DNATorsionPotential.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file   core/scoring/dna/DNATorsionPotential.hh
/// @brief  DNATorsionPotential potential class delcaration
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu)

#ifndef INCLUDED_core_scoring_dna_DNATorsionPotential_HH
#define INCLUDED_core_scoring_dna_DNATorsionPotential_HH

// Unit Headers
#include <core/scoring/dna/DNATorsionPotential.fwd.hh>

// Project Headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/AmberPeriodicFunc.hh>
#include <core/scoring/constraints/HarmonicFunc.fwd.hh>
#include <core/scoring/constraints/HarmonicFunc.hh>

// Utility Headers
#include <utility/pointer/ReferenceCount.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray4D.hh>

namespace core {
namespace scoring {
namespace dna {

//enum{ WHATEVER, ALPHA, BETA, GAMMA, DELTA, EPSILON, ZETA, CHI, NU0, NU1, NU2, NU3, NU4 };

class DNATorsionPotential : public utility::pointer::ReferenceCount
{

public:
  DNATorsionPotential();
  ~DNATorsionPotential() {}


    /* Undefinded, comented out to make python bindings complile
  void
  eval_dna_torsion_score_residue(
    conformation::Residue const & rsd,
    Size const dna_torsion_number,
    Real & score,
    Real & deriv ) const;


  void
  eval_ribose_closure_score( conformation::Residue const & rsd, Real & score ) const;


  void
  eval_ribose_closure_derivative(
    id::AtomID const & id,
    pose::Pose const & pose,
    Vector & f1,
    Vector & f2 ) const;
    */

  //  void update_constraints( pose::Pose & pose ) const;

  void
  setup_constraints( pose::Pose & pose, constraints::ConstraintSetOP & dna_torsion_constraints,
   constraints::ConstraintSetOP & dna_sugar_close_constraints, constraints::ConstraintSetOP & dna_base_distance_constraints ) const;

  Real delta_cutoff() const { return DELTA_CUTOFF_; }

  utility::vector1< constraints::AmberPeriodicFuncOP > & alpha_components() { return alpha_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & beta_components() { return beta_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & gamma_components() { return gamma_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & delta_components() { return delta_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & epsilon_components() { return epsilon_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & zeta_components() { return zeta_components_; }

  utility::vector1< constraints::AmberPeriodicFuncOP > & nu0_components() { return nu0_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & nu1_components() { return nu1_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & nu2_components() { return nu2_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & nu3_components() { return nu3_components_; }
  utility::vector1< constraints::AmberPeriodicFuncOP > & nu4_components() { return nu4_components_; }

  void
  add_sugar_ring_closure_constraints( conformation::Residue const & rsd, constraints::ConstraintSet & cst_set ) const;

private:

  void
  add_sugar_ring_closure_constraints( pose::Pose & pose, constraints::ConstraintSet & cst_set ) const;

  void
  add_dna_base_distance_constraints( pose::Pose & pose, constraints::ConstraintSet & cst_set ) const;

  void
  add_dna_torsion_tethers(
    pose::Pose & pose,
    constraints::ConstraintSet & cst_set ) const;

  void
  add_DNA_torsion_constraint(
       pose::Pose & pose,
       Size const i,
       constraints::ConstraintSet & cst_set,
       Size const dna_torsion_number,
       utility::vector1< constraints::AmberPeriodicFuncOP > const & gaussian_parameter_set ) const;


  bool
  get_atom_ids_by_torsion(
    Size const dna_torsion_number,
    pose::Pose & pose,
    Size const resid,
    id::AtomID & id1,
    id::AtomID & id2,
    id::AtomID & id3,
    id::AtomID & id4 ) const;

  void
  init_dna_torsion_parameters();

  utility::vector1< constraints::AmberPeriodicFuncOP > alpha_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > beta_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > gamma_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > delta_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > epsilon_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > zeta_components_;

  utility::vector1< constraints::AmberPeriodicFuncOP > nu0_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > nu1_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > nu2_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > nu3_components_;
  utility::vector1< constraints::AmberPeriodicFuncOP > nu4_components_;

  utility::vector1< std::string > alpha_atom_names_;
  utility::vector1< std::string > beta_atom_names_;
  utility::vector1< std::string > gamma_atom_names_;
  utility::vector1< std::string > delta_atom_names_;
  utility::vector1< std::string > epsilon_atom_names_;
  utility::vector1< std::string > zeta_atom_names_;

  utility::vector1< std::string > nu0_atom_names_;
  utility::vector1< std::string > nu1_atom_names_;
  utility::vector1< std::string > nu2_atom_names_;
  utility::vector1< std::string > nu3_atom_names_;
  utility::vector1< std::string > nu4_atom_names_;

  // alpha, beta, gamma, delta, epsilon, zeta
  Real const DELTA_CUTOFF_;
  Real const scale_dna_torsion_tether_;
  Real const scale_dna_torsion_sd_;

  // Ribose closure
  Distance const c2star_c3star_bond_length_;
  Distance const c2star_c3star_sd_;
  constraints::HarmonicFuncOP c2star_c3star_dist_harm_func_;

  Real const c4star_c3star_c2star_bond_angle_;
  constraints::HarmonicFuncOP c4star_c3star_c2star_angle_harm_func_;
  Real const o3star_c3star_c2star_bond_angle_;
  constraints::HarmonicFuncOP o3star_c3star_c2star_angle_harm_func_;
  Real const c3star_c2star_c1star_bond_angle_;
  constraints::HarmonicFuncOP c3star_c2star_c1star_angle_harm_func_;

  bool const verbose_;

};

}
}
}

#endif