| #ifndef H_TABIPB_MOLECULE_STRUCT_H |
| #define H_TABIPB_MOLECULE_STRUCT_H |
|
|
| #include <vector> |
| #include <string> |
| #include <fstream> |
| #include <cstddef> |
|
|
| #include "timer.h" |
| #include "params.h" |
|
|
| #ifdef TABIPB_APBS |
| #include "generic/valist.h" |
| #endif |
|
|
| struct Timers_Molecule; |
|
|
| class Molecule |
| { |
| private: |
| const struct Params& params_; |
| struct Timers_Molecule& timers_; |
| |
| std::size_t num_atoms_; |
| std::vector<double> coords_; |
| std::vector<double> charge_; |
| std::vector<double> radius_; |
|
|
| double coulombic_energy_; |
|
|
| public: |
| Molecule(struct Params&, struct Timers_Molecule&); |
| ~Molecule() = default; |
| |
| #ifdef TABIPB_APBS |
| Molecule(Valist*, struct Params&, struct Timers_Molecule&); |
| #endif |
| |
| void build_xyzr_file() const; |
| |
| std::size_t num_atoms() const { return num_atoms_; }; |
| double coulombic_energy() const { return coulombic_energy_; }; |
| const double* coords_ptr() const { return coords_.data(); }; |
| const double* charge_ptr() const { return charge_.data(); }; |
| const double* radius_ptr() const { return radius_.data(); }; |
| |
| void compute_coulombic_energy(); |
| void copyin_to_device() const; |
| void delete_from_device() const; |
| }; |
|
|
|
|
| struct Timers_Molecule |
| { |
| Timer ctor; |
| Timer compute_coulombic_energy; |
| Timer build_xyzr_file; |
| Timer copyin_to_device; |
| Timer delete_from_device; |
| |
| void print() const; |
| std::string get_durations() const; |
| std::string get_headers() const; |
|
|
| Timers_Molecule() = default; |
| ~Timers_Molecule() = default; |
| }; |
|
|
| #endif |
|
|
