StepWiseRNA_Minimizer.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 SWA_ResidueSampler.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_Minimizer_HH
#define INCLUDED_protocols_swa_rna_StepWiseRNA_Minimizer_HH

//#include <numeric/xyzMatrix.hh>
//#include <numeric/xyzVector.hh>
#include <protocols/swa/rna/StepWiseRNA_Util.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_BaseCentroidScreener.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.hh>     //Feb 02, 2012: Need this to pass rosetta_tools/python_cc_reader/test_all_headers_compile.py
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.fwd.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/io/silent/SilentFileData.fwd.hh>
#include <utility/vector1.hh>
#include <protocols/moves/Mover.hh>
#include <string>
#include <map>

namespace protocols {
namespace swa {
namespace rna {

  //  typedef std::map< std::string, core::pose::PoseOP > PoseList;

  /////////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////////
  class StepWiseRNA_Minimizer: public protocols::moves::Mover {
  public:


    //constructor!
    StepWiseRNA_Minimizer(
            utility::vector1 <pose_data_struct2> const & pose_data_list,
            StepWiseRNA_JobParametersCOP & job_parameters );

    //destructor -- necessary?
    ~StepWiseRNA_Minimizer();

    /// @brief Apply the minimizer to one pose
    virtual void apply( core::pose::Pose & pose_to_visualize );

    virtual std::string get_name() const;

    void
    set_silent_file( std::string const & silent_file );

    void
    set_move_map_list(utility::vector1 <core::kinematics::MoveMap> const & move_map_list);

    void
    set_scorefxn( core::scoring::ScoreFunctionOP const & scorefxn );

    core::io::silent::SilentFileDataOP & silent_file_data();

    void
    set_base_centroid_screener( StepWiseRNA_BaseCentroidScreenerOP & screener );

    void
    set_native_edensity_score_cutoff( core::Real const & setting); //Fang's electron density code

    void
    set_verbose( bool const setting){verbose_=setting;}

    void
    set_centroid_screen(bool const setting){centroid_screen_=setting;} //For testing purposes.

    void
    set_perform_o2star_pack(bool const setting){ perform_o2star_pack_=setting;} //For testing purposes.

    void
    set_output_before_o2star_pack(bool const setting){output_before_o2star_pack_=setting;} //For testing purposes.

    void
    set_rm_virt_phosphate(bool const setting){rm_virt_phosphate_=setting;}

    void
    set_perform_minimize(bool const setting){perform_minimize_=setting;}

    void
    set_num_pose_minimize(Size const setting){num_pose_minimize_=setting;}

    void
    set_minimize_and_score_sugar(bool const setting){minimize_and_score_sugar_=setting;}

    void
    set_native_rmsd_screen( bool const setting ){native_screen_=setting;}

    void
    set_native_screen_rmsd_cutoff( core::Real const setting ){native_screen_rmsd_cutoff_=setting;}

    void
    set_user_input_VDW_bin_screener(StepWiseRNA_VDW_Bin_ScreenerOP const & user_input_VDW_bin_screener){ user_input_VDW_bin_screener_= user_input_VDW_bin_screener; }

    void
    set_rename_tag( bool const setting ){ rename_tag_=setting;}

  private:

    utility::vector1 <core::kinematics::MoveMap>
    Get_default_movemap( core::pose::Pose const & pose ) const;

    void
    Figure_out_moving_residues( core::kinematics::MoveMap & mm, core::pose::Pose const & pose ) const;

    bool
    pass_all_pose_screens(core::pose::Pose & pose, std::string const in_tag, core::io::silent::SilentFileData & silent_file_data) const;

    void
    Freeze_sugar_torsions(core::kinematics::MoveMap & mm, Size const nres) const;

    void
    output_empty_minimizer_silent_file() const; //FEB 09, 2012

    void
    output_pose_data_wrapper(std::string & tag, char tag_first_char, core::pose::Pose & pose, core::io::silent::SilentFileData & silent_file_data, std::string const out_silent_file) const;

    core::Size
    figure_out_actual_five_prime_chain_break_res(core::pose::Pose const & pose) const;

    bool
    native_edensity_score_screener(core::pose::Pose & pose, core::pose::Pose & native_pose) const; //Fang's electron density code

  private:

    utility::vector1 <pose_data_struct2> const pose_data_list_;
    StepWiseRNA_JobParametersCOP job_parameters_;

    core::io::silent::SilentFileDataOP sfd_;
    utility::vector1 <core::kinematics::MoveMap> move_map_list_;
    core::scoring::ScoreFunctionOP scorefxn_;
    std::string silent_file_;
    bool verbose_;
    bool screen_verbose_;
    bool native_screen_;
    core::Real native_screen_rmsd_cutoff_;

    bool perform_electron_density_screen_, rm_virt_phosphate_; //Fang's electron density code
    core::Real native_edensity_score_cutoff_; //Fang's electron density code

    bool centroid_screen_; //for testing purposes

    bool perform_o2star_pack_; //Jan 19, 2012
    bool output_before_o2star_pack_; //for testing purposes

    bool perform_minimize_; //Parin Mar 12, 2012

    core::Size num_pose_minimize_;
    bool minimize_and_score_sugar_;
    bool rename_tag_;

    std::map< core::id::AtomID, core::id::AtomID > pose_to_native_map_;

    utility::vector1< core::Size > fixed_res_;

    StepWiseRNA_BaseCentroidScreenerOP base_centroid_screener_;

    StepWiseRNA_VDW_Bin_ScreenerOP user_input_VDW_bin_screener_;


  };

}
} //swa
} // protocols

#endif