RNA_Util.cc File Reference

#include <core/scoring/rna/RNA_Util.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/VariantType.hh>
#include <core/id/TorsionID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/AtomPointer.fwd.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomType.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/AA.hh>
#include <numeric/constants.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/FoldTree.hh>
#include <utility/vector1.hh>
#include <numeric/xyz.functions.hh>
#include <ObjexxFCL/string.functions.hh>

Go to the source code of this file.

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::scoring
	core::scoring::rna

Constant Groups
	core
	A class for defining atom parameters, known as atom_types.
	core::scoring
	core::scoring::rna

Functions
Size	core::scoring::rna::convert_acgu_to_1234 (char const c)
char	core::scoring::rna::get_edge_from_num (Size const num)
std::string	core::scoring::rna::get_full_edge_from_num (Size const num)
char	core::scoring::rna::get_orientation_from_num (Size const num)
std::string	core::scoring::rna::get_full_orientation_from_num (Size const num)
std::string	core::scoring::rna::get_full_LW_orientation_from_num (Size const num)
std::string const	core::scoring::rna::first_base_atom (conformation::Residue const &rsd)
bool	core::scoring::rna::is_purine (conformation::Residue const &rsd)
Size	core::scoring::rna::first_base_atom_index (conformation::Residue const &rsd)
std::string const	core::scoring::rna::chi1_torsion_atom (conformation::Residue const &rsd)
Size	core::scoring::rna::chi1_torsion_atom_index (conformation::Residue const &rsd)
std::string const	core::scoring::rna::default_jump_atom (conformation::Residue const &rsd)
bool	core::scoring::rna::possibly_canonical (chemical::AA const &aa1, chemical::AA const &aa2)
bool	core::scoring::rna::possibly_canonical_strict (chemical::AA const &aa1, chemical::AA const &aa2)
void	core::scoring::rna::get_watson_crick_base_pair_atoms (chemical::AA const &aa1, chemical::AA const &aa2, std::string &atom1, std::string &atom2)
void	core::scoring::rna::get_watson_crick_base_pair_atoms (chemical::AA const &aa1, chemical::AA const &aa2, utility::vector1< std::string > &atom_ids1, utility::vector1< std::string > &atom_ids2)
bool	core::scoring::rna::is_cutpoint_open (core::pose::Pose const &pose, Size const i)
bool	core::scoring::rna::is_rna_chainbreak (core::pose::Pose const &pose, Size const i)
void	core::scoring::rna::initialize_non_main_chain_sugar_atoms ()
void	core::scoring::rna::fix_sugar_coords_WORKS_BUT_SLOW (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< utility::vector1< id::DOF_Type > > which_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::Size const &i)
void	core::scoring::rna::prepare_scratch_residue (core::conformation::ResidueOP &scratch_rsd, core::conformation::Residue const &start_rsd, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose const &pose)
void	core::scoring::rna::fix_sugar_coords (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::pose::Pose const &reference_pose, core::Size const &i)
void	core::scoring::rna::initialize_atoms_for_which_we_need_new_dofs (utility::vector1< std::string > &atoms_for_which_we_need_new_dofs, pose::Pose const &pose, Size const &i)
void	core::scoring::rna::apply_non_main_chain_sugar_coords (utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::pose::Pose const &reference_pose, core::Size const &i)
void	core::scoring::rna::apply_ideal_c2endo_sugar_coords (core::pose::Pose &pose, core::Size const &i)
void	core::scoring::rna::get_fade_correction (Real const z, Real const cutoff_lower, Real const cutoff_upper, Real const fade_zone, Real &fade_value, Real &fade_deriv)
Vector	core::scoring::rna::get_rna_base_centroid (conformation::Residue const &rsd, bool verbose)
numeric::xyzMatrix< core::Real >	core::scoring::rna::get_rna_base_coordinate_system (conformation::Residue const &rsd, Vector const &centroid)
bool	core::scoring::rna::Is_base_phosphate_atom_pair (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const atomno_1, Size const atomno_2)

Variables
utility::vector1< std::string >	core::scoring::rna::non_main_chain_sugar_atoms