TemperedDocking.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   TemperedDocking.hh
///
/// @brief allows low-resolution docking using simulated or parallel tempering
/// @author Oliver Lange

#ifndef INCLUDED_protocols_docking_TemperedDocking_hh
#define INCLUDED_protocols_docking_TemperedDocking_hh

// Unit Headers
#include <protocols/docking/TemperedDocking.fwd.hh>

// Package Headers
#include <protocols/docking/types.hh>

// Project Headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/kinematics/FoldTree.hh>

#include <protocols/moves/Mover.hh>
#include <protocols/rigid/RigidBodyMover.fwd.hh>
#include <protocols/canonical_sampling/MetropolisHastingsMover.fwd.hh>
#include <protocols/canonical_sampling/TemperingBase.fwd.hh>

#include <utility/tag/Tag.fwd.hh>


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

// Numeric Headers

// ObjexxFCL Headers

// C++ headers

namespace protocols {
namespace docking {

/// @brief allows docking using simulated or parallel tempering
/// @detailed
class TemperedDocking : public moves::Mover
{
public:
  /// @brief Associates relevant options with the TemperedDocking class
  static void register_options();

  /// @brief default constructor fills values with the expected defaults
  TemperedDocking();

  /// @brief clone
  virtual protocols::moves::MoverOP clone() const;

  ///@brief copy ctor
  TemperedDocking( TemperedDocking const & rhs );

  ///@brief assignment operator
  TemperedDocking & operator=( TemperedDocking const & rhs );

  /// @brief Assigns default values to primitive members
  void set_defaults();

  /// @brief Instantiates non-primitive members based on the value of the primitive members
  void sync_objects_with_flags();

  /// @brief Sets the score function that will be used in the low-resolution phase
  void set_lowres_scorefxn( core::scoring::ScoreFunctionOP docking_scorefxn_low );

  /// @brief Sets the score function that will be used in the high-resolution phase.
  ///   The same score function will be used for evaluating moves, packing and discriminating
  void set_highres_scorefxn( core::scoring::ScoreFunctionOP docking_scorefxn_high );

  /// @brief Sets the score function that will be used in the high-resolution phase.
  ///   The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing
  void set_highres_scorefxn(
    core::scoring::ScoreFunctionCOP docking_scorefxn_high,
    core::scoring::ScoreFunctionCOP docking_scorefxn_pack );

  /// @brief Sets the score function that will be used in the high-resolution phase.
  ///   The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating
  void set_highres_scorefxn(
    core::scoring::ScoreFunctionCOP docking_scorefxn_high,
    core::scoring::ScoreFunctionCOP docking_scorefxn_pack,
    core::scoring::ScoreFunctionCOP docking_scorefxn_output);

  void set_sc_min( bool sc_min );

  virtual void apply( core::pose::Pose & pose );


  //getters for const access to movers and data of docking protocol
  protocols::moves::MoverCOP to_centroid() const;

  std::string partners() const { return partners_;} /// @brief returns the docking partners chain identifiers

  virtual std::string get_name() const { return "TemperedDocking"; }

  DockJumps & movable_jumps(){ return movable_jumps_;} ///@brief returns ref to the jumps vector for docking

  DockJumps const & movable_jumps() const { return movable_jumps_; } ///@ return const ref to the jumps vector for docking


  //setters
  void set_autofoldtree( bool setting ){ autofoldtree_ = setting; }

  void set_partners( std::string const& setting ){ partners_=setting; }

  void set_movable_jumps( DockJumps const& setting ){ movable_jumps_ = setting; }

  void set_use_constraints( bool setting );


  void add_jump( core::SSize const jump_number ){ movable_jumps_.push_back( int( jump_number ) ); }
  void show( std::ostream & out=std::cout );
  friend std::ostream & operator<<(std::ostream& out, const TemperedDocking & dp );

  // function for the parser with lots of accessors
  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 & );

protected:
  /// @brief Assigns user specified values to primitive members using command line options
  void init_from_options();

  /// @brief Performs the portion of setup of non-primitive members that requires a pose - called on apply
  void finalize_setup( core::pose::Pose & pose );

  /// @brief Sets up the instance of TemperedDocking and initializes all members based on values passed in at construction
  ///   or via the command line.
  void init(
    DockJumps const movable_jumps,
    core::scoring::ScoreFunctionCOP docking_score_low,
    core::scoring::ScoreFunctionCOP docking_score_high
  );

  void copy( TemperedDocking & lhs, TemperedDocking const & rhs);

  void setup_objects();

private:
  /// information about the mode
  bool autofoldtree_;

  bool flags_and_objects_are_in_sync_;
  bool first_apply_with_current_setup_;

  bool sc_min_;

  /// how many cycles of monte-carlo per trajectory in the sampler ?
  core::Size n_cycles_;

  core::kinematics::FoldTree fold_tree_;
  std::string partners_;

  std::string previous_sequence_;

  /// jumps that rigid_body transformations can occur over
  DockJumps movable_jumps_;

  // score functions
  core::scoring::ScoreFunctionCOP docking_scorefxn_low_;
  core::scoring::ScoreFunctionCOP docking_scorefxn_high_;
  core::scoring::ScoreFunctionCOP docking_scorefxn_pack_;
  core::scoring::ScoreFunctionCOP docking_scorefxn_output_;

  // constraint set mover
  protocols::moves::MoverOP docking_constraint_;

  protocols::rigid::RigidBodyPerturbNoCenterMoverOP rb_mover_;
  protocols::canonical_sampling::TemperingBaseOP tempering_;
  protocols::canonical_sampling::MetropolisHastingsMoverOP sampler_;
  //if side-chains are to be taken from specified pdb file... it is set here...
  std::string recover_sidechains_filename_;

  protocols::moves::MoverOP to_centroid_;

  bool use_csts_;

  core::Real rigid_rot_mag_;
  core::Real rigid_trans_mag_;

  static bool options_registered_;

};
} // docking
} // protocols

#endif