Index

A

add() (in module rinchi_tools.tools) add_addition() (in module rinchi_add) add_changes() (in module rinchi_changes) add_convert() (in module rinchi_convert) add_db() (in module rinchi_database)

add_search() (in module rinchi_search) add_stats() (in module rinchi_stats) addition_ops() (in module rinchi_add) Atom (class in rinchi_tools.atom)

B

Backup (class in rinchi_tools.matcher) backup() (rinchi_tools.matcher.Backup method) bonds_compatible() (rinchi_tools.matcher.Matcher method) breadth_first_search() (rinchi_tools.molecule.Molecule static method)

build_rauxinfo() (in module rinchi_tools.tools) build_rinchi() (in module rinchi_tools.tools) build_rinchi_rauxinfo() (in module rinchi_tools.tools) busy (rinchi_tools.utils.Spinner attribute)

C

calculate_edges() (rinchi_tools.molecule.Molecule method) calculate_reaction_fingerprint() (rinchi_tools.reaction.Reaction method) calculate_rings() (rinchi_tools.molecule.Molecule method) calculate_rings_by_atoms() (rinchi_tools.molecule.Molecule method) call_command() (in module rinchi_tools.utils) change_across_reaction() (rinchi_tools.reaction.Reaction method) changes_ops() (in module rinchi_changes) chemical_formula_to_dict() (rinchi_tools.molecule.Molecule method) compare_fingerprints() (in module rinchi_tools.database) composite_to_simple() (rinchi_tools.molecule.Molecule static method) consolidate() (in module rinchi_tools.utils) construct_output_text() (in module rinchi_tools.utils) convert_all() (in module rinchi_tools.v02_tools)

convert_ops() (in module rinchi_convert) convert_rauxinfo() (in module rinchi_tools.v02_tools) convert_rinchi() (in module rinchi_tools.v02_tools) convert_v02_v03() (in module rinchi_tools.database) count_centres() (rinchi_tools.molecule.Molecule method) count_compatable() (rinchi_tools.matcher.Matcher method) count_rings() (rinchi_tools.molecule.Molecule method) count_sp2() (rinchi_tools.molecule.Molecule method) count_sp3() (rinchi_tools.molecule.Molecule method) counter_to_print_string() (in module rinchi_tools.utils) create_csv_from_directory() (in module rinchi_tools.conversion) create_output_file() (in module rinchi_tools.utils) csv_to_sql() (in module rinchi_tools.database)

D

db_ops() (in module rinchi_database) dedupe_rinchi() (in module rinchi_tools.tools) delay (rinchi_tools.utils.Spinner attribute)

depth() (rinchi_tools.matcher.Backup method) depth_first_search() (rinchi_tools.molecule.Molecule method) detect_reaction() (rinchi_tools.reaction.Reaction method)

E

edge_list_to_atoms_spanned() (rinchi_tools.molecule.Molecule static method) edge_list_to_vector() (rinchi_tools.molecule.Molecule method)

edges_to_atoms() (rinchi_tools.molecule.Molecule static method)

F

file_text_from_rinchi() (rinchi_tools.rinchi_lib.RInChI method) find_initial_ring_set() (rinchi_tools.molecule.Molecule method) find_initial_ring_set_trial() (rinchi_tools.molecule.Molecule method) find_linearly_independent() (rinchi_tools.molecule.Molecule method)

find_rings_from_back_edges() (rinchi_tools.molecule.Molecule method) find_shortest_path() (rinchi_tools.molecule.Molecule method) from_param() (rinchi_tools.rinchi_lib.StringHandler class method)

G

gen_possible_mappings() (rinchi_tools.matcher.Matcher method) gen_rauxinfo() (in module rinchi_tools.database) gen_test_state() (rinchi_tools.matcher.Matcher method) generate_edge_list() (rinchi_tools.molecule.Molecule method) generate_rauxinfo() (in module rinchi_tools.tools) (in module rinchi_tools.v02_tools) generate_svg_image() (rinchi_tools.reaction.Reaction method) get_attached_edges() (rinchi_tools.atom.Atom method) get_backup_mappings() (rinchi_tools.matcher.Matcher method) get_formula() (rinchi_tools.molecule.Molecule method)

get_hybrid_count() (rinchi_tools.molecule.Molecule method) get_hybridisation() (rinchi_tools.atom.Atom method) get_ring_count() (rinchi_tools.molecule.Molecule method) get_ring_count_inc_elements() (rinchi_tools.molecule.Molecule method) get_terminal_atoms() (rinchi_tools.matcher.Matcher static method) get_terminal_mappings() (rinchi_tools.matcher.Matcher method) get_valence() (rinchi_tools.atom.Atom method) get_valence_count() (rinchi_tools.molecule.Molecule method)

H

has_isotopic_inchi() (rinchi_tools.reaction.Reaction method) has_isotopic_layer() (rinchi_tools.molecule.Molecule method) has_ring() (rinchi_tools.reaction.Reaction method)

has_substructures() (rinchi_tools.reaction.Reaction method) has_substructures_by_populations() (rinchi_tools.reaction.Reaction method) Hashable (class in rinchi_tools.utils)

I

inchi_2_auxinfo() (in module rinchi_tools.tools) inchi_to_chemical_formula() (rinchi_tools.molecule.Molecule method) inchi_to_layer() (rinchi_tools.molecule.Molecule method) inchis_from_rinchi() (rinchi_tools.rinchi_lib.RInChI method) initialize() (rinchi_tools.molecule.Molecule method)

is_agent() (rinchi_tools.reaction.Reaction method) is_balanced() (rinchi_tools.reaction.Reaction method) is_compatible() (rinchi_tools.matcher.Matcher method) is_covering() (rinchi_tools.matcher.Matcher method) is_sub() (rinchi_tools.matcher.Matcher method)

L

longkey() (rinchi_tools.reaction.Reaction method)

M

master_to_sub() (rinchi_tools.matcher.Matcher method) match() (rinchi_tools.matcher.Matcher method)

Matcher (class in rinchi_tools.matcher) Molecule (class in rinchi_tools.molecule)

N

new() (rinchi_tools.molecule.Molecule static method)

new_state() (rinchi_tools.matcher.Matcher method)

O

output() (in module rinchi_tools.utils)

P

path_to_cycle_edge_list() (rinchi_tools.molecule.Molecule static method) present_in_layer() (rinchi_tools.reaction.Reaction static method)

present_in_reaction() (rinchi_tools.reaction.Reaction method) process_stats() (in module rinchi_tools.tools)

R

rdf_to_csv() (in module rinchi_tools.conversion) rdf_to_csv_append() (in module rinchi_tools.conversion) rdf_to_rinchis() (in module rinchi_tools.conversion) rdf_to_sql() (in module rinchi_tools.database) Reaction (class in rinchi_tools.reaction) read_input_file() (in module rinchi_tools.utils) recall_fingerprints() (in module rinchi_tools.database) remove_stereo() (in module rinchi_tools.tools) restore() (rinchi_tools.matcher.Backup method) RInChI (class in rinchi_tools.rinchi_lib) rinchi (module) rinchi_2_longkey() (in module rinchi_tools.v02_rinchi_key) rinchi_2_shortkey() (in module rinchi_tools.v02_rinchi_key) rinchi_add (module) rinchi_changes (module) rinchi_convert (module) rinchi_database (module) rinchi_errorcheck() (rinchi_tools.rinchi_lib.RInChI method) rinchi_from_file_text() (rinchi_tools.rinchi_lib.RInChI method) rinchi_search (module)

rinchi_stats (module) rinchi_to_dict_list() (in module rinchi_tools.tools) rinchi_to_file() (in module rinchi_tools.conversion) rinchi_tools (module) rinchi_tools.atom (module) rinchi_tools.conversion (module) rinchi_tools.database (module) rinchi_tools.matcher (module) rinchi_tools.molecule (module) rinchi_tools.reaction (module) rinchi_tools.rinchi_lib (module) rinchi_tools.tools (module) rinchi_tools.utils (module) rinchi_tools.v02_rinchi_key (module) rinchi_tools.v02_tools (module) rinchikey_from_file_text() (rinchi_tools.rinchi_lib.RInChI method) rinchikey_from_rinchi() (rinchi_tools.rinchi_lib.RInChI method) rinchis_to_keys() (in module rinchi_tools.conversion) ring_change() (rinchi_tools.reaction.Reaction method) rxn_to_rinchi() (in module rinchi_tools.conversion)

S

search_for_roles() (in module rinchi_tools.database) search_for_roles_advanced() (in module rinchi_tools.database) search_master() (in module rinchi_tools.database) search_ops() (in module rinchi_search) search_rinchis() (in module rinchi_tools.database) set_atomic_hydrogen() (rinchi_tools.molecule.Molecule method) set_atoms() (rinchi_tools.molecule.Molecule method) shortkey() (rinchi_tools.reaction.Reaction method) Spinner (class in rinchi_tools.utils) spinning_cursor() (rinchi_tools.utils.Spinner static method) split_rinchi() (in module rinchi_tools.tools) split_rinchi_inc_auxinfo() (in module rinchi_tools.tools)

split_rinchi_only_auxinfo() (in module rinchi_tools.tools) sql_key_to_rinchi() (in module rinchi_tools.database) start() (rinchi_tools.utils.Spinner method) stats_ops() (in module rinchi_stats) stereo_change() (rinchi_tools.reaction.Reaction method) stop() (rinchi_tools.utils.Spinner method) string_to_dict() (in module rinchi_tools.utils) StringHandler (class in rinchi_tools.rinchi_lib) sub_count() (rinchi_tools.matcher.Matcher method) sub_count_unique() (rinchi_tools.matcher.Matcher method) sub_to_master() (rinchi_tools.matcher.Matcher method)

U

update_fingerprints() (in module rinchi_tools.database)

V

vector_to_edge_list() (rinchi_tools.molecule.Molecule method)

W

webkey() (rinchi_tools.reaction.Reaction method)