This is the complete list of members for stormm::topology::AtomGraphStage, including all inherited members.

addAnglParameters(double k_eq_in, double th_eq_in, const char4 atom_i_type=unknown_atom_type, const char4 atom_j_type=unknown_atom_type, const char4 atom_k_type=unknown_atom_type)	stormm::topology::AtomGraphStage
addAtom(int z_number, int placement=-1, const char4 atom_name={ 'U', 'N', 'K', ' ' }, const char4 atom_type={ 'U', 'N', 'K', ' ' }, const char4 res_name={ 'U', 'N', 'K', ' ' }, int charge_index=-1, int lennard_jones_index=-1, double atomic_charge=0.0)	stormm::topology::AtomGraphStage
addAtoms(const std::vector< int > &z_numbers, int placement=-1, const std::vector< int > &added_residue_limits={}, const std::vector< char4 > &added_atom_names={}, const std::vector< char4 > &added_atom_types={}, const std::vector< char4 > &added_residue_names={}, const std::vector< int > &added_charge_indices={}, const std::vector< int > &added_lennard_jones_indices={}, const std::vector< double > &added_atomic_charges={})	stormm::topology::AtomGraphStage
addBondParameters(double k_eq_in, double l_eq_in, const char4 atom_i_type=unknown_atom_type, const char4 atom_j_type=unknown_atom_type)	stormm::topology::AtomGraphStage
addCImpParameters(double k_eq_in, double phi_in, const char4 atom_i_type=unknown_atom_type, const char4 atom_j_type=unknown_atom_type, const char4 atom_k_type=unknown_atom_type, const char4 atom_l_type=unknown_atom_type)	stormm::topology::AtomGraphStage
addCmapParameters(const int dimension_in, const std::vector< double > &surf_in, const char4 atom_i_type=unknown_atom_type, const char4 atom_j_type=unknown_atom_type, const char4 atom_k_type=unknown_atom_type, const char4 atom_l_type=unknown_atom_type, const char4 atom_m_type=unknown_atom_type)	stormm::topology::AtomGraphStage
addDiheParameters(double ampl_in, double period_in, double phi_in, const char4 atom_i_type=unknown_atom_type, const char4 atom_j_type=unknown_atom_type, const char4 atom_k_type=unknown_atom_type, const char4 atom_l_type=unknown_atom_type)	stormm::topology::AtomGraphStage
addUbrdParameters(double k_eq_in, double l_eq_in, const char4 atom_i_type=unknown_atom_type, const char4 atom_k_type=unknown_atom_type)	stormm::topology::AtomGraphStage
addVirtualSite(int parameter_index, int frame1_atom, int frame2_atom, int frame3_atom=-1, int frame4_atom=-1)	stormm::topology::AtomGraphStage
addVirtualSites(const std::vector< int > &parameter_indices, const std::vector< int > &frame1_atoms, const std::vector< int > &frame2_atoms, const std::vector< int > &frame3_atoms, const std::vector< int > &frame4_atoms)	stormm::topology::AtomGraphStage
AtomGraphStage(int atom_count_in=0, const std::vector< int > &residue_limits_in={}, ExceptionResponse policy_in=ExceptionResponse::DIE)	stormm::topology::AtomGraphStage
AtomGraphStage(const AtomGraph *ag_in, ExceptionResponse policy_in=ExceptionResponse::DIE) (defined in stormm::topology::AtomGraphStage)	stormm::topology::AtomGraphStage
AtomGraphStage(const AtomGraph &ag_in, ExceptionResponse policy_in=ExceptionResponse::DIE) (defined in stormm::topology::AtomGraphStage)	stormm::topology::AtomGraphStage
AtomGraphStage(const MdlMol *cmpd_in, ExceptionResponse policy_in=ExceptionResponse::DIE) (defined in stormm::topology::AtomGraphStage)	stormm::topology::AtomGraphStage
AtomGraphStage(const MdlMol &cmpd_in, ExceptionResponse policy_in=ExceptionResponse::DIE) (defined in stormm::topology::AtomGraphStage)	stormm::topology::AtomGraphStage
AtomGraphStage(const AtomGraphStage &original)=default	stormm::topology::AtomGraphStage
AtomGraphStage(AtomGraphStage &&original)=default (defined in stormm::topology::AtomGraphStage)	stormm::topology::AtomGraphStage
exportTopology(int minimum_solute_size=default_minimum_solute_atoms, const std::vector< char4 > &solute_included_residue_names={}, double hmass_repartition_factor=1.0) const	stormm::topology::AtomGraphStage
getAtomCount() const	stormm::topology::AtomGraphStage
getElectrostatic14Screening() const	stormm::topology::AtomGraphStage
getMoleculeCount() const	stormm::topology::AtomGraphStage
getOutputFile() const	stormm::topology::AtomGraphStage
getResidueCount() const	stormm::topology::AtomGraphStage
getTitle() const	stormm::topology::AtomGraphStage
getVanDerWaals14Screening() const	stormm::topology::AtomGraphStage
operator=(const AtomGraphStage &other)=default (defined in stormm::topology::AtomGraphStage)	stormm::topology::AtomGraphStage
operator=(AtomGraphStage &&other)=default (defined in stormm::topology::AtomGraphStage)	stormm::topology::AtomGraphStage
setBond(int atom_i, int atom_j, int parameter_index)	stormm::topology::AtomGraphStage
setBonds(const std::vector< int > &atom_i, const std::vector< int > &atom_j, const std::vector< int > &parameter_index)	stormm::topology::AtomGraphStage
setElectrostatic14Screening(double screening_factor_in)	stormm::topology::AtomGraphStage
setOutputFile(const std::string &output_file_in)	stormm::topology::AtomGraphStage
setTitle(const std::string &title_in)	stormm::topology::AtomGraphStage
setVanDerWaals14Screening(double screening_factor_in)	stormm::topology::AtomGraphStage