| calculate_fingerprint(LigandIdentifier const &id) | protocols::ligand_evolution::FragmentLibrary | |
| create_ligand(std::string const &smiles, bool create_rotamers) const | protocols::ligand_evolution::FragmentLibrary | private |
| create_ligand_pose(LigandIdentifier const &id, bool create_rotamers, char ligand_chain) const | protocols::ligand_evolution::FragmentLibrary | |
| create_ligand_pose(std::string const &smiles, bool create_rotamers, char ligand_chain) const | protocols::ligand_evolution::FragmentLibrary | |
| create_pose(core::conformation::Residue &ligand, char ligand_chain) const | protocols::ligand_evolution::FragmentLibrary | private |
| fingerprints_ | protocols::ligand_evolution::FragmentLibrary | private |
| FragmentLibrary() | protocols::ligand_evolution::FragmentLibrary | |
| FragmentLibrary(FragmentLibrary const &other)=delete | protocols::ligand_evolution::FragmentLibrary | |
| generate_rotamers(core::chemical::MutableResidueType &new_ligand) const | protocols::ligand_evolution::FragmentLibrary | private |
| get_similar_reagents(core::Size reagent_id, core::Size reaction_id, core::Size position) const | protocols::ligand_evolution::FragmentLibrary | |
| identifier_to_smiles(LigandIdentifier const &identifier) const | protocols::ligand_evolution::FragmentLibrary | |
| initialize_from_options(EvolutionOptionsOP options, core::Size external_scoring, core::Size rank) | protocols::ligand_evolution::FragmentLibrary | |
| load_data(std::string const &reaction_file_path, std::string const &reagent_file_path, core::Size rank) | protocols::ligand_evolution::FragmentLibrary | |
| load_reactions(std::string const &reaction_file_name) | protocols::ligand_evolution::FragmentLibrary | private |
| load_reagents(std::string const &reagent_file_path) | protocols::ligand_evolution::FragmentLibrary | private |
| load_smiles(std::string const &path_to_data) | protocols::ligand_evolution::FragmentLibrary | |
| max_positions() const | protocols::ligand_evolution::FragmentLibrary | |
| max_reagents_ | protocols::ligand_evolution::FragmentLibrary | private |
| n_unscored_smiles() const | protocols::ligand_evolution::FragmentLibrary | |
| operator=(FragmentLibrary const &other)=delete | protocols::ligand_evolution::FragmentLibrary | |
| pose_ | protocols::ligand_evolution::FragmentLibrary | private |
| random_ligand() const | protocols::ligand_evolution::FragmentLibrary | |
| random_reaction() const | protocols::ligand_evolution::FragmentLibrary | |
| random_reaction(std::set< core::Size > const &exclude) const | protocols::ligand_evolution::FragmentLibrary | |
| reaction_id(core::Size reaction_id) const | protocols::ligand_evolution::FragmentLibrary | |
| reaction_name_to_index(std::string const &reaction_name) const | protocols::ligand_evolution::FragmentLibrary | |
| reaction_name_to_index_ | protocols::ligand_evolution::FragmentLibrary | private |
| reaction_positions(core::Size reaction_id) const | protocols::ligand_evolution::FragmentLibrary | |
| reactions_ | protocols::ligand_evolution::FragmentLibrary | private |
| reactions_size() const | protocols::ligand_evolution::FragmentLibrary | |
| reagent_id(core::Size reagent_id) const | protocols::ligand_evolution::FragmentLibrary | |
| reagent_name_to_index(core::Size reaction_index, core::Size position, std::string const &reagent_name) const | protocols::ligand_evolution::FragmentLibrary | |
| reagents_ | protocols::ligand_evolution::FragmentLibrary | private |
| reagents_size() const | protocols::ligand_evolution::FragmentLibrary | |
| reagents_size(core::Size reaction_index) const | protocols::ligand_evolution::FragmentLibrary | |
| reagents_size(core::Size reaction_index, core::Size position) const | protocols::ligand_evolution::FragmentLibrary | |
| run_reaction(LigandIdentifier const &identifier) const | protocols::ligand_evolution::FragmentLibrary | |
| set_pose(core::pose::PoseCOP pose) | protocols::ligand_evolution::FragmentLibrary | |
| similarity(LigandIdentifier const &id1, LigandIdentifier const &id2) | protocols::ligand_evolution::FragmentLibrary | |
| smiles_ | protocols::ligand_evolution::FragmentLibrary | private |
| weighted_sampler_ | protocols::ligand_evolution::FragmentLibrary | private |
| ~FragmentLibrary() | protocols::ligand_evolution::FragmentLibrary | |
