bounded_restraint.h

// -*-c++-*-
#ifndef STORMM_NMR_RESTRAINT_H
#define STORMM_NMR_RESTRAINT_H
 
#include <string>
#include "copyright.h"
#include "Chemistry/chemical_features.h"
#include "DataTypes/stormm_vector_types.h"
#include "Trajectory/coordinateframe.h"
#include "Topology/atomgraph.h"
 
namespace stormm {
namespace restraints {
 
using chemistry::ChemicalFeatures;
using topology::AtomGraph;
using trajectory::CoordinateFrameReader;
 
class BoundedRestraint {
public:

  BoundedRestraint(const AtomGraph *ag_in);
  
  BoundedRestraint(const std::string &mask_i_in, const std::string &mask_j_in, 
                   const std::string &mask_k_in, const std::string &mask_l_in,
                   const AtomGraph *ag_in, const ChemicalFeatures &chemfe,
                   const CoordinateFrameReader &cfr, int init_step_in, int final_step_in,
                   double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in,
                   double init_r3_in, double init_r4_in, double final_k2_in,
                   double final_k3_in, double final_r1_in, double final_r2_in,
                   double final_r3_in, double final_r4_in,
                   const double3 init_ref_crd_in = { 0.0, 0.0, 0.0 },
                   const double3 final_ref_crd_in = { 0.0, 0.0, 0.0 });
 
  BoundedRestraint(const std::string &mask_i_in, const std::string &mask_j_in, 
                   const std::string &mask_k_in, const AtomGraph *ag_in,
                   const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr,
                   int init_step_in, int final_step_in, double init_k2_in, double init_k3_in,
                   double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in,
                   double final_k2_in, double final_k3_in, double final_r1_in,
                   double final_r2_in, double final_r3_in, double final_r4_in);
 
  BoundedRestraint(const std::string &mask_i_in, const std::string &mask_j_in, 
                   const AtomGraph *ag_in, const ChemicalFeatures &chemfe,
                   const CoordinateFrameReader &cfr, int init_step_in, int final_step_in,
                   double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in,
                   double init_r3_in, double init_r4_in, double final_k2_in,
                   double final_k3_in, double final_r1_in, double final_r2_in,
                   double final_r3_in, double final_r4_in);
 
  BoundedRestraint(const std::string &mask_i_in, const AtomGraph *ag_in,
                   const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr,
                   int init_step_in, int final_step_in, double init_k2_in, double init_k3_in,
                   double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in,
                   double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in,
                   double final_r3_in, double final_r4_in, const double3 init_ref_crd_in,
                   const double3 final_ref_crd_in);
  
  BoundedRestraint(const std::string &mask_i_in, const std::string &mask_j_in, 
                   const std::string &mask_k_in, const std::string &mask_l_in,
                   const AtomGraph *ag_in, const ChemicalFeatures &chemfe,
                   const CoordinateFrameReader &cfr, double k2_in, double k3_in,
                   double r1_in, double r2_in, double r3_in, double r4_in);
 
  BoundedRestraint(const std::string &mask_i_in, const std::string &mask_j_in,
                   const std::string &mask_k_in, const AtomGraph *ag_in,
                   const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, double k2_in,
                   double k3_in, double r1_in, double r2_in, double r3_in, double r4_in);
 
  BoundedRestraint(const std::string &mask_i_in, const std::string &mask_j_in,
                   const AtomGraph *ag_in, const ChemicalFeatures &chemfe,
                   const CoordinateFrameReader &cfr, double k2_in, double k3_in,
                   double r1_in, double r2_in, double r3_in, double r4_in);
 
  BoundedRestraint(const std::string &mask_i_in, const AtomGraph *ag_in,
                   const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, double k2_in,
                   double k3_in, double r1_in, double r2_in, double r3_in, double r4_in,
                   const double3 ref_crd_in);
 
  BoundedRestraint(const std::string &mask_i_in, const AtomGraph *ag_in,
                   const ChemicalFeatures &chemfe, const CoordinateFrameReader &cfr, double k2_in,
                   double k3_in, double r1_in, double r2_in, double r3_in, double r4_in,
                   const std::string & mask_ref_in);
 
  BoundedRestraint(int atom_i_in, int atom_j_in, int atom_k_in, int atom_l_in,
                   const AtomGraph *ag_in, int init_step_in, int final_step_in, double init_k2_in,
                   double init_k3_in, double init_r1_in, double init_r2_in, double init_r3_in,
                   double init_r4_in, double final_k2_in, double final_k3_in,
                   double final_r1_in, double final_r2_in, double final_r3_in,
                   double final_r4_in, const double3 init_ref_crd_in = { 0.0, 0.0, 0.0},
                   const double3 final_ref_crd_in = { 0.0, 0.0, 0.0 });
 
  BoundedRestraint(int atom_i_in, int atom_j_in, int atom_k_in, const AtomGraph *ag_in,
                   int init_step_in, int final_step_in, double init_k2_in, double init_k3_in,
                   double init_r1_in, double init_r2_in, double init_r3_in, double init_r4_in,
                   double final_k2_in, double final_k3_in, double final_r1_in, double final_r2_in,
                   double final_r3_in, double final_r4_in);
 
  BoundedRestraint(int atom_i_in, int atom_j_in, const AtomGraph *ag_in, int init_step_in,
                   int final_step_in, double init_k2_in, double init_k3_in, double init_r1_in,
                   double init_r2_in, double init_r3_in, double init_r4_in, double final_k2_in,
                   double final_k3_in, double final_r1_in, double final_r2_in, double final_r3_in,
                   double final_r4_in);
 
  BoundedRestraint(int atom_i_in, const AtomGraph *ag_in, int init_step_in, int final_step_in,
                   double init_k2_in, double init_k3_in, double init_r1_in, double init_r2_in,
                   double init_r3_in, double init_r4_in, double final_k2_in, double final_k3_in,
                   double final_r1_in, double final_r2_in, double final_r3_in, double final_r4_in,
                   const double3 init_ref_crd_in, const double3 final_ref_crd_in);
 
  BoundedRestraint(int atom_i_in, int atom_j_in, int atom_k_in, int atom_l_in,
                   const AtomGraph *ag_in, double k2_in, double k3_in, double r1_in,
                   double r2_in, double r3_in, double r4_in);
 
  BoundedRestraint(int atom_i_in, int atom_j_in, int atom_k_in, const AtomGraph *ag_in,
                   double k2_in, double k3_in, double r1_in, double r2_in, double r3_in,
                   double r4_in);
 
  BoundedRestraint(int atom_i_in, int atom_j_in, const AtomGraph *ag_in, double k2_in,
                   double k3_in, double r1_in, double r2_in, double r3_in, double r4_in);
  
  BoundedRestraint(int atom_i_in, const AtomGraph *ag_in, double k2_in, double k3_in, double r1_in,
                   double r2_in, double r3_in, double r4_in, const double3 ref_crd_in);
 
  BoundedRestraint(int atom_index, const AtomGraph *ag_in, const CoordinateFrameReader &cfr,
                   double k2_in, double k3_in, double r1_in, double r2_in, double r3_in,
                   double r4_in, int refr_index = -1);

  BoundedRestraint(const BoundedRestraint &original) = default;
  BoundedRestraint(BoundedRestraint &&original) = default;
  BoundedRestraint& operator=(const BoundedRestraint &original) = default;
  BoundedRestraint& operator=(BoundedRestraint &&original) = default;
  
  int getAtomIndex(int restrained_atom_number) const;

  int getOrder() const;

  int getInitialStep() const;

  int getFinalStep() const;

  double2 getStiffness(int step_number = 0) const;

  double2 getInitialStiffness() const;

  double2 getFinalStiffness() const;

  double4 getDisplacements(int step_number = 0) const;

  double4 getInitialDisplacements() const;

  double4 getFinalDisplacements() const;

  double3 getTargetSite(int step_number = 0) const;
  
  double3 getInitialTargetSite() const;

  double3 getFinalTargetSite() const;

  const AtomGraph* getTopologyPointer() const;

  void setInitialStep(int new_init_step);

  void setFinalStep(int new_final_step);

  void setStiffness(double new_keq);

  void setStiffnesses(double new_k2, double new_k3);

  void setInitialStiffness(double new_init_keq);

  void setInitialStiffnesses(double new_init_k2, double new_init_k3);

  void setFinalStiffness(double new_init_keq);

  void setFinalStiffnesses(double new_init_k2, double new_init_k3);

  void setDisplacements(double new_r1, double new_r2, double new_r3, double new_r4);

  void setInitialDisplacements(double new_r1, double new_r2, double new_r3, double new_r4);

  void setFinalDisplacements(double new_r1, double new_r2, double new_r3, double new_r4);

  void setTargetSite(double new_ref_x, double new_ref_y, double new_ref_z);
  void setTargetSite(double3 new_ref_crd);

  void setInitialTargetSite(double new_ref_x, double new_ref_y, double new_ref_z);
  void setInitialTargetSite(double3 new_ref_crd);

  void setFinalTargetSite(double new_ref_x, double new_ref_y, double new_ref_z);
  void setFinalTargetSite(double3 new_ref_crd);
 
private:
  int atom_i;             
  int atom_j;             
  int atom_k;             
  int atom_l;             
  int order;              
  int initial_step;       
  int final_step;         
  double2 initial_keq;    
  double4 initial_r;      
  double2 final_keq;      
  double4 final_r;        
  double3 initial_center; 
  double3 final_center;   
  
  const AtomGraph *ag_pointer;  

  std::string reportAtomList();

  void checkDisplacementLimits(double4 *rval);
};
 
} // namespace restraints
} // namespace stormm
 
#endif