RNA_ProtocolUtil.hh File Reference

#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <utility/io/ozstream.fwd.hh>
#include <string>
#include <utility/vector1.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>

Go to the source code of this file.

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

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

Typedefs
typedef numeric::xyzVector < core::Real >	protocols::rna::Vector

Functions
void	protocols::rna::figure_out_reasonable_rna_fold_tree (pose::Pose &pose)
void	protocols::rna::figure_out_secstruct (pose::Pose &pose)
void	protocols::rna::get_base_pairing_info (core::pose::Pose const &pose, core::Size const &seqpos, char &secstruct, ObjexxFCL::FArray1D< bool > &edge_is_base_pairing)
void	protocols::rna::get_base_pairing_list (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &base_pairing_list)
void	protocols::rna::create_rna_vall_torsions (pose::Pose &pose, utility::io::ozstream &torsions_out, utility::vector1< Size > const &exclude_res_list)
void	protocols::rna::create_rna_vall_torsions (pose::Pose &pose, std::string const outfile, utility::vector1< Size > const &exclude_res_list)
Real	protocols::rna::get_o1p_o2p_sign (pose::Pose const &pose)
Real	protocols::rna::get_o1p_o2p_sign (pose::Pose const &pose, Size res_num)
void	protocols::rna::assert_phosphate_nomenclature_matches_mini (pose::Pose const &pose)
void	protocols::rna::ensure_phosphate_nomenclature_matches_mini (pose::Pose &pose)
void	protocols::rna::make_phosphate_nomenclature_matches_mini (pose::Pose &pose)
void	protocols::rna::export_packer_results (utility::vector1< std::pair< core::Real, std::string > > &results, utility::vector1< core::pose::PoseOP > pose_list, core::scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dumo=false)
void	protocols::rna::check_base_pair (core::pose::Pose &pose, ObjexxFCL::FArray1D_int &struct_type)
void	protocols::rna::setup_base_pair_constraints (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const &pairings, core::Real const suppress_factor=1.0)
void	protocols::rna::setup_coarse_chainbreak_constraints (pose::Pose &pose, Size const &n)
std::string const	protocols::rna::convert_based_on_match_type (std::string const RNA_string, Size const type)
bool	protocols::rna::compare_RNA_char (char const char1, char const char2)
bool	protocols::rna::compare_RNA_secstruct (char const char1, char const char2)
Vector	protocols::rna::get_sugar_centroid (core::conformation::Residue const &rsd)
void	protocols::rna::make_extended_coarse_pose (pose::Pose &coarse_pose, std::string const &full_sequence)
void	protocols::rna::make_coarse_pose (pose::Pose const &pose, pose::Pose &coarse_pose)
void	protocols::rna::print_internal_coords (core::pose::Pose const &pose)
void	protocols::rna::remove_cutpoint_closed (pose::Pose &pose, Size const i)
void	protocols::rna::remove_cutpoints_closed (pose::Pose &pose)
void	protocols::rna::virtualize_5prime_phosphates (pose::Pose &pose)
bool	protocols::rna::possible_root (core::kinematics::FoldTree const &f, core::Size const &n)
bool	protocols::rna::is_num_in_list (core::Size const i, utility::vector1< core::Size > const &list)
utility::vector1< Size >	protocols::rna::get_rigid_body_jumps (core::pose::Pose const &pose)
bool	protocols::rna::let_rigid_body_jumps_move (core::kinematics::MoveMap &movemap, pose::Pose const &pose, bool const move_first_rigid_body)
void	protocols::rna::translate_virtual_anchor_to_first_rigid_body (pose::Pose &pose)

Detailed Description

Detailed:

Author

Rhiju Das

Definition in file RNA_ProtocolUtil.hh.