ContextIndependentGeometricSolEnergy.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/ContextIndependentGeometricSolEnergy.hh
/// @brief  Hydrogen bond energy method class declaration
/// @author Parin Sripakdeevong (sripakpa@stanford.edu), Rhiju Das (rhiju@stanford.edu)



#ifndef INCLUDED_core_scoring_geometric_solvation_ContextIndependentGeometricSolEnergy_hh
#define INCLUDED_core_scoring_geometric_solvation_ContextIndependentGeometricSolEnergy_hh

// Unit Headers
#include <core/scoring/geometric_solvation/ContextIndependentGeometricSolEnergy.fwd.hh>
#include <core/types.hh>

// Package headers
// AUTO-REMOVED #include <core/scoring/hbonds/constants.hh>
#include <core/scoring/hbonds/types.hh>
#include <core/scoring/hbonds/HBondDatabase.fwd.hh>
#include <core/scoring/hbonds/hbonds_geom.hh>
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>

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

//Auto Headers
#include <core/scoring/methods/EnergyMethodOptions.fwd.hh>


namespace core {
namespace scoring {
namespace geometric_solvation {

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

  ///
  ContextIndependentGeometricSolEnergy( methods::EnergyMethodOptions const & options );

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

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

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

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

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

  /// This evaluates everything for now,
  /// but eventually may want to split this
  /// based on backbone/backbone vs. others,
  /// as is carried out in HBondEnergy.cc
  virtual
  void
  residue_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const &,
    EnergyMap & emap
  ) const;

  void
  eval_atom_derivative_intra_RNA(
     id::AtomID const & atom_id,
     pose::Pose const & pose,
     EnergyMap const & weights,
     Vector & F1,
     Vector & F2
  ) const;

  /// f1 and f2 are zeroed
  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;

  Real
  eval_atom_energy(
    id::AtomID const & atom_id,
    pose::Pose const & pose
  ) 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 & ,
    EnergyMap & emap
  ) const;

  virtual
  Distance
  atomic_interaction_cutoff() const;

  // Undefined, commenting out to fix PyRosetta build  Real hydrogen_interaction_cutoff2() const;

  ///@brief ContextIndependentGeometricSolEnergy is NOT context sensitive
  virtual
  void indicate_required_context_graphs(
    utility::vector1< bool > & /*context_graphs_required*/ ) const;

private:

  inline
  Real
  res_res_geometric_sol_one_way(
    conformation::Residue const & polar_rsd,
    conformation::Residue const & occ_rsd,
    pose::Pose const & pose ) const;

  inline
  Real
  donorRes_occludingRes_geometric_sol_one_way(
    conformation::Residue const & don_rsd,
    conformation::Residue const & occ_rsd,
    pose::Pose const & pose ) const;

  inline
  Real
  acceptorRes_occludingRes_geometric_sol_one_way(
    conformation::Residue const & acc_rsd,
    conformation::Residue const & occ_rsd,
    pose::Pose const & pose ) const;

  inline
  Real
  occluded_water_hbond_penalty(
    bool const & is_donor,
    hbonds::HBEvalTuple const & hbond_eval_type,
    Vector const & polar_atm_xyz,
    Vector const & base_atm_xyz,
    Vector const & occluding_atm_xyz,
    bool const update_deriv = false,
    hbonds::HBondDerivs & deriv = hbonds::DUMMY_DERIVS) const;

  inline
  void
  set_water_base_atm(
    Vector const & base_v,
    Vector const & atom_v,
    Vector const & water_v,
    Vector & water_base_v,
    Real const & xH /*cos(theta)*/,
    Distance const & bond_length ) const;

  inline
  Real
  get_water_cos(
    Vector const & base_atm_xyz,
    Vector const & polar_atm_xyz,
    Vector const & occluding_atm_xyz ) const;

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

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

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

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


  void
  get_atom_atom_geometric_solvation_for_donor(
    Size const & don_h_atm,
    conformation::Residue const & don_rsd,
    Size const & occ_atm,
    conformation::Residue const & occ_rsd,
    pose::Pose const & pose,
    Real & energy,
    bool const update_deriv = false,
    hbonds::HBondDerivs & deriv = hbonds::DUMMY_DERIVS
  ) const;

  void
  get_atom_atom_geometric_solvation_for_acceptor(
    Size const & acc_atm,
    conformation::Residue const & acc_rsd,
    Size const & occ_atm,
    conformation::Residue const & occ_rsd,
    pose::Pose const & pose,
    Real & energy,
    bool const update_deriv = false,
    hbonds::HBondDerivs & deriv = hbonds::DUMMY_DERIVS
  ) const;


  Real
  donorRes_occludingRes_geometric_sol_RNA_intra(
    conformation::Residue const & rsd,
    pose::Pose const & pose ) const;

  Real
  acceptorRes_occludingRes_geometric_sol_RNA_intra(
    conformation::Residue const & rsd,
    pose::Pose const & pose ) const;

  Vector
  get_acceptor_base_atm_xyz( conformation::Residue const & acc_rsd, Size const & acc_atm ) const;

private:

  /////////////////////////////////////////////////////////////////////////////
  // data
  /////////////////////////////////////////////////////////////////////////////
  methods::EnergyMethodOptionsOP options_;


  // no Hbonds longer than sqrt of this (the square)
  hbonds::HBondDatabaseCOP hb_database_;
  Real const dist_cut2_;
  Real const geometric_sol_scale_;

  bool const correct_geom_sol_acceptor_base_;
  bool const verbose_;

  virtual
  core::Size version() const;

};

} // hbonds
} // scoring
} // core

#endif