RotamerSubset.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/pack/rotamer_set/RotamerSet_.hh
/// @brief  rotamer set implementation class
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu)


#ifndef INCLUDED_core_pack_rotamer_set_RotamerSubset_hh
#define INCLUDED_core_pack_rotamer_set_RotamerSubset_hh

//Unit headers
#include <core/pack/rotamer_set/RotamerSubset.fwd.hh>

// Package headers
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>


//Project headers
#include <core/conformation/Residue.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
// AUTO-REMOVED #include <core/pack/dunbrack/RotamerLibrary.fwd.hh>
// AUTO-REMOVED #include <core/scoring/trie/RotamerTrieBase.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/graph/Graph.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>

#ifdef WIN32
  #include <core/pack/rotamer_set/RotamerSet.fwd.hh>
  #include <core/pack/rotamer_set/RotamerSet.hh>
  #include <core/graph/Graph.hh>
#endif

namespace core {
namespace pack {
namespace rotamer_set {

/// @brief Container for a subset of rotamers that have been created
/// by another rotamer set.  This subset object copies pointers to
/// the rotamers contained in another set, as opposed to cloning the
/// rotamers.  It's main purpose is to manage the bookkeeping involved
/// in packing with a subset of rotamers (when it might be faster
/// to use a subset and to create an interaction graph specifically
/// for that subset than to simply pass an abreviated list of rotamers
/// to the SimAnnealer with the "rot_to_pack" vector).
class RotamerSubset : public RotamerSet
{
public:
  typedef conformation::ResidueOP ResidueOP;
  typedef conformation::ResidueCOP ResidueCOP;
  typedef scoring::trie::RotamerTrieBaseOP RotamerTrieBaseOP;

public:
  RotamerSubset(
    RotamerSet & rotset,
    utility::vector1< Size > const & rotamer_subset
  );

  virtual ~RotamerSubset();

  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_restype ) const;

  virtual
  Size
  get_n_rotamers_for_residue_group( Size which_resgroup ) const;

  ///@brief given a rotamer id, return an int which represents a type for this rotamer.
  virtual
  Size
  get_residue_type_index_for_rotamer( Size which_rotamer ) const ;

  virtual
  Size
  get_residue_group_index_for_rotamer( Size which_rotamer ) 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:
  /// @brief (private) No copy-constructor
  RotamerSubset( RotamerSubset const & );

  /// @brief declare that a new block of residue types has begun, and that new residues
  /// are about to be pushed back. NOT IMPLEMENTED.
  //void
  //declare_new_residue_type();

  /// @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. NOT IMPLEMENTED.
  //void
  //push_back_rotamer( conformation::ResidueOP );

  /// @brief Borrow (steal) a rotamer held by another RotamerSet
  /// without cloning that rotamer.  That is, both sets will now point
  /// at the same rotamer object, so if that rotamer changes for one set,
  /// it changes for both.
  void
  steal_rotamer( conformation::ResidueOP rotamer );


  /// @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;



public: // noop functions:

  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
  );

  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
  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;



// DATA
private:

  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