MMLJEnergyInter.hh

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//
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/// @file   core/scoring/methods/MMLJEnergyInter.hh
/// @brief  molecular mechanics lj energy
/// @author P. Douglas Renfrew (renfrew@unc.edu)

#ifndef INCLUDED_core_scoring_methods_MMLJEnergyInter_hh
#define INCLUDED_core_scoring_methods_MMLJEnergyInter_hh

// Unit headers
#include <core/scoring/methods/MMLJEnergyInter.fwd.hh>
// AUTO-REMOVED #include <core/scoring/mm/MMLJLibrary.hh>
#include <core/scoring/mm/MMLJEnergyTable.hh>

#include <core/scoring/mm/mmtrie/MMEnergyTableAtom.hh>

// Package headers
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
#include <core/scoring/etable/count_pair/CountPairFunction.fwd.hh>

#include <core/scoring/trie/RotamerTrieBase.fwd.hh>
// AUTO-REMOVED #include <core/scoring/trie/RotamerTrie.fwd.hh>
// AUTO-REMOVED #include <core/scoring/trie/TrieCountPairBase.hh>

// Project headers
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>

// C++ headers
#include <iostream>

#include <core/scoring/trie/TrieCountPairBase.fwd.hh>
#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace methods {

class MMLJEnergyInter : public ContextIndependentTwoBodyEnergy {
public:
  typedef ContextIndependentTwoBodyEnergy  parent;
public:

  /// ctor
  MMLJEnergyInter();

  /// clone
  virtual
  EnergyMethodOP
  clone() const;

  void
  setup_for_minimizing(
    pose::Pose & pose,
    ScoreFunction const & sfxn,
    kinematics::MinimizerMapBase const & min_map
  ) const;

  ///
  virtual
  void
  setup_for_packing(
    pose::Pose & pose,
    utility::vector1< bool > const &,
    utility::vector1< bool > const &
  ) const;

  // Creates a rotamer trie for the input set of rotamers and stores the trie
  // in the rotamer set.
  virtual
  void
  prepare_rotamers_for_packing(
    pose::Pose const & pose,
    conformation::RotamerSetBase & set ) const;

  // Updates the cached rotamer trie for a residue if it has changed during the course of
  // a repacking
  virtual
  void
  update_residue_for_packing( pose::Pose & pose, Size resid ) const;

  ///
  virtual
  void
  residue_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const &,
    EnergyMap & emap
  ) const;

  virtual
  void
  eval_atom_derivative(
    id::AtomID const & id,
    pose::Pose const & pose,
    kinematics::DomainMap const & /* domain_map*/,
    ScoreFunction const & /*sfxn*/,
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2
  ) const;

  virtual
  bool
  defines_intrares_energy( EnergyMap const & ) const;

  virtual
  void
  eval_intrares_energy(
    conformation::Residue const & rsd,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap & emap
  ) const;

  virtual
  void
  evaluate_rotamer_pair_energies(
    conformation::RotamerSetBase const & set1,
    conformation::RotamerSetBase const & set2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap const & weights,
    ObjexxFCL::FArray2D< core::PackerEnergy > & energy_table
  ) const;

  //@brief overrides default rotamer/background energy calculation and uses
  // the trie-vs-trie algorithm instead
  virtual
  void
  evaluate_rotamer_background_energies(
    conformation::RotamerSetBase const & set,
    conformation::Residue const & residue,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap const & weights,
    utility::vector1< core::PackerEnergy > & energy_vector
  ) const;

  /// @brief MMLJEnergyInter does not have an atomic interation threshold
  virtual
  Distance
  atomic_interaction_cutoff() const;

  /// @brief MMLJEnergyInter is context independent; indicates that no context graphs are required
  virtual
  void
  indicate_required_context_graphs( utility::vector1< bool > & ) const;

  /// @brief required for neighbor list and to be more lke the ETable
  etable::count_pair::CountPairFunctionCOP
  get_count_pair_function(
    Size res1,
    Size res2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn
  ) const;

  /// @brief required for neighbor list and to be more lke the ETable
  etable::count_pair::CountPairFunctionCOP
  get_count_pair_function(
    conformation::Residue const & res1,
    conformation::Residue const & res2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn
  ) const;

  /// @brief required for neighbor list and to be more lke the ETable
  etable::count_pair::CountPairFunctionOP
  get_intrares_countpair(
    conformation::Residue const & res,
    pose::Pose const & pose,
    ScoreFunction const & sfxn
  ) const;

  trie::RotamerTrieBaseOP
  create_rotamer_trie(
    conformation::RotamerSetBase const & rotset,
    pose::Pose const & pose
  ) const;

  trie::RotamerTrieBaseOP
  create_rotamer_trie(
    conformation::Residue const & res,
    pose::Pose const & pose
  ) const;

   // Hooks for trie algorithms

  ///  How close do two heavy atoms have to be such that their hydrogen atoms might interact?
  ///  max heavy-to-hydrogen distance ( MAGIC NUMBER!!!! FIX IT ) + atom-pair interaction distance.
  Real
  hydrogen_interaction_cutoff2() const
  {
    return ( hydrogen_interaction_cutoff() )*( hydrogen_interaction_cutoff() );
  }

  Real
  hydrogen_interaction_cutoff() const
  {
    return ( potential_.max_dist() + 2 * 1.468 ); // HR3 has the largest hydrogen radii @ 1.468
  }

  trie::TrieCountPairBaseOP
  get_count_pair_function_trie(
    conformation::Residue const & res1,
    conformation::Residue const & res2,
    trie::RotamerTrieBaseCOP trie1,
    trie::RotamerTrieBaseCOP trie2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn
  ) const;

  trie::TrieCountPairBaseOP
  get_count_pair_function_trie(
    conformation::RotamerSetBase const & set1,
    conformation::RotamerSetBase const & set2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn
  ) const;

  inline
  Energy heavyatom_heavyatom_energy(
    core::scoring::mm::mmtrie::MMEnergyTableAtom const & at1,
    core::scoring::mm::mmtrie::MMEnergyTableAtom const & at2,
    DistanceSquared & d2,
    Size & path_dist
  ) const
  {
    Real rep(0), atr(0);
    potential_.score( at1.mm_atom_type(), at2.mm_atom_type(), path_dist, d2, rep, atr );
    return rep + atr;

  }

  inline
  Energy heavyatom_hydrogenatom_energy(
    core::scoring::mm::mmtrie::MMEnergyTableAtom const & at1,
    core::scoring::mm::mmtrie::MMEnergyTableAtom const & at2,
    Size & path_dist
  ) const
  {
    Real dist_squared( at1.xyz().distance_squared( at2.xyz() ) );
    Real rep(0), atr(0);
    potential_.score( at1.mm_atom_type(), at2.mm_atom_type(), path_dist, dist_squared, rep, atr );
    return rep + atr;
  }

  inline
  Energy hydrogenatom_heavyatom_energy(
    core::scoring::mm::mmtrie::MMEnergyTableAtom const & at1,
    core::scoring::mm::mmtrie::MMEnergyTableAtom const & at2,
    Size & path_dist
  ) const
  {
    Real dist_squared( at1.xyz().distance_squared( at2.xyz() ) );
    Real rep(0), atr(0);
    potential_.score( at1.mm_atom_type(), at2.mm_atom_type(), path_dist, dist_squared, rep, atr );
    return rep + atr;
  }

  inline
  Energy hydrogenatom_hydrogenatom_energy(
    core::scoring::mm::mmtrie::MMEnergyTableAtom const & at1,
    core::scoring::mm::mmtrie::MMEnergyTableAtom const & at2,
    Size & path_dist
  ) const
  {
    Real dist_squared( at1.xyz().distance_squared( at2.xyz() ) );
    Real rep(0), atr(0);
    potential_.score( at1.mm_atom_type(), at2.mm_atom_type(), path_dist, dist_squared, rep, atr );
    return rep + atr;
  }


  // stuff for bump check
  virtual
  void
  bump_energy_full(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap & emap
  ) const;

  virtual
  void
  bump_energy_backbone(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap & emap
  ) const;

private:
  core::scoring::mm::MMLJEnergyTable const & potential_;
virtual
core::Size version() const;

};

} // namespace methods
} // namespace scoring
} // namespace core


#endif // INCLUDED_core_scoring_methods_MMLJEnergyInter_HH