nml_conformer.h

// -*-c++-*-
#ifndef STORMM_NML_CONFORMER_H
#define STORMM_NML_CONFORMER_H
 
#include "copyright.h"
#include "Constants/behavior.h"
#include "Constants/symbol_values.h"
#include "Structure/structure_enumerators.h"
#include "Synthesis/synthesis_enumerators.h"
#include "Parsing/textfile.h"
#include "namelist_element.h"
#include "namelist_emulator.h"
 
namespace stormm {
namespace namelist {
 
using constants::ExceptionResponse;
using parse::TextFile;
using parse::WrapTextSearch;
using structure::SamplingIntensity;
using synthesis::SystemGrouping;
using synthesis::VariableTorsionAdjustment;

constexpr int default_conf_rotation_samples       = 3;
constexpr int default_conf_cis_trans_samples      = 2;
constexpr int default_conf_max_rotatable_bonds    = 4;
constexpr int default_conf_max_seeding_attempts   = 3;
constexpr int default_conf_clash_pairs            = 0;
constexpr int default_conf_max_system_trials      = 16384;
constexpr int default_conf_sample_trials          = 512;
constexpr int default_conf_running_states         = 16;
constexpr int default_conf_final_states           = 100;
constexpr int default_conf_reshuffle_iterations   = 0;
constexpr int active_states_limit                 = 524288;
constexpr int seeding_attempts_limit              = 100;
constexpr double default_conf_rmsd_tolerance      = 1.5;
constexpr double default_conf_core_restraint      = 16.0;
constexpr char default_conf_chirality[]           = "false";
constexpr char default_conf_cis_trans[]           = "false";
constexpr char default_conf_stop_hbonds[]         = "false";
constexpr char default_conf_output_grouping[]     = "system";
constexpr char default_conf_sampling_effort[]     = "light";
constexpr char default_conf_adjustment_method[]   = "none";
constexpr char default_conf_rotation_set_zero[]   = "60.0";
constexpr char default_conf_rotation_set_one[]    = "180.0";
constexpr char default_conf_rotation_set_two[]    = "-60.0";
constexpr char default_conf_cis_trans_set_zero[]  = "0.0";
constexpr char default_conf_cis_trans_set_one[]   = "180.0";
constexpr char default_conf_rotation_snap[]       = "10.0";
constexpr char default_conf_cis_trans_snap[]      = "5.0";

class ConformerControls {
public:

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

  ConformerControls(const ConformerControls &original) = default;
  ConformerControls(ConformerControls &&original) = default;
  ConformerControls& operator=(const ConformerControls &original) = default;
  ConformerControls& operator=(ConformerControls &&original) = default;
  
  const std::string& getCoreAtomMask() const;

  const std::string& getCoreDataItemName() const;

  double getCoreRK2Value() const;

  double getCoreRK3Value() const;

  double getCoreR2Value() const;

  double getCoreR3Value() const;

  bool sampleChirality() const;

  bool sampleCisTrans() const;

  bool preventHydrogenBonding() const;

  int getRunningStateCount() const;

  int getFinalStateCount() const;

  int getRotationSampleCount() const;

  int getCisTransSampleCount() const;

  const std::vector<double>& getRotationSampleValues() const;

  const std::vector<double>& getCisTransSampleValues() const;

  int getRotatableBondLimit() const;

  int getMaxSeedingAttempts() const;

  int getClashPairTolerance() const;
  
  int getSamplingTrialLimit() const;

  int getMaximumTrialLimit() const;
  
  double getRMSDTolerance() const;

  SystemGrouping getGroupingMethod() const;

  SamplingIntensity getSamplingIntensity() const;

  double getRotatableBondSnapThreshold() const;

  double getCisTransBondSnapThreshold() const;

  VariableTorsionAdjustment getTorsionAdjustmentProtocol() const;
  
  const NamelistEmulator& getTranscript() const;
  
private:
  ExceptionResponse policy;         
  std::string core_atom_mask;       
  std::string core_data_item;       
  double core_rk2;                  
  double core_rk3;                  
  double core_r2;                   
  double core_r3;                   
  std::string anchor_conformation;  
  bool sample_chirality;            
  bool sample_cis_trans;            
  bool prevent_hbonds;              
  int running_states;               
  int final_states;                 
  int rotation_sample_count;        
  int rotatable_bond_limit;         
  int cis_trans_sample_count;       
  int max_seeding_attempts;         
  int clash_pair_tolerance;         
  int sampling_trial_limit;         
  int maximum_trial_limit;          
  double rmsd_tolerance;            
  std::string group_method;         
  std::string sample_effort;        
  double rotation_snap_threshold;   
  double cis_trans_snap_threshold;  
  std::string adjustment_method;    

  std::vector<double> rotation_sample_values;

  std::vector<double> cis_trans_sample_values;

  NamelistEmulator nml_transcript;
  
  void validateCoreRestraint() const;
  
  void validateSampleChirality(const std::string &directive) const;

  void validateSampleCisTrans(const std::string &directive) const;

  void validatePreventHBonds(const std::string &directive) const;  
  
  void validateStateCounts();

  void validateGroupingMethod();

  void validateSeedingAttempts();

  void validateClashCounts();
  
  void validateSamplingIntensity();

  void validateTorsionSnapping(double *snap_setting, const std::string &desc) const;

  void validateTorsionAdjustmentProtocol();
  
  void processSamplingValues(int *sample_count, const std::string &count_keyword,
                             std::vector<double> *sample_values, const std::string &value_keyword,
                             double value_stride, double value_notch,
                             const NamelistEmulator &t_nml);
};

NamelistEmulator conformerInput(const TextFile &tf, int *start_line, bool *found,
                                ExceptionResponse policy = ExceptionResponse::DIE,
                                WrapTextSearch wrap = WrapTextSearch::NO);
  
} // namespace namelist
} // namespace stormm
 
#endif