StepWiseRNA_ResidueSampler.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 res 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 Parin Sripakdeevong
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_ResidueSampler_HH
#define INCLUDED_protocols_swa_rna_StepWiseRNA_ResidueSampler_HH

//#include <numeric/xyzMatrix.hh>
//#include <numeric/xyzVector.hh>
#include <protocols/swa/rna/StepWiseRNA_Util.hh>
#include <protocols/swa/rna/StepWiseRNA_VirtualRiboseSampler.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_BaseCentroidScreener.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_RotamerGenerator_Wrapper.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_FloatingBase_Sampler_Util.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/pack/task/PackerTask.fwd.hh>
#include <protocols/simple_moves/GreenPacker.fwd.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_ResidueSampler: public protocols::moves::Mover {
  public:

    //constructor!
    StepWiseRNA_ResidueSampler( StepWiseRNA_JobParametersCOP & job_parameters_ );

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

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

    virtual std::string get_name() const;

    void
    set_centroid_screen( bool const setting){ centroid_screen_=setting;}

    void
    set_allow_base_pair_only_centroid_screen( bool const setting){ allow_base_pair_only_centroid_screen_=setting;}

    void
    set_VDW_atr_rep_screen( bool const setting){ VDW_atr_rep_screen_=setting;}

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

    void
    set_output_filename( std::string const & output_filename);

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

    void
    set_fast( bool const & setting );

    void
    set_medium_fast( bool const & setting);

    void
    set_native_rmsd_screen( bool const & setting );

    void
    set_native_screen_rmsd_cutoff( core::Real const & setting);

    void
    set_integration_test_mode( bool const & setting);

    void
    set_verbose( bool const & setting );

    void
    set_perform_o2star_pack( bool const & setting );

    void
    set_cluster_rmsd( core::Real const & setting );

    void
    set_allow_bulge_at_chainbreak( bool const & setting );

    utility::vector1< pose_data_struct2 > &
    get_pose_data_list();

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

    void output_pose_data_list( std::string const final_sampler_output_silent_file ) const;

    void set_num_pose_kept( core::Size const & num_pose_kept );

    void
    set_base_centroid_screener( StepWiseRNA_BaseCentroidScreenerOP & screener );

    void
    set_parin_favorite_output( bool const & setting){ parin_favorite_output_=setting ; }

    void
    set_floating_base( bool const & setting){ floating_base_=setting ; }

    void
    set_include_syn_chi( bool const & setting){ include_syn_chi_=setting ; }

    void
    set_allow_syn_pyrimidine(  bool const & setting){ allow_syn_pyrimidine_ =setting; }

    void
    set_distinguish_pucker( bool const & setting){ distinguish_pucker_=setting ; }

    void
    set_finer_sampling_at_chain_closure( bool const & setting){ finer_sampling_at_chain_closure_=setting; }

    void
    set_PBP_clustering_at_chain_closure( bool const & setting){ PBP_clustering_at_chain_closure_ =setting; }

    void
    set_reinitialize_CCD_torsions( bool const & setting){ reinitialize_CCD_torsions_ =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_extra_epsilon_rotamer( bool const & setting){ extra_epsilon_rotamer_ = setting; }

    void
    set_extra_beta_rotamer( bool const & setting){ extra_beta_rotamer_ = setting; }

    void
    set_extra_anti_chi_rotamer( bool const & setting){ extra_anti_chi_rotamer_ = setting; }

    void
    set_extra_syn_chi_rotamer( bool const & setting){ extra_syn_chi_rotamer_ = setting; }

    void
    set_sample_both_sugar_base_rotamer( bool const & setting){ sample_both_sugar_base_rotamer_ = setting; }

    void
    set_include_torsion_value_in_tag( bool const & setting){ include_torsion_value_in_tag_ = setting; }

    void
    set_rebuild_bulge_mode( bool const & setting){ rebuild_bulge_mode_ = setting; }

    void
    set_debug_eplison_south_sugar_mode( bool const & setting){ debug_eplison_south_sugar_mode_ = setting; }

    void
    set_exclude_alpha_beta_gamma_sampling( bool const & setting){ exclude_alpha_beta_gamma_sampling_ = setting; }

    void
    set_combine_long_loop_mode( bool const & setting){ combine_long_loop_mode_ = setting; }

    void
    set_do_not_sample_multiple_virtual_sugar( bool const & setting){ do_not_sample_multiple_virtual_sugar_ = setting; }

    void
    set_sample_ONLY_multiple_virtual_sugar( bool const & setting){ sample_ONLY_multiple_virtual_sugar_ = setting; }

    void
    set_assert_no_virt_ribose_sampling( bool const & setting){ assert_no_virt_ribose_sampling_ = setting; }

    void
    set_output_pdb( bool const setting){ output_pdb_=setting;}


  private:

    void
    initialize_scorefunctions();

    void
    Copy_CCD_torsions(core::pose::Pose & pose, core::pose::Pose const & template_pose) const;

    void
    Copy_CCD_torsions_general(core::pose::Pose & pose, core::pose::Pose const & template_pose, core::Size const five_prime_res, core::Size const three_prime_res) const;

    bool
    Chain_break_screening(core::pose::Pose & chain_break_screening_pose, core::scoring::ScoreFunctionOP const & constraint_scorefxn );

    bool
    Chain_break_screening_general( core::pose::Pose & chain_break_screening_pose, core::scoring::ScoreFunctionOP const & chainbreak_scorefxn, core::Size const five_prime_res);

    void
    standard_sampling_WRAPPER( core::pose::Pose & pose,
                              FloatingBaseChainClosureJobParameter const & prev_sugar_FB_JP,
                              FloatingBaseChainClosureJobParameter const & curr_sugar_FB_JP,
                              FloatingBaseChainClosureJobParameter const & five_prime_CB_sugar_FB_JP,
                              FloatingBaseChainClosureJobParameter const & three_prime_CB_sugar_FB_JP);

    void
    standard_sampling(core::pose::Pose & pose, utility::vector1< pose_data_struct2 > & pose_data_list, std::string const sugar_tag );


    void
    floating_base_sampling(core::pose::Pose & pose, FloatingBaseChainClosureJobParameter const & prev_sugar_FB_JP);

    void
    get_base_atr_rep_score(core::pose::Pose const & pose, core::Real & base_atr_score, core::Real & base_rep_score);

    bool
    Full_atom_van_der_Waals_screening_REPLICATE(
                                      core::pose::Pose & current_pose_screen,
                                      core::Real const & base_rep_score,
                                      core::Real const &  base_atr_score,
                                      core::Real & delta_rep_score,
                                      core::Real & delta_atr_score,
                                      core::Size const & gap_size,
                                      bool const & Is_internal);


    bool
    Full_atom_van_der_Waals_screening(
                                      core::pose::Pose & current_pose_screen,
                                      core::Real const & base_rep_score,
                                      core::Real const &  base_atr_score,
                                      core::Real & delta_rep_score,
                                      core::Real & delta_atr_score,
                                      core::Size const & gap_size,
                                      bool const & Is_internal);

    void
    initialize_o2star_packer_task( core::pose::Pose const & pose );

    void
    initialize_o2star_green_packer( core::pose::Pose & pose );

    void
    sample_o2star_hydrogen( core::pose::Pose & pose , core::pose::Pose & pose_with_original_HO2star_torsion );

    core::Real
    Pose_selection_by_full_score(utility::vector1< pose_data_struct2 >& pose_data_list, core::pose::Pose & current_pose, std::string const & tag);

    bool
    apply_bulge_variant( core::pose::Pose & pose, core::Real const & delta_atr_score );

    void
    Update_pose_data_list(std::string const & tag, utility::vector1< pose_data_struct2 > & pose_data_list, core::pose::Pose const & current_pose, core::Real const & current_score) const;

    void
    cluster_pose_data_list(utility::vector1< pose_data_struct2 > & pose_data_list);

    std::string
    create_tag(std::string const prestring, StepWiseRNA_RotamerGenerator_WrapperOP const & rotamer_generator) const;

    core::kinematics::Stub
    get_reference_stub(core::Size const reference_res, core::pose::Pose const & pose) const;


    std::string //silly function to convert to real to string
    create_torsion_value_string(core::Real const & torsion_value) const;

    std::string
    create_rotamer_string( core::pose::Pose const & pose) const;

    /////////////////////////////////////function related to sampling/setup virtual sugar /////////////////////////////////////////////////////////////////
    bool
    Is_previous_sugar_virtual( core::pose::Pose const & pose ) const;

    bool
    Is_current_sugar_virtual( core::pose::Pose const & pose ) const;

    bool
    Is_five_prime_chain_break_sugar_virtual( core::pose::Pose const & pose ) const;

    bool
    Is_three_prime_chain_break_sugar_virtual( core::pose::Pose const & pose ) const;

    utility::vector1< pose_data_struct2 >
    previous_floating_base_chain_closure(core::pose::Pose & viewer_pose, FloatingBaseChainClosureJobParameter const & FB_job_params, std::string const name);

    ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


  private:

    StepWiseRNA_JobParametersCOP job_parameters_; //need to use the full_to_sub map...should convert to const style.. Parin Feb 28, 2010

    core::io::silent::SilentFileDataOP sfd_;
    utility::vector1< pose_data_struct2 > pose_data_list_;

    core::scoring::ScoreFunctionOP scorefxn_;
    core::scoring::ScoreFunctionOP atr_rep_screening_scorefxn_;
    core::scoring::ScoreFunctionOP chainbreak_scorefxn_;
    core::scoring::ScoreFunctionOP sampling_scorefxn_;
    core::scoring::ScoreFunctionOP o2star_pack_scorefxn_;

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

    SillyCountStruct count_data_;
    std::string silent_file_;
    std::string output_filename_;
    core::Real const bin_size_; /*ALWAYS 20!!!*/
    core::Real const rep_cutoff_;
    core::Size num_pose_kept_;
    core::Size const multiplier_;
    core::Real cluster_rmsd_;
    bool verbose_;
    bool native_rmsd_screen_;
    core::Real native_screen_rmsd_cutoff_;

    bool perform_o2star_pack_;
    core::pack::task::PackerTaskOP o2star_pack_task_;
    protocols::simple_moves::GreenPackerOP o2star_green_packer_;
    bool const use_green_packer_;
    bool allow_bulge_at_chainbreak_;
    bool fast_;
    bool medium_fast_;
    bool integration_test_mode_;
    bool floating_base_;

    StepWiseRNA_BaseCentroidScreenerOP base_centroid_screener_;

    bool parin_favorite_output_;
    bool centroid_screen_;
    bool allow_base_pair_only_centroid_screen_;
    bool VDW_atr_rep_screen_;
    bool include_syn_chi_;
    bool allow_syn_pyrimidine_;
    bool distinguish_pucker_;
    bool build_pose_from_scratch_;
    core::Real current_score_cutoff_;
    bool finer_sampling_at_chain_closure_;
    bool PBP_clustering_at_chain_closure_;
    bool reinitialize_CCD_torsions_;
    bool extra_epsilon_rotamer_;
    bool extra_beta_rotamer_;
    bool extra_anti_chi_rotamer_;
    bool extra_syn_chi_rotamer_;
    bool sample_both_sugar_base_rotamer_;
    bool include_torsion_value_in_tag_;
    bool rebuild_bulge_mode_;
    bool debug_eplison_south_sugar_mode_;
    bool exclude_alpha_beta_gamma_sampling_;
    bool combine_long_loop_mode_;
    bool do_not_sample_multiple_virtual_sugar_;
    bool sample_ONLY_multiple_virtual_sugar_;
    bool assert_no_virt_ribose_sampling_;
    bool output_pdb_;

    StepWiseRNA_VDW_Bin_ScreenerOP user_input_VDW_bin_screener_;


  };

}
} //swa
} // protocols

#endif