Index
_
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A
|
B
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C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
R
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S
|
U
|
V
|
W
_
__getnewargs__() (md_harmonize.KEGG_parser.reaction_center method)
__init__() (md_harmonize.aromatics.AromaticManager method)
(md_harmonize.compound.Atom method)
(md_harmonize.compound.Bond method)
(md_harmonize.compound.Compound method)
(md_harmonize.harmonization.CompoundHarmonizationManager method)
(md_harmonize.harmonization.HarmonizationManager method)
(md_harmonize.harmonization.HarmonizedCompoundEdge method)
(md_harmonize.harmonization.HarmonizedEdge method)
(md_harmonize.harmonization.HarmonizedReactionEdge method)
(md_harmonize.harmonization.ReactionHarmonizationManager method)
(md_harmonize.KEGG_parser.RpairParser method)
(md_harmonize.reaction.Reaction method)
__new__() (md_harmonize.KEGG_parser.reaction_center static method)
__repr__() (md_harmonize.KEGG_parser.reaction_center method)
A
add_aromatic_substructures() (md_harmonize.aromatics.AromaticManager method)
add_edge() (md_harmonize.harmonization.CompoundHarmonizationManager method)
(md_harmonize.harmonization.HarmonizationManager method)
add_invalid() (md_harmonize.harmonization.CompoundHarmonizationManager method)
add_neighbors() (md_harmonize.compound.Atom method)
AromaticManager (class in md_harmonize.aromatics)
Atom (class in md_harmonize.compound)
atom_mappings_parser() (in module md_harmonize.MetaCyc_parser)
B
backbone_color_identifier() (md_harmonize.compound.Compound method)
Bond (class in md_harmonize.compound)
break_cycle() (md_harmonize.compound.Compound method)
C
calculate_bond_stereochemistry() (md_harmonize.compound.Compound method)
calculate_distance_to_r_groups() (md_harmonize.compound.Compound method)
calculate_y_coordinate() (md_harmonize.compound.Compound static method)
circular_pair_relationship() (md_harmonize.compound.Compound method)
circular_pair_relationship_helper() (md_harmonize.compound.Compound method)
clone() (md_harmonize.compound.Atom method)
(md_harmonize.compound.Bond method)
collect_atomic_weights_of_neighbors() (md_harmonize.compound.Compound method)
color_atom() (md_harmonize.compound.Atom method)
color_compound() (md_harmonize.compound.Compound method)
color_groups() (md_harmonize.compound.Compound method)
color_h() (md_harmonize.compound.Compound method)
color_metal() (md_harmonize.compound.Compound method)
combine_atom_mappings() (md_harmonize.KEGG_parser.RpairParser method)
compare_branch_weights() (md_harmonize.compound.Compound method)
compare_chemical_details() (md_harmonize.compound.Compound static method)
compare_chemical_details_with_mapping() (md_harmonize.compound.Compound method)
compare_ecs() (md_harmonize.harmonization.ReactionHarmonizationManager static method)
composition() (md_harmonize.compound.Compound property)
Compound (class in md_harmonize.compound)
compound_mappings() (md_harmonize.harmonization.ReactionHarmonizationManager method)
compound_pair_mappings() (in module md_harmonize.KEGG_parser)
CompoundHarmonizationManager (class in md_harmonize.harmonization)
connected_components() (md_harmonize.compound.Compound method)
construct_aromatic_entity() (md_harmonize.aromatics.AromaticManager static method)
construct_component() (md_harmonize.KEGG_parser.RpairParser static method)
contains_r_groups() (md_harmonize.compound.Compound method)
count_changed_atom_identifiers() (md_harmonize.KEGG_parser.RpairParser method)
create_atom_mappings() (in module md_harmonize.KEGG_parser)
create_compound_kcf() (in module md_harmonize.KEGG_parser)
create_key() (md_harmonize.harmonization.HarmonizationManager static method)
create_manager() (md_harmonize.harmonization.CompoundHarmonizationManager static method)
create_reaction_centers() (md_harmonize.KEGG_parser.RpairParser static method)
create_reactions() (in module md_harmonize.KEGG_parser)
(in module md_harmonize.MetaCyc_parser)
curate_invalid_n() (md_harmonize.compound.Compound method)
curate_invalid_symmetric_atoms() (md_harmonize.compound.Compound method)
curate_molfile() (in module md_harmonize.KEGG_database_scraper)
D
decode() (md_harmonize.aromatics.AromaticManager static method)
define_bond_stereochemistry() (md_harmonize.compound.Compound method)
detect_abnormal_atom() (md_harmonize.compound.Compound method)
detect_aromatic_substructures() (md_harmonize.aromatics.AromaticManager method)
detect_aromatic_substructures_timeout() (md_harmonize.aromatics.AromaticManager method)
detect_components() (md_harmonize.KEGG_parser.RpairParser static method)
determine_relationship() (md_harmonize.compound.Compound static method)
(md_harmonize.harmonization.ReactionHarmonizationManager static method)
difference (md_harmonize.KEGG_parser.reaction_center attribute)
distance_matrix() (md_harmonize.compound.Compound property)
download() (in module md_harmonize.KEGG_database_scraper)
E
encode() (md_harmonize.aromatics.AromaticManager method)
(md_harmonize.compound.Compound method)
entry_list() (in module md_harmonize.KEGG_database_scraper)
extract_aromatic_bonds() (md_harmonize.compound.Compound method)
extract_aromatic_substructures() (md_harmonize.aromatics.AromaticManager method)
extract_double_bond_connecting_cycle() (md_harmonize.compound.Compound method)
F
find_center_atoms() (md_harmonize.KEGG_parser.RpairParser method)
find_compound() (md_harmonize.harmonization.CompoundHarmonizationManager static method)
find_critical_atom_in_cycle() (md_harmonize.compound.Compound method)
find_cycles() (md_harmonize.compound.Compound method)
find_cycles_helper() (md_harmonize.compound.Compound method)
find_double_bond_linked_atom() (md_harmonize.compound.Compound method)
find_mappings() (md_harmonize.compound.Compound method)
find_mappings_reversed() (md_harmonize.compound.Compound method)
find_target_atom() (md_harmonize.KEGG_parser.RpairParser static method)
first_round_color() (md_harmonize.compound.Compound method)
formula() (md_harmonize.compound.Compound property)
fuse_cycles() (md_harmonize.aromatics.AromaticManager static method)
G
generate_atom_color_with_neighbors() (md_harmonize.compound.Compound method)
generate_atom_mapping_by_atom_color() (md_harmonize.compound.Compound method)
generate_atom_mappings() (md_harmonize.KEGG_parser.RpairParser method)
generate_atom_zero_layer_color() (md_harmonize.compound.Compound method)
generate_kat_neighbors() (md_harmonize.KEGG_parser.RpairParser static method)
generate_one_to_one_mappings() (in module md_harmonize.MetaCyc_parser)
get_center_list() (md_harmonize.KEGG_parser.RpairParser static method)
get_chemical_details() (md_harmonize.compound.Compound method)
get_edge_list() (md_harmonize.harmonization.CompoundHarmonizationManager method)
get_next_layer_neighbors() (md_harmonize.compound.Compound method)
H
h_color_identifier() (md_harmonize.compound.Compound method)
h_index() (md_harmonize.compound.Compound property)
HarmonizationManager (class in md_harmonize.harmonization)
harmonize_compound_list() (in module md_harmonize.harmonization)
harmonize_reaction() (md_harmonize.harmonization.ReactionHarmonizationManager method)
harmonize_reaction_list() (in module md_harmonize.harmonization)
HarmonizedCompoundEdge (class in md_harmonize.harmonization)
HarmonizedEdge (class in md_harmonize.harmonization)
HarmonizedReactionEdge (class in md_harmonize.harmonization)
has_isolated_atoms() (md_harmonize.compound.Compound method)
has_visited() (md_harmonize.harmonization.CompoundHarmonizationManager method)
heavy_atoms() (md_harmonize.compound.Compound property)
I
i (md_harmonize.KEGG_parser.reaction_center attribute)
index_of_heavy_atoms() (md_harmonize.compound.Compound property)
indigo_aromatic_bonds() (md_harmonize.aromatics.AromaticManager method)
indigo_aromatize() (md_harmonize.aromatics.AromaticManager method)
invalid_symmetric_atoms() (md_harmonize.compound.Compound method)
J
jaccard() (md_harmonize.harmonization.ReactionHarmonizationManager method)
K
kat (md_harmonize.KEGG_parser.reaction_center attribute)
kegg_aromatize() (md_harmonize.aromatics.AromaticManager method)
kegg_data_parser() (in module md_harmonize.KEGG_parser)
kegg_kcf_parser() (in module md_harmonize.KEGG_parser)
L
label (md_harmonize.KEGG_parser.reaction_center attribute)
M
map_atom_by_colors() (md_harmonize.KEGG_parser.RpairParser method)
map_components() (md_harmonize.KEGG_parser.RpairParser method)
map_r_correspondents() (md_harmonize.compound.Compound method)
map_resonance() (md_harmonize.compound.Compound method)
map_resonance_helper() (md_harmonize.compound.Compound method)
map_whole_compound() (md_harmonize.KEGG_parser.RpairParser method)
match (md_harmonize.KEGG_parser.reaction_center attribute)
match_unmapped_compounds() (md_harmonize.harmonization.ReactionHarmonizationManager method)
md_harmonize (module)
md_harmonize.aromatics (module)
md_harmonize.compound (module)
md_harmonize.harmonization (module)
md_harmonize.KEGG_database_scraper (module)
md_harmonize.KEGG_parser (module)
md_harmonize.MetaCyc_parser (module)
md_harmonize.reaction (module)
metal_color_identifier() (md_harmonize.compound.Compound method)
metal_index() (md_harmonize.compound.Compound property)
molfile_name() (md_harmonize.compound.Compound static method)
N
name() (md_harmonize.compound.Compound property)
(md_harmonize.reaction.Reaction property)
O
one_to_one_compound_mappings() (md_harmonize.harmonization.ReactionHarmonizationManager method)
optimal_mapping_with_r() (md_harmonize.compound.Compound method)
optimal_resonant_mapping() (md_harmonize.compound.Compound method)
P
pair_atom_mappings() (md_harmonize.harmonization.HarmonizedCompoundEdge method)
pair_components() (md_harmonize.KEGG_parser.RpairParser static method)
pair_relationship() (md_harmonize.harmonization.HarmonizedEdge method)
parse_equation() (in module md_harmonize.KEGG_parser)
preliminary_atom_mappings_check() (md_harmonize.KEGG_parser.RpairParser static method)
R
r_groups() (md_harmonize.compound.Compound property)
Reaction (class in md_harmonize.reaction)
reaction_center (class in md_harmonize.KEGG_parser)
reaction_parser() (in module md_harmonize.MetaCyc_parser)
reaction_side_parser() (in module md_harmonize.MetaCyc_parser)
ReactionHarmonizationManager (class in md_harmonize.harmonization)
remove_different_bonds() (md_harmonize.KEGG_parser.RpairParser static method)
remove_edge() (md_harmonize.harmonization.CompoundHarmonizationManager method)
(md_harmonize.harmonization.HarmonizationManager method)
remove_neighbors() (md_harmonize.compound.Atom method)
reset_color() (md_harmonize.compound.Atom method)
(md_harmonize.compound.Compound method)
restore_cycle() (md_harmonize.compound.Compound method)
reversed_mappings() (md_harmonize.harmonization.HarmonizedCompoundEdge property)
reversed_relationship() (md_harmonize.harmonization.HarmonizedEdge property)
RpairParser (class in md_harmonize.KEGG_parser)
S
same_structure_relationship() (md_harmonize.compound.Compound method)
save_manager() (md_harmonize.harmonization.HarmonizationManager method)
search() (md_harmonize.harmonization.HarmonizationManager method)
separate_connected_components() (md_harmonize.compound.Compound method)
structure_matrix() (md_harmonize.compound.Compound method)
U
unmapped_compounds() (md_harmonize.harmonization.ReactionHarmonizationManager method)
update_aromatic_bond_type() (md_harmonize.compound.Compound method)
update_atom_number() (md_harmonize.compound.Atom method)
update_atom_symbol() (md_harmonize.compound.Compound method)
update_bond_type() (md_harmonize.compound.Bond method)
update_color_tuple() (md_harmonize.compound.Compound method)
update_cycle() (md_harmonize.compound.Atom method)
update_entity() (in module md_harmonize.KEGG_database_scraper)
update_first_atom() (md_harmonize.compound.Bond method)
update_kat() (md_harmonize.compound.Atom method)
update_second_atom() (md_harmonize.compound.Bond method)
update_stereochemistry() (md_harmonize.compound.Atom method)
(md_harmonize.compound.Bond method)
update_symbol() (md_harmonize.compound.Atom method)
V
validate_component_atom_mappings() (md_harmonize.KEGG_parser.RpairParser static method)
validate_mapping_with_r() (md_harmonize.compound.Compound method)
W
with_r_pair_relationship() (md_harmonize.compound.Compound method)
with_r_pair_relationship_helper() (md_harmonize.compound.Compound method)
md_harmonize
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