| add_atom(MolFileIOAtomOP atom) | core::chemical::sdf::MolFileIOMolecule | |
| add_bond(MolFileIOBondOP bond) | core::chemical::sdf::MolFileIOMolecule | |
| add_str_str_data(std::string const &key, std::string const &value) | core::chemical::sdf::MolFileIOMolecule | |
| atom_index(AtomIndex index) | core::chemical::sdf::MolFileIOMolecule | |
| convert_to_ResidueType(chemical::AtomTypeSetCOP atom_types, chemical::ElementSetCOP elements, chemical::MMAtomTypeSetCOP mm_atom_types) | core::chemical::sdf::MolFileIOMolecule | inline |
| convert_to_ResidueType(std::map< AtomIndex, std::string > &index_name_map, chemical::AtomTypeSetCOP atom_types, chemical::ElementSetCOP elements, chemical::MMAtomTypeSetCOP mm_atom_types) | core::chemical::sdf::MolFileIOMolecule | |
| create_dummy_atom(MutableResidueTypeOP restype, std::string atom_name, core::Vector const &xyz_offset, chemical::ElementSetCOP elements, chemical::MMAtomTypeSetCOP mm_atom_types) | core::chemical::sdf::MolFileIOMolecule | private |
| get_str_str_data() const | core::chemical::sdf::MolFileIOMolecule | inline |
| index_atom_map_ | core::chemical::sdf::MolFileIOMolecule | private |
| index_valid(AtomIndex index, MutableResidueType const &restype, std::map< mioAD, core::chemical::VD > &restype_from_mio) | core::chemical::sdf::MolFileIOMolecule | private |
| molecule_string_data_ | core::chemical::sdf::MolFileIOMolecule | private |
| MolFileIOMolecule() | core::chemical::sdf::MolFileIOMolecule | |
| molgraph_ | core::chemical::sdf::MolFileIOMolecule | private |
| name() const | core::chemical::sdf::MolFileIOMolecule | inline |
| name(std::string name) | core::chemical::sdf::MolFileIOMolecule | inline |
| name_ | core::chemical::sdf::MolFileIOMolecule | private |
| normalize() | core::chemical::sdf::MolFileIOMolecule | |
| parse_multi(std::istream &estream, utility::vector1< std::string > &parsed, std::string label) const | core::chemical::sdf::MolFileIOMolecule | private |
| set_from_extra_data(MutableResidueType &restype, std::map< mioAD, core::chemical::VD > &restype_from_mio) | core::chemical::sdf::MolFileIOMolecule | private |
| ~MolFileIOMolecule() override | core::chemical::sdf::MolFileIOMolecule | |