RotamerSet.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file   core/pack/RotamerSet/RotamerSet.hh
/// @brief  Residue Set class
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu)


#ifndef INCLUDED_core_pack_rotamer_set_RotamerSet_hh
#define INCLUDED_core_pack_rotamer_set_RotamerSet_hh

// Unit Headers
#include <core/pack/rotamer_set/RotamerSet.fwd.hh>

// Package Headers

#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>

// Project Headers
#include <core/types.hh>

#include <core/conformation/RotamerSetBase.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/graph/Graph.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
// AUTO-REMOVED #include <core/scoring/hbonds/HBondSet.fwd.hh>
// AUTO-REMOVED #include <core/scoring/trie/RotamerTrieBase.fwd.hh>

#ifdef WIN32 //VC++ needs full class declaration
#include <core/scoring/trie/RotamerTrieBase.hh>
#include <core/conformation/Residue.hh> // WIN32 INCLUDE
#endif

//#include <basic/datacache/BasicDataCache.hh>

// ObjexxFCL Headers
// AUTO-REMOVED #include <ObjexxFCL/FArray2.fwd.hh>

// Utility headers
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.fwd.hh>

#include <utility/vector1.hh>


namespace core {
namespace pack {
namespace rotamer_set {


class RotamerSet : public conformation::RotamerSetBase
{

private: // typedefs
  typedef conformation::RotamerSetBase parent;

public:
  RotamerSet();
  virtual ~RotamerSet();

  void set_resid( Size resid );

  virtual
  void build_rotamers(
    pose::Pose const & the_pose,
    scoring::ScoreFunction const & scorefxn,
    task::PackerTask const & task,
    graph::GraphCOP packer_neighbor_graph,
    bool use_neighbor_context = true
  ) = 0;

  virtual
  void build_dependent_rotamers(
    RotamerSets const & rotamer_sets,
    pose::Pose const & pose,
    scoring::ScoreFunction const & scorefxn,
    task::PackerTask const & task,
    graph::GraphCOP packer_neighbor_graph
  ) = 0;

  virtual
  void
  add_rotamer(
    conformation::Residue const & rotamer
  ) = 0;

  /// @brief Return the number of different residue types; two residue types are considered
  /// different if they have a different address.
  virtual
  Size
  get_n_residue_types() const = 0;

  /// @brief Return the number of different residue groups.  Two residue types are considered
  /// to be part of the same block of residues if 1. they have the same address or 2. they have
  /// the same "name3" and the same neighbor radius.
  virtual
  Size
  get_n_residue_groups() const = 0;

  /// @brief Return the first rotamer of a particular residue type
  virtual
  Size
  get_residue_type_begin( Size which_restype ) const = 0;

  /// @brief Return the first rotamer that belongs to a particular rotamer group
  virtual
  Size
  get_residue_group_begin( Size which_resgroup ) const = 0;

  virtual
  Size
  get_n_rotamers_for_residue_type( Size which_restype ) const = 0;

  virtual
  Size
  get_n_rotamers_for_residue_group( Size which_resgroup ) const = 0;

  /// @brief Rotamers i to i+j of all the same residue type are grouped together.
  /// This function returns the index of the residue type in a contiguous block
  /// of rotamers.  E.g. rotamers 100 to 120 might all be lysine rotamers, and might
  /// be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99.
  /// If new lysine rotamers are appended to the end of the rotamer set, they are
  /// considered to be in a separate residue type block.  Lysine rotamers 200 to 210 might
  /// be block 15 while lysine rotamers 100 to 120 are still block 7.
  virtual
  Size
  get_residue_type_index_for_rotamer( Size which_rotamer ) const = 0;

  /// @brief Return the index of the rotamer group for a particular rotamer.
  virtual
  Size
  get_residue_group_index_for_rotamer( Size which_rotamer ) const = 0;

  virtual
  void
  compute_one_body_energies(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scorefxn,
    task::PackerTask const & task,
    graph::GraphCOP packer_neighbor_graph,
    utility::vector1< core::PackerEnergy > & energies ) const = 0;

  /// for OptE
  virtual
  void
  compute_one_body_energy_maps(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scorefxn,
    task::PackerTask const & task,
    graph::GraphCOP packer_neighbor_graph,
    utility::vector1< scoring::EnergyMap > & energies ) const = 0;

  virtual
  Size
  num_rotamers() const = 0;

  virtual
  Size
  id_for_current_rotamer() const = 0;

  virtual
  Size resid() const { return resid_;}

  virtual
  conformation::ResidueCOP
  rotamer( Size rot_id ) const = 0;

  // iterate over rotamers directly
  virtual Rotamers::const_iterator begin() const = 0;
  virtual Rotamers::const_iterator end() const = 0;

  /// @brief mutatable access to a single rotamer in the set.
  virtual
  conformation::ResidueOP
  nonconst_rotamer( Size rot_id ) = 0;

  virtual
  void
  store_trie( Size method_enum_id, conformation::AbstractRotamerTrieOP trie ) = 0;

  virtual
  conformation::AbstractRotamerTrieCOP
  get_trie( Size method_enum_id ) const = 0;

  /// @brief removes a single rotamer and causes a rotamer index update
  virtual
  void
  drop_rotamer( Size rot_id ) = 0;

  /// @brief rotamers_to_delete must be of size nrotmaers -- each position
  /// in the array that's "true" is removed from the set of rotamers
  virtual
  void
  drop_rotamers( utility::vector1< bool > const & rotamers_to_delete ) = 0;

  /// @brief deletes the rotamers in the list with the given indices.
  /// The indices of these rotamers is presumed to be those before any delete operation.
  /// e.g. if there are four rotamers, and rotamer_indices_to_delete includes 1 & 3,
  /// then the rotamers that will remain are the rotamers originally indexed as 2 and 4,
  /// even though their new indices will be 1 & 2.
  virtual
  void
  drop_rotamers_by_index( utility::vector1< Size > const & rotamer_indices_to_delete ) = 0;

private:
  // deny use of the copy constructor (no pass-by-value)
  RotamerSet( RotamerSet const & );

  Size resid_; //which residue is this?

  /// @brief BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh
  /// @warning DataCache must always be initialized with the number of cacheable
  ///  data types -- see the last enum entry.
  //BasicDataCache data_cache_;

};


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


#endif // INCLUDED_core_pack_RotamerSet_RotamerSet_HH