StepWiseRNA_RotamerGenerator.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
/// @author Parin Sripakdeevong


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_RotamerGenerator_hh
#define INCLUDED_protocols_swa_rna_StepWiseRNA_RotamerGenerator_hh

#include <protocols/swa/rna/StepWiseRNA_Classes.hh> 

#include <core/types.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/id/TorsionID.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>

#include <string>
#include <map>



namespace protocols {
namespace swa {
namespace rna {

  class StepWiseRNA_RotamerGenerator: public utility::pointer::ReferenceCount {
  public:

    StepWiseRNA_RotamerGenerator( Size const moving_suite,
                                bool const sample_lower_sugar_and_base,
                                bool const sample_upper_sugar_and_base,
                                PuckerState const pucker1,
                                PuckerState const pucker2); 


    virtual ~StepWiseRNA_RotamerGenerator();

    utility::vector1< core::id::TorsionID > const & torsion_ids() const;

    bool has_another_rotamer() const;

    void update_to_next_rotamer();

    utility::vector1< Torsion_Info > const & get_current_rotamer(){ return rotamer_list_; }

    void reset();

//    void set_Is_bulge( bool const & setting ){ Is_bulge_ = setting; }

    void set_sample_extra_rotamers( bool const setting ){ sample_extra_rotamers_ = setting; }

    void set_fast( bool const setting ){ fast_ = setting; }

    void set_sample_chi_torsion( bool const setting) { sample_chi_torsion_= setting; }

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

    void set_force_syn_chi_res_list( utility::vector1< core::Size > const & setting){ force_syn_chi_res_list_ = setting; } //April 29, 2011

    void set_bin_size( core::Size const setting){ bin_size_=setting;} 

    void set_extra_epsilon( bool const setting){ extra_epsilon_ =setting; }

    void set_extra_beta( bool const setting){ extra_beta_ =setting; }

    void set_extra_anti_chi( bool const setting){ extra_anti_chi_ =setting; }

    void set_extra_syn_chi( bool const setting){ extra_syn_chi_ =setting; }

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

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

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

    core::Size num_rotamer_centers();
    core::Size const & group_rotamer();
    core::Size const & subgroup_rotamer();
    core::Size const & moving_suite();

    PuckerState pucker_state(std::string const which_sugar);



  private:
/*
    void
    initialize_puckers(
                       core::pose::Pose const & pose,
                       bool const & sample_sugar_and_base1,
                       bool const & sample_sugar_and_base2 );
*/
    void
    initialize_sample_base_states( core::pose::Pose const & pose );

    void
    initialize_rotamers();

    void
    initialize_extra_rotamer_perturbations();

    void 
    add_torsion_id(core::id::TorsionID const torsion_id);

  private:

    core::Size const moving_suite_;

    bool const sample_lower_sugar_and_base_;
    bool const sample_upper_sugar_and_base_;

    PuckerState const pucker1_specified_; 
    PuckerState const pucker2_specified_;


    bool sample_extra_rotamers_;
    bool fast_;

    core::Size bin_size_;
    int bins1_, bins2_, bins3_, eps_bins_, beta_bins_; //int because they are compared to ints in torsion definition loops.
    bool verbose_;

    utility::vector1< core::id::TorsionID > torsion_ids_;
    utility::vector1< utility::vector1< core::Real > > rotamer_centers_;

    utility::vector1< core::id::TorsionID > perturb_torsion_ids_;
    utility::vector1< utility::vector1< core::Real > > extra_rotamer_perturbations_;

    core::Size group_rotamer_;
    core::Size subgroup_rotamer_;

    utility::vector1< Torsion_Info > rotamer_list_;
    bool sample_chi_torsion_;
    bool include_syn_chi_;
    utility::vector1< core::Size > force_syn_chi_res_list_; //April 29, 2011
    bool extra_epsilon_;
    bool extra_beta_;
    bool extra_anti_chi_;
    bool extra_syn_chi_;
    bool exclude_alpha_beta_gamma_sampling_;
    bool allow_syn_pyrimidine_;
    BaseState lower_base_state_;
    BaseState upper_base_state_;

  };

} //rna
} //swa
} // protocols

#endif