RotamerSet_.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file   core/pack/rotamer_set/RotamerSet_.hh
/// @brief  rotamer set implementation 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/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/BumpSelector.hh>
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>


//Project headers
#include <core/conformation/Residue.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/pack/dunbrack/RotamerLibrary.fwd.hh>
#ifdef WIN32
#include <core/scoring/trie/RotamerTrieBase.hh>
#endif

#include <core/scoring/EnergyMap.fwd.hh>

// Utility headers
#include <utility/pointer/owning_ptr.hh>
// AUTO-REMOVED #include <utility/vector1.hh>

#include <core/scoring/trie/RotamerTrieBase.fwd.hh>
#include <utility/vector1.hh>


namespace core {
namespace pack {
namespace rotamer_set {

/// @brief Container for a set of rotamers for use in packing.
/// Rotamers are sorted into groups of the same residue type.
/// Offsets into these rotamer groups are maintained by this class, as is
/// information concerning the "original rotamer" -- the rotamer
/// present on the input pose before packing began.
class RotamerSet_ : public RotamerSet
{
public:
  typedef conformation::ResidueOP ResidueOP;
  typedef conformation::ResidueCOP ResidueCOP;
  typedef pack::dunbrack::ChiSetOP ChiSetOP;
  typedef scoring::trie::RotamerTrieBaseOP RotamerTrieBaseOP;

public:
  RotamerSet_();
  virtual ~RotamerSet_();

  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
  );


  /// @brief  Build rotamers that depend on positions of rotamers built in a previous pass
  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
  );


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

  virtual
  Size
  get_n_residue_types() const;

  virtual
  Size
  get_n_residue_groups() const;

  virtual
  Size
  get_residue_type_begin( Size which_restype ) const;

  virtual
  Size
  get_residue_group_begin( Size which_resgroup ) const;

  virtual
  Size
  get_n_rotamers_for_residue_type( Size which_resgroup ) const;

  virtual
  Size
  get_n_rotamers_for_residue_group( Size which_resgroup ) const;

  virtual
  Size
  get_residue_type_index_for_rotamer( Size which_rotamer ) const ;

  virtual
  Size
  get_residue_group_index_for_rotamer( Size which_rotamer ) const ;


  /// @brief Computes the packers "one body energies" for the set of rotamers.
  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;


  /// 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;

  /*
  virtual
  void
  compute_two_body_energies(
    RotamerSet const & other,
    pose::Pose const & pose,
    scoring::ScoreFunction const & scorefxn,
    ObjexxFCL::FArray2< Energy > & pair_energy_table ) const;
  */

  virtual
  Size
  num_rotamers() const;

  virtual
  Size
  id_for_current_rotamer() const;

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

  virtual Rotamers::const_iterator begin() const { return rotamers_.begin(); }
  virtual Rotamers::const_iterator end() const { return rotamers_.end(); }

  virtual
  conformation::ResidueOP
  nonconst_rotamer( Size rot_id );

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

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

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

  /// @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 );

  /// @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 );

private:
  RotamerSet_( RotamerSet_ const & );


protected:
  /// @brief Creates a set of rotamers for a particular residue type
  /// (the concrete residue type) while relying on the rotamer-
  /// building instructions within the PackerTask.
  /// Use the residue in the input pose at position resid_ as the existing residue.
  virtual
  void build_rotamers_for_concrete_virt(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scorefxn,
    task::PackerTask const & task,
    chemical::ResidueTypeCOP concrete_residue,
    graph::GraphCOP packer_neighbor_graph,
    bool use_neighbor_context = true
  );

  /// @brief Creates a set of rotamers for a particular residue type
  /// (the concrete residue type) while relying on the rotamer-
  /// building instructions within the PackerTask.
  void build_rotamers_for_concrete(
    pose::Pose const & pose,
    scoring::ScoreFunction const & scorefxn,
    task::PackerTask const & task,
    chemical::ResidueTypeCOP concrete_residue,
    conformation::Residue const & existing_residue,
    graph::GraphCOP packer_neighbor_graph,
    bool use_neighbor_context = true
  );


  /// @brief  Build rotamers of a specific type that depend on positions of rotamers built in a previous pass
  /// Use an input "existing residue" which may or may not reflect the coordinates of the residue at
  /// pose.residue( resid_ );
  void
  build_dependent_rotamers_for_concrete(
    RotamerSets const & rotamer_sets,
    pose::Pose const & pose,
      scoring::ScoreFunction const &, // scorefxn,
    task::PackerTask const & task,
    conformation::Residue const & existing_residue,
    chemical::ResidueTypeCOP concrete_residue,
    graph::GraphCOP packer_neighbor_graph
  );


  /// @brief Creates a sets of rotamers for an "optimize H" repacking
  void
  build_optimize_H_rotamers(
    pose::Pose const & pose,
    task::PackerTask const & task,
    chemical::ResidueTypeCOP concrete_residue,
    conformation::Residue const & existing_residue
  );

public:
  /// @brief Pushes standard-deviation multiples that should be sampled
  /// for this residue -- if this residue has more neighbors within 10A
  /// than the task-specified cutoff for buriedness, then extra rotamer
  /// samples are added to the extra_chi_steps vector, otherwise, the
  /// vector is not modified.
  void set_extra_samples(
    task::PackerTask const & task,
    int num_10A_neighbors,
    int chi,
    chemical::ResidueTypeCOP concrete_residue,
    utility::vector1< Real > & extra_chi_steps
  ) const;

public:
  /// @brief Computes the "bump energy" of a rotamer: the bump energy is the
  /// sum of rotamer's interactions with 1) the backbone-and-side chains of
  /// neighboring residues that are held fixed during this repacking optimization
  /// and 2) the backbones of neighboring residues that are changable during this
  /// repacking optimization.
  virtual
  core::PackerEnergy
  bump_check(
    ResidueCOP rotamer,
    scoring::ScoreFunction const & sf,
    pose::Pose const & pose,
    task::PackerTask const & task,
    graph::GraphCOP packer_neighbor_graph
  ) const;

private:

  /// @brief declare that a new block of residue types has begun, and that new residues
  /// are about to be pushed back.
  void
  prepare_for_new_residue_type( core::chemical::ResidueType const & restype );

  /// @brief should two residue types be considered the same residue type?
  bool
  different_restype( core::chemical::ResidueType const & rt1, core::chemical::ResidueType const & rt2 ) const;

  /// @brief should two residue types be considered to belong to the same residue-type group?
  bool
  different_resgroup( core::chemical::ResidueType const & rt1, core::chemical::ResidueType const & rt2 ) const;

  /// @brief This function should not be called directly -- it ought to be called only from prepare_for_new_residue_type
  void
  new_residue_type();

  /// @brief This function should not be called directly -- it ought to be called only from prepare_for_new_residue_type
  void
  new_residue_group();

  /// @brief appends a rotamer to the list of rotamers, and increments the count
  /// for the number of rotamers for the current value of n_residue_types.
  void
  push_back_rotamer( conformation::ResidueOP );

  void
  update_rotamer_offsets() const;

// DATA
private:

  BumpSelector bump_selector_;
  Rotamers rotamers_;

  mutable Size n_residue_types_;
  mutable Size n_residue_groups_;
  mutable utility::vector1< Size > residue_type_rotamers_begin_;
  mutable utility::vector1< Size > residue_group_rotamers_begin_;
  mutable utility::vector1< Size > n_rotamers_for_restype_;
  mutable utility::vector1< Size > n_rotamers_for_resgroup_;

  mutable utility::vector1< Size > residue_type_for_rotamers_;
  mutable utility::vector1< Size > residue_group_for_rotamers_;

  utility::vector1< conformation::AbstractRotamerTrieOP > cached_tries_;

  mutable Size id_for_current_rotamer_;

  ResidueOP current_rotamer_copy_;
  mutable bool rotamer_offsets_require_update_;
};

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


#endif // INCLUDED_core_pack_RotamerSet_RotamerSet__HH