StepWiseRNA_PoseSetup.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_PoseSetup.hh
/// @brief
/// @detailed
///
/// @author Parin Sripakdeevong
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_PoseSetup_hh
#define INCLUDED_protocols_swa_rna_StepWiseRNA_PoseSetup_hh

#include <protocols/swa/rna/StepWiseRNA_Util.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.fwd.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <protocols/moves/Mover.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>
#include <ObjexxFCL/FArray1D.hh>

#include <string>
#include <map>


namespace protocols {
namespace swa {
namespace rna {

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

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

    //constructor!
    StepWiseRNA_PoseSetup(StepWiseRNA_JobParametersOP & job_parameters);

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

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

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

    virtual std::string get_name() const;

    void
    set_input_tags( utility::vector1< std::string > const & setting){ input_tags_=setting; } //Only called if COPY_DOF is true

    void
    set_silent_files_in( utility::vector1< std::string > const & setting){ silent_files_in_= setting; } //Only called if COPY_DOF is true

    void
    set_bulge_res( utility::vector1 < core::Size > const & bulge_res ){ bulge_res_ = bulge_res; }

    void
    set_virtual_res( utility::vector1 < core::Size > const & virtual_res_list){ virtual_res_list_ = virtual_res_list; }

    void
    set_native_virtual_res( utility::vector1 < core::Size > const & native_virtual_res_list ){ native_virtual_res_list_ = native_virtual_res_list; } //Parin Mar 22, 2010

    void
    set_copy_DOF( bool const setting){ copy_DOF_=setting;} //Parin Mar 29, 2010

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

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

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

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

    void
    set_apply_virtual_res_variant_at_dinucleotide( bool const setting){ apply_virtual_res_variant_at_dinucleotide_=setting;}

    void
    set_align_to_native( bool const setting){ align_to_native_=setting;}

    private:

    void
    Import_pose( Size const & i, core::pose::Pose & import_pose) const; //Only called if COPY_DOF is true

    void
    make_pose( core::pose::Pose & pose ); //Only called if COPY_DOF is true

    void
    read_input_pose_and_copy_dofs( core::pose::Pose & pose ); //Only called if COPY_DOF is true

    void
    apply_cutpoint_variants( core::pose::Pose & pose , core::pose::Pose & pose_without_cutpoints);

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

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

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

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

    void
    correctly_copy_HO2star_positions( core::pose::Pose & full_pose , utility::vector1<core::pose::Pose> const & start_pose_list);

    core::Real
    get_nearest_dist_to_O2star( core::Size const O2star_seq_num, core::pose::Pose const & input_pose, utility::vector1< core::Size > const input_res_list , utility::vector1< core::Size > const & common_res_list);

    //void
    //ensure_idealize_bond_length_bond_angle_at_cutpoint( core::pose::Pose & working_pose);

    void
    add_protonated_H1_adenosine_variants( core::pose::Pose & pose ) const;

    void
    verify_protonated_H1_adenosine_variants( core::pose::Pose & pose ) const;

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

  private:

//    utility::vector1< utility::vector1< Size > > input_res_vectors_;

    core::chemical::ResidueTypeSetCAP rsd_set_;
    utility::vector1< std::string > input_tags_;
    utility::vector1< std::string > silent_files_in_;
    StepWiseRNA_JobParametersOP job_parameters_;
    bool copy_DOF_;
    bool verbose_;

    utility::vector1< Size > bulge_res_;
    utility::vector1< Size > virtual_res_list_;
    utility::vector1< Size > native_virtual_res_list_;

    bool rebuild_bulge_mode_;
    bool output_pdb_;
    bool apply_virtual_res_variant_at_dinucleotide_;
    bool align_to_native_;

  };

}
} //swa
} // protocols

#endif