Index

A

a() (graph_tool.PropertyMap property) add_edge() (graph_tool.Graph method) add_edge_list() (graph_tool.Graph method) add_partition() (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) add_vertex() (graph_tool.Graph method) (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) adjacency() (in module graph_tool.spectral) AdjacencyOperator (class in graph_tool.spectral) align_mode() (graph_tool.inference.partition_modes.PartitionModeState method) align_nested_partition_labels() (in module graph_tool.inference.partition_modes) align_partition_labels() (in module graph_tool.inference.partition_modes) 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.blockmodel.BlockPairHist method) (graph_tool.inference.blockmodel.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) augmented_graph() (in module graph_tool.inference.overlap_blockmodel) avg_combined_corr() (in module graph_tool.correlations) avg_neighbor_corr() (in module graph_tool.correlations) avg_neighbour_corr() (in module graph_tool.correlations) AxelrodState (class in graph_tool.dynamics)

B

back_edge() (graph_tool.search.DFSVisitor method) base() (graph_tool.GraphView property) bellman_ford_search() (in module graph_tool.search) BellmanFordVisitor (class in graph_tool.search) bethe_entropy() (in module graph_tool.inference.blockmodel) 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)

BinaryThresholdState (class in graph_tool.dynamics) bisection_minimize() (in module graph_tool.inference.bisection) black_target() (graph_tool.search.AStarVisitor method) (graph_tool.search.BFSVisitor method) BlockPairHist (class in graph_tool.inference.blockmodel) BlockState (class in graph_tool.inference.blockmodel) BooleanState (class in graph_tool.dynamics) 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) CIsingGlauberBlockState (class in graph_tool.inference.uncertain_blockmodel) CIsingGlauberState (class in graph_tool.dynamics) classify_partition() (graph_tool.inference.partition_modes.ModeClusterState method) 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) coerce_type() (graph_tool.PropertyMap method) collect_edge_marginals() (graph_tool.inference.blockmodel.BlockState method) collect_marginal() (graph_tool.inference.uncertain_blockmodel.DynamicsBlockStateBase method) (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) collect_marginal_multigraph() (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) collect_partition_histogram() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) collect_vertex_marginals() (graph_tool.inference.blockmodel.BlockState method) combined_corr_hist() (in module graph_tool.correlations) CompactHashimotoOperator (class in graph_tool.spectral) complete_graph() (in module graph_tool.generation) condensation_graph() (in module graph_tool.generation)

contingency_graph() (in module graph_tool.inference.partition_modes) continuous_map() (in module graph_tool.inference.util) ContinuousStateBase (class in graph_tool.dynamics) copy() (graph_tool.dynamics.ContinuousStateBase method) (graph_tool.dynamics.DiscreteStateBase method) (graph_tool.Graph method) (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.modularity.ModularityState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) (graph_tool.inference.partition_centroid.PartitionCentroidState method) (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) (graph_tool.inference.planted_partition.PPBlockState method) (graph_tool.inference.uncertain_blockmodel.DynamicsBlockStateBase method) (graph_tool.inference.uncertain_blockmodel.EpidemicsBlockState method) (graph_tool.inference.uncertain_blockmodel.LatentMultigraphBlockState method) (graph_tool.inference.uncertain_blockmodel.MeasuredBlockState method) (graph_tool.inference.uncertain_blockmodel.MixedMeasuredBlockState method) (graph_tool.inference.uncertain_blockmodel.UncertainBlockState method) (graph_tool.PropertyMap method) copy_property() (graph_tool.Graph method) corr_hist() (in module graph_tool.correlations) count_shortest_paths() (in module graph_tool.topology)

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.nested_blockmodel.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) DictState (class in graph_tool.inference.util) 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) DiscreteStateBase (class in graph_tool.dynamics)

distance_histogram() (in module graph_tool.stats) dmask() (in module graph_tool.inference.util) 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.blockmodel.BlockState method) (graph_tool.inference.blockmodel_em.EMBlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.modularity.ModularityState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) (graph_tool.inference.planted_partition.PPBlockState method) draw_hierarchy() (in module graph_tool.draw) duplicate_level() (graph_tool.inference.nested_blockmodel.NestedBlockState method) DynamicsBlockStateBase (class in graph_tool.inference.uncertain_blockmodel)

E

e_iter() (graph_tool.inference.blockmodel_em.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) EdgePropertyMap (class in graph_tool) 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.blockmodel_em)

EMBlockState (class in graph_tool.inference.blockmodel_em) entropies() (graph_tool.inference.mcmc.TemperingState method) entropy() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.mcmc.TemperingState method) (graph_tool.inference.modularity.ModularityState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) (graph_tool.inference.planted_partition.PPBlockState method) (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) ep (graph_tool.Graph attribute) EpidemicsBlockState (class in graph_tool.inference.uncertain_blockmodel) EpidemicStateBase (class in graph_tool.dynamics) examine_edge() (graph_tool.search.AStarVisitor method) (graph_tool.search.BellmanFordVisitor method) (graph_tool.search.BFSVisitor 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.blockmodel.BlockState method) extended_clustering() (in module graph_tool.clustering) extract_largest_component() (in module graph_tool.topology)

F

fa() (graph_tool.PropertyMap property) find_edge() (in module graph_tool.util) find_edge_range() (in module graph_tool.util) find_new_level() (graph_tool.inference.nested_blockmodel.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_knn() (in module graph_tool.generation) generate_maxent_sbm() (in module graph_tool.generation) generate_sbm() (in module graph_tool.generation) geometric_graph() (in module graph_tool.generation) get_2d_array() (graph_tool.PropertyMap method) get_active() (graph_tool.dynamics.DiscreteStateBase method) get_ak() (graph_tool.inference.blockmodel_em.EMBlockState method) get_all_edges() (graph_tool.Graph method) get_all_neighbors() (graph_tool.Graph method) get_allowed_energies() (graph_tool.inference.mcmc.MulticanonicalState method) get_array() (graph_tool.PropertyMap method) get_B() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.modularity.ModularityState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) (graph_tool.inference.partition_centroid.PartitionCentroidState method) (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) (graph_tool.inference.planted_partition.PPBlockState method) get_bclabel() (graph_tool.inference.blockmodel.BlockState method) get_Be() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.modularity.ModularityState method) (graph_tool.inference.partition_centroid.PartitionCentroidState method) (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.planted_partition.PPBlockState method) get_bg() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) get_block_edge_gradient() (in module graph_tool.inference.overlap_blockmodel) get_block_state() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) get_blocks() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.planted_partition.PPBlockState method) get_bpclabel() (graph_tool.inference.blockmodel.BlockState method) get_bs() (graph_tool.inference.nested_blockmodel.NestedBlockState method) get_bstack() (graph_tool.inference.nested_blockmodel.NestedBlockState method) get_clabel() (graph_tool.inference.nested_blockmodel.NestedBlockState method) get_coupled_state() (graph_tool.inference.partition_modes.PartitionModeState method) get_data_path() (in module graph_tool.collection) get_density() (graph_tool.inference.mcmc.MulticanonicalState method) get_diff() (graph_tool.dynamics.ContinuousStateBase method) get_E() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) get_edge_blocks() (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) get_edge_filter() (graph_tool.Graph method) get_edge_prob() (graph_tool.inference.uncertain_blockmodel.DynamicsBlockStateBase method) (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) get_edges() (graph_tool.Graph method) get_edges_prob() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) get_energies() (graph_tool.inference.mcmc.MulticanonicalState method) get_er() (graph_tool.inference.blockmodel.BlockState method) get_ers() (graph_tool.inference.blockmodel.BlockState method) get_fast_edge_removal() (graph_tool.Graph method) get_fe() (graph_tool.inference.blockmodel_em.EMBlockState method) get_flatness() (graph_tool.inference.mcmc.MulticanonicalState method) get_graph() (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) (graph_tool.PropertyMap method) get_group_sizes() (graph_tool.inference.blockmodel_em.EMBlockState method) get_hierarchy_control_points() (in module graph_tool.draw) get_hierarchy_tree() (in module graph_tool.inference.nested_blockmodel) get_hist() (graph_tool.inference.mcmc.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.nested_blockmodel.NestedBlockState method) get_M() (graph_tool.inference.partition_modes.PartitionModeState method) get_majority_blocks() (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) get_MAP() (graph_tool.inference.blockmodel_em.EMBlockState method) get_marginal() (graph_tool.inference.partition_modes.PartitionModeState method) get_matrix() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.blockmodel_em.EMBlockState method) get_max() (graph_tool.inference.partition_modes.PartitionModeState method) get_max_nested() (graph_tool.inference.partition_modes.PartitionModeState method) get_mode() (graph_tool.inference.partition_modes.ModeClusterState method) get_modes() (graph_tool.inference.partition_modes.ModeClusterState method) get_move_prob() (graph_tool.inference.blockmodel.BlockState method) get_N() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) get_nested_partition() (graph_tool.inference.partition_modes.PartitionModeState method) get_nested_partitions() (graph_tool.inference.partition_modes.PartitionModeState method) get_nonempty_B() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) (graph_tool.inference.planted_partition.PPBlockState method) get_nonoverlap_blocks() (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) get_nr() (graph_tool.inference.blockmodel.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.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method)

get_p_posterior() (graph_tool.inference.uncertain_blockmodel.MeasuredBlockState method) get_partition() (graph_tool.inference.partition_modes.PartitionModeState method) get_partitions() (graph_tool.inference.partition_modes.PartitionModeState method) get_perm_hist() (graph_tool.inference.mcmc.MulticanonicalState method) get_posterior() (graph_tool.inference.mcmc.MulticanonicalState method) get_q_posterior() (graph_tool.inference.uncertain_blockmodel.MeasuredBlockState method) get_r_phi() (graph_tool.dynamics.KuramotoState method) get_range() (graph_tool.inference.mcmc.MulticanonicalState method) get_rec_params() (graph_tool.inference.blockmodel.BlockState method) get_state() (graph_tool.dynamics.ContinuousStateBase method) (graph_tool.dynamics.DiscreteStateBase method) (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) (graph_tool.inference.planted_partition.PPBlockState method) get_total_degrees() (graph_tool.Graph method) get_vertex_filter() (graph_tool.Graph method) get_vertex_marginals() (graph_tool.inference.blockmodel_em.EMBlockState method) get_vertices() (graph_tool.Graph method) get_wr() (graph_tool.inference.partition_modes.ModeClusterState method) get_x() (graph_tool.inference.uncertain_blockmodel.DynamicsBlockStateBase method) (graph_tool.inference.uncertain_blockmodel.EpidemicsBlockState method) (graph_tool.inference.uncertain_blockmodel.IsingBaseBlockState method) gibbs_sweep() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.mcmc.TemperingState method) (graph_tool.inference.nested_blockmodel.NestedBlockState 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.dynamics module graph_tool.flow module graph_tool.generation module graph_tool.inference module graph_tool.inference.bisection module graph_tool.inference.blockmodel module graph_tool.inference.blockmodel_em module graph_tool.inference.latent_multigraph module graph_tool.inference.layered_blockmodel module graph_tool.inference.mcmc module graph_tool.inference.minimize module graph_tool.inference.modularity module graph_tool.inference.nested_blockmodel module graph_tool.inference.overlap_blockmodel module graph_tool.inference.partition_centroid module graph_tool.inference.partition_modes module graph_tool.inference.planted_partition module graph_tool.inference.uncertain_blockmodel module graph_tool.inference.util 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) GraphPropertyMap (class in graph_tool) 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.overlap_blockmodel) hashimoto() (in module graph_tool.spectral)

HashimotoOperator (class in graph_tool.spectral) hierarchy_minimize() (in module graph_tool.inference.nested_blockmodel) hits() (in module graph_tool.centrality)

I

in_degree() (graph_tool.Vertex method) in_edges() (graph_tool.Vertex method) in_neighbors() (graph_tool.Vertex method) incidence() (in module graph_tool.spectral) IncidenceOperator (class in 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) IsingBaseBlockState (class in graph_tool.inference.uncertain_blockmodel) IsingGlauberBlockState (class in graph_tool.inference.uncertain_blockmodel) IsingGlauberState (class in graph_tool.dynamics) IsingMetropolisState (class in graph_tool.dynamics) isomorphism() (in module graph_tool.topology) iterate_async() (graph_tool.dynamics.DiscreteStateBase method) iterate_sync() (graph_tool.dynamics.DiscreteStateBase method)

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) KirmanState (class in graph_tool.dynamics) konect_data (in module graph_tool.collection) KuramotoState (class in graph_tool.dynamics)

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) LaplacianOperator (class in graph_tool.spectral) latent_multigraph() (in module graph_tool.inference.latent_multigraph) LatentMultigraphBlockState (class in graph_tool.inference.uncertain_blockmodel) lattice() (in module graph_tool.generation)

LayeredBlockState (class in graph_tool.inference.layered_blockmodel) layout_callback() (graph_tool.draw.GraphWidget method) lbinom() (in module graph_tool.inference.util) learn() (graph_tool.inference.blockmodel_em.EMBlockState method) level_entropy() (graph_tool.inference.nested_blockmodel.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.blockmodel_em.EMBlockState method) ma() (graph_tool.PropertyMap property) MajorityVoterState (class in graph_tool.dynamics) make_maximal_planar() (in module graph_tool.topology) map_property_values() (in module graph_tool) marginal_multigraph_entropy() (in module graph_tool.inference.uncertain_blockmodel) mark_subgraph() (in module graph_tool.topology) max_cardinality_matching() (in module graph_tool.topology) max_cliques() (in module graph_tool.topology) max_independent_vertex_set() (in module graph_tool.topology) mcmc_anneal() (in module graph_tool.inference.mcmc) mcmc_equilibrate() (in module graph_tool.inference.mcmc) mcmc_multilevel() (in module graph_tool.inference.mcmc) mcmc_sweep() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.mcmc.TemperingState method) (graph_tool.inference.modularity.ModularityState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) (graph_tool.inference.partition_centroid.PartitionCentroidState method) (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.planted_partition.PPBlockState method) (graph_tool.inference.uncertain_blockmodel.EpidemicsBlockState method) (graph_tool.inference.uncertain_blockmodel.IsingBaseBlockState method) (graph_tool.inference.uncertain_blockmodel.MixedMeasuredBlockState method) (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) MeasuredBlockState (class in graph_tool.inference.uncertain_blockmodel) merge_sweep() (graph_tool.inference.blockmodel.BlockState method) merge_vertices() (graph_tool.inference.blockmodel.BlockState method) mf_entropy() (in module graph_tool.inference.blockmodel) microstate_entropy() (in module graph_tool.inference.blockmodel) 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) minimize_nested_blockmodel_dl() (in module graph_tool.inference.minimize) MixedMeasuredBlockState (class in graph_tool.inference.uncertain_blockmodel) ModeClusterState (class in graph_tool.inference.partition_modes) model_entropy() (in module graph_tool.inference.blockmodel) modularity() (graph_tool.inference.modularity.ModularityState method) (in module graph_tool.inference.modularity) modularity_matrix() (in module graph_tool.spectral) ModularityState (class in graph_tool.inference.modularity) module graph_tool graph_tool.centrality graph_tool.clustering graph_tool.collection graph_tool.correlations graph_tool.draw graph_tool.dynamics graph_tool.flow graph_tool.generation graph_tool.inference graph_tool.inference.bisection graph_tool.inference.blockmodel graph_tool.inference.blockmodel_em graph_tool.inference.latent_multigraph graph_tool.inference.layered_blockmodel graph_tool.inference.mcmc graph_tool.inference.minimize graph_tool.inference.modularity graph_tool.inference.nested_blockmodel graph_tool.inference.overlap_blockmodel graph_tool.inference.partition_centroid graph_tool.inference.partition_modes graph_tool.inference.planted_partition graph_tool.inference.uncertain_blockmodel graph_tool.inference.util graph_tool.search graph_tool.spectral graph_tool.stats graph_tool.topology graph_tool.util

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.blockmodel.BlockState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) (graph_tool.inference.planted_partition.PPBlockState method) multicanonical_B_sweep() (graph_tool.inference.blockmodel.BlockState method) multicanonical_equilibrate() (in module graph_tool.inference.mcmc) multicanonical_sweep() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) MulticanonicalState (class in graph_tool.inference.mcmc) multiflip_mcmc_sweep() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.mcmc.TemperingState method) (graph_tool.inference.modularity.ModularityState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) (graph_tool.inference.partition_centroid.PartitionCentroidState method) (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.planted_partition.PPBlockState method) (graph_tool.inference.uncertain_blockmodel.UncertainBaseState method) mutual_information() (in module graph_tool.inference.partition_centroid)

N

nested_partition_clear_null() (in module graph_tool.inference.partition_modes) nested_partition_overlap() (in module graph_tool.inference.partition_modes) nested_partition_overlap_center() (in module graph_tool.inference.partition_modes) NestedBlockState (class in graph_tool.inference.nested_blockmodel) 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) ns (in module graph_tool.collection) ns_info (in module graph_tool.collection) 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)

order_nested_partition_labels() (in module graph_tool.inference.partition_modes) order_partition_labels() (in module graph_tool.inference.partition_modes) out_degree() (graph_tool.Vertex method) out_edges() (graph_tool.Vertex method) out_neighbors() (graph_tool.Vertex method) OverlapBlockState (class in graph_tool.inference.overlap_blockmodel)

P

pagerank() (in module graph_tool.centrality) partition_overlap() (in module graph_tool.inference.partition_modes) partition_overlap_center() (in module graph_tool.inference.partition_modes) PartitionCentroidState (class in graph_tool.inference.partition_centroid) PartitionHist (class in graph_tool.inference.blockmodel) PartitionModeState (class in graph_tool.inference.partition_modes) perfect_prop_hash() (in module graph_tool) planar_layout() (in module graph_tool.draw) pmap() (in module graph_tool.inference.util) pos_from_device() (graph_tool.draw.GraphWidget method) pos_to_device() (graph_tool.draw.GraphWidget method) posterior_cdev() (graph_tool.inference.partition_modes.PartitionModeState method) posterior_entropy() (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) posterior_lprob() (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) PottsGlauberState (class in graph_tool.dynamics) PottsMetropolisState (class in graph_tool.dynamics)

PPBlockState (class in graph_tool.inference.planted_partition) predecessor_tree() (in module graph_tool.generation) price_network() (in module graph_tool.generation) print_summary() (graph_tool.inference.nested_blockmodel.NestedBlockState method) project_level() (graph_tool.inference.nested_blockmodel.NestedBlockState method) project_partition() (graph_tool.inference.nested_blockmodel.NestedBlockState method) prop_map() (graph_tool.PropertyArray property) prop_to_size() (in module graph_tool.draw) propagate_clabel() (graph_tool.inference.nested_blockmodel.NestedBlockState method) properties (graph_tool.Graph attribute) PropertyArray (class in graph_tool) PropertyMap (class in graph_tool) pseudo_diameter() (in module graph_tool.topology) PseudoCIsingBlockState (class in graph_tool.inference.uncertain_blockmodel) PseudoIsingBlockState (class in graph_tool.inference.uncertain_blockmodel) 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_shortest_path() (in module graph_tool.topology) random_spanning_tree() (in module graph_tool.topology) reduced_mutual_information() (in module graph_tool.inference.partition_centroid) regenerate_surface() (graph_tool.draw.GraphWidget method) reindex_edges() (graph_tool.Graph method) relabel() (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) relabel_partition() (graph_tool.inference.partition_modes.PartitionModeState method) remove_edge() (graph_tool.Graph method) remove_labeled_edges() (in module graph_tool.stats) remove_parallel_edges() (in module graph_tool.stats)

remove_partition() (graph_tool.inference.partition_modes.PartitionModeState method) remove_self_loops() (in module graph_tool.stats) remove_vertex() (graph_tool.Graph method) (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.nested_blockmodel.NestedBlockState method) replace_level() (graph_tool.inference.nested_blockmodel.NestedBlockState method) replace_partitions() (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) reserve() (graph_tool.PropertyMap method) reset_active() (graph_tool.dynamics.DiscreteStateBase method) reset_hist() (graph_tool.inference.mcmc.MulticanonicalState method) reset_layout() (graph_tool.draw.GraphWidget method) resize() (graph_tool.PropertyMap method) reverse_map() (in module graph_tool.inference.util) rotate_begin() (graph_tool.draw.GraphWidget method) rotate_end() (graph_tool.draw.GraphWidget method)

S

sample_graph() (graph_tool.inference.blockmodel.BlockState method) sample_nested_partition() (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) sample_partition() (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) sample_vertex_move() (graph_tool.inference.blockmodel.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_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_hparams() (graph_tool.inference.uncertain_blockmodel.MeasuredBlockState method) (graph_tool.inference.uncertain_blockmodel.MixedMeasuredBlockState method) set_params() (graph_tool.inference.uncertain_blockmodel.DynamicsBlockStateBase method) (graph_tool.inference.uncertain_blockmodel.EpidemicsBlockState method) set_rec_params() (graph_tool.inference.blockmodel.BlockState method) set_reversed() (graph_tool.Graph method) set_state() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.nested_blockmodel.NestedBlockState 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.blockmodel.BlockState method) (graph_tool.inference.layered_blockmodel.LayeredBlockState method) (graph_tool.inference.overlap_blockmodel.OverlapBlockState method) shrink_to_fit() (graph_tool.Graph method) (graph_tool.PropertyMap method) shuffle_nested_partition_labels() (in module graph_tool.inference.partition_modes) shuffle_partition_labels() (in module graph_tool.inference.partition_modes) similarity() (in module graph_tool.topology) SIRSState (class in graph_tool.dynamics) SIRState (class in graph_tool.dynamics) SISState (class in graph_tool.dynamics) SIState (class in graph_tool.dynamics) solve() (graph_tool.dynamics.ContinuousStateBase method) solve_euler() (graph_tool.dynamics.ContinuousStateBase method) solve_sbm_fugacities() (in module graph_tool.generation) source() (graph_tool.Edge method) start_vertex() (graph_tool.search.DFSVisitor method) states_move() (graph_tool.inference.mcmc.TemperingState method) states_swap() (graph_tool.inference.mcmc.TemperingState method) StopSearch subgraph_isomorphism() (in module graph_tool.topology) swap() (graph_tool.PropertyMap method)

T

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

UncertainBaseState (class in graph_tool.inference.uncertain_blockmodel) UncertainBlockState (class in graph_tool.inference.uncertain_blockmodel)

ungroup_vector_property() (in module graph_tool) update() (graph_tool.draw.GraphWidget method)

V

value_type() (graph_tool.PropertyMap method) value_types() (in module graph_tool) variation_information() (in module graph_tool.inference.partition_centroid) 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) VertexPropertyMap (class in graph_tool) vertices() (graph_tool.Graph method) virtual_add_partition() (graph_tool.inference.partition_modes.ModeClusterState method) (graph_tool.inference.partition_modes.PartitionModeState method) virtual_remove_partition() (graph_tool.inference.partition_modes.PartitionModeState method) virtual_vertex_move() (graph_tool.inference.blockmodel.BlockState method) (graph_tool.inference.planted_partition.PPBlockState method) VoterState (class in graph_tool.dynamics) vp (graph_tool.Graph attribute)

Z

zoom_begin() (graph_tool.draw.GraphWidget method)

zoom_end() (graph_tool.draw.GraphWidget method)