RNA_Motif.hh File Reference

find RNA motifs (u-turns, T-loops, etc.) in a pose More...

#include <utility/VirtualBase.hh>
#include <core/scoring/rna/RNA_Motif.fwd.hh>
#include <core/chemical/rna/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <core/pose/util.hh>
#include <core/pose/rna/RNA_FilteredBaseBaseInfo.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/rna/RNA_LowResolutionPotential.hh>

Classes
class	core::scoring::rna::RNA_Motif
class	core::scoring::rna::RNA_Motifs

Namespaces
	core
	A class for reading in the atom type properties.
	core::scoring
	core::scoring::rna

Enumerations
enum	core::scoring::rna::RNA_MotifType {   core::scoring::rna::U_TURN, core::scoring::rna::UA_HANDLE, core::scoring::rna::T_LOOP, core::scoring::rna::INTERCALATED_T_LOOP,   core::scoring::rna::LOOP_E_SUBMOTIF, core::scoring::rna::BULGED_G, core::scoring::rna::GNRA_TETRALOOP, core::scoring::rna::STRICT_WC_STACKED_PAIR,   core::scoring::rna::WC_STACKED_PAIR, core::scoring::rna::A_MINOR, core::scoring::rna::PLATFORM, core::scoring::rna::TL_RECEPTOR,   core::scoring::rna::TETRALOOP_TL_RECEPTOR, core::scoring::rna::Z_TURN, core::scoring::rna::TANDEM_GA_SHEARED, core::scoring::rna::TANDEM_GA_WATSON_CRICK,   core::scoring::rna::GA_MINOR, core::scoring::rna::DOUBLE_T_LOOP }

Functions
std::string	core::scoring::rna::to_string (RNA_MotifType type)
std::ostream &	core::scoring::rna::operator<< (std::ostream &out, RNA_Motif const &s)
bool	core::scoring::rna::operator< (RNA_Motif const &lhs, RNA_Motif const &rhs)
std::ostream &	core::scoring::rna::operator<< (std::ostream &out, RNA_Motifs const &s)
bool	core::scoring::rna::check_rna_loop (core::pose::Pose const &pose, core::Size const n, core::Size const nloop)
bool	core::scoring::rna::check_stack (Size const i, Size const j, core::pose::rna::RNA_BaseStackList const &base_stack_list)
void	core::scoring::rna::output_rna_motif (pose::Pose const &pose, RNA_Motif const &motif)
void	core::scoring::rna::output_rna_motifs_detailed (pose::Pose const &pose, RNA_Motifs const &motifs)
bool	core::scoring::rna::check_watson_crick_sequence (pose::Pose const &pose, Size const res1, Size const res2, bool const strict=false)
RNA_Motifs	core::scoring::rna::get_rna_motifs (pose::Pose const &pose, core::scoring::rna::RNA_LowResolutionPotential const &potential, core::pose::rna::RNA_FilteredBaseBaseInfo const &filtered_base_base_info)
	identify RNA motifs inside pose More...
Real	core::scoring::rna::get_rna_motif_score (pose::Pose const &pose, core::scoring::rna::RNA_LowResolutionPotential const &potential, core::pose::rna::RNA_FilteredBaseBaseInfo const &filtered_base_base_info)
	wrapper around get_rna_motifs – outputs score. More...
void	core::scoring::rna::output_rna_motifs (std::ostream &out, core::pose::Pose const &pose, RNA_Motifs const &rna_motifs, bool const output_WC_stacked_pair)
void	core::scoring::rna::output_motifs_to_pymol (std::ostream &out, core::pose::Pose const &pose, RNA_Motifs const &rna_motifs)
	sets up .pml file that will color motifs. More...

Variables
std::map< RNA_MotifType, core::Real > const	core::scoring::rna::rna_motif_bonus
std::map< RNA_MotifType, std::string > const	core::scoring::rna::motif_color

Detailed Description

find RNA motifs (u-turns, T-loops, etc.) in a pose

Author

Rhiju Das, rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu