RNA_Util.cc File Reference

#include <core/pose/rna/RNA_Util.hh>
#include <core/pose/util.hh>
#include <core/types.hh>
#include <core/chemical/ResidueSelector.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/id/TorsionID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/AtomPointer.fwd.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Stub.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomType.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/pose/rna/RNA_IdealCoord.hh>
#include <core/chemical/AA.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <utility/vector1.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/string.functions.hh>

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

Functions
bool	core::pose::rna::mutate_position (pose::Pose &pose, Size const i, char const &new_seq)
void	core::pose::rna::figure_out_reasonable_rna_fold_tree (pose::Pose &pose)
void	core::pose::rna::virtualize_5prime_phosphates (pose::Pose &pose)
bool	core::pose::rna::is_cutpoint_open (Pose const &pose, Size const i)
bool	core::pose::rna::is_rna_chainbreak (Pose const &pose, Size const i)
void	core::pose::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, Pose &pose, Size const i)
void	core::pose::rna::prepare_scratch_residue (core::conformation::ResidueOP &scratch_rsd, core::conformation::Residue const &start_rsd, utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose const &pose)
void	core::pose::rna::fix_sugar_coords (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose &pose, Pose const &reference_pose, Size const i)
void	core::pose::rna::initialize_atoms_for_which_we_need_new_dofs (utility::vector1< std::string > &atoms_for_which_we_need_new_dofs, Pose const &pose, Size const i)
void	core::pose::rna::apply_non_main_chain_sugar_coords (utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose &pose, Pose const &reference_pose, Size const i)
void	core::pose::rna::apply_ideal_c2endo_sugar_coords (Pose &pose, Size const i)
PuckerState	core::pose::rna::assign_pucker (Pose const &pose, Size const rsd_id)
void	core::pose::rna::apply_pucker (Pose &pose, Size const i, PuckerState pucker_state, bool const skip_same_state, bool const idealize_coord)
void	core::pose::rna::correctly_position_cutpoint_phosphate_torsions (pose::Pose &current_pose, Size const five_prime_chainbreak)
void	core::pose::rna::correctly_add_cutpoint_variants (core::pose::Pose &pose, Size const res_to_add, bool const check_fold_tree)

Variables
static basic::Tracer	TR ("core.pose.rna.RNA_Util")
static const RNA_FittedTorsionInfo	torsion_info

Detailed Description

Author

Rhiju Das

Variable Documentation

const RNA_FittedTorsionInfo torsion_info

static

Referenced by core::pose::rna::apply_pucker(), core::pose::rna::assign_pucker(), core::chemical::rna::get_epsilon_torsions(), and core::pose::rna::RNA_IdealCoord::init().

basic::Tracer TR("core.pose.rna.RNA_Util")

static