CarbonHBondEnergy.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   core/scoring/methods/CarbonHBondEnergy.hh
/// @brief  Hydrogen bond energy method class declaration
/// @author Phil Bradley
/// @author Andrew Leaver-Fay


#ifndef INCLUDED_core_scoring_carbon_hbonds_CarbonHBondEnergy_hh
#define INCLUDED_core_scoring_carbon_hbonds_CarbonHBondEnergy_hh

#include <core/types.hh>

// Unit Headers
#include <core/scoring/carbon_hbonds/CarbonHBondEnergy.fwd.hh>

// Package headers
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
// AUTO-REMOVED #include <core/scoring/carbon_hbonds/CarbonHBondPotential.hh>
#include <core/scoring/MinimizationData.fwd.hh>


// Project headers
#include <core/pose/Pose.fwd.hh>
// AUTO-REMOVED #include <core/scoring/EnergyMap.hh>

#include <core/scoring/carbon_hbonds/CarbonHBondPotential.fwd.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>

namespace core {
namespace scoring {
namespace carbon_hbonds {

static core::Vector DUMMY_VECTOR;

///
class CarbonHBondEnergy : public methods::ContextIndependentTwoBodyEnergy  {
public:
  typedef methods::ContextIndependentTwoBodyEnergy  parent;

public:

  ///
  CarbonHBondEnergy();

  ///@brief copy c-tor
  CarbonHBondEnergy( CarbonHBondEnergy const & src );

  /// clone
  virtual
  methods::EnergyMethodOP
  clone() const;

  ///
  virtual
  void
  setup_for_scoring( pose::Pose & pose, ScoreFunction const & ) const;

  /////////////////////////////////////////////////////////////////////////////
  // scoring
  /////////////////////////////////////////////////////////////////////////////

  /// @brief Evaluate the cbond energy between two residues
  virtual
  void
  residue_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const &,
    EnergyMap & emap
  ) const;


  /// @brief Splitting out based on bb/bb for the OnTheFly IGs
  virtual
  void
  backbone_backbone_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap & emap
  ) const;


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

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

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

  virtual
  bool
  minimize_in_whole_structure_context( pose::Pose const & ) const;

  /// @brief Evaluate all atom-pair derivatives for any interactions between the two residues
  virtual
  void
  eval_residue_pair_derivatives(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    ResSingleMinimizationData const &,
    ResSingleMinimizationData const &,
    ResPairMinimizationData const & min_data,
    pose::Pose const & pose,
    EnergyMap const & weights,
    utility::vector1< DerivVectorPair > & r1_atom_derivs,
    utility::vector1< DerivVectorPair > & r2_atom_derivs
  ) const;

  virtual
  void
  eval_intrares_derivatives(
    conformation::Residue const & rsd,
    ResSingleMinimizationData const & min_data,
    pose::Pose const & pose,
    EnergyMap const & weights,
    utility::vector1< DerivVectorPair > & atom_derivs
  ) const;

  ///
  //  virtual
  //  void
  //  finalize_total_energy(
  //    pose::Pose & pose,
  //    ScoreFunction const &,
  //    EnergyMap & totals
  //  ) const;

  virtual
  bool
  defines_intrares_energy( EnergyMap const & /*weights*/ ) const;

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

  virtual
  Distance
  atomic_interaction_cutoff() const;

  virtual
  bool
  divides_backbone_and_sidechain_energetics() const
  {
    return true;
  }

  // Real hydrogen_interaction_cutoff2() const;

  ///@brief CarbonHBondEnergy is context sensitive
  virtual
  void indicate_required_context_graphs(
    utility::vector1< bool > & context_graphs_required ) const;

  bool
  use_orientation_dep_rna_ch_o_bonds(conformation::Residue const & don_rsd, conformation::Residue const & acc_rsd) const;

private:

  bool
  path_distance_OK(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    Size const ii,
    Size const jj
  ) const;

  Real
  res_res_carbon_hbond_one_way(
    conformation::Residue const & don_rsd,
    conformation::Residue const & acc_rsd,
    Real & bb_bb,
    Real & bb_sc,
    Real & sc_sc
  ) const;

  Real
  bb_bb_carbon_hbond_one_way(
    conformation::Residue const & don_rsd,
    conformation::Residue const & acc_rsd
  ) const;

  Real
  sc_bb_carbon_hbond_one_way(
    conformation::Residue const & don_rsd, // sidechain atoms on donor
    conformation::Residue const & acc_rsd  // backbone atoms on acceptor
  ) const;

  Real
  bb_sc_carbon_hbond_one_way(
    conformation::Residue const & don_rsd, // backbone atoms on donor
    conformation::Residue const & acc_rsd  // sidechain atoms on acceptor
  ) const;

  Real
  sc_sc_carbon_hbond_one_way(
    conformation::Residue const & don_rsd,
    conformation::Residue const & acc_rsd
  ) const;


  void
  res_res_carbon_hbond_derivs_one_way(
    conformation::Residue const & don_rsd,
    conformation::Residue const & acc_rsd,
    EnergyMap const & weights,
    utility::vector1< DerivVectorPair > & don_atom_derivs,
    utility::vector1< DerivVectorPair > & acc_atom_derivs
  ) const;


  bool
  atom_is_apolar_h( conformation::Residue const & rsd, Size const atm ) const;

  bool
  atom_is_acceptor( conformation::Residue const & rsd, Size const atm ) const;

  /// @details Atom pair interaction energy; returns true if the interaction energy
  /// is nonzero.  The f2 vector returned when update_deriv is true is the force on
  /// the hydrogen atom; f2 for the acceptor is -1 * f2 for the hydrogen.  f1 may
  /// be computed by taking the cross product of f2 with the coordinate of the
  /// acceptor/hydrogen respectively.
  bool
  get_atom_atom_carbon_hbond_energy(
    Size const don_h_atm,
    conformation::Residue const & don_rsd,
    Size const acc_atm,
    conformation::Residue const & acc_rsd,
    Real & energy,
    bool const update_deriv = false,
    Vector & f2 = DUMMY_VECTOR
  ) const;


private:

  /////////////////////////////////////////////////////////////////////////////
  // data
  /////////////////////////////////////////////////////////////////////////////

  // const-ref to scoring database
  carbon_hbonds::CarbonHBondPotential const & carbon_hbond_potential_;
  Real const max_dis_;
  Real const max_dis2_;

  Size const path_dist_cutoff_;

  bool const orientation_dep_rna_ch_o_bonds_;
  bool const verbose_;

  /// apl -- enmethods should not know what weights to use; they should use the weights they're given
  /// This will allow (near future) reweighting between arbitrary residue pairs
  //mutable Real wbb_bb_;
  //mutable Real wbb_sc_;
  //mutable Real wsc_sc_;

virtual
core::Size version() const;
};

} // carbon_hbonds
} // scoring
} // core

#endif