FullatomCustomPairDistanceEnergy.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/FullatomCustomPairDistanceEnergy.hh
/// @brief  Custom atom pair distance energy
/// @author David E Kim


#ifndef INCLUDED_core_scoring_custom_pair_distance_FullatomCustomPairDistanceEnergy_hh
#define INCLUDED_core_scoring_custom_pair_distance_FullatomCustomPairDistanceEnergy_hh

// Unit Headers
#include <core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergy.fwd.hh>

// Package headers

// Project headers
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
#include <core/scoring/constraints/Func.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

#include <core/kinematics/MinimizerMapBase.fwd.hh>

#include <core/chemical/ResidueType.fwd.hh>
// AUTO-REMOVED #include <basic/datacache/CacheableData.hh>

// Utility headers
// AUTO-REMOVED #include <utility/OrderedTuple.hh>
// AUTO-REMOVED #include <utility/fixedsizearray1.hh>
#include <numeric/interpolation/Histogram.hh>

// C++ headers
#include <map>
#include <list>

#include <utility/OrderedTuple.fwd.hh>
#include <utility/fixedsizearray1.fwd.hh>
#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace custom_pair_distance {

struct atoms_and_func_struct
{
  Size resA_atom_index_;
  Size resB_atom_index_;
  DistanceFuncCOP func_;
};

struct resatom_and_func_struct
{
  Size res_index_;
  Size atom_index_;
  DistanceFuncCOP func_;
};

class AtomPairFuncList : public utility::pointer::ReferenceCount
{
public:
  AtomPairFuncList();
  virtual ~AtomPairFuncList();

  std::list< atoms_and_func_struct > const & ats_n_func_list() const {
    return interacting_atompair_list_;
  }

  void
  add_interaction( atoms_and_func_struct const & interacting_pair );

private:
  std::list< atoms_and_func_struct > interacting_atompair_list_;
};

typedef utility::pointer::owning_ptr< AtomPairFuncList > AtomPairFuncListOP;
typedef utility::pointer::owning_ptr< AtomPairFuncList const > AtomPairFuncListCOP;

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

public:
  typedef utility::fixedsizearray1< Size, 2 > ResAtomIndex;
  typedef utility::OrderedTuple< ResAtomIndex > ResAtomIndexTuple;
  typedef std::map< ResAtomIndexTuple, std::list< resatom_and_func_struct > > ResAtomIndexFuncMap;

  typedef utility::fixedsizearray1< chemical::ResidueTypeCOP, 2 > ResTypePair;
  typedef utility::OrderedTuple< ResTypePair > ResTypePairTuple;

  typedef std::map< ResTypePairTuple, AtomPairFuncListOP > PairFuncMap;

  ///
  FullatomCustomPairDistanceEnergy();

  FullatomCustomPairDistanceEnergy( FullatomCustomPairDistanceEnergy const & src );

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


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

  // necessary pure virtual functions
  virtual
  void indicate_required_context_graphs( utility::vector1< bool > & /*context_graphs_required*/ ) const {}

  virtual
  bool
  defines_intrares_energy( EnergyMap const & /*weights*/ ) const { return false; }

  virtual
  void
  eval_intrares_energy(
    conformation::Residue const &,
    pose::Pose const &,
    ScoreFunction const &,
    EnergyMap &
  ) const {}

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

  virtual
  Distance
  atomic_interaction_cutoff() const;

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

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

  /// @brief Returns true if there are atoms on residue 1 & 2 that have interactions defined between them,
  /// and false otherwise.  This avoids unnecessary calls to residue_pair_energy_ext during minimization
  /// between pairs of atoms that have no interactons
  virtual
  bool
  defines_score_for_residue_pair(
    conformation::Residue const & res1,
    conformation::Residue const & res2,
    bool res_moving_wrt_eachother
  ) const;

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

  /// @brief Returns true.  This class takes advantage of the opportunity to store sequence-specific data
  /// in a ResiduePairMinimiazationObject listing the atom-pair interactions for a particular residue pair
  /// and to extract that data from cache for easy use inside residue_pair_energy_ext.
  virtual
  bool
  use_extended_residue_pair_energy_interface() const;

  /// @brief Extract the cached std::list< atoms_and_func_struct > object from the ResPairMinimizationData
  /// object that was stored for this particular residue pair in setup_for_minimizing_for_residue_pair, and
  /// use this cached list to evaluate the atom-pair interactions.
  virtual
  void
  residue_pair_energy_ext(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    ResPairMinimizationData const & min_data,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap & emap
  ) const;

  /// @brief Find the list of atom-pair interactions from the pair_and_func_map_ for the given
  /// residue-type pair and cache that list in the input ResPairMinimizationData object.
  virtual
  void
  setup_for_minimizing_for_residue_pair(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    kinematics::MinimizerMapBase const & minmap,
    ResSingleMinimizationData const & res1_data_cache,
    ResSingleMinimizationData const & res2_data_cache,
    ResPairMinimizationData & data_cache
  ) const;


  /// @brief Evaluate all f1/f2 derivative vector pairs for all interacting atoms
  /// on the input residue pair.
  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, // provides context
    EnergyMap const & weights,
    utility::vector1< DerivVectorPair > & r1_atom_derivs,
    utility::vector1< DerivVectorPair > & r2_atom_derivs
  ) const;

private:

  PairFuncMap::const_iterator
  find(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2
  ) const;

  bool
  interaction_defined(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2 ) const;

  void
  set_pair_and_func_map();

// DATA

private:

  PairFuncMap pair_and_func_map_;
  Real max_dis_;
  virtual
  core::Size version() const;
};



// stolen from Spencer's centroid disulfide stuff
class DistanceFunc : public constraints::Func
{
public:
  DistanceFunc( std::string const name );
  virtual ~DistanceFunc();
  constraints::FuncOP clone() const { return new DistanceFunc( *this ); }
  virtual Real func( Real const ) const;
  virtual Real dfunc( Real const ) const;
  virtual Real max_dis() const;
  virtual Real min_dis() const;
private:
  numeric::interpolation::HistogramCOP<Real,Real>::Type scores_hist_;
};



/*class CacheableAtomPairFuncMap : public basic::datacache::CacheableData
{
public:
  typedef utility::fixedsizearray1< Size, 2 > ResAtomIndex;
  typedef utility::OrderedTuple< ResAtomIndex > ResAtomIndexTuple;
  typedef std::map< ResAtomIndexTuple, std::list< resatom_and_func_struct > > ResAtomIndexFuncMap;

  CacheableAtomPairFuncMap(){};
  virtual ~CacheableAtomPairFuncMap(){};
  virtual basic::datacache::CacheableDataOP clone() const { return new CacheableAtomPairFuncMap( *this ); }
  ResAtomIndexFuncMap & map() { return map_; }
  ResAtomIndexFuncMap const & map() const { return map_; }
private:
  ResAtomIndexFuncMap map_;
virtual
core::Size version() const;
};*/


}
}
}


#endif