ConformationSearch.h

Go to the documentation of this file.

 
#ifndef PNAB_CONFORMATIONSEARCH_H
#define PNAB_CONFORMATIONSEARCH_H
 
#include "Chain.h"
 
#define BOLTZMANN 0.0019872041 // kcal/(mol.K)
 
namespace PNAB {
    class ConformationSearch {
 
    public:
        ConformationSearch(PNAB::RuntimeParameters &runtime_params, PNAB::Backbone &backbone,
                           PNAB::HelicalParameters &helical_params, PNAB::Bases bases,
                           std::string prefix = "test", bool verbose = true);
 
        std::string run();
 
    private:
        bool verbose_; 
        PNAB::RuntimeParameters runtime_params_; 
        std::array<unsigned, 2> backbone_range_; 
        PNAB::Backbone backbone_; 
        PNAB::HelicalParameters helical_params_; 
        PNAB::Bases bases_; 
        std::mt19937_64 rng_; 
        int number_of_candidates = 0; 
        OpenBabel::matrix3x3 step_rot_, 
                             glbl_rot_; 
        OpenBabel::vector3 step_translate_, 
                           glbl_translate_; 
        OpenBabel::OBConversion conv_; 
        unsigned monomer_num_coords_; 
        std::string prefix_; 
 
        BaseUnit unit; 
        OpenBabel::OBMol bu_a_mol; 
        unsigned head, 
                 tail; 
        std::string output_string; 
        double* coords; 
        OpenBabel::OBRotorList rl; 
        std::vector<OpenBabel::OBRotor*> rotor_vector; 
 
        void SystematicSearch();
 
        void RandomSearch(bool weighted);
 
        void MonteCarloSearch(bool weighted);
 
        void GeneticAlgorithmSearch();
 
        std::vector <std::piecewise_linear_distribution<double>> WeightedDistributions();
 
        double measureDistance(double *coords, unsigned head, unsigned tail);
 
        void reportData(PNAB::ConformerData &conf_data);
 
        void printProgress(std::size_t search_index, std::size_t search_size);
    };
}
 
#endif //PNAB_MONTECARLOROTORSEARCH_H