nml_restraint.h

// -*-c++-*-
#ifndef STORMM_NML_RESTRAINT_H
#define STORMM_NML_RESTRAINT_H
 
#include "copyright.h"
#include "input.h"
#include "namelist_emulator.h"
#include "namelist_enumerators.h"
#include "Chemistry/chemical_features.h"
#include "Parsing/textfile.h"
#include "Restraints/bounded_restraint.h"
#include "Restraints/restraint_enumerators.h"
#include "Topology/atomgraph.h"
#include "Topology/atomgraph_abstracts.h"
#include "Trajectory/coordinateframe.h"
#include "Trajectory/phasespace.h"
 
namespace stormm {
namespace namelist {
 
using chemistry::ChemicalFeatures;
using parse::WrapTextSearch;
using restraints::BoundedRestraint;
using restraints::RestraintEnsemble;
using topology::AtomGraph;
using topology::NonbondedKit;
using trajectory::CoordinateFrame;
using trajectory::CoordinateFrameReader;
using trajectory::PhaseSpace;

constexpr char default_heavy_atom_mask[] = "@/2-200";
constexpr double default_restraint_ensemble_penalty = 1.0;
constexpr double default_restraint_ensemble_half_width = 0.0;
constexpr double default_restraint_ensemble_hbond_proximity = 3.0;
constexpr double default_restraint_ensemble_distance_cutoff = 6.0;

class RestraintControls {
public:

  RestraintControls(ExceptionResponse policy_in = ExceptionResponse::DIE);
  
  RestraintControls(const TextFile &tf, int *start_line, bool *found_nml,
                    ExceptionResponse policy_in = ExceptionResponse::DIE,
                    WrapTextSearch wrap = WrapTextSearch::NO);
  
  RestraintControls(const RestraintControls &original) = default;
  RestraintControls(RestraintControls &&original) = default;
  RestraintControls& operator=(const RestraintControls &original) = default;
  RestraintControls& operator=(RestraintControls &&original) = default;

  int getOrder() const;
  
  std::string getSystemLabel() const;

  std::vector<BoundedRestraint> getRestraint(const AtomGraph *ag, const ChemicalFeatures &chemfe,
                                             const CoordinateFrameReader &cf) const;
 
  std::vector<BoundedRestraint> getRestraint(const AtomGraph *ag, const ChemicalFeatures &chemfe,
                                             const CoordinateFrame &cf) const;
 
  std::vector<BoundedRestraint> getRestraint(const AtomGraph *ag, const ChemicalFeatures &chemfe,
                                             const PhaseSpace &ps) const;

  const NamelistEmulator& getTranscript() const;
  
private:
 
  // General information about the status of the restraint
  ExceptionResponse policy;   
  bool restraint_is_valid;    
  std::string system;         
  RestraintEnsemble domain;   
 
  // Parameters for a typical Amber flat-bottom well NMR restraint applied to specific atoms
  std::string mask_i;         
  std::string mask_j;         
  std::string mask_k;         
  std::string mask_l;         
  std::string ensemble_mask;  
  int atom_i;                 
  int atom_j;                 
  int atom_k;                 
  int atom_l;                 
  int order;                  
  int initiation_step;        
  int maturation_step;        
  double initial_k2;          
  double initial_k3;          
  double initial_r1;          
  double initial_r2;          
  double initial_r3;          
  double initial_r4;          
  double mature_k2;           
  double mature_k3;           
  double mature_r1;           
  double mature_r2;           
  double mature_r3;           
  double mature_r4;           
  double3 initial_crd;        
  double3 mature_crd;         
 
  // Parameters for ensembles of restraints
  double penalty;                 
  double flat_bottom_half_width;  
  double cutoff;                  
  double proximity;               

  NamelistEmulator nml_transcript;
  
  RestraintAnchoring getAtomSpecification() const;

  void enforceSpecification();

  void checkFinalRestraintSettings(bool nstep1_found, bool r2a_found, bool r3a_found,
                                   bool k2a_found, bool k3a_found, int starting_line,
                                   const std::string &filename);
};
 
NamelistEmulator restraintInput(const TextFile &tf, int *start_line, bool *found,
                                ExceptionResponse policy = ExceptionResponse::DIE,
                                WrapTextSearch wrap = WrapTextSearch::NO);
 
} // namespace namelist
} // namespace stormm
 
#endif