RemodelMover.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   protocols/forge/remodel/RemodelMover.hh
/// @brief
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

#ifndef INCLUDED_protocols_forge_remodel_RemodelMover_hh
#define INCLUDED_protocols_forge_remodel_RemodelMover_hh

// unit headers
#include <protocols/forge/remodel/RemodelMover.fwd.hh>
#include <protocols/forge/remodel/RemodelData.hh>
#include <protocols/forge/remodel/RemodelWorkingSet.hh>
#include <protocols/forge/remodel/RemodelDesignMover.hh>
#include <protocols/forge/remodel/RemodelAccumulator.hh>

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

// package headers
#include <protocols/forge/build/BuildInstruction.fwd.hh>
#include <protocols/forge/build/BuildManager.hh>
#include <protocols/forge/components/VarLengthBuild.fwd.hh>

// project headers
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <protocols/moves/Mover.hh>

#include <basic/datacache/DataMap.fwd.hh> //parser

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

// C++ headers
#include <string>


namespace protocols {
namespace forge {
namespace remodel {


class RemodelMover : public protocols::moves::Mover {


private: // typedefs


  typedef protocols::moves::Mover Super;


public: // typedefs


  typedef std::string String;

  typedef core::Real Real;
  typedef core::Size Size;
  typedef core::pack::task::TaskFactoryOP TaskFactoryOP;
  typedef core::pose::Pose Pose;
  typedef core::scoring::ScoreFunction ScoreFunction;
  typedef core::scoring::ScoreFunctionOP ScoreFunctionOP;

  typedef protocols::forge::build::BuildInstructionOP BuildInstructionOP;
  typedef protocols::forge::build::BuildManager BuildManager;
  typedef protocols::forge::build::BuildManager::Original2Modified Original2Modified;
  typedef protocols::forge::build::Interval Interval;
  typedef protocols::moves::MoverOP MoverOP;
  typedef protocols::forge::components::VarLengthBuildOP VarLengthBuildOP;
  typedef protocols::forge::components::VarLengthBuild VarLengthBuild;
  typedef protocols::forge::remodel::RemodelData RemodelData;
  typedef protocols::forge::remodel::RemodelWorkingSet RemodelWorkingSet;

  /// @brief A pair storing a instruction's original interval and a string
  ///  denoting the sequence during design.
  /// @remarks This is only for instructions such as SegmentRebuild or
  ///  SegmentInsert.  Non-applicable instructions will not have any data
  ///  stored here.
  typedef std::pair< Interval, String > OriginalInterval2DesignString;
  typedef utility::vector1< OriginalInterval2DesignString > DesignInfo;

  //parser fabio
  typedef utility::tag::TagCOP TagCOP;
  typedef protocols::filters::Filters_map Filters_map;
  typedef basic::datacache::DataMap DataMap;
  typedef protocols::moves::Movers_map Movers_map;

public: // construct/destruct


  /// @brief default constructor
  RemodelMover();


  /// @brief copy constructor
  RemodelMover( RemodelMover const & rval );


  /// @brief default destructor
  virtual
  ~RemodelMover();


private: // disallow assignment


  /// @brief copy assignment
  /// @remarks Mover base class prevents this from working properly...
  RemodelMover & operator =( RemodelMover const & rval );


public: // virtual constructors

  /// @brief clone this object, for parser
  virtual
  MoverOP clone() const;


  /// @brief create this type of object, for parser
  virtual
  MoverOP fresh_instance() const;


  /// @brief clone this object
  virtual
  MoverOP clone();


  /// @brief create this type of object
  virtual
  MoverOP fresh_instance();


public: // accessors

  /*
  /// @brief use full-mer fragments when building the loop? (default false)
  inline
  bool use_fullmer() const {
  return use_fullmer_;
  }


  /// @brief use sequence biased fragments when building the loop? (default false)
  inline
  bool use_sequence_bias() const {
  return use_sequence_bias_;
  }


  /// @brief the maximum allowed linear chainbreak (default 0.07)
  inline
  Real max_linear_chainbreak() const {
  return max_linear_chainbreak_;
  }


  /// @brief the loop mover string to use during centroid build
  ///  (default "RemodelLoopMover")
  /// @remarks set to either a string the create_loop_mover() LoopMoverFactory
  ///  recognizes or the "RemodelLoopMover"
  inline
  String const & centroid_loop_mover_str() const {
  return centroid_loop_mover_str_;
  }


  /// @brief redesign the neighborhood around the loop?  if false, then just
  ///  repacks during the design phase (default true)
  inline
  bool redesign_loop_neighborhood() const {
  return redesign_loop_neighborhood_;
  }


  /// @brief name of the resfile to use during design-refine; empty string
  ///  implies no resfile
  inline
  String const & resfile() const {
  return resfile_;
  }


  /// @brief the number of design-refine cycles to perform, default 3
  inline
  Size dr_cycles() const {
  return dr_cycles_;
  }
  */

  /// @brief the centroid level score function, default "remodel_cen"
  ScoreFunction const & centroid_scorefunction() const;


  /// @brief the full-atom level score function
  ScoreFunction const & fullatom_scorefunction() const;


public: // mutators


  /// @brief add instruction to the manager of this RemodelMover (no copy)
  /// @param[in] bi BuildInstruction
  /// @param[in] aa_during_design_refine The allowed amino acid sequence
  ///  during design.  Only applicable to BuildInstructions like
  ///  SegmentRebuild and SegmentInsert.  Make sure the length of this
  ///  string matches up properly, and remember to use any special characters,
  ///  e.g. the insertion character for SegmentInsert
  /*
  void add_instruction(
  BuildInstructionOP bi,
  String const & aa_during_design_refine = String()
  );


  /// @brief create directed dependency between two instructions
  void create_directed_dependency(
  BuildInstructionOP u,
  BuildInstructionOP v
  );
  */
  /*
  /// @brief use full-mer fragments when building the loop?
  inline
  void use_fullmer( bool const flag ) {
  use_fullmer_ = flag;
  }


  /// @brief use sequence biased fragments when building the loop? (default false)
  inline
  void use_sequence_bias( bool const flag ) {
  use_sequence_bias_ = flag;
  }
  */

  /// @brief the maximum allowed linear chainbreak
  inline
  void max_linear_chainbreak( Real const threshold ) {
    max_linear_chainbreak_ = threshold;
  }


  /// @brief the loop mover string to use during centroid build
  /// @remarks set to either a string the create_loop_mover() LoopMoverFactory
  ///  recognizes or the "RemodelLoopMover"
  inline
  void centroid_loop_mover_str( String const & loop_mover_str ) {
    centroid_loop_mover_str_ = loop_mover_str;
  }


  /// @brief redesign the neighborhood around the loop?  if false, then just
  ///  repacks during the design phase
  inline
  void redesign_loop_neighborhood( bool const flag ) {
    redesign_loop_neighborhood_ = flag;
  }

  /*
  /// @brief name of the resfile to use during design-refine; empty string
  ///  implies no resfile
  inline
  void resfile( String const & filename ) {
  resfile_ = filename;
  }
  */
  /// @brief set the number of design-refine cycles to perform
  /// @remarks set this to 0 to skip design-refine
  inline
  void dr_cycles( Size const cycles ) {
    dr_cycles_ = cycles;
  }


  /// @brief set the centroid level score function
  void centroid_scorefunction( ScoreFunction const & sfx );


  /// @brief set the centroid level score function
  void centroid_scorefunction( ScoreFunctionOP const & sfx );


  /// @brief set the full-atom level score function
  void fullatom_scorefunction( ScoreFunction const & sfx );


  /// @brief set the full-atom level score function
  void fullatom_scorefunction( ScoreFunctionOP const & sfx );


public: // calculators


  /// @brief the name for the loops' neighborhood calculator
  inline
  static
  String neighborhood_calc_name() {
    return "RemodelMover_loops_neighborhood_calc";
  }


  /// @brief the name for the loops' buried unsatisfied polars
  ///  calculator
  inline
  static
  String loops_buns_polar_calc_name() {
    return "RemodelMover_loops_bup";
  }


  /// @brief the name for the loops' neighborhood buried unsatisfied polars
  ///  calculator
  inline
  static
  String neighborhood_buns_polar_calc_name() {
    return "RemodelMover_loops_neighborhood_bup";
  }


public: // virtual main methods


  /// @brief apply defined moves to given Pose
  virtual
  void apply( Pose & pose );

  virtual std::string get_name() const;

  bool confirm_sequence(core::pose::Pose & pose );


private: // protocol methods
  bool SamePose(Pose const & pose1, Pose const & pose2);

  void register_user_options();

  bool centroid_build(
    Pose & pose,
    protocols::forge::build::BuildManager & manager
  );


  /// @brief run the centroid level build stage
  /// @return true if loop closed, false otherwise
  bool centroid_build(
    Pose & pose
  );

  bool design_refine_seq_relax(
    Pose & pose,
    RemodelDesignMover & designMover
  );

  bool design_refine_cart_relax(
    Pose & pose,
    RemodelDesignMover & designMover
  );


  /// @brief run the design-refine stage
  /// @return currently always true
  bool design_refine(
    Pose & pose,
    RemodelDesignMover & designMover
  );


  /// @brief return a TaskFactory useable as a starting point for either
  ///  design or refinement
  TaskFactoryOP generic_taskfactory();


private: // design methods


  /// @brief process a continuous design string, adding appropriate operations
  ///  to the TaskFactory
  void process_continuous_design_string(
    Interval const & original_interval,
    String const & design_str,
    Original2Modified const & original2modified_interval_endpoints,
    TaskFactoryOP design_tf
  );


  /// @brief process a design string containing an insert, adding appropriate
  ///  operations to the TaskFactory
  void process_insert_design_string(
    Interval const & original_interval,
    String const & design_str,
    Original2Modified const & original2modified_interval_endpoints,
    TaskFactoryOP design_tf
  );


  /// @brief return a boolean vector specifying allowed a.a. when designing
  ///  on the surface
  static
  utility::vector1< bool > const & allowed_surface_aa();


private: // data


  /// @brief the BuildManager
  // try to get this from Remodel OB
  BuildManager manager_;

  Pose native_pose_;

  /// @brief holds all the blueprint info, contains build manager
  RemodelData remodel_data_;

  /// @brief working set holds all the modified index that is required for the
  /// remodeling task
  RemodelWorkingSet working_model_;


  /// @brief Stores instructions' original interval and a string denoting
  ///  the sequence during design.
  /// @remarks This is only for instructions such as SegmentRebuild or
  ///  SegmentInsert.  Non-applicable instructions will not have any data
  ///  stored here.
  DesignInfo design_info_;


  /// @brief use sequence biased fragments when building the loop? (default false)
  ///bool use_sequence_bias_;


  /// @brief the maximum allowed linear chainbreak (default 0.07)
  Real max_linear_chainbreak_;


  /// @brief the loop mover string to use during centroid build
  ///  (default "RemodelLoopMover")
  /// @remarks set to either a string the create_loop_mover() LoopMoverFactory
  ///  recognizes or the "RemodelLoopMover"
  String centroid_loop_mover_str_;


  /// @brief redesign the neighborhood around the loop?  if false, then just
  ///  repacks during the design phase (default true)
  bool redesign_loop_neighborhood_;


  /// @brief name of the resfile to use during design-refine; empty string
  ///  implies no resfile
  ///String resfile_;


  /// @brief the number of design-refine cycles to perform, default 3
  Size dr_cycles_;


  /// @brief the centroid scorefunction to use, default "remodel_cen"
  ScoreFunctionOP centroid_sfx_;


  /// @brief the full-atom scorefunction to use
  ScoreFunctionOP fullatom_sfx_;


  //blueprint
  String blueprint_;


  //For parsing rosetta scripts input
  bool rosetta_scripts_quick_and_dirty_ ;
  bool rosetta_scripts_build_disulfide_ ;
  bool rosetta_scripts_fast_disulfide_ ;
  bool rosetta_scripts_bypass_fragments_ ;
  core::Real rosetta_scripts_match_rt_limit_ ;
  Size rosetta_scripts_min_disulfides_ ;
  Size rosetta_scripts_max_disulfides_ ;
  bool rosetta_scripts_include_current_ds_ ;
  bool rosetta_scripts_keep_current_ds_ ;
  Size rosetta_scripts_min_loop_ ;
  bool rosetta_scripts_ ;
  //for saving results from multiple runs
  core::pose::PoseOP last_input_pose_;

  forge::remodel::RemodelAccumulator accumulator_;
  bool relax_bb_for_disulf_;
  bool use_match_rt_ ;
  bool use_disulf_fa_score_;
  core::Real disulf_fa_max_ ;


  struct instruction_flags {
    Size num_trajectory;
    Size num_report ;
    Size num_frag_moves;
    bool nojumps_;
    bool automatic_;
    bool use_bp_seq_; // use blueprint sequence for fragment picking
    bool randomize_equiv_frag_; // randomize identical scoring fragments, otherwise will get the same top 'n' fragments each time
    bool has_ligand_;
    bool no_repack_;
    bool fast_build_;
    bool backrub_;
    bool help_;
    bool checkpoint_;
    bool rigid_min_;
    bool no_design_;
    bool no_frags_;
    bool matchingFrags_;
    bool use_ccd_refine_;
    bool pose_relax_;
    bool allow_chi_during_relax_;
    bool pose_frag_moves_;
    bool dsspSS_;
    bool inserting_pdb_;
    bool neighbor_design_;
    bool rank_by_bsasa_;
    bool neighbor_repack_;
    bool skip_ccd_moves_;
    bool rigid_segment_in_refinement_;
    bool staged_manual_design_;
    bool use_ccd_trim_;
    Real ccd_cutoff_;

    /// @brief use full-mer fragments when building the loop? (default false)
    bool use_fullmer_;

    // added by Nobu
    bool silent_;
    bool output_fragfiles_;
    bool read_fragfiles_;

    String cstfile_;
    String insert_pdb_;
    String prefix_;
  };

private: // per-stage movers


  /// @brief VLB for centroid_build
  /// @remarks Store it here instead of re-instantiation each centroid_build()
  ///  call so fragment caching works.
  /// @warning Remember to set this to null if the BuildManager changes.
  VarLengthBuildOP vlb_;


public: // parser

  virtual void parse_my_tag( TagCOP tag, basic::datacache::DataMap & data, Filters_map const &, Movers_map const &, Pose const & );

private:

  void set_param_from_options();

};


} // namespace components
} // namespace forge
} // namespace protocols


#endif /* INCLUDED_protocols_forge_components_RemodelMover_HH */