Index

A

add_all_chembl_compound_properties() (in module add_chembl_compound_properties) add_annotations_to_drug_mechanisms_cti() (in module get_drug_mechanism_ct_pairs) add_aromaticity_descriptors() (in module add_rdkit_compound_descriptors) add_built_in_descriptors() (in module add_rdkit_compound_descriptors) add_chembl_compound_properties module add_chembl_target_class_annotations module add_chembl_target_class_annotations() (in module add_chembl_target_class_annotations) add_dataset_sizes() (in module get_stats) add_debugging_info() (in module get_stats) add_dm_filtering_columns() (in module get_drug_mechanism_ct_pairs)

add_drug_mechanism_ct_pairs() (in module get_drug_mechanism_ct_pairs) add_dti_annotations module add_dti_annotations() (in module add_dti_annotations) add_filtering_columns module add_filtering_columns() (in module add_filtering_columns) add_rdkit_compound_descriptors module add_rdkit_compound_descriptors() (in module add_rdkit_compound_descriptors) add_subset_filtering_columns() (in module add_filtering_columns) arguments module

C

calculate_aromatic_atoms() (in module add_rdkit_compound_descriptors) calculate_ligand_efficiency_metrics() (in module add_chembl_compound_properties) calculate_rdkit (arguments.CalculationArgs attribute) CalculationArgs (class in arguments) check_atc() (in module sanity_checks) check_compound_props() (in module sanity_checks) check_for_mixed_types() (in module sanity_checks) check_ligand_efficiency_metrics() (in module sanity_checks)

check_null_values() (in module sanity_checks) check_pairs_without_pchembl_are_in_drug_mechanisms() (in module sanity_checks) check_rdkit_props() (in module sanity_checks) check_target_classes() (in module sanity_checks) chembl_version (arguments.CalculationArgs attribute) clean_dataset module clean_dataset() (in module clean_dataset) clean_none_values() (in module clean_dataset)

D

dataset module Dataset (class in dataset) delimiter (arguments.OutputArgs attribute)

df_result (dataset.Dataset attribute) df_sizes_all (dataset.Dataset attribute) df_sizes_pchembl (dataset.Dataset attribute) drug_mechanism_pairs_set (dataset.Dataset attribute) drug_mechanism_targets_set (dataset.Dataset attribute)

G

get_activity_ct_pairs module get_aggregated_activity_ct_pairs() (in module get_activity_ct_pairs) get_aggregated_compound_target_pairs_with_pchembl() (in module get_activity_ct_pairs) get_aggregated_target_classes() (in module add_chembl_target_class_annotations) get_args() (in module arguments) get_atc_classification() (in module add_chembl_compound_properties) get_average_info() (in module get_activity_ct_pairs) get_chembl_properties_and_structures() (in module add_chembl_compound_properties) get_compound_target_pairs_with_pchembl() (in module get_activity_ct_pairs) get_ct_pair_dataset() (in module get_dataset) get_data_subsets() (in module add_filtering_columns) get_dataset module

get_dataset_sizes() (in module get_stats) get_drug_mechanism_ct_pairs module get_drug_mechanism_ct_pairs() (in module get_drug_mechanism_ct_pairs) get_drug_mechanisms_interactions() (in module get_drug_mechanism_ct_pairs) get_first_publication_cpd_date() (in module add_chembl_compound_properties) get_relevant_tid_mappings() (in module get_drug_mechanism_ct_pairs) get_stats module get_stats_columns() (in module get_stats) get_stats_for_column() (in module get_stats) get_target_class_table() (in module add_chembl_target_class_annotations)

L

limit_to_literature (arguments.CalculationArgs attribute)

limited_flag (arguments.CalculationArgs attribute)

M

main module main() (in module main) min_nof_cpds_b (arguments.CalculationArgs attribute) min_nof_cpds_bf (arguments.CalculationArgs attribute) module add_chembl_compound_properties add_chembl_target_class_annotations add_dti_annotations add_filtering_columns add_rdkit_compound_descriptors arguments clean_dataset dataset get_activity_ct_pairs get_dataset get_drug_mechanism_ct_pairs get_stats main output sanity_checks

O

output module output_ambiguous_target_classes() (in module add_chembl_target_class_annotations)

output_path (arguments.OutputArgs attribute) output_stats() (in module output) OutputArgs (class in arguments)

P

parse_args() (in module arguments)

R

remove_compounds_without_smiles_and_mixtures() (in module clean_dataset)

reorder_columns() (in module clean_dataset) round_floats() (in module clean_dataset)

S

sanity_checks module

sanity_checks() (in module sanity_checks) set_types_to_int() (in module clean_dataset)

T

test_equality() (in module sanity_checks)

W

write_and_check_output() (in module output) write_b (arguments.OutputArgs attribute) write_bf (arguments.OutputArgs attribute) write_debug_sizes() (in module output)

write_full_dataset (arguments.OutputArgs attribute) write_full_dataset_to_file() (in module output) write_output() (in module output) write_to_csv (arguments.OutputArgs attribute) write_to_excel (arguments.OutputArgs attribute)