Index

A

add_OCH3() (in module ligning.monomer) add_random_monomer() (ligning.polymer.Polymer method) add_random_ring() (ligning.polymer.Polymer method) add_specific_linkage() (ligning.polymer.Polymer method)

add_specific_monomer() (ligning.polymer.Polymer method) add_specific_ring() (ligning.polymer.Polymer method) adjust_indices() (in module ligning.utils) analyze() (ligning.characterization.Population method)

B

BOOptimizer (class in ligning.optimization)

C

cal_all() (ligning.characterization.Characterize method) (ligning.characterization.CharacterizeGraph method) cal_branching() (ligning.characterization.Characterize method) cal_CI() (in module ligning.utils) cal_distance() (in module ligning.utils) cal_metrics() (ligning.characterization.CharacterizeGraph method) cal_MW() (ligning.characterization.Characterize method) (ligning.characterization.CharacterizeGraph method) Characterize (class in ligning.characterization) characterize_all() (ligning.characterization.Population method) CharacterizeGraph (class in ligning.characterization) clean_csv_cache() (in module ligning.utils) connect_C1_C2() (ligning.polymer.PolymerGraph method)

count_connections() (ligning.characterization.Characterize method) count_linkages() (ligning.characterization.Characterize method) (ligning.characterization.CharacterizeGraph method) count_monomers() (ligning.characterization.Characterize method) (ligning.characterization.CharacterizeGraph method) count_OCH3() (ligning.characterization.Characterize method) (ligning.characterization.CharacterizeGraph method) count_OH() (ligning.characterization.Characterize method) (ligning.characterization.CharacterizeGraph method) count_types() (ligning.characterization.Characterize method) (ligning.characterization.CharacterizeGraph method) counts_to_metrics() (in module ligning.utils) create() (ligning.monomer.Monomer method)

D

draw_atomic_graph() (in module ligning.utils)

draw_big_graph() (in module ligning.utils) draw_graph() (in module ligning.utils)

F

find_available_C1_in_polymer() (ligning.polymer.PolymerGraph method) find_available_C2_in_monomer() (ligning.polymer.PolymerGraph method) find_available_monomer_types() (ligning.polymer.PolymerGraph method)

find_C2_index_in_polymer() (ligning.polymer.PolymerGraph method) find_O_index_in_polymer() (ligning.polymer.PolymerGraph method) formula_to_MW() (in module ligning.utils)

G

generate_random_branching_state() (in module ligning.utils) generate_random_linkage() (in module ligning.utils) generate_random_monomer() (in module ligning.utils) generate_random_size_from_distribution() (in module ligning.utils) get_counts() (ligning.characterization.Characterize method) (ligning.characterization.Population method)

get_counts_polymer() (in module ligning.characterization) get_metrics() (ligning.characterization.Characterize method) get_metrics_mean() (ligning.characterization.Population method) get_metrics_polymer() (in module ligning.characterization) graph_to_mol() (in module ligning.utils) graph_to_smile() (in module ligning.utils)

J

join_two() (in module ligning.utils)

L

ligning.characterization module ligning.monomer module ligning.optimization module

ligning.polymer module ligning.utils module

M

make_available() (in module ligning.utils) make_multi_available() (in module ligning.utils) make_unavailable() (in module ligning.utils) MaskedFunc (class in ligning.optimization) metrics_array_to_dict() (in module ligning.utils) module ligning.characterization ligning.monomer ligning.optimization ligning.polymer ligning.utils

Monomer (class in ligning.monomer) monomer_G() (in module ligning.monomer) monomer_graph() (in module ligning.monomer) monomer_H() (in module ligning.monomer) monomer_S() (in module ligning.monomer) MW_array_to_number_average() (in module ligning.utils) MW_array_to_weight_average() (in module ligning.utils)

O

optimize() (ligning.optimization.BOOptimizer method)

P

ParameterMask (class in ligning.optimization) plot_distance_trajectory() (in module ligning.utils) plot_metrics() (in module ligning.utils) plot_single_distribution() (in module ligning.utils) Polymer (class in ligning.polymer)

PolymerGraph (class in ligning.polymer) Population (class in ligning.characterization) predict() (ligning.optimization.MaskedFunc method) (ligning.optimization.VectorizedFunc method) prepare_X() (ligning.optimization.ParameterMask method)

R

run() (ligning.optimization.Simulation method)

run_MCMC() (ligning.optimization.Trajectory method) run_MCMC_ring() (ligning.optimization.Trajectory method)

S

select_one_from_many() (in module ligning.utils) select_one_from_many_with_index() (in module ligning.utils) select_random_monomer() (in module ligning.monomer)

set_random_state() (in module ligning.utils) Simulation (class in ligning.optimization) smiles_to_formula() (in module ligning.utils)

T

Trajectory (class in ligning.optimization)

try_adding_new() (ligning.polymer.Polymer method)

U

update_available_C1_in_polymer() (ligning.polymer.PolymerGraph method)

update_branching_C_in_polymer() (ligning.polymer.PolymerGraph method) update_units() (ligning.polymer.Polymer method)

V

VectorizedFunc (class in ligning.optimization)

W

write_output_on_individual() (in module ligning.utils)