useful_rdkit_utils
Getting Started
Installation
REOS
Ring Systems
Fingerprints and Descriptors
Scaffold Finder
Cross-validation and data splitting
Reactions
Molecular Geometry
Miscellaneous Utilities
Jupyter
Pandas
Seaborn
Stats
Units
SALI
Model Comparison
Descriptor Preprocessor
useful_rdkit_utils
Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
K
|
L
|
M
|
P
|
R
|
S
|
T
|
U
|
V
A
add_molecule_and_errors() (in module useful_rdkit_utils.pandas_utils)
align_mols_to_template() (in module useful_rdkit_utils.misc_utils)
B
bootstrap_confidence_interval() (in module useful_rdkit_utils.stat_utils)
boxplot_base64_image() (in module useful_rdkit_utils.misc_utils)
build_ring_systems_dataframe() (in module useful_rdkit_utils.ring_systems)
C
calc_mol() (RDKitDescriptors method)
(RDKitProperties method)
(Ro5Calculator method)
calc_smiles() (RDKitDescriptors method)
(RDKitProperties method)
(Ro5Calculator method)
calculate_sali() (in module useful_rdkit_utils.sali)
clean_and_scale_descriptors() (in module useful_rdkit_utils.descriptors)
clean_descriptors() (in module useful_rdkit_utils.descriptors)
cleanup_fragment() (in module useful_rdkit_utils.scaffold_finder)
cleanup_fragments() (RingSystemFinder method)
cleave_linker_bonds() (RingSystemFinder static method)
compare_datasets() (in module useful_rdkit_utils.descriptors)
count_fragments() (in module useful_rdkit_utils.misc_utils)
create_ring_dictionary() (in module useful_rdkit_utils.ring_systems)
cross_validate() (in module useful_rdkit_utils.split_utils)
D
demo_block_logs() (in module useful_rdkit_utils.misc_utils)
drop_rule() (REOS method)
E
enumerate_library() (in module useful_rdkit_utils.reactions)
enumerate_library_sample() (in module useful_rdkit_utils.reactions)
F
find_ring_systems() (RingSystemFinder method)
find_scaffolds() (in module useful_rdkit_utils.scaffold_finder)
fix_bond_stereo() (RingSystemFinder static method)
G
gen_3d() (in module useful_rdkit_utils.geometry)
gen_conformers() (in module useful_rdkit_utils.geometry)
generate_fragments() (in module useful_rdkit_utils.scaffold_finder)
get_active_rule_sets() (REOS method)
get_available_rule_sets() (REOS method)
get_bemis_murcko_clusters() (in module useful_rdkit_utils.split_utils)
get_butina_clusters() (in module useful_rdkit_utils.split_utils)
get_center() (in module useful_rdkit_utils.geometry)
get_conformer_energies() (in module useful_rdkit_utils.geometry)
get_count_fp() (Smi2Fp method)
get_fp() (Smi2Fp method)
get_kmeans_clusters() (in module useful_rdkit_utils.split_utils)
get_largest_fragment() (in module useful_rdkit_utils.misc_utils)
get_min_ring_frequency() (in module useful_rdkit_utils.ring_systems)
get_molecules_with_scaffold() (in module useful_rdkit_utils.scaffold_finder)
get_np() (Smi2Fp method)
get_np_counts() (Smi2Fp method)
get_random_clusters() (in module useful_rdkit_utils.split_utils)
get_rule_file_location() (REOS method)
get_rules_dict() (REOS method)
get_scaffold() (in module useful_rdkit_utils.split_utils)
get_shape_moments() (in module useful_rdkit_utils.geometry)
get_spiro_atoms() (in module useful_rdkit_utils.ring_systems)
get_unit_multiplier() (in module useful_rdkit_utils.units)
GroupKFoldShuffle (class in useful_rdkit_utils.split_utils)
K
kcal_to_ki() (in module useful_rdkit_utils.units)
ki_to_kcal() (in module useful_rdkit_utils.units)
L
label_atoms() (in module useful_rdkit_utils.misc_utils)
M
main() (in module useful_rdkit_utils.scaffold_finder)
max_possible_correlation() (in module useful_rdkit_utils.stat_utils)
max_ring_size() (in module useful_rdkit_utils.ring_systems)
mcs_align() (in module useful_rdkit_utils.misc_utils)
mcs_rmsd() (in module useful_rdkit_utils.geometry)
module
useful_rdkit_utils.descriptors
useful_rdkit_utils.geometry
useful_rdkit_utils.jupyter_utils
useful_rdkit_utils.misc_utils
useful_rdkit_utils.pandas_utils
useful_rdkit_utils.reactions
useful_rdkit_utils.reos
useful_rdkit_utils.ring_systems
useful_rdkit_utils.sali
useful_rdkit_utils.scaffold_finder
useful_rdkit_utils.seaborn_utils
useful_rdkit_utils.split_utils
useful_rdkit_utils.stat_utils
useful_rdkit_utils.units
mol2morgan_fp() (in module useful_rdkit_utils.descriptors)
mol2numpy_fp() (in module useful_rdkit_utils.descriptors)
mol_to_3D_view() (in module useful_rdkit_utils.geometry)
mol_to_base64_image() (in module useful_rdkit_utils.misc_utils)
P
pandas_mols() (RDKitDescriptors method)
(RDKitProperties method)
(REOS method)
(RingSystemLookup method)
(Ro5Calculator method)
pandas_smiles() (RDKitDescriptors method)
(RDKitProperties method)
(REOS method)
(RingSystemLookup method)
(Ro5Calculator method)
parse_smarts() (REOS method)
pearson_confidence() (in module useful_rdkit_utils.stat_utils)
plot_sali_pairs() (in module useful_rdkit_utils.sali)
process_mol() (REOS method)
(RingSystemLookup method)
process_smiles() (REOS method)
(RingSystemLookup method)
R
rd_enable_png() (in module useful_rdkit_utils.jupyter_utils)
rd_enable_svg() (in module useful_rdkit_utils.jupyter_utils)
rd_make_structures_pretty() (in module useful_rdkit_utils.jupyter_utils)
rd_set_image_size() (in module useful_rdkit_utils.jupyter_utils)
rd_setup_jupyter() (in module useful_rdkit_utils.jupyter_utils)
rd_show_atom_indices() (in module useful_rdkit_utils.jupyter_utils)
rd_show_cip_stereo() (in module useful_rdkit_utils.jupyter_utils)
rd_shut_the_hell_up() (in module useful_rdkit_utils.misc_utils)
RDKitDescriptors (class in useful_rdkit_utils.descriptors)
RDKitProperties (class in useful_rdkit_utils.descriptors)
read_rules() (REOS method)
refine_conformers() (in module useful_rdkit_utils.geometry)
remove_dummy_atoms() (in module useful_rdkit_utils.misc_utils)
REOS (class in useful_rdkit_utils.reos)
ring_stats() (in module useful_rdkit_utils.ring_systems)
RingSystemFinder (class in useful_rdkit_utils.ring_systems)
RingSystemLookup (class in useful_rdkit_utils.ring_systems)
Ro5Calculator (class in useful_rdkit_utils.descriptors)
S
scale_descriptors() (in module useful_rdkit_utils.descriptors)
set_active_rule_sets() (REOS method)
set_min_priority() (REOS method)
set_output_smarts() (REOS method)
set_sns_defaults() (in module useful_rdkit_utils.seaborn_utils)
set_sns_size() (in module useful_rdkit_utils.seaborn_utils)
Smi2Fp (class in useful_rdkit_utils.descriptors)
smi2mol_with_errors() (in module useful_rdkit_utils.misc_utils)
smi2morgan_fp() (in module useful_rdkit_utils.descriptors)
smi2numpy_fp() (in module useful_rdkit_utils.descriptors)
smi_to_base64_image() (in module useful_rdkit_utils.misc_utils)
split() (GroupKFoldShuffle method)
T
tag_atoms() (in module useful_rdkit_utils.misc_utils)
tag_bonds_to_preserve() (RingSystemFinder method)
taylor_butina_clustering() (in module useful_rdkit_utils.misc_utils)
test_ring_system_finder() (in module useful_rdkit_utils.ring_systems)
test_ring_system_lookup() (in module useful_rdkit_utils.ring_systems)
U
ug_ml_to_uM() (in module useful_rdkit_utils.units)
update_descriptors() (RDKitDescriptors method)
useful_rdkit_utils.descriptors
module
useful_rdkit_utils.geometry
module
useful_rdkit_utils.jupyter_utils
module
useful_rdkit_utils.misc_utils
module
useful_rdkit_utils.pandas_utils
module
useful_rdkit_utils.reactions
module
useful_rdkit_utils.reos
module
useful_rdkit_utils.ring_systems
module
useful_rdkit_utils.sali
module
useful_rdkit_utils.scaffold_finder
module
useful_rdkit_utils.seaborn_utils
module
useful_rdkit_utils.split_utils
module
useful_rdkit_utils.stat_utils
module
useful_rdkit_utils.units
module
V
value_counts_df() (in module useful_rdkit_utils.pandas_utils)