#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <string>
#include <map>
#include <core/chemical/AA.hh>
#include <core/io/silent/RNA_SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <numeric/angle.functions.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/conformation/Residue.hh>
#include <set>
#include <ObjexxFCL/string.functions.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <protocols/swa/rna/StepWiseRNA_Util.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/rna/RNA_Util.hh>

Classes
struct	protocols::swa::rna::Anchor_ribose_stub

struct	protocols::swa::rna::Euler_angles

struct	protocols::swa::rna::Base_bin

struct	protocols::swa::rna::compare_base_bin

struct	protocols::swa::rna::compare_int_pair

struct	protocols::swa::rna::compare_test

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.

	protocols::swa

	protocols::swa::rna

Constant Groups
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.

	protocols::swa

	protocols::swa::rna

Macros
#define	centroid_bin_size 1.0

#define	euler_angle_bin_size 20

#define	euler_z_bin_size 0.05

Typedefs
typedef numeric::xyzMatrix < core::Real >	Matrix

Functions
bool	protocols::swa::rna::Is_base_stack (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF)

bool	protocols::swa::rna::Is_base_pair (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, core::Real const base_axis_CUTOFF, core::Real const base_planarity_CUTOFF)

bool	protocols::swa::rna::Is_strong_base_stack (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list)

bool	protocols::swa::rna::Base_centroid_screening (core::kinematics::Stub const &moving_res_base, utility::vector1< core::kinematics::Stub > const &other_residues_base_list, Size const num_nucleotides, SillyCountStruct &count_data, bool const allow_base_pair_only_screen)

Base_bin	protocols::swa::rna::Get_euler_stub_bin (numeric::xyzVector< core::Real > const &centriod, Euler_angles const &euler_angles)

core::kinematics::Stub	protocols::swa::rna::Get_ribose_stub (conformation::Residue const &rsd, bool const Is_prepend, bool const verbose)

int	protocols::swa::rna::DOF_bin_value (std::map< Base_bin, int, compare_base_bin >::const_iterator const &base_bin_it, std::string const &DOF)

Real	protocols::swa::rna::DOF_bin_size (std::string const &DOF)

void	protocols::swa::rna::Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const foldername)

void	protocols::swa::rna::Analyze_base_bin_map (std::map< Base_bin, int, compare_base_bin > const &base_bin_map, std::string const &DOF_one, std::string const &DOF_two, std::string const foldername)

void	protocols::swa::rna::translate_then_rotate_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &vector, numeric::xyzMatrix< core::Real > const matrix, bool const verbose)

void	protocols::swa::rna::set_to_origin (pose::Pose &pose, Size const seq_num, bool verbose)

Euler_angles	protocols::swa::rna::Get_euler_angles (numeric::xyzMatrix< core::Real > const &coordinate_matrix)

void	protocols::swa::rna::convert_euler_to_coordinate_matrix (Euler_angles const &E, numeric::xyzMatrix< core::Real > &coordinate_matrix)

void	protocols::swa::rna::get_specific_atom_coordinate (std::string const &atom_name, numeric::xyzVector< core::Real > &atom_pos, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)

core::Real	protocols::swa::rna::get_max_centroid_to_atom_distance (utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, std::string const atom_name)

utility::vector1 < core::conformation::ResidueOP >	protocols::swa::rna::setup_residue_at_origin_list (pose::Pose const &pose, Size const &moving_res, bool const extra_anti_chi_rotamer, bool const extra_syn_chi_rotamer, std::string const pose_name)

bool	protocols::swa::rna::check_floating_base_chain_closable (core::Size const &reference_res, core::pose::Pose const &pose, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const Is_prepend, Size const gap_size)

bool	protocols::swa::rna::check_floating_base_chain_closable (core::Size const &reference_res, utility::vector1< pose_data_struct2 > pose_data_list, utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, core::kinematics::Stub const &moving_res_base_stub, bool const Is_prepend, core::Size const gap_size)

void	protocols::swa::rna::set_base_coordinate_frame (pose::Pose &pose, Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)