surface_area.h

// -*-c++-*-
#ifndef STORMM_SURFACE_AREA_H
#define STORMM_SURFACE_AREA_H
 
#include "copyright.h"
#include "Constants/behavior.h"
#include "Math/geodesic.h"
#include "Math/series_ops.h"
#include "Math/vector_ops.h"
#include "Potential/scorecard.h"
#include "Synthesis/atomgraph_synthesis.h"
#include "Synthesis/phasespace_synthesis.h"
#include "Synthesis/synthesis_abstracts.h"
#include "Topology/atomgraph.h"
#include "Topology/atomgraph_abstracts.h"
#include "Trajectory/phasespace.h"
#include "energy_enumerators.h"
 
namespace stormm {
namespace energy {
 
using constants::PrecisionModel;
using stmath::indexingArray;
using stmath::maxValue;
using stmath::minValue;
using stmath::surfaceDistribution;
using synthesis::AtomGraphSynthesis;
using synthesis::PhaseSpaceSynthesis;
using synthesis::PsSynthesisWriter;
using synthesis::SyNonbondedKit;
using topology::AtomGraph;
using topology::ChemicalDetailsKit;
using topology::ImplicitSolventKit;
using topology::NonbondedKit;
using trajectory::PhaseSpaceWriter;
using trajectory::PhaseSpace;
  
constexpr double default_sasa_energy = 0.05;

constexpr double default_sasa_probe_radius = 1.4;

constexpr int default_sasa_point_count = 272;

constexpr SasaReference default_sasa_radii = SasaReference::LENNARD_JONES_SIGMA;

constexpr PrecisionModel default_sasa_precision = PrecisionModel::SINGLE;

constexpr int sasa_neighbor_list_buffer_size = 8192;

template <typename Tcalc, typename Tcalc2, typename Tcalc3>
void surfaceArea(PsSynthesisWriter *poly_psw, ScoreCard *sc,
                 const SyNonbondedKit<Tcalc, Tcalc2> &synbk, const uint* sasa_mask,
                 const std::vector<Tcalc3> &sphere_pts,
                 double probe_radius = default_sasa_probe_radius,
                 double weight = default_sasa_energy, EvaluateForce eval_frc = EvaluateForce::NO,
                 SasaReference radii_source = default_sasa_radii);
 
void surfaceArea(PhaseSpaceSynthesis *poly_ps, ScoreCard *sc, const AtomGraphSynthesis *poly_ag,
                 const std::vector<int> &molecule_idx = {}, int n_pts = default_sasa_point_count,
                 double probe_radius = default_sasa_probe_radius,
                 double weight = default_sasa_energy, EvaluateForce eval_frc = EvaluateForce::NO,
                 SasaReference radii_source = default_sasa_radii,
                 PrecisionModel prec = default_sasa_precision);
  
template <typename Tcalc, typename Tcalc3>
double surfaceArea(PhaseSpaceWriter *psw, const std::vector<bool> &sasa_mask,
                   const std::vector<Tcalc3> &sphere_pts, const Tcalc* atomic_radii,
                   double probe_radius = default_sasa_probe_radius,
                   double weight = default_sasa_energy,
                   EvaluateForce eval_frc = EvaluateForce::NO,
                   const int* radii_idx = nullptr);
 
template <typename Tcalc, typename Tcalc3>
double surfaceArea(PhaseSpaceWriter *psw, const std::vector<bool> &sasa_mask,
                   const NonbondedKit<Tcalc> &nbk, const std::vector<Tcalc3> &sphere_pts,
                   double probe_radius = default_sasa_probe_radius,
                   double weight = default_sasa_energy,
                   EvaluateForce eval_frc = EvaluateForce::NO);
 
template <typename Tcalc, typename Tcalc3>
double surfaceArea(PhaseSpaceWriter *psw, const std::vector<bool> &sasa_mask,
                   const ImplicitSolventKit<Tcalc> &isk, const std::vector<Tcalc3> &sphere_pts,
                   double probe_radius = default_sasa_probe_radius,
                   double weight = default_sasa_energy,
                   EvaluateForce eval_frc = EvaluateForce::NO);
 
double surfaceArea(PhaseSpace *ps, const AtomGraph *ag, const std::vector<int> &molecule_idx = {},
                   int n_pts = default_sasa_point_count,
                   double probe_radius = default_sasa_probe_radius,
                   double weight = default_sasa_energy, EvaluateForce eval_frc = EvaluateForce::NO,
                   SasaReference radii_source = default_sasa_radii,
                   PrecisionModel prec = default_sasa_precision);
                   
double surfaceArea(PhaseSpace *ps, const AtomGraph &ag, const std::vector<int> &molecule_idx = {},
                   int n_pts = default_sasa_point_count,
                   double probe_radius = default_sasa_probe_radius,
                   double weight = default_sasa_energy, EvaluateForce eval_frc = EvaluateForce::NO,
                   SasaReference radii_source = default_sasa_radii,
                   PrecisionModel prec = default_sasa_precision);
  
} // namespace energy
} // namespace energy
 
#include "surface_area.tpp"
 
#endif