Index

A

add_edge() (Grouper.utils.nxGroupGraph method) add_group() (Grouper.libraries.Libraries.BasisSet method) add_node() (Grouper.utils.nxGroupGraph method) all_group_indices (Grouper.fragmentation.MatchState attribute)

all_group_names (Grouper.fragmentation.MatchState attribute) all_matched_atoms (Grouper.fragmentation.MatchState attribute) all_unmatched_atoms (Grouper.fragmentation.MatchState attribute) apply_enumeration_theorem() (Grouper.counting.GraphBase method)

B

BasisSet (class in Grouper.libraries.Libraries)

C

calculate_centrality() (in module Grouper.visualization.visualize_space) calculate_diversity_index() (in module Grouper.visualization.visualize_space) calculate_edge_density() (in module Grouper.visualization.visualize_space) calculate_modularity() (in module Grouper.visualization.visualize_space) calculate_network_properties() (in module Grouper.visualization.visualize_space)

calculate_port_positions() (in module Grouper.visualization.visualize_graph) calculate_substructure_frequencies() (in module Grouper.visualization.visualize_space) chemical_space_network() (in module Grouper.visualization.visualize_space) convert_edges_to_nodetype() (in module Grouper.utils) convert_to_nx() (in module Grouper.utils)

D

data_to_gg_edge() (in module Grouper.utils)

DelayImportError doi (Grouper.libraries.Libraries.GroupExtension attribute)

E

EmbedError

extended_smarts (Grouper.libraries.Libraries.GroupExtension attribute)

F

filter() (Grouper.group_graph_set.GroupGraphSet method) filter_inventory() (Grouper.counting.GraphBase method)

find_shortest_paths() (in module Grouper.visualization.visualize_space) fragment() (in module Grouper.fragmentation) fragment_smiles() (Grouper.libraries.Libraries.BasisSet method)

G

generate_inventory() (Grouper.counting.GraphBase method) generate_permutations() (Grouper.counting.GraphBase method) generate_svg() (in module Grouper.visualization.visualize_graph) generate_svg_for_node() (in module Grouper.visualization.visualize_graph) get_cycle_index() (Grouper.counting.GraphBase method) get_edges() (Grouper.counting.GraphBase method) get_groups() (Grouper.libraries.Libraries.BasisSet method) GraphBase (class in Grouper.counting) group (Grouper.libraries.Libraries.GroupExtension attribute) group_bonds (Grouper.fragmentation.MatchState attribute) group_traces (Grouper.libraries.Libraries.BasisSet property) group_traces_ (Grouper.libraries.Libraries.BasisSet attribute) Grouper.counting module Grouper.exports module Grouper.fragmentation module Grouper.group_graph_set module

Grouper.io module Grouper.libraries module Grouper.libraries.Libraries module Grouper.utils module Grouper.visualization module Grouper.visualization.visualize_graph module Grouper.visualization.visualize_node module Grouper.visualization.visualize_space module GrouperError GroupExtension (class in Grouper.libraries.Libraries) GroupGraphSet (class in Grouper.group_graph_set)

I

import_() (in module Grouper.io)

isFullyFragmented() (Grouper.fragmentation.MatchState method)

J

Joback (class in Grouper.libraries.Libraries)

M

make_undirected() (Grouper.utils.nxGroupGraph method) MatchState (class in Grouper.fragmentation) module Grouper.counting Grouper.exports Grouper.fragmentation Grouper.group_graph_set Grouper.io Grouper.libraries Grouper.libraries.Libraries Grouper.utils Grouper.visualization Grouper.visualization.visualize_graph Grouper.visualization.visualize_node Grouper.visualization.visualize_space

N

n_free_ports() (Grouper.utils.nxGroupGraph method) n_groups (Grouper.libraries.Libraries.BasisSet property) NodeColoredGraph (class in Grouper.counting)

nodeDefs_indices (Grouper.fragmentation.MatchState attribute) nx_visualize() (in module Grouper.visualization.visualize_graph) nxGroupGraph (class in Grouper.utils)

P

parse_vcolg_line() (in module Grouper.utils) plot() (Grouper.counting.GraphBase method)

plot_feature_similarity() (in module Grouper.visualization.visualize_space) priority (Grouper.libraries.Libraries.GroupExtension attribute)

Q

query_groups() (Grouper.libraries.Libraries.BasisSet method)

S

SaftGammaMie (class in Grouper.libraries.Libraries)

sample() (Grouper.group_graph_set.GroupGraphSet method) spring_layout() (in module Grouper.visualization.visualize_graph)

T

to_3d_mol() (in module Grouper.exports) to_csv() (Grouper.group_graph_set.GroupGraphSet method) to_dataframe() (Grouper.group_graph_set.GroupGraphSet method) to_inchi() (in module Grouper.exports) to_inchi_key() (in module Grouper.exports) to_jsonl() (Grouper.group_graph_set.GroupGraphSet method) to_mol() (in module Grouper.exports)

to_pdb() (in module Grouper.exports) to_PyG_Data() (Grouper.utils.nxGroupGraph method) to_sdf() (Grouper.group_graph_set.GroupGraphSet method) (in module Grouper.exports) to_smarts() (in module Grouper.exports) to_smiles_list() (Grouper.group_graph_set.GroupGraphSet method) to_xyz() (in module Grouper.exports)

U

Unifac (class in Grouper.libraries.Libraries)

V

visualize() (in module Grouper.visualization.visualize_graph) visualize_chemical_space() (in module Grouper.visualization.visualize_space) visualize_cytoscape() (in module Grouper.visualization.visualize_graph)

visualize_group() (in module Grouper.visualization.visualize_node) visualize_group_extension() (in module Grouper.visualization.visualize_node) visualize_library() (Grouper.libraries.Libraries.BasisSet method) visualize_substructure_correlation() (in module Grouper.visualization.visualize_space)