Index

A

AbsoluteModifier() (in module navicatGA.score_modifiers) addLoggingLevel() (in module navicatGA.logger) allowed_mutation_genes (navicatGA.base_solver.GenAlgSolver attribute)

allowed_selection_strategies (in module navicatGA.base_solver) AlphabetGenAlgSolver (class in navicatGA.alphabet_solver) assembler (navicatGA.base_solver.GenAlgSolver attribute)

B

best_fitness (navicatGA.helpers.GAResult attribute) best_fitness_ (navicatGA.base_solver.GenAlgSolver attribute) best_individual (navicatGA.helpers.GAResult attribute) best_individual_ (navicatGA.base_solver.GenAlgSolver attribute)

best_pfitness (navicatGA.helpers.GAResult attribute) best_pfitness_ (navicatGA.base_solver.GenAlgSolver attribute) build_solver() (in module navicatGA.config) build_solver_from_yaml() (in module navicatGA.config)

C

calculate_fitness() (navicatGA.base_solver.GenAlgSolver method) calculate_fitness_cache() (in module navicatGA.cache) calculate_one_fitness_cache() (in module navicatGA.cache) check_error() (in module navicatGA.helpers) check_input_base() (navicatGA.base_solver.GenAlgSolver method) check_selfie_chars() (in module navicatGA.chemistry_selfies) check_smiles_chars() (in module navicatGA.wrappers_smiles) check_xyz() (in module navicatGA.chemistry_xyz) chromosome_to_smiles() (in module navicatGA.wrappers_smiles) chromosome_to_xyz() (in module navicatGA.wrappers_xyz) chromosomize() (navicatGA.alphabet_solver.AlphabetGenAlgSolver method) (navicatGA.selfies_solver.SelfiesGenAlgSolver method)

close_logger() (in module navicatGA.logger) close_solver_logger() (navicatGA.base_solver.GenAlgSolver method) concatenate_list() (in module navicatGA.helpers) configure_logger() (in module navicatGA.logger) COORD_THRESHOLD (in module navicatGA.queue_wrappers_xyz) (in module navicatGA.wrappers_xyz) count_selfie_chars() (in module navicatGA.chemistry_selfies) create_offspring() (navicatGA.base_solver.GenAlgSolver static method) (navicatGA.float_solver.FloatGenAlgSolver method) (navicatGA.selfies_solver.SelfiesGenAlgSolver method) (navicatGA.smiles_solver.SmilesGenAlgSolver method) (navicatGA.xyz_solver.XYZGenAlgSolver method)

D

decode_selfies_list() (in module navicatGA.chemistry_selfies) diagnose_mol() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles)

draw_selfies() (in module navicatGA.chemistry_selfies) draw_smiles() (in module navicatGA.chemistry_smiles) draw_xyz() (in module navicatGA.chemistry_xyz)

E

encode_smiles_list() (in module navicatGA.chemistry_selfies)

error_message (navicatGA.timeout.timeout attribute) exception_messages (in module navicatGA.exception_messages)

F

fitness (navicatGA.helpers.GAResult attribute) fitness_ (navicatGA.base_solver.GenAlgSolver attribute) fitness_function_float() (in module navicatGA.fitness_functions_float) fitness_function_selfies() (in module navicatGA.fitness_functions_selfies) fitness_function_target_property() (in module navicatGA.fitness_functions_selfies) (in module navicatGA.fitness_functions_xyz)

fitness_function_target_selfies() (in module navicatGA.fitness_functions_selfies) fitness_function_xyz() (in module navicatGA.fitness_functions_xyz) FixedSubmitProcess (class in navicatGA.queue_wrappers_xyz) FloatGenAlgSolver (class in navicatGA.float_solver)

G

GAResult (class in navicatGA.helpers) GaussianModifier() (in module navicatGA.score_modifiers) GenAlgSolver (class in navicatGA.base_solver) generations (navicatGA.helpers.GAResult attribute) generations_ (navicatGA.base_solver.GenAlgSolver attribute) geom2angle() (in module navicatGA.wrappers_xyz) geom2bond() (in module navicatGA.wrappers_xyz) geom2dihedral() (in module navicatGA.wrappers_xyz) geom2ehl() (in module navicatGA.quantum_wrappers_xyz) geom2ehomo() (in module navicatGA.quantum_wrappers_xyz) geom2elumo() (in module navicatGA.quantum_wrappers_xyz) geom2gap() (in module navicatGA.quantum_wrappers_xyz) geom2opt() (in module navicatGA.quantum_wrappers_xyz) (in module navicatGA.queue_wrappers_xyz) geom2pyscf() (in module navicatGA.quantum_wrappers_xyz) geom2sub_sterimol() (in module navicatGA.wrappers_xyz) get_alphabet_from_path() (in module navicatGA.chemistry_xyz) get_boltzmann_probabilities() (navicatGA.base_solver.GenAlgSolver method) get_conformer_rmsd() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) get_confs_ff() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) get_crossover_points() (navicatGA.alphabet_solver.AlphabetGenAlgSolver method) (navicatGA.base_solver.GenAlgSolver method) (navicatGA.float_solver.FloatGenAlgSolver method)

get_default_alphabet() (in module navicatGA.chemistry_xyz) get_ECFP4() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) get_elapsed_time() (in module navicatGA.helpers) get_input_dimensions() (in module navicatGA.helpers) get_interatomic_distances() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) get_number_mutations() (navicatGA.base_solver.GenAlgSolver method) get_selection_probabilities() (navicatGA.base_solver.GenAlgSolver method) get_selfie_chars() (in module navicatGA.chemistry_selfies) get_starting_xyz_from_file() (in module navicatGA.chemistry_xyz) get_starting_xyz_from_path() (in module navicatGA.chemistry_xyz) get_starting_xyz_from_smi() (in module navicatGA.chemistry_xyz) get_structure_ff() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) gl2ehl() (in module navicatGA.quantum_wrappers_xyz) gl2ehomo() (in module navicatGA.quantum_wrappers_xyz) gl2elumo() (in module navicatGA.quantum_wrappers_xyz) gl2gap() (in module navicatGA.quantum_wrappers_xyz) gl2geom() (in module navicatGA.wrappers_xyz) gl2opt() (in module navicatGA.quantum_wrappers_xyz)

H

h_positions (in module navicatGA.quantum_wrappers_xyz) handle_timeout() (navicatGA.timeout.timeout method) handler() (in module navicatGA.timeout)

has_transition_metals() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) Hashable_Geometry (class in navicatGA.chemistry_xyz) (class in navicatGA.wrappers_xyz)

I

initialize_population() (navicatGA.alphabet_solver.AlphabetGenAlgSolver method) (navicatGA.base_solver.GenAlgSolver method) (navicatGA.float_solver.FloatGenAlgSolver method)

interval_selection() (navicatGA.base_solver.GenAlgSolver method) InvalidInput is_transition_metal() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles)

L

lg (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) (in module navicatGA.quantum_wrappers_selfies) (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) load_yaml() (in module navicatGA.config) logger (in module navicatGA.alphabet_solver) (in module navicatGA.cache) (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) (in module navicatGA.chemistry_xyz) (in module navicatGA.fitness_functions_selfies) (in module navicatGA.fitness_functions_xyz) (in module navicatGA.float_solver) (in module navicatGA.quantum_wrappers_selfies) (in module navicatGA.quantum_wrappers_xyz) (in module navicatGA.queue_wrappers_xyz) (in module navicatGA.score_modifiers) (in module navicatGA.selfies_solver) (in module navicatGA.smiles_solver) (in module navicatGA.timeout) (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) (in module navicatGA.wrappers_xyz) (in module navicatGA.xyz_solver) (navicatGA.base_solver.GenAlgSolver attribute)

M

make_array() (in module navicatGA.helpers) max_conv (navicatGA.base_solver.GenAlgSolver attribute) max_counter (navicatGA.selfies_solver.SelfiesGenAlgSolver attribute) (navicatGA.smiles_solver.SmilesGenAlgSolver attribute) (navicatGA.xyz_solver.XYZGenAlgSolver attribute) max_fitness_ (navicatGA.base_solver.GenAlgSolver attribute) max_gen (navicatGA.base_solver.GenAlgSolver attribute) mean_fitness_ (navicatGA.base_solver.GenAlgSolver attribute) message (navicatGA.exceptions.InvalidInput attribute) (navicatGA.exceptions.NoAssembler attribute) (navicatGA.exceptions.NoFitnessFunction attribute) module navicatGA navicatGA.alphabet_solver navicatGA.base_solver navicatGA.cache navicatGA.chemistry_selfies navicatGA.chemistry_smiles navicatGA.chemistry_xyz navicatGA.config navicatGA.exception_messages navicatGA.exceptions navicatGA.fitness_functions_float navicatGA.fitness_functions_selfies navicatGA.fitness_functions_xyz navicatGA.float_solver navicatGA.helpers navicatGA.logger navicatGA.quantum_wrappers_selfies navicatGA.quantum_wrappers_xyz navicatGA.queue_wrappers_xyz navicatGA.score_modifiers navicatGA.selfies_solver navicatGA.smiles_solver navicatGA.timeout navicatGA.wrappers_selfies navicatGA.wrappers_smiles navicatGA.wrappers_xyz navicatGA.xyz_solver

mol_structure2cm() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) mol_structure2depictions() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) mol_structure2pyscf() (in module navicatGA.quantum_wrappers_selfies) mutate_population() (navicatGA.alphabet_solver.AlphabetGenAlgSolver method) (navicatGA.base_solver.GenAlgSolver method) (navicatGA.float_solver.FloatGenAlgSolver method) mutation_rate (navicatGA.base_solver.GenAlgSolver attribute)

N

n_crossover_points (navicatGA.base_solver.GenAlgSolver attribute) n_genes (navicatGA.base_solver.GenAlgSolver attribute) n_matings (navicatGA.base_solver.GenAlgSolver attribute) n_mutations (navicatGA.base_solver.GenAlgSolver attribute) navicatGA module navicatGA.alphabet_solver module navicatGA.base_solver module navicatGA.cache module navicatGA.chemistry_selfies module navicatGA.chemistry_smiles module navicatGA.chemistry_xyz module navicatGA.config module navicatGA.exception_messages module navicatGA.exceptions module navicatGA.fitness_functions_float module navicatGA.fitness_functions_selfies module navicatGA.fitness_functions_xyz module

navicatGA.float_solver module navicatGA.helpers module navicatGA.logger module navicatGA.quantum_wrappers_selfies module navicatGA.quantum_wrappers_xyz module navicatGA.queue_wrappers_xyz module navicatGA.score_modifiers module navicatGA.selfies_solver module navicatGA.smiles_solver module navicatGA.timeout module navicatGA.wrappers_selfies module navicatGA.wrappers_smiles module navicatGA.wrappers_xyz module navicatGA.xyz_solver module NoAssembler NoFitnessFunction

O

opt() (in module navicatGA.quantum_wrappers_xyz)

P

pad_xyz_list() (in module navicatGA.chemistry_xyz) plot_fitness_results() (navicatGA.base_solver.GenAlgSolver static method) plot_results (navicatGA.base_solver.GenAlgSolver attribute) pop_keep (navicatGA.base_solver.GenAlgSolver attribute) pop_size (navicatGA.base_solver.GenAlgSolver attribute) population (navicatGA.helpers.GAResult attribute) population_ (navicatGA.base_solver.GenAlgSolver attribute) print_stats() (navicatGA.base_solver.GenAlgSolver method)

printable_fitness (navicatGA.base_solver.GenAlgSolver attribute) prob_intervals (navicatGA.base_solver.GenAlgSolver attribute) problem_type (navicatGA.base_solver.GenAlgSolver attribute) progress_bars (navicatGA.base_solver.GenAlgSolver attribute) prune_duplicates (navicatGA.base_solver.GenAlgSolver attribute) prune_mol_conformers() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) pyscf2geom() (in module navicatGA.quantum_wrappers_xyz)

Q

queue_env_var (in module navicatGA.queue_wrappers_xyz) (in module navicatGA.wrappers_xyz)

QUEUE_TYPE (in module navicatGA.queue_wrappers_xyz) (in module navicatGA.wrappers_xyz)

R

random_merge_xyz() (in module navicatGA.chemistry_xyz) randomize_selfies() (in module navicatGA.chemistry_selfies) randomize_smiles() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles)

refill_population() (navicatGA.alphabet_solver.AlphabetGenAlgSolver method) resolve() (in module navicatGA.config) runtime (navicatGA.helpers.GAResult attribute) runtime_ (navicatGA.base_solver.GenAlgSolver attribute)

S

sanitize_multiple_smiles() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) sanitize_smiles() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) sc2cm() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2depictions() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2ehomo() (in module navicatGA.quantum_wrappers_selfies) sc2elumo() (in module navicatGA.quantum_wrappers_selfies) sc2gap() (in module navicatGA.quantum_wrappers_selfies) sc2ilogp() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2krr() (in module navicatGA.wrappers_selfies) sc2levenshtein_to_target() (in module navicatGA.wrappers_selfies) sc2logp() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2mol_structure() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2mv() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2mw() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2mwilogp() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2nmw() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2selfies() (in module navicatGA.wrappers_selfies)

sc2smiles() (in module navicatGA.wrappers_selfies) (in module navicatGA.wrappers_smiles) sc2tanimoto_to_target() (in module navicatGA.wrappers_selfies) scalarizer (navicatGA.base_solver.GenAlgSolver attribute) score_modifier() (in module navicatGA.score_modifiers) seconds (navicatGA.timeout.timeout attribute) select_parents() (navicatGA.base_solver.GenAlgSolver method) selection_rate (navicatGA.base_solver.GenAlgSolver attribute) selection_strategy (navicatGA.base_solver.GenAlgSolver attribute) SelfiesGenAlgSolver (class in navicatGA.selfies_solver) set_dative_bonds() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles) set_lru_cache() (in module navicatGA.cache) show_stats (navicatGA.base_solver.GenAlgSolver attribute) smiles2logp() (in module navicatGA.wrappers_smiles) smiles2mol_structure() (in module navicatGA.wrappers_smiles) smiles2xyz() (in module navicatGA.wrappers_smiles) SmilesGenAlgSolver (class in navicatGA.smiles_solver) solve() (navicatGA.base_solver.GenAlgSolver method) SOLVERS (in module navicatGA.config) sort_by_fitness() (navicatGA.base_solver.GenAlgSolver static method) SquaredModifier() (in module navicatGA.score_modifiers) starting_population (navicatGA.smiles_solver.SmilesGenAlgSolver attribute) (navicatGA.xyz_solver.XYZGenAlgSolver attribute) starting_random (navicatGA.selfies_solver.SelfiesGenAlgSolver attribute) (navicatGA.smiles_solver.SmilesGenAlgSolver attribute) (navicatGA.xyz_solver.XYZGenAlgSolver attribute) submit() (navicatGA.queue_wrappers_xyz.FixedSubmitProcess method)

T

temperature (navicatGA.base_solver.GenAlgSolver attribute) test_bohachevsky() (in module navicatGA.float_solver) timed_decoder() (in module navicatGA.chemistry_selfies) timed_sanitizer() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles)

timeout (class in navicatGA.timeout) timer_alarm() (in module navicatGA.timeout) tournament_selection() (navicatGA.base_solver.GenAlgSolver method) tournament_selection_helper() (navicatGA.base_solver.GenAlgSolver static method) track_evaluations() (in module navicatGA.helpers)

U

UNAVAILABLE_SOLVERS (in module navicatGA.config)

USER (in module navicatGA.queue_wrappers_xyz) (in module navicatGA.wrappers_xyz)

V

variables_limits (navicatGA.float_solver.FloatGenAlgSolver attribute)

verbose (navicatGA.base_solver.GenAlgSolver attribute)

W

write_population() (navicatGA.selfies_solver.SelfiesGenAlgSolver method) (navicatGA.smiles_solver.SmilesGenAlgSolver method) (navicatGA.xyz_solver.XYZGenAlgSolver method)

X

XYZGenAlgSolver (class in navicatGA.xyz_solver)