LoopRelaxMover.hh

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// vi: set ts=2 noet:
//
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/// @brief LoopRelaxMover.hh
/// @author James Thompson

#ifndef INCLUDED_protocols_comparative_modeling_LoopRelaxMover_hh
#define INCLUDED_protocols_comparative_modeling_LoopRelaxMover_hh

#include <core/types.hh>
#include <core/fragment/FragSet.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <protocols/loops/Loops.fwd.hh>
#include <protocols/loops/LoopsFileIO.fwd.hh>
#include <protocols/comparative_modeling/LoopRelaxMover.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>

#include <string>

#include <utility/vector1.hh>

#include <protocols/loops/Loops.hh>


namespace protocols {
namespace comparative_modeling {

class LoopRelaxMover : public moves::Mover {

public:

  // constructor
  LoopRelaxMover();

  /// @brief Alternative constructor.
  /// BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS().
  /// AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL
  /// NOT BE INITIALIZED.
  LoopRelaxMover(
    std::string const & remodel,
    std::string const & intermedrelax,
    std::string const & refine,
    std::string const & relax,
    loops::Loops const & loops
  );

  /// @brief Unresolved-loop-index constructor.
  /// BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS().
  /// AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL
  /// NOT BE INITIALIZED.
  LoopRelaxMover(
    std::string const & remodel,
    std::string const & intermedrelax,
    std::string const & refine,
    std::string const & relax,
    loops::LoopsFileData const & loops_from_file
  );

  /// @brief GuardedLoopsOP constructor.  This constructor copies the pointer
  /// to a GuardedLoops object; Loop indices must be resolved by the time
  /// that the guarded_loops_ object is accessed, but, they need not
  /// have been resolved at the time of this object's construction.
  /// BE WARNED: THIS CONSTRUCTOR DOES NOT CALL SET_DEFAULTS().
  /// AS A RESULT, THE SCORE FUNCTIONS (AMONG OTHER THINGS) WILL
  /// NOT BE INITIALIZED.
  LoopRelaxMover(
    std::string const & remodel,
    std::string const & intermedrelax,
    std::string const & refine,
    std::string const & relax,
    loops::GuardedLoopsFromFileOP guarded_loops
  );

  /// @brief Copy-ctor; Shallow copy of all data.
  LoopRelaxMover( LoopRelaxMover const & src );

  /// @brief assignment operator; Shallow copy of all data.
  LoopRelaxMover const & operator = ( LoopRelaxMover const & rhs );


  //destructor
  virtual ~LoopRelaxMover();

  /// @brief Apply the loop-relax protocol to a Pose.  At the call to this function, the
  /// loop indices originating from the loop file (which may list indices with PDB identifiers
  /// i.e. res+insertioncode+chain ) will be resolved. Until this point, the Loops object
  /// in the LoopRelaxMover cannot be used.
  virtual void apply( core::pose::Pose & pose );
  virtual std::string get_name() const;

  // getters and setters
  void scorefxns( core::scoring::ScoreFunctionOP cen_scorefxn, core::scoring::ScoreFunctionOP fa_scorefxn );
  void fa_scorefxn( core::scoring::ScoreFunctionOP fa_scorefxn );
  void cen_scorefxn( core::scoring::ScoreFunctionOP cen_scorefxn );

  void cmd_line_csts( bool setting ) {
    cmd_line_csts_ = setting;
  }

  void copy_sidechains( bool setting ) {
    copy_sidechains_ = setting;
  }

  void rebuild_filter( core::Real setting ) {
    rebuild_filter_ = setting;
  }

  void n_rebuild_tries( core::Size setting ) {
    n_rebuild_tries_ = setting;
  }

  void remodel( std::string val ) {
    remodel_ = val;
  }

  void intermedrelax( std::string val ) {
    intermedrelax_ = val;
  }

  void refine( std::string val ) {
    refine_ = val;
  }

  void relax( std::string val ) {
    relax_ = val;
  }

  /// @brief Must be called before the Loops data can be read from.
  void resolve_loopfile_indices( core::pose::Pose const & pose );

  /// @brief set the Loops object (with resolved indices) directly.  This would override
  /// the unresolved-indices held in the LoopsFileData if that data were set in the constructor
  void loops( protocols::loops::LoopsOP const val );

  /// @brief Set the loop file data.  This will require that a Pose be presented to
  /// the LoopRelax object before get_loops() can be called.
  void loops_file_data( loops::LoopsFileData const & loopfiledata );

  void frag_libs( utility::vector1< core::fragment::FragSetOP > new_libs );

  bool cmd_line_csts() const {
     return cmd_line_csts_;
  }

  bool copy_sidechains() const {
     return copy_sidechains_;
  }

  core::Size n_rebuild_tries() const {
     return n_rebuild_tries_;
  }

  core::Real rebuild_filter() const {
     return rebuild_filter_;
  }

  /// @brief Loops accessor.  May only be retrieved after the loop indices have been resolved
  /// in a call to apply.
  protocols::loops::LoopsOP get_loops();

  /// @brief Loops accessor.  May only be retrieved after the loop indices have been resolved
  /// in a call to apply.
  protocols::loops::LoopsCOP get_loops() const;

  std::string remodel () const {
    return remodel_;
  }

  std::string relax() const {
    return relax_;
  }

  std::string intermedrelax() const {
    return intermedrelax_;
  }

  std::string refine() const {
    return refine_;
  }

  utility::vector1< core::fragment::FragSetOP > frag_libs() const;

  protocols::moves::MoverOP clone() const;
  protocols::moves::MoverOP fresh_instance() const;
  void compute_rmsd( bool const c ){ compute_rmsd_ = c; }
  bool compute_rmsd() const { return compute_rmsd_; }

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

//  void task_factory( core::pack::task::TaskFactoryOP tf ); /// currently taskfactory is not supported
//  core::pack::task::TaskFactoryOP task_factory() const;

private:
  void set_defaults_();

  bool cmd_line_csts_;
  bool copy_sidechains_;

  core::Size n_rebuild_tries_;
  core::Real rebuild_filter_;

  std::string remodel_;
  std::string intermedrelax_;
  std::string refine_;
  std::string relax_;

  loops::GuardedLoopsFromFileOP guarded_loops_;

  core::scoring::ScoreFunctionOP cen_scorefxn_;
  core::scoring::ScoreFunctionOP fa_scorefxn_;

  utility::vector1< core::fragment::FragSetOP > frag_libs_;
  bool compute_rmsd_; //dflt true; but set to false if you change the pose length between start and rmsd measurements;
//  core::pack::task::TaskFactoryOP task_factory_; //dflt NULL; a way to restrict packing from outside the mover
};

} // namespace loops
} // namespace protocols

#endif // INCLUDED_protocols_loops_LoopRelaxMover_HH