| add_orbitals_to_restype(core::Size const atm_index2, core::Size const atm_index3, core::chemical::AtomType const &atmtype, std::string const atom_hybridization, utility::vector1< numeric::xyzVector< core::Real > > const orbital_xyz_vectors) | core::chemical::orbitals::AssignOrbitals | |
| Aindex_ | core::chemical::orbitals::AssignOrbitals | private |
| AObondedatoms_ | core::chemical::orbitals::AssignOrbitals | private |
| AOdist_ | core::chemical::orbitals::AssignOrbitals | private |
| AOhybridization_ | core::chemical::orbitals::AssignOrbitals | private |
| assign_only_pi_orbitals_to_atom(core::chemical::AtomType const &atmtype) | core::chemical::orbitals::AssignOrbitals | |
| assign_orbitals() | core::chemical::orbitals::AssignOrbitals | |
| assign_sp2_orbitals_to_one_bonded_atom(core::chemical::AtomType const &atmtype) | core::chemical::orbitals::AssignOrbitals | |
| assign_sp2_sp_orbitals_to_one_bonded_atom(core::chemical::AtomType const &atmtype) | core::chemical::orbitals::AssignOrbitals | |
| AssignOrbitals(core::chemical::ResidueTypeOP const restype) | core::chemical::orbitals::AssignOrbitals | |
| calculate_orbital_icoor(numeric::xyzVector< core::Real > const orbital_xyz, core::Size const atm_index1, core::Size const atm_index2, core::Size const atm_index3, std::string const orbital_element_name) | core::chemical::orbitals::AssignOrbitals | |
| Coordinates_Tetrahedral_bondedto3atoms_helper(core::Size const atm_index1, core::Size const atm_index2, core::Size const atm_index3, core::Size const atm_index4, core::Real const dist) | core::chemical::orbitals::AssignOrbitals | |
| Coordinates_TriganolPlanar_bondedto1atom_helper(core::Size const atm_index1, core::Size const atm_index2, core::Size const atm_index3, core::Real const dist) | core::chemical::orbitals::AssignOrbitals | |
| cross_product_helper(core::Size const atm_index1, core::Size const atm_index2, core::Size const atm_index3, core::Real const dist) | core::chemical::orbitals::AssignOrbitals | |
| make_orbital_element_name() | core::chemical::orbitals::AssignOrbitals | private |
| make_orbital_type_name(AtomType const &atmtype, std::string const orbitaltype, core::Size const hybridization) | core::chemical::orbitals::AssignOrbitals | private |
| n_orbitals_ | core::chemical::orbitals::AssignOrbitals | private |
| Orbtype_ | core::chemical::orbitals::AssignOrbitals | private |
| restype_ | core::chemical::orbitals::AssignOrbitals | private |
| set_orbital_type_and_bond(core::Size atom_index, std::string orbital_element_name, std::string orbital_type_full_name) | core::chemical::orbitals::AssignOrbitals | private |