraphWidget method)

key_release_event() (graph_tool.draw.GraphWidget method) key_type() (graph_tool.PropertyMap method) konect_data (in module graph_tool.collection)

L

label_biconnected_components() (in module graph_tool.topology) label_components() (in module graph_tool.topology) label_largest_component() (in module graph_tool.topology) label_out_component() (in module graph_tool.topology) label_parallel_edges() (in module graph_tool.stats) label_self_loops() (in module graph_tool.stats) laplacian() (in module graph_tool.spectral) lattice() (in module graph_tool.generation) LayeredBlockState (class in graph_tool.inference)

layout_callback() (graph_tool.draw.GraphWidget method) learn() (graph_tool.inference.EMBlockState method) level_entropy() (graph_tool.inference.NestedBlockState method) line_graph() (in module graph_tool.generation) list_properties() (graph_tool.Graph method) load() (graph_tool.Graph method) load_graph() (in module graph_tool) load_graph_from_csv() (in module graph_tool) local_clustering() (in module graph_tool.clustering)

M

m_iter() (graph_tool.inference.EMBlockState method) ma (graph_tool.PropertyMap attribute) make_maximal_planar() (in module graph_tool.topology) map_property_values() (in module graph_tool) mark_subgraph() (in module graph_tool.topology) max_cardinality_matching() (in module graph_tool.topology) max_independent_vertex_set() (in module graph_tool.topology) mcmc_anneal() (in module graph_tool.inference) mcmc_equilibrate() (in module graph_tool.inference) mcmc_multilevel() (in module graph_tool.inference) mcmc_sweep() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.NestedBlockState method) (graph_tool.inference.OverlapBlockState method) (graph_tool.inference.TemperingState method) merge_sweep() (graph_tool.inference.BlockState method) merge_vertices() (graph_tool.inference.BlockState method) mf_entropy() (in module graph_tool.inference) microstate_entropy() (in module graph_tool.inference)

min_cut() (in module graph_tool.flow) min_spanning_tree() (in module graph_tool.topology) min_st_cut() (in module graph_tool.flow) minimize_blockmodel_dl() (in module graph_tool.inference) minimize_nested_blockmodel_dl() (in module graph_tool.inference) model_entropy() (in module graph_tool.inference) modularity() (in module graph_tool.inference) modularity_matrix() (in module graph_tool.spectral) motif_significance() (in module graph_tool.clustering) motifs() (in module graph_tool.clustering) motion_notify_event() (graph_tool.draw.GraphWidget method) move_vertex() (graph_tool.inference.BlockState method) (graph_tool.inference.NestedBlockState method) multicanonical_equilibrate() (in module graph_tool.inference) multicanonical_sweep() (graph_tool.inference.BlockState method) (graph_tool.inference.NestedBlockState method) MulticanonicalState (class in graph_tool.inference) multiflip_mcmc_sweep() (graph_tool.inference.BlockState method) (graph_tool.inference.NestedBlockState method) (graph_tool.inference.TemperingState method)

N

NestedBlockState (class in graph_tool.inference) new_edge_property() (graph_tool.Graph method) new_ep() (graph_tool.Graph method) new_gp() (graph_tool.Graph method) new_graph_property() (graph_tool.Graph method)

new_property() (graph_tool.Graph method) new_vertex_property() (graph_tool.Graph method) new_vp() (graph_tool.Graph method) non_tree_edge() (graph_tool.search.BFSVisitor method) num_edges() (graph_tool.Graph method) num_vertices() (graph_tool.Graph method)

O

openmp_enabled() (in module graph_tool) openmp_get_num_threads() (in module graph_tool) openmp_get_schedule() (in module graph_tool) openmp_set_num_threads() (in module graph_tool)

openmp_set_schedule() (in module graph_tool) out_degree() (graph_tool.Vertex method) out_neighbors() (graph_tool.Vertex method) OverlapBlockState (class in graph_tool.inference)

P

pagerank() (in module graph_tool.centrality) PartitionHist (class in graph_tool.inference) perfect_prop_hash() (in module graph_tool) planar_layout() (in module graph_tool.draw) pos_from_device() (graph_tool.draw.GraphWidget method) pos_to_device() (graph_tool.draw.GraphWidget method) predecessor_tree() (in module graph_tool.generation) price_network() (in module graph_tool.generation) print_summary() (graph_tool.inference.NestedBlockState method) project_level() (graph_tool.inference.NestedBlockState method) project_partition() (graph_tool.inference.NestedBlockState method)

prop_map (graph_tool.PropertyArray attribute) prop_to_size() (in module graph_tool.draw) propagate_clabel() (graph_tool.inference.NestedBlockState method) properties (graph_tool.Graph attribute) PropertyArray (class in graph_tool) PropertyMap (class in graph_tool) pseudo_diameter() (in module graph_tool.topology) purge_edges() (graph_tool.Graph method) purge_vertices() (graph_tool.Graph method) push_relabel_max_flow() (in module graph_tool.flow) python_value_type() (graph_tool.PropertyMap method)

R

radial_tree_layout() (in module graph_tool.draw) random_graph() (in module graph_tool.generation) random_layout() (in module graph_tool.draw) random_rewire() (in module graph_tool.generation) random_spanning_tree() (in module graph_tool.topology) regenerate_surface() (graph_tool.draw.GraphWidget method) reindex_edges() (graph_tool.Graph method) remove_edge() (graph_tool.Graph method) remove_labeled_edges() (in module graph_tool.stats) remove_parallel_edges() (in module graph_tool.stats)

remove_self_loops() (in module graph_tool.stats) remove_vertex() (graph_tool.Graph method) (graph_tool.inference.BlockState method) (graph_tool.inference.NestedBlockState method) replace_level() (graph_tool.inference.NestedBlockState method) reserve() (graph_tool.PropertyMap method) reset_hist() (graph_tool.inference.MulticanonicalState method) reset_layout() (graph_tool.draw.GraphWidget method) resize() (graph_tool.PropertyMap method) rotate_begin() (graph_tool.draw.GraphWidget method) rotate_end() (graph_tool.draw.GraphWidget method)

S

sample_graph() (graph_tool.inference.BlockState method) sample_vertex_move() (graph_tool.inference.BlockState method) save() (graph_tool.Graph method) scalar_assortativity() (in module graph_tool.correlations) scale_changed() (graph_tool.draw.GraphWidget method) scroll_event() (graph_tool.draw.GraphWidget method) sequential_vertex_coloring() (in module graph_tool.topology) set_2d_array() (graph_tool.PropertyMap method) set_blocks() (graph_tool.inference.BlockState method) set_directed() (graph_tool.Graph method) set_edge_filter() (graph_tool.Graph method) set_fast_edge_removal() (graph_tool.Graph method) set_filters() (graph_tool.Graph method) set_rec_params() (graph_tool.inference.BlockState method) set_reversed() (graph_tool.Graph method) set_value() (graph_tool.PropertyMap method)

set_vertex_filter() (graph_tool.Graph method) sfdp_layout() (in module graph_tool.draw) shortest_distance() (in module graph_tool.topology) shortest_path() (in module graph_tool.topology) show_config() (in module graph_tool) shrink() (graph_tool.inference.BlockState method) (graph_tool.inference.LayeredBlockState method) (graph_tool.inference.OverlapBlockState method) shrink_to_fit() (graph_tool.Graph method) (graph_tool.PropertyMap method) similarity() (in module graph_tool.topology) source() (graph_tool.Edge method) start_vertex() (graph_tool.search.DFSVisitor method) states_move() (graph_tool.inference.TemperingState method) states_swap() (graph_tool.inference.TemperingState method) StopSearch subgraph_isomorphism() (in module graph_tool.topology)

T

target() (graph_tool.Edge method) TemperingState (class in graph_tool.inference) topological_sort() (in module graph_tool.topology) transition() (in module graph_tool.spectral) transitive_closure() (in module graph_tool.topology)

tree_edge() (graph_tool.search.BFSVisitor method) (graph_tool.search.DFSVisitor method) triangulation() (in module graph_tool.generation) trust_transitivity() (in module graph_tool.centrality) tsp_tour() (in module graph_tool.topology)

U

ungroup_vector_property() (in module graph_tool)

V

value_type() (graph_tool.PropertyMap method) value_types() (in module graph_tool) Vertex (class in graph_tool) vertex() (graph_tool.Graph method) vertex_average() (in module graph_tool.stats) vertex_hist() (in module graph_tool.stats)

vertex_index (graph_tool.Graph attribute) vertex_percolation() (in module graph_tool.topology) vertex_properties (graph_tool.Graph attribute) vertex_similarity() (in module graph_tool.topology) vertices() (graph_tool.Graph method) virtual_vertex_move() (graph_tool.inference.BlockState method) vp (graph_tool.Graph attribute)

Z

zoom_begin() (graph_tool.draw.GraphWidget method)

zoom_end() (graph_tool.draw.GraphWidget method)