PackRotamersMover.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
/// @brief
/// @author Monica Berrondo
/// @author Modified by Sergey Lyskov

#ifndef INCLUDED_protocols_simple_moves_PackRotamersMover_hh
#define INCLUDED_protocols_simple_moves_PackRotamersMover_hh

// Unit headers
#include <protocols/simple_moves/PackRotamersMover.fwd.hh>
#include <protocols/moves/Mover.hh>

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

// AUTO-REMOVED #include <core/pack/interaction_graph/InteractionGraphBase.hh>
// AUTO-REMOVED #include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/pack/task/PackerTask.fwd.hh>
//#ifdef __clang__
// AUTO-REMOVED #include <core/pack/task/PackerTask.hh>
//#endif
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

#include <core/pack/interaction_graph/InteractionGraphBase.fwd.hh>
#include <core/pack/rotamer_set/RotamerSets.fwd.hh>




namespace protocols {
namespace simple_moves {

/// @brief A protocols::moves::Mover that packs the side-chains using a rotamer library
/// It uses a ScoreFunction for packing and a PackerTask,
/// or a TaskFactory that generates a PackerTask, for instructions on
/// what rotamer sets are allowed at each residue position during packing
///
/// Common Methods:
///     PackRotamersMover.apply
class PackRotamersMover : public protocols::moves::Mover {
/// @brief please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here!
/// @author ashworth (current form)
public:
  typedef core::pack::interaction_graph::InteractionGraphBaseOP InteractionGraphBaseOP;
  typedef core::pack::interaction_graph::InteractionGraphBaseCOP InteractionGraphBaseCOP;
  typedef core::pack::rotamer_set::RotamerSetsOP RotamerSetsOP;
  typedef core::pack::rotamer_set::RotamerSetsCOP RotamerSetsCOP;
  typedef core::pack::task::PackerTaskCOP PackerTaskCOP;
  typedef core::pack::task::TaskFactoryCOP TaskFactoryCOP;
  typedef core::scoring::ScoreFunctionCOP ScoreFunctionCOP;

public:
  /// @brief default constructor
  PackRotamersMover();
  /// @brief constructor with typename
  PackRotamersMover( std::string const & );

  /// @brief Constructs a PackRotamersMover with PackerTask  <task>
  /// evaluated using  <scorefxn>
  ///
  /// ScoreFunction  scorefxn   /function to minimize while changine rotamers
  /// PackerTask     task       /object specifying what to design/pack
  /// Size (int)     nloop      /number of loops in the Pose (???)
  PackRotamersMover(
    ScoreFunctionCOP scorefxn,
    PackerTaskCOP task = 0,
    core::Size nloop = 1
  );

  // destructor (important for properly forward-declaring smart-pointer members)
  virtual ~PackRotamersMover();

  // copy constructor
  PackRotamersMover( PackRotamersMover const & other );

  // methods

  /// @brief Performs side-chain packing based on the input PackerTask
  /// using the input ScoreFunction
  ///
  /// example(s):
  ///     packmover.apply(pose)
  /// See Also:
  ///     PackerTask
  ///     ScoreFunction
  virtual void apply( Pose & pose );
  virtual std::string get_name() const;
  bool task_is_valid( Pose const & pose ) const; // should this be virtual?

  virtual void parse_def( utility::lua::LuaObject const & def,
          utility::lua::LuaObject const & score_fxns,
          utility::lua::LuaObject const & tasks,
          protocols::moves::MoverCacheSP cache );

  /// @brief allow non-const access to the internal minimizer options object

  ///@brief parse XML (specifically in the context of the parser/scripting scheme)
  virtual void parse_my_tag(
    TagPtr const,
    protocols::moves::DataMap &,
    Filters_map const &,
    protocols::moves::Movers_map const &,
    Pose const & );

  ///@brief parse "scorefxn" XML option (can be employed virtually by derived Packing movers)
  virtual void parse_score_function(
    TagPtr const,
    protocols::moves::DataMap const &,
    Filters_map const &,
    protocols::moves::Movers_map const &,
    Pose const & );

  ///@brief parse "task_operations" XML option (can be employed virtually by derived Packing movers)
  virtual void parse_task_operations(
    TagPtr const,
    protocols::moves::DataMap const &,
    Filters_map const &,
    protocols::moves::Movers_map const &,
    Pose const & );

  ///@brief required in the context of the parser/scripting scheme
  virtual protocols::moves::MoverOP fresh_instance() const;
  ///@brief required in the context of the parser/scripting scheme
  virtual protocols::moves::MoverOP clone() const;

  // setters

  /// @brief Sets the ScoreFunction to  <sf>
  ///
  /// example(s):
  ///     packmover.score_function(scorefxn)
  /// See Also:
  ///     PackRotamersMover
  ///     PackRotamersMover.task
  void score_function( ScoreFunctionCOP sf );
  /// @brief Sets the TaskFactory to  <tf>
  ///
  /// example(s):
  ///     packmover.task_factory(task_design)
  /// See Also:
  ///     PackRotamersMover
  ///     PackRotamersMover.task
  void task_factory( TaskFactoryCOP tf );
  /// @brief Sets the PackerTask to  <t>
  ///
  /// example(s):
  ///     packmover.task(task_pack)
  /// See Also:
  ///     PackRotamersMover
  ///     PackRotamersMover.task_factory
  void task( PackerTaskCOP t );
  void nloop( core::Size nloop_in );


  // accessors

  /// @brief Returns the ScoreFunction
  ///
  /// example(s):
  ///     packmover.score_function()
  /// See Also:
  ///     PackRotamersMover
  ///     PackRotamersMover.task
  ScoreFunctionCOP score_function() const;
  /// @brief Returns the PackerTask
  ///
  /// example(s):
  ///     packmover.task()
  /// See Also:
  ///     PackRotamersMover
  ///     PackRotamersMover.task_factory
  PackerTaskCOP task() const;
  core::Size nloop() const { return nloop_; }
  /// @brief Returns the TaskFactory
  ///
  /// example(s):
  ///     packmover.task_factory()
  /// See Also:
  ///     PackRotamersMover
  ///     PackRotamersMover.task
  TaskFactoryCOP task_factory() const;
  RotamerSetsCOP rotamer_sets() const;
  InteractionGraphBaseCOP ig() const;
  friend std::ostream &operator<< (std::ostream &os, PackRotamersMover const &mover);

protected:
  ///@brief get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask.
  virtual void setup( Pose & pose );
  // need a more elegant rot_to_pack implementation than this
  virtual core::PackerEnergy run(
    Pose & pose,
    utility::vector0< int > rot_to_pack = utility::vector0< int >()
  ) const;
  virtual void note_packertask_settings( Pose const & );

private:
  // pointers to data that are passed in
  ScoreFunctionCOP scorefxn_;
  PackerTaskCOP task_;
  core::Size nloop_;
  TaskFactoryCOP task_factory_;

  // 'really private:' packer data, actually created and owned by this class
  RotamerSetsOP rotamer_sets_;
  InteractionGraphBaseOP ig_;

};

// note: it is better to create new files, instead of adding additional classes here

} // moves
} // protocols

#endif