stormm::synthesis::Pdb Member List

This is the complete list of members for stormm::synthesis::Pdb, including all inherited members.

exportCoordinateFrame(int model_index, HybridFormat layout=default_hpc_format) const	stormm::synthesis::Pdb
exportPhaseSpace(int model_index, HybridFormat layout=default_hpc_format) const	stormm::synthesis::Pdb
getAtomCount() const	stormm::synthesis::Pdb
getCoordinateSeries(const std::vector< int > model_sequence={}) const	stormm::synthesis::Pdb
getFormalChargePrinting() const	stormm::synthesis::Pdb
getModelCount() const	stormm::synthesis::Pdb
loadCoordinates(const T *xcrd_in, const T *ycrd_in, const T *zcrd_in, int model_index=0, double gpos_scale=1.0)	stormm::synthesis::Pdb
loadCoordinates(const llint *xcrd_in, const llint *ycrd_in, const llint *zcrd_in, const int *xcrd_ovrf, const int *ycrd_ovrf, const int *zcrd_ovrf, double gpos_scale=1.0, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const CoordinateFrame *cf, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const CoordinateFrame &cf, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const PhaseSpace *ps, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const PhaseSpace &ps, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const CoordinateSeries< T > *cs, const std::vector< int2 > &frame_mapping={}) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const CoordinateSeries< T > &cs, const std::vector< int2 > &frame_mapping={}) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const PhaseSpaceSynthesis *poly_ps, int system_index, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const PhaseSpaceSynthesis &poly_ps, int system_index, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const Condensate *cdns, int system_index, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadCoordinates(const Condensate &cdns, int system_index, int model_index=0) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
loadTopologicalData(const AtomGraph *ag)	stormm::synthesis::Pdb
loadTopologicalData(const AtomGraph &ag) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(int atom_count_in=0, int model_count_in=1)	stormm::synthesis::Pdb
Pdb(const std::string &file_name_in, int model_index=-1, const std::vector< char > &alternate_prefs={ ' ', 'A' }) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const std::string &file_name_in, const std::vector< int > &model_indices, const std::vector< char > &alternate_prefs={ ' ', 'A' }) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(int atom_count_in, int model_count_in, const std::vector< double > &x_coordinates_in, const std::vector< double > &y_coordinates_in, const std::vector< double > &z_coordinates_in, const std::vector< char4 > &atom_names_in, const std::vector< char4 > &residue_names_in, const std::vector< char > &chain_names_in, const std::vector< double > &occupancies_in, const std::vector< double > &b_factors_in, const std::vector< char2 > &elements_in={}, const std::vector< int > &atom_numbers_in={}, const std::vector< int > &residue_numbers_in={}, const std::vector< int > &anisotropy_matrices_in={}, const std::vector< PdbAtomKind > &atom_classes_in={}, const std::vector< std::string > &header_in={}, const std::vector< std::string > &remark_in={}, const std::vector< std::string > &extras_in={}) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const AtomGraph *ag, const CoordinateFrame *cf) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const AtomGraph &ag, const CoordinateFrame &cf) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const AtomGraph *ag, const PhaseSpace *ps) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const AtomGraph &ag, const PhaseSpace &ps) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const AtomGraph *ag, const CoordinateSeries< T > *cf, const std::vector< int > &frames={}) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const AtomGraph &ag, const CoordinateSeries< T > &cf, const std::vector< int > &frames={}) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const AtomGraph *ag, const CoordinateSeries< T > *cs, int frame_number) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
Pdb(const AtomGraph &ag, const CoordinateSeries< T > &cs, int frame_number) (defined in stormm::synthesis::Pdb)	stormm::synthesis::Pdb
setFormalChargePrinting(bool print_formal_charges_in=true)	stormm::synthesis::Pdb
writeToFile(const std::string &file_name, PrintSituation expectation, const std::vector< int > &model_indices={}) const	stormm::synthesis::Pdb