Chain.h

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#ifndef PNAB_CHAIN_H
#define PNAB_CHAIN_H
 
#include <algorithm>
#include <openbabel/forcefield.h>
#include <openbabel/rotor.h>
#include <openbabel/generic.h>
#include <openbabel/obiter.h>
#include "Containers.h"
#define KJ_TO_KCAL 0.239006
 
namespace PNAB {
 
    class Chain {
 
    public:
        Chain(PNAB::Bases bases, const PNAB::Backbone &backbone, std::vector<std::string> strand,
              std::string ff_type, std::array<unsigned, 2> &range, bool hexad,
              std::vector<bool> build_strand = {true, false, false, false, false, false},
              std::vector<bool> strand_orientation = {true, true, true, true, true, true},
              double glycosidic_bond_distance = 0.0);
 
        ~Chain() {
            for (auto v : v_base_coords_vec_) {
                for (auto i : v)
                    delete[] i;
            }
        }
 
        PNAB::ConformerData generateConformerData(double *xyz, PNAB::HelicalParameters &hp, std::vector<double> energy_filter);
 
    private:
        std::vector<OpenBabel::OBMol> v_chain_ = std::vector<OpenBabel::OBMol>(6); 
        OpenBabel::OBMol combined_chain_; 
        std::vector<std::vector<unsigned>> v_new_bond_ids_ = std::vector<std::vector<unsigned>>(6); 
        std::vector<std::vector<unsigned>> v_deleted_atoms_ids_ = std::vector<std::vector<unsigned>>(6); 
        std::vector<std::vector<unsigned>> v_num_bu_A_mol_atoms_ = std::vector<std::vector<unsigned>>(6); 
        std::vector<std::vector<std::vector<unsigned>>> v_fixed_bonds = std::vector<std::vector<std::vector<unsigned>>>(6); 
        std::vector<std::vector<double*>> v_base_coords_vec_ = std::vector<std::vector<double*>>(6); 
        unsigned chain_length_, 
                 n_chains_; 
        bool isKCAL_, 
             hexad_; 
        std::vector<bool> strand_orientation_; 
        double glycosidic_bond_distance_; 
        OpenBabel::OBForceField *pFF_; 
        std::array<unsigned, 2> monomer_bb_index_range_; 
        std::vector<std::vector<unsigned>> v_bb_start_index_ = std::vector<std::vector<unsigned>>(6); 
        std::string ff_type_; 
        std::vector<std::vector<unsigned int>> all_angles_, 
                                               all_torsions_; 
        std::vector<bool> is_fixed_bond; 
        std::vector<bool> build_strand_; 
 
        OpenBabel::OBFFConstraints constraintsBond_, 
                                   constraintsAng_, 
                                   constraintsTor_, 
                                   constraintsTot_; 
 
        void fillConformerEnergyData(double *xyz, PNAB::ConformerData &conf_data, std::vector<double> energy_filter);
 
        void setupChain(std::vector<PNAB::Base> &strand, OpenBabel::OBMol &chain, std::vector<unsigned> &new_bond_ids,
                            std::vector<unsigned> &deleted_atoms_ids, std::vector<unsigned> &num_base_unit_atoms,
                            std::vector<unsigned> &bb_start_index, std::vector<double *> &base_coords_vec,
                            std::vector<std::vector<unsigned>> &fixed_bonds_vec, const Backbone &backbone, unsigned chain_index);
        void setupFFConstraints(OpenBabel::OBMol &chain, std::vector<unsigned> &new_bond_ids, std::vector<std::vector<unsigned>> &fixed_bonds_vec, unsigned offset = 0);
 
        void setCoordsForChain(double *xyz, double *conf, PNAB::HelicalParameters &hp, std::vector<unsigned> &num_bu_atoms,
                               std::vector<unsigned> &bb_start_index, std::vector<double *> &base_coords_vec,
                               std::vector<unsigned> &deleted_atoms_ids, unsigned chain_index);
 
        void orderResidues(OpenBabel::OBMol* molecule);
    };
 
}
 
#endif //PNAB_CHAIN_H