Index

_

__init__() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) _calculate_gmic() (TACTICS.thompson_sampling.strategies._thermal.GMICCriticalityMixin method)

_calculate_gmic_details() (TACTICS.thompson_sampling.strategies._thermal.GMICCriticalityMixin method) _rotation_flexibility() (TACTICS.thompson_sampling.strategies._thermal.ThermalCyclingMixin method)

A

adapt_heated_scale() (TACTICS.thompson_sampling.strategies.top_two_selection.TopTwoSelection method) adapt_temperatures() (TACTICS.thompson_sampling.strategies.roulette_wheel.RouletteWheelSelection method) (TACTICS.thompson_sampling.strategies.top_two_selection.TopTwoSelection method)

add_score() (TACTICS.thompson_sampling.core.reagent.Reagent method) auto_detect_compatibility() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) AutoDetectionResult (class in TACTICS.library_enumeration.enumeration_utils)

B

BalancedWarmup (class in TACTICS.thompson_sampling.warmup.balanced) BalancedWarmupConfig (class in TACTICS.thompson_sampling.warmup.config) baseline() (TACTICS.thompson_sampling.presets.ConfigPresets static method)

BayesUCBConfig (class in TACTICS.thompson_sampling.strategies.config) BayesUCBSelection (class in TACTICS.thompson_sampling.strategies.bayes_ucb_selection) bind_worker_context() (TACTICS.thompson_sampling.core.parallel_evaluator.ParallelEvaluator method)

C

close() (TACTICS.thompson_sampling.core.parallel_evaluator.ParallelEvaluator method) (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) compare_trajectory_vs_snapshot() (in module TACTICS.thompson_sampling.diagnostics) compute_convergence_point() (in module TACTICS.thompson_sampling.diagnostics) compute_disagreement_convergence() (in module TACTICS.thompson_sampling.diagnostics) compute_posterior_entropy() (in module TACTICS.thompson_sampling.diagnostics) compute_scale_adaptation() (in module TACTICS.thompson_sampling.diagnostics) ConfigPresets (class in TACTICS.thompson_sampling.presets) counter (TACTICS.thompson_sampling.core.evaluators.CustomEvaluator property) (TACTICS.thompson_sampling.core.evaluators.DBEvaluator property) (TACTICS.thompson_sampling.core.evaluators.Evaluator property) (TACTICS.thompson_sampling.core.evaluators.FPEvaluator property) (TACTICS.thompson_sampling.core.evaluators.FredEvaluator property) (TACTICS.thompson_sampling.core.evaluators.LookupEvaluator property) (TACTICS.thompson_sampling.core.evaluators.MLClassifierEvaluator property) (TACTICS.thompson_sampling.core.evaluators.MWEvaluator property) (TACTICS.thompson_sampling.core.evaluators.ROCSEvaluator property)

coverage_stats (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef property) create_evaluator() (in module TACTICS.thompson_sampling.factories) create_strategy() (in module TACTICS.thompson_sampling.factories) create_warmup() (in module TACTICS.thompson_sampling.factories) CustomEvaluator (class in TACTICS.thompson_sampling.core.evaluators) CustomEvaluatorConfig (class in TACTICS.thompson_sampling.core.evaluator_config)

D

DBEvaluator (class in TACTICS.thompson_sampling.core.evaluators) DBEvaluatorConfig (class in TACTICS.thompson_sampling.core.evaluator_config)

DeprotectionSpec (class in TACTICS.library_enumeration.smarts_toolkit.config) detailed_message() (TACTICS.library_enumeration.enumeration_utils.EnumerationError method)

E

EnhancedWarmup (class in TACTICS.thompson_sampling.warmup.enhanced) EnhancedWarmupConfig (class in TACTICS.thompson_sampling.warmup.config) enumerate() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) enumerate_batch() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) enumerate_from_smiles() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) enumerate_library() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) enumerate_products() (in module TACTICS.library_enumeration.generate_products) enumerate_single() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) enumerate_single_from_smiles() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) EnumerationError (class in TACTICS.library_enumeration.enumeration_utils) EnumerationResult (class in TACTICS.library_enumeration.enumeration_utils) EpsilonGreedyConfig (class in TACTICS.thompson_sampling.strategies.config) EpsilonGreedySelection (class in TACTICS.thompson_sampling.strategies.epsilon_greedy)

evaluate() (TACTICS.thompson_sampling.core.evaluators.CustomEvaluator method) (TACTICS.thompson_sampling.core.evaluators.DBEvaluator method) (TACTICS.thompson_sampling.core.evaluators.Evaluator method) (TACTICS.thompson_sampling.core.evaluators.FPEvaluator method) (TACTICS.thompson_sampling.core.evaluators.FredEvaluator method) (TACTICS.thompson_sampling.core.evaluators.LookupEvaluator method) (TACTICS.thompson_sampling.core.evaluators.MLClassifierEvaluator method) (TACTICS.thompson_sampling.core.evaluators.MWEvaluator method) (TACTICS.thompson_sampling.core.evaluators.ROCSEvaluator method) (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) evaluate_batch() (TACTICS.thompson_sampling.core.parallel_evaluator.ParallelEvaluator method) (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) Evaluator (class in TACTICS.thompson_sampling.core.evaluators)

F

failures_to_dataframe() (in module TACTICS.library_enumeration.enumeration_utils) format_sar_report() (in module TACTICS.thompson_sampling.diagnostics) FPEvaluator (class in TACTICS.thompson_sampling.core.evaluators) FPEvaluatorConfig (class in TACTICS.thompson_sampling.core.evaluator_config)

FredEvaluator (class in TACTICS.thompson_sampling.core.evaluators) FredEvaluatorConfig (class in TACTICS.thompson_sampling.core.evaluator_config) from_config() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler class method) from_worker_data() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline class method)

G

gen_line_plot_performance_data() (TACTICS.library_analysis.visualization.TS_Benchmarks method) gen_TS_runs_data() (TACTICS.library_analysis.visualization.TS_Benchmarks method) generate_all_combinations() (in module TACTICS.library_enumeration.generate_products) generate_warmup_combinations() (TACTICS.thompson_sampling.warmup.balanced.BalancedWarmup method) (TACTICS.thompson_sampling.warmup.base.WarmupStrategy method) (TACTICS.thompson_sampling.warmup.enhanced.EnhancedWarmup method) get_all_protecting_group_names() (in module TACTICS.library_enumeration.smarts_toolkit.constants) get_barplot_TS_results_data() (TACTICS.library_analysis.visualization.TS_Benchmarks method) get_compatibility_map() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) get_compatible_patterns() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) get_compatible_reagents() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef method) get_component_criticality() (TACTICS.thompson_sampling.strategies._thermal.GMICCriticalityMixin method) (TACTICS.thompson_sampling.strategies.base_strategy.SelectionStrategy method) (TACTICS.thompson_sampling.strategies.bayes_ucb_selection.BayesUCBSelection method) get_component_state() (TACTICS.thompson_sampling.strategies.base_strategy.SelectionStrategy method) (TACTICS.thompson_sampling.strategies.bayes_ucb_selection.BayesUCBSelection method) (TACTICS.thompson_sampling.strategies.roulette_wheel.RouletteWheelSelection method) (TACTICS.thompson_sampling.strategies.top_two_selection.TopTwoSelection method) get_description() (TACTICS.thompson_sampling.warmup.base.WarmupStrategy method) get_diagnostics() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method)

get_expected_evaluations() (TACTICS.thompson_sampling.warmup.balanced.BalancedWarmup method) (TACTICS.thompson_sampling.warmup.base.WarmupStrategy method) (TACTICS.thompson_sampling.warmup.enhanced.EnhancedWarmup method) get_incompatible_reagents() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef method) get_inputs_for_step() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig method) get_name() (TACTICS.thompson_sampling.warmup.balanced.BalancedWarmup method) (TACTICS.thompson_sampling.warmup.base.WarmupStrategy method) (TACTICS.thompson_sampling.warmup.enhanced.EnhancedWarmup method) get_num_prods() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) get_posterior_landscape() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) get_preset() (in module TACTICS.thompson_sampling.presets) get_primary_reaction() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig method) get_protecting_group() (in module TACTICS.library_enumeration.smarts_toolkit.constants) get_reactant_template() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef method) get_reactions_for_step() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig method) get_sar_summary() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) get_validator() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) GMICCriticalityMixin (class in TACTICS.thompson_sampling.strategies._thermal) GreedyConfig (class in TACTICS.thompson_sampling.strategies.config) GreedySelection (class in TACTICS.thompson_sampling.strategies.greedy_selection)

H

has_alternatives (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline property)

has_alternatives_at_step() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig method)

I

init_prior() (TACTICS.thompson_sampling.core.reagent.Reagent method) InputSource (class in TACTICS.library_enumeration.smarts_toolkit.config) install() (in module TACTICS._lazy) is_multi_step (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig property) (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline property)

is_product_deprotection (TACTICS.library_enumeration.smarts_toolkit.config.DeprotectionSpec property) is_valid() (TACTICS.library_enumeration.smarts_toolkit._validator.ValidationResult method) is_validated (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef property)

L

load_product_library() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method)

LookupEvaluator (class in TACTICS.thompson_sampling.core.evaluators) LookupEvaluatorConfig (class in TACTICS.thompson_sampling.core.evaluator_config)

M

MLClassifierEvaluator (class in TACTICS.thompson_sampling.core.evaluators) MLClassifierEvaluatorConfig (class in TACTICS.thompson_sampling.core.evaluator_config) module TACTICS._lazy TACTICS.library_analysis.diagnostic_plots TACTICS.library_enumeration.enumeration_utils TACTICS.library_enumeration.file_writer TACTICS.library_enumeration.generate_products TACTICS.library_enumeration.smarts_toolkit.config TACTICS.library_enumeration.smarts_toolkit.constants TACTICS.thompson_sampling.core.evaluator_config TACTICS.thompson_sampling.core.evaluators TACTICS.thompson_sampling.diagnostics TACTICS.thompson_sampling.factories TACTICS.thompson_sampling.strategies.config TACTICS.thompson_sampling.warmup.config

MWEvaluator (class in TACTICS.thompson_sampling.core.evaluators) MWEvaluatorConfig (class in TACTICS.thompson_sampling.core.evaluator_config)

N

num_components (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline property) (TACTICS.thompson_sampling.config.ThompsonSamplingConfig property) num_reactants (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef property)

num_steps (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig property) (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline property) (TACTICS.thompson_sampling.config.ThompsonSamplingConfig property)

O

overlay() (TACTICS.thompson_sampling.core.evaluators.ROCSEvaluator method)

P

ParallelEvaluator (class in TACTICS.thompson_sampling.core.parallel_evaluator) pattern_ids (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline property) plot_adaptive_intensity() (in module TACTICS.library_analysis.diagnostic_plots) plot_barplot_TS_results() (TACTICS.library_analysis.visualization.TS_Benchmarks method) plot_criticality_trajectory() (in module TACTICS.library_analysis.diagnostic_plots) plot_gmic_directed_exploration() (in module TACTICS.library_analysis.diagnostic_plots) plot_line_performance_with_error_bars() (TACTICS.library_analysis.visualization.TS_Benchmarks method)

plot_reagent_usage_action_panel() (in module TACTICS.library_analysis.diagnostic_plots) plot_rws_diagnostic() (in module TACTICS.library_analysis.diagnostic_plots) plot_snr_trajectory() (in module TACTICS.library_analysis.diagnostic_plots) plot_temperature_decomposition() (in module TACTICS.library_analysis.diagnostic_plots) plot_ttts_diagnostic() (in module TACTICS.library_analysis.diagnostic_plots) prepare_scores() (TACTICS.thompson_sampling.strategies.base_strategy.SelectionStrategy method) prepare_worker_data() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) ProtectingGroupInfo (class in TACTICS.library_enumeration.smarts_toolkit.config)

R

reactant_index (TACTICS.library_enumeration.smarts_toolkit.config.DeprotectionSpec property) ReactionConfig (class in TACTICS.library_enumeration.smarts_toolkit.config) ReactionDef (class in TACTICS.library_enumeration.smarts_toolkit.config) reactions (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline property) read_reagent_file() (in module TACTICS.library_enumeration.enumeration_utils) read_reagents() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) Reagent (class in TACTICS.thompson_sampling.core.reagent) reagent_file_list (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline property) (TACTICS.thompson_sampling.config.ThompsonSamplingConfig property) recommended() (TACTICS.thompson_sampling.presets.ConfigPresets static method) recommended_rws() (TACTICS.thompson_sampling.presets.ConfigPresets static method)

register_compatibility() (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) reset_percentiles() (TACTICS.thompson_sampling.strategies.bayes_ucb_selection.BayesUCBSelection method) reset_temperature() (TACTICS.thompson_sampling.strategies.roulette_wheel.RouletteWheelSelection method) (TACTICS.thompson_sampling.strategies.top_two_selection.TopTwoSelection method) results_to_dataframe() (in module TACTICS.library_enumeration.enumeration_utils) ROCSEvaluator (class in TACTICS.thompson_sampling.core.evaluators) ROCSEvaluatorConfig (class in TACTICS.thompson_sampling.core.evaluator_config) rotate_component() (TACTICS.thompson_sampling.strategies._thermal.ThermalCyclingMixin method) rotate_component_weighted() (TACTICS.thompson_sampling.strategies._thermal.ThermalCyclingMixin method) RouletteWheelConfig (class in TACTICS.thompson_sampling.strategies.config) RouletteWheelSelection (class in TACTICS.thompson_sampling.strategies.roulette_wheel)

S

sample() (TACTICS.thompson_sampling.core.reagent.Reagent method) search() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) select_batch() (TACTICS.thompson_sampling.strategies.base_strategy.SelectionStrategy method) select_reagent() (TACTICS.thompson_sampling.strategies.base_strategy.SelectionStrategy method) (TACTICS.thompson_sampling.strategies.bayes_ucb_selection.BayesUCBSelection method) (TACTICS.thompson_sampling.strategies.epsilon_greedy.EpsilonGreedySelection method) (TACTICS.thompson_sampling.strategies.greedy_selection.GreedySelection method) (TACTICS.thompson_sampling.strategies.roulette_wheel.RouletteWheelSelection method) (TACTICS.thompson_sampling.strategies.top_two_selection.TopTwoSelection method) (TACTICS.thompson_sampling.strategies.ucb_selection.UCBSelection method) SelectionStrategy (class in TACTICS.thompson_sampling.strategies.base_strategy)

set_evaluator() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) set_hide_progress() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) set_max_confs() (TACTICS.thompson_sampling.core.evaluators.FredEvaluator method) (TACTICS.thompson_sampling.core.evaluators.ROCSEvaluator method) step_indices (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig property) StepInput (class in TACTICS.library_enumeration.smarts_toolkit.config) steps_with_alternatives (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig property) stripplot_TS_results() (TACTICS.library_analysis.visualization.TS_Benchmarks method) success (TACTICS.library_enumeration.enumeration_utils.EnumerationResult property) summarize_failures() (in module TACTICS.library_enumeration.enumeration_utils) summary() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef method) SynthesisPipeline (class in TACTICS.library_enumeration.synthesis_pipeline)

T

TACTICS._lazy module TACTICS.library_analysis.diagnostic_plots module TACTICS.library_enumeration.enumeration_utils module TACTICS.library_enumeration.file_writer module TACTICS.library_enumeration.generate_products module TACTICS.library_enumeration.smarts_toolkit.config module TACTICS.library_enumeration.smarts_toolkit.constants module TACTICS.thompson_sampling.core.evaluator_config module TACTICS.thompson_sampling.core.evaluators module

TACTICS.thompson_sampling.diagnostics module TACTICS.thompson_sampling.factories module TACTICS.thompson_sampling.strategies.config module TACTICS.thompson_sampling.warmup.config module ThermalCyclingMixin (class in TACTICS.thompson_sampling.strategies._thermal) ThompsonSampler (class in TACTICS.thompson_sampling.core.sampler) ThompsonSamplingConfig (class in TACTICS.thompson_sampling.config) to_dict() (TACTICS.library_enumeration.enumeration_utils.EnumerationError method) TopTwoConfig (class in TACTICS.thompson_sampling.strategies.config) TopTwoSelection (class in TACTICS.thompson_sampling.strategies.top_two_selection) total_compatible (TACTICS.library_enumeration.smarts_toolkit._validator.ValidationResult property) total_incompatible (TACTICS.library_enumeration.smarts_toolkit._validator.ValidationResult property) TS_Benchmarks (class in TACTICS.library_analysis.visualization)

U

UCBConfig (class in TACTICS.thompson_sampling.strategies.config)

UCBSelection (class in TACTICS.thompson_sampling.strategies.ucb_selection)

V

validate_all() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig method) (TACTICS.library_enumeration.synthesis_pipeline.SynthesisPipeline method) validate_config() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionConfig method) validate_reaction() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef method)

validate_source_fields() (TACTICS.library_enumeration.smarts_toolkit.config.StepInput method) validation_result (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef property) ValidationResult (class in TACTICS.library_enumeration.smarts_toolkit._validator) visualize_reaction() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef method) visualize_template_match() (TACTICS.library_enumeration.smarts_toolkit.config.ReactionDef method)

W

warm_up() (TACTICS.thompson_sampling.core.sampler.ThompsonSampler method) WarmupStrategy (class in TACTICS.thompson_sampling.warmup.base)

write_enumerated_library() (in module TACTICS.library_enumeration.file_writer) write_products_chunked() (in module TACTICS.library_enumeration.file_writer)