Index

A

AbsoluteModifier() (in module navicatGA.score_modifiers)

addLoggingLevel() (in module navicatGA.logger)

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

close_logger() (in module navicatGA.logger) close_solve_logger() (navicatGA.base_solver.GenAlgSolver method) concatenate_list() (in module navicatGA.helpers) configure_logger() (in module navicatGA.logger) count_selfie_chars() (in module navicatGA.chemistry_selfies) create_offspring() (navicatGA.base_solver.GenAlgSolver static 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)

F

fitness_function_float() (in module navicatGA.fitness_functions_float)

G

GaussianModifier() (in module navicatGA.score_modifiers) GenAlgSolver (class in navicatGA.base_solver) geom2angle() (in module navicatGA.wrappers_xyz) geom2bond() (in module navicatGA.wrappers_xyz) geom2dihedral() (in module navicatGA.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.base_solver.GenAlgSolver method) (navicatGA.selfies_solver.SelfiesGenAlgSolver method) (navicatGA.smiles_solver.SmilesGenAlgSolver method) (navicatGA.xyz_solver.XYZGenAlgSolver 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) gl2geom() (in module navicatGA.wrappers_xyz)

H

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.base_solver.GenAlgSolver method) (navicatGA.selfies_solver.SelfiesGenAlgSolver method) (navicatGA.smiles_solver.SmilesGenAlgSolver method) (navicatGA.xyz_solver.XYZGenAlgSolver method)

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

M

make_array() (in module navicatGA.helpers) module navicatGA navicatGA.base_solver navicatGA.cache navicatGA.chemistry_selfies navicatGA.chemistry_smiles navicatGA.chemistry_xyz navicatGA.exception_messages navicatGA.exceptions navicatGA.fitness_functions_float navicatGA.helpers navicatGA.logger navicatGA.progress_bars 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) mutate_population() (navicatGA.base_solver.GenAlgSolver method) (navicatGA.selfies_solver.SelfiesGenAlgSolver method) (navicatGA.smiles_solver.SmilesGenAlgSolver method) (navicatGA.xyz_solver.XYZGenAlgSolver method)

N

navicatGA module navicatGA.base_solver module navicatGA.cache module navicatGA.chemistry_selfies module navicatGA.chemistry_smiles module navicatGA.chemistry_xyz module navicatGA.exception_messages module navicatGA.exceptions module navicatGA.fitness_functions_float module navicatGA.helpers module navicatGA.logger module

navicatGA.progress_bars 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

P

pad_xyz_list() (in module navicatGA.chemistry_xyz) plot_fitness_results() (navicatGA.base_solver.GenAlgSolver static method)

print_stats() (navicatGA.base_solver.GenAlgSolver method) prune_mol_conformers() (in module navicatGA.chemistry_selfies) (in module navicatGA.chemistry_smiles)

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

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) 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) score_modifier() (in module navicatGA.score_modifiers) select_parents() (navicatGA.base_solver.GenAlgSolver method) 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) set_progress_bars() (in module navicatGA.progress_bars) smiles2mol_structure() (in module navicatGA.wrappers_smiles) SmilesGenAlgSolver (class in navicatGA.smiles_solver) solve() (navicatGA.base_solver.GenAlgSolver method) solve_progress() (in module navicatGA.progress_bars) sort_by_fitness() (navicatGA.base_solver.GenAlgSolver static method) SquaredModifier() (in module navicatGA.score_modifiers)

T

test_benzene_selfies() (in module navicatGA.selfies_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)

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)