RotamerSets.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file   core/pack/RotamerSet/RotamerSets.hh
/// @brief  RotamerSets class declaration
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu)


#ifndef INCLUDED_core_pack_rotamer_set_RotamerSets_hh
#define INCLUDED_core_pack_rotamer_set_RotamerSets_hh

// Unit Headers
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>
//#include <core/pack/rotamer_set/rotamer_building_functions.hh> // WHY IS THIS IN THE .HH?

// Package Headers

#include <core/pack/rotamer_set/RotamerSet.fwd.hh>
#include <core/pack/rotamer_set/FixbbRotamerSets.hh>
//#include <core/pack/rotamer_set/RotamerSetsBase.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/interaction_graph/InteractionGraphBase.fwd.hh>
#include <core/pack/interaction_graph/PrecomputedPairEnergiesInteractionGraph.fwd.hh>
#include <core/pack/interaction_graph/OnTheFlyInteractionGraph.fwd.hh>

#ifdef WIN32 //VC++ needs full class declaration
#include <core/pack/rotamer_set/RotamerSet.hh> // WIN32 INCLUDE
#endif

// Project Headers
#include <core/conformation/Residue.fwd.hh>
// AUTO-REMOVED #include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/graph/Graph.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

// Utility Headers
// AUTO-REMOVED #include <utility/vector1.hh>
#include <core/types.hh>

#include <utility/vector1.hh>


namespace core {
namespace pack {
namespace rotamer_set {

class RotamerSets : public FixbbRotamerSets
{
public:
  typedef task::PackerTaskCOP PackerTaskCOP;

public:
  RotamerSets();
  ~RotamerSets();

  void
  set_task( task::PackerTaskCOP task);

  void
  build_rotamers(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scfxn,
    graph::GraphCOP packer_neighbor_graph
  );

  void
  compute_energies(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scfxn,
    graph::GraphCOP packer_neighbor_graph,
    interaction_graph::InteractionGraphBaseOP ig
  );

  void
  dump_pdb( pose::Pose const & pose, std::string const & filename ) const;

  virtual uint nrotamers() const;
  virtual uint nrotamers_for_moltenres( uint ) const;

  virtual uint nmoltenres() const;
  virtual uint total_residue() const;

  virtual
  uint
  moltenres_2_resid( uint ) const;

  virtual
  uint
  resid_2_moltenres( uint ) const;

  virtual
  uint
  moltenres_for_rotamer( uint ) const;

  virtual
  uint
  res_for_rotamer( uint ) const;

  virtual
  core::conformation::ResidueCOP
  rotamer( uint ) const;

  virtual
  core::conformation::ResidueCOP
  rotamer_for_moltenres( uint moltenres_id, uint rotamerid ) const;

  virtual
  uint
  nrotamer_offset_for_moltenres( uint ) const;

  virtual
  RotamerSetCOP
  rotamer_set_for_residue( uint resid ) const;

  virtual
  RotamerSetOP
  rotamer_set_for_residue( uint resid );

  virtual
  RotamerSetCOP
  rotamer_set_for_moltenresidue( uint moltenresid ) const;

  virtual
  RotamerSetOP
  rotamer_set_for_moltenresidue( uint moltenresid );

  virtual
  RotamerSetVector::const_iterator begin()
  { return set_of_rotamer_sets_.begin(); }

  virtual
  RotamerSetVector::const_iterator end()
  { return set_of_rotamer_sets_.end(); }

  /// convert rotid in full rotamer enumeration into rotamer id on its source residue
  virtual
  uint
  rotid_on_moltenresidue( uint rotid ) const;

  /// convert moltenres rotid to id in full rotamer enumeration
  virtual
  uint
  moltenres_rotid_2_rotid( uint moltenres, uint moltenresrotid ) const;

  /// access to packer_task_
  PackerTaskCOP
  task() const;

  void prepare_sets_for_packing( pose::Pose const & pose, scoring::ScoreFunction const &);

private:
  void update_offset_data();


public:

  void
  compute_one_body_energies(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scfxn,
    graph::GraphCOP packer_neighbor_graph,
    interaction_graph::InteractionGraphBaseOP ig
  );

  /// @brief precomputes all rotamer pair energies between neighboring RotamerSets( residues )
  /// and stores those energies in an intereaction graph capable of storing them
  /// public so it can be used by the GreenPacker.
  void
  precompute_two_body_energies(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scfxn,
    graph::GraphCOP packer_neighbor_graph,
    interaction_graph::PrecomputedPairEnergiesInteractionGraphOP pig,
    bool const finalize_edges = true
  );

private:
  /// @brief Marks all protein vertices in the on-the-fly interaction graph as ones
  /// that should distinguish between the backbones and sidechains.  Then, adds edges to
  /// the on-the-fly interaction graph between neighboring RotamerSets,
  /// and figures out, for those edges, which pairs of rotamer groups (e.g. ala1/arg2, ser1/phe2)
  /// are close enough to interact for their energies to need calculation.
  void
  prepare_otf_graph(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scfxn,
    graph::GraphCOP packer_neighbor_graph,
    interaction_graph::OnTheFlyInteractionGraphOP otfig
  );

  /// @brief computes one body energies for the on-the-fly graph, calculating proline-correction
  /// terms for protien-residues that allow prolines and storing them on the otf edges
  void
  compute_proline_correction_energies_for_otf_graph(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scfxn,
    graph::GraphCOP packer_neighbor_graph,
    interaction_graph::OnTheFlyInteractionGraphOP otfig
  );

public:

  static
  core::PackerEnergy
  get_bb_bbE(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scfxn,
    conformation::Residue const & res1,
    conformation::Residue const & res2
  );

  static
  core::PackerEnergy
  get_sc_bbE(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scfxn,
    conformation::Residue const & res1,
    conformation::Residue const & res2
  );

public: // WHY? G++, WHY?!

  virtual
  utility::vector1< uint > const &
  resid_2_moltenres_vector() const {
    return resid_2_moltenres_;
  }

  virtual
  utility::vector1< uint > const &
  moltenres_2_resid_vector() const {
    return moltenres_2_resid_;
  }

private:
  uint nmoltenres_;
  uint total_residue_;

  uint nrotamers_;

  RotamerSetVector set_of_rotamer_sets_;
  utility::vector1< uint > resid_2_moltenres_;
  utility::vector1< uint > moltenres_2_resid_;
  utility::vector1< uint > nrotamer_offsets_;

   // originating moltenres for a particular rotamer in the enumeration of all rotamers
  utility::vector1< uint > moltenres_for_rotamer_;
  utility::vector1< uint > nrotamers_for_moltenres_;

  PackerTaskCOP task_;
};

} // namespace rotamer_set
} // namespace pack
} // namespace core


#endif // INCLUDED_core_pack_RotamerSet_RotamerSets_HH