Index

A

align() (utils.analysis.PSAStretcherAligner method) aligned_query (utils.analysis.StretcherAlignment attribute) aligned_subject (utils.analysis.StretcherAlignment attribute) AnalysisResult (class in utils.analysis)

AnalyzerConfig (class in utils.analysis) audit_config() (utils.rank_fragility.config.RunConfig method) audit_dataset() (in module utils.rank_fragility.audit) AuditConfig (class in utils.rank_fragility.config)

B

baseline_model (utils.rank_fragility.config.MetricConfig attribute) (utils.rank_fragility.config.RunConfig attribute) BaselineParams (class in utils.baselines)

BaseLoader (class in utils.loader) build_analyzer() (in module utils) build_arg_parser() (in module utils.rank_fragility.run) build_loader() (in module utils)

C

canonicalize() (utils.cleaner.SMILESCleaner method) canonicalize_all() (utils.cleaner.SMILESCleaner method) clean_benchmark_splits() (in module utils) (in module utils.benchmark_cleaning) cliffs_rows (utils.analysis.AnalysisResult attribute)

compute_advantage_decomposition() (in module utils.rank_fragility.attribution) compute_fragility_summary() (in module utils.rank_fragility.fragility) compute_metric() (in module utils.rank_fragility.metrics) config_from_args() (in module utils.rank_fragility.run) conflicts_rows (utils.analysis.AnalysisResult attribute)

D

data (utils.rank_fragility.config.RunConfig attribute) deduplicate_all() (utils.cleaner.SMILESCleaner method) DEFAULT_ID_COLS (utils.loader.TabularLoader attribute) DEFAULT_LABEL_COLS (utils.loader.TabularLoader attribute) DEFAULT_SEQUENCE_COLS (utils.loader.TabularLoader attribute)

DEFAULT_SMILES_COLS (utils.loader.TabularLoader attribute) DEFAULT_TARGET_ID_COLS (utils.loader.TabularLoader attribute) discover_yaml_files() (in module run) drop_rule() (utils.cleaner.REOS method) DTIAnalyzer (class in utils.analysis) DTILoader (class in utils.loader)

E

echo_config() (in module run) eval_baselines_generic() (in module utils.baselines)

eval_baselines_polaris() (in module utils.baselines) evaluate_models() (in module utils.rank_fragility.leaderboard)

F

foldseek_m8_path (utils.analysis.AnalyzerConfig attribute) fp_nbits (utils.analysis.AnalyzerConfig attribute) (utils.baselines.BaselineParams attribute)

fp_radius (utils.analysis.AnalyzerConfig attribute) (utils.baselines.BaselineParams attribute)

G

gaps_pct (utils.analysis.StretcherAlignment attribute) generate_counterfactual_panels() (in module utils.rank_fragility.panels) get_active_rule_sets() (utils.cleaner.REOS method) get_available_rule_sets() (utils.cleaner.REOS method) get_data() (utils.cleaner.SMILESCleaner method)

get_rule_file_location() (utils.cleaner.REOS method) get_splits() (utils.loader.BaseLoader method) (utils.loader.PolarisLoader method) (utils.loader.TabularLoader method) (utils.loader.TDCLoader method) get_valid() (utils.cleaner.SMILESCleaner method)

H

higher_is_better() (in module utils.rank_fragility.metrics)

I

id_col (utils.analysis.AnalyzerConfig attribute) (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.PanelConfig attribute) (utils.rank_fragility.config.RunConfig attribute)

identity_pct (utils.analysis.StretcherAlignment attribute)

J

json_default() (in module utils)

L

label_col (utils.analysis.AnalyzerConfig attribute) (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.PanelConfig attribute) (utils.rank_fragility.config.RunConfig attribute) label_cols (utils.analysis.AnalyzerConfig attribute) length (utils.analysis.StretcherAlignment attribute)

lgbm_colsample (utils.baselines.BaselineParams attribute) lgbm_estimators (utils.baselines.BaselineParams attribute) lgbm_leaves (utils.baselines.BaselineParams attribute) lgbm_lr (utils.baselines.BaselineParams attribute) lgbm_subsample (utils.baselines.BaselineParams attribute) load_prediction_directory() (in module utils.rank_fragility.predictions) load_yaml() (in module run)

M

main() (in module run) (in module utils.rank_fragility.run) make_logger() (in module utils) merge_predictions_with_audit() (in module utils.rank_fragility.predictions) metric (utils.rank_fragility.config.MetricConfig attribute) (utils.rank_fragility.config.RunConfig attribute) metric_config() (utils.rank_fragility.config.RunConfig method) MetricConfig (class in utils.rank_fragility.config) mlp_hidden (utils.baselines.BaselineParams attribute) mlp_max_iter (utils.baselines.BaselineParams attribute) module run utils utils.analysis utils.baselines utils.benchmark_cleaning utils.cleaner utils.config_models utils.loader utils.pydantic_compat utils.rank_fragility.attribution utils.rank_fragility.audit utils.rank_fragility.config utils.rank_fragility.counterfactual utils.rank_fragility.fragility utils.rank_fragility.leaderboard utils.rank_fragility.metrics utils.rank_fragility.panels utils.rank_fragility.predictions utils.rank_fragility.run utils.splitting

mol_to_inchi() (utils.cleaner.SMILESCleaner static method) mol_to_molblock() (utils.cleaner.SMILESCleaner static method) mol_to_smiles() (utils.cleaner.SMILESCleaner static method) molblock_to_mol() (utils.cleaner.SMILESCleaner static method) morgan_fps() (in module utils.analysis)

N

n_gaps (utils.analysis.StretcherAlignment attribute) n_panels (utils.rank_fragility.config.PanelConfig attribute) (utils.rank_fragility.config.RunConfig attribute) name (utils.analysis.AnalyzerConfig attribute) near_leak_thresholds (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.RunConfig attribute)

normalize_echo_config() (in module utils.config_models) normalize_loader_config() (in module utils.config_models) normalize_runtime_config() (in module utils.config_models) normalize_split_column() (in module utils.config_models)

O

original_leaderboard() (in module utils.rank_fragility.leaderboard)

output_dir (utils.rank_fragility.config.PanelConfig attribute) (utils.rank_fragility.config.RunConfig attribute)

P

pandas_smiles() (utils.cleaner.REOS method) panel_config() (utils.rank_fragility.config.RunConfig method) panel_size (utils.rank_fragility.config.PanelConfig attribute) (utils.rank_fragility.config.RunConfig attribute) PanelConfig (class in utils.rank_fragility.config) parse_smarts() (utils.cleaner.REOS method) per_record_df (utils.analysis.AnalysisResult attribute) per_sample_loss() (in module utils.rank_fragility.metrics)

PolarisLoader (class in utils.loader) pred_dir (utils.rank_fragility.config.RunConfig attribute) primary_near_leak_threshold (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.RunConfig attribute) process_mol() (utils.cleaner.REOS method) process_smiles() (utils.cleaner.REOS method) PSAStretcherAligner (class in utils.analysis) pydantic_model_dump() (in module utils.pydantic_compat) pydantic_model_validate() (in module utils.pydantic_compat)

Q

query_end (utils.analysis.StretcherAlignment attribute)

query_start (utils.analysis.StretcherAlignment attribute)

R

random_seed (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.PanelConfig attribute) (utils.rank_fragility.config.RunConfig attribute) random_split_indices() (in module utils.splitting) rank_models() (in module utils.rank_fragility.leaderboard) read_rules() (utils.cleaner.REOS method) regression_conflict_threshold (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.RunConfig attribute) regression_conflict_threshold_sensitivity (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.RunConfig attribute) REOS (class in utils.cleaner) reos_filter_all() (utils.cleaner.SMILESCleaner method)

resolve_output_dir() (in module utils) ResultWriter (class in utils) rf_estimators (utils.baselines.BaselineParams attribute) run module run() (utils.analysis.DTIAnalyzer method) (utils.analysis.SMILESAnalyzer method) run_analysis() (in module utils.rank_fragility.run) run_baselines() (in module utils) (in module utils.baselines) run_counterfactual_evaluation() (in module utils.rank_fragility.counterfactual) run_one_config() (in module run) RunConfig (class in utils.rank_fragility.config)

S

scaffold_fps() (in module utils.analysis) scaffold_split_indices() (in module utils.splitting) score (utils.analysis.StretcherAlignment attribute) seed (utils.baselines.BaselineParams attribute) sequence_alignment_rows (utils.analysis.AnalysisResult attribute) sequence_alignment_workers (utils.analysis.AnalyzerConfig attribute) sequence_col (utils.analysis.AnalyzerConfig attribute) set_active_rule_sets() (utils.cleaner.REOS method) set_min_priority() (utils.cleaner.REOS method) set_output_smarts() (utils.cleaner.REOS method) sim_threshold (utils.analysis.AnalyzerConfig attribute) similarity_pct (utils.analysis.StretcherAlignment attribute) smiles_col (utils.analysis.AnalyzerConfig attribute) (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.RunConfig attribute) smiles_to_mol() (utils.cleaner.SMILESCleaner static method)

SMILESAnalyzer (class in utils.analysis) SMILESCleaner (class in utils.cleaner) sota_model (utils.rank_fragility.config.MetricConfig attribute) (utils.rank_fragility.config.RunConfig attribute) split_col (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.RunConfig attribute) split_indices() (in module utils.splitting) standardize() (utils.cleaner.SMILESCleaner static method) standardize_all() (utils.cleaner.SMILESCleaner method) standardize_mol() (utils.cleaner.SMILESCleaner static method) StretcherAlignment (class in utils.analysis) structure_alignment_rows (utils.analysis.AnalysisResult attribute) structure_check() (utils.cleaner.SMILESCleaner static method) subject_end (utils.analysis.StretcherAlignment attribute) subject_start (utils.analysis.StretcherAlignment attribute) summarize_audit() (in module utils.rank_fragility.audit) summary (utils.analysis.AnalysisResult attribute)

T

TabularLoader (class in utils.loader) target_id_col (utils.analysis.AnalyzerConfig attribute) target_rates (utils.rank_fragility.config.PanelConfig attribute) (utils.rank_fragility.config.RunConfig attribute) task (utils.rank_fragility.config.AuditConfig attribute) (utils.rank_fragility.config.MetricConfig attribute) (utils.rank_fragility.config.PanelConfig attribute) (utils.rank_fragility.config.RunConfig attribute)

task_type (utils.analysis.AnalyzerConfig attribute) TDCLoader (class in utils.loader) typ (utils.analysis.AnalyzerConfig attribute)

U

unique_sequences_jsonl (utils.analysis.AnalyzerConfig attribute) utils module utils.analysis module utils.baselines module utils.benchmark_cleaning module utils.cleaner module utils.config_models module utils.loader module utils.pydantic_compat module utils.rank_fragility.attribution module

utils.rank_fragility.audit module utils.rank_fragility.config module utils.rank_fragility.counterfactual module utils.rank_fragility.fragility module utils.rank_fragility.leaderboard module utils.rank_fragility.metrics module utils.rank_fragility.panels module utils.rank_fragility.predictions module utils.rank_fragility.run module utils.splitting module

V

validate_yaml_mapping() (in module utils.config_models)

W

write_analysis() (utils.ResultWriter method) write_performance() (utils.ResultWriter method)

write_records() (utils.ResultWriter method) write_summary() (utils.ResultWriter method)