SidechainMoverBase.hh

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// vi: set ts=2 noet:
//
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/// @file protocols/simple_moves/sidechain_moves/SidechainMoverBase.hh
/// @brief definition of SidechainMoverBase class and functions
/// @author Oliver Lange (oliver.lange@tum.de) adapted from Colin A. Smith's code


#ifndef INCLUDED_protocols_simple_moves_sidechain_moves_SidechainMoverBase_hh
#define INCLUDED_protocols_simple_moves_sidechain_moves_SidechainMoverBase_hh

// Unit Headers
#include <protocols/simple_moves/sidechain_moves/SidechainMoverBase.fwd.hh>

// Protocols Headers
#include <protocols/canonical_sampling/MetropolisHastingsMover.fwd.hh>
#include <protocols/canonical_sampling/ThermodynamicMover.hh>

// Core Headers
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pose/Pose.fwd.hh>

#include <core/pack/dunbrack/DunbrackRotamer.hh>
#include <core/id/DOF_ID_Range.fwd.hh>

#include <core/pack/dunbrack/DunbrackRotamer.fwd.hh>
#include <core/pack/dunbrack/RotamerLibrary.fwd.hh>

// Numeric Headers
#include <numeric/random/random.hh>

// Utility headers
#include <utility/vector1.hh>

namespace protocols {
namespace simple_moves {
namespace sidechain_moves {

/// @brief class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions
class SidechainMoverBase : public protocols::canonical_sampling::ThermodynamicMover {

public:
//
  typedef utility::vector1< core::Real > ChiVector;

  /// @brief default constructor
  SidechainMoverBase();

  /// @brief constructor with user provided rotamer library
  SidechainMoverBase(
    core::pack::dunbrack::RotamerLibrary const & rotamer_library
  );

  SidechainMoverBase(
    SidechainMoverBase const & mover
  );

  ~SidechainMoverBase();

  virtual
  void
  parse_my_tag(
    utility::tag::TagPtr const tag,
    protocols::moves::DataMap & data,
    protocols::filters::Filters_map const & filters,
    protocols::moves::Movers_map const & movers,
    core::pose::Pose const & pose
  );

  /// @brief initialize the packer task if necessary
  void
  init_task(
    core::pose::Pose const & pose
  );

  virtual
  void
  initialize_simulation(
    core::pose::Pose &pose,
    protocols::canonical_sampling::MetropolisHastingsMover const & metropolis_hastings_mover,
    core::Size cycle   //non-zero if trajectory is restarted
  );

  virtual core::conformation::ResidueOP
  make_move( core::conformation::ResidueOP res );

  virtual void
  make_chi_move(
    core::conformation::Residue const& residue,
    ChiVector const& old_chi,
    ChiVector&  new_chi
  ) = 0;

  virtual core::Size suggest_residue_number( core::pose::Pose const& ) const;

  /// @brief apply a sidechain move to a Pose object
  virtual void apply( core::pose::Pose& pose );

  virtual std::string get_name() const;

  virtual core::Real
  compute_proposal_density(
    core::conformation::Residue const & new_residue,
    core::Size const resnum,
    core::chemical::ResidueType const & old_res_type,
    ChiVector const & old_chi
  ) const = 0;

  /// @brief idealize sidechains that might be altered
  void idealize_sidechains( core::pose::Pose& pose );

  /// @brief get the rotamer library
  core::pack::dunbrack::RotamerLibrary const& rotamer_library() const;

  /// @brief get the task factory
  core::pack::task::TaskFactoryCOP task_factory() const;

  /// @brief set the task factory
  void
  set_task_factory( core::pack::task::TaskFactoryCOP task_factory );

  /// @brief get the packer task
  core::pack::task::PackerTaskCOP task() const;

  /// @brief set the task
  void set_task(  core::pack::task::PackerTaskCOP task );

  /// @brief get whether detailed balance is preserved (i.e. proposal density ratio calculated)
  bool
  preserve_detailed_balance() const;

  /// @brief set whether detailed balance is preserved (i.e. proposal density ratio calculated)
  void
  set_preserve_detailed_balance( bool setting );

  ///@brief perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.
  bool change_chi_without_replacing_residue() const;

  ///@brief perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.
  void
  set_change_chi_without_replacing_residue( bool setting );

  ///@brief return true if your last move has mutated residue --- make sure the residue is replaced entirely
  virtual bool have_mutated_residue() const { return false; }

  /// @brief get the TorsionIDs perturbed by the mover during moves, along with their ranges
  virtual
  utility::vector1<core::id::TorsionID_Range>
  torsion_id_ranges(
    core::pose::Pose & pose
  );

  /// @brief get the DOF_IDs perturbed by the mover during moves, along with their ranges
  virtual
  utility::vector1<core::id::DOF_ID_Range>
  dof_id_ranges(
    core::pose::Pose & pose
  );

  /// @brief get the residues that can be changed by this mover
  utility::vector1<core::Size> const &
  packed_residues() const;

  /// @brief get a vector indicating whether each residue can be packed
  utility::vector1<bool> const &
  residue_packed() const;

  /// @brief get the ratio of proposal densities for the last move
  virtual
  core::Real
  last_proposal_density_ratio();

protected:


  //  void set_last_proposal_density_ratio( core::Real setting ) {
  //    last_proposal_density_ratio_ = setting;
  //  }

private:

  void set_defaults();
  void init_from_options();

  core::pack::dunbrack::RotamerLibrary const & rotamer_library_;
  core::pack::task::TaskFactoryCOP task_factory_;
  core::pack::task::PackerTaskCOP task_;
  utility::vector1<core::Size> packed_residues_;
  utility::vector1<bool> residue_packed_;

  bool preserve_detailed_balance_;
  bool change_chi_without_replacing_residue_;

  utility::vector1<core::Real> last_chi_angles_;
  core::Size last_nchi_;

  core::Real last_proposal_density_ratio_;

}; //SidechainMoverBase


} // sidechain_moves
} // simple_moves
} // protocols

#endif