RNA_BasePairClassifier.cc File Reference

#include <core/pose/rna/RNA_BasePairClassifier.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pose/rna/RNA_BaseDoubletClasses.hh>
#include <core/chemical/rna/util.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/scoring/rna/RNA_CentroidInfo.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <utility/pointer/owning_ptr.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/conversions.hh>
#include <vector>
#include <string>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>

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

Typedefs
using	core::pose::rna::Matrix = numeric::xyzMatrix< Real >

Functions
static basic::Tracer	TR ("core.pose.rna.RNA_BasePairClassifier")
void	core::pose::rna::update_edge_hbond_numbers (conformation::Residue const &rsd, Size const &atm, Size &N_W, Size &N_H, Size &N_S)
void	core::pose::rna::update_edge_hbond_numbers_careful_hydrogen (conformation::Residue const &rsd, Size const &atm, conformation::Residue const &other_rsd, Size const &other_atm, Size &N_W, Size &N_H, Size &N_S)
bool	core::pose::rna::atom_is_polar (core::conformation::Residue const &rsd, Size const atm)
bool	core::pose::rna::heavy_atom_is_polar (core::conformation::Residue const &rsd, Size const atm)
bool	core::pose::rna::atom_is_acceptor (core::conformation::Residue const &rsd, Size const atm)
void	core::pose::rna::figure_out_number_base_contacts (conformation::Residue const &rsd_i, conformation::Residue const &rsd_j, BaseEdge &edge_classification)
BaseDoubletOrientation	core::pose::rna::figure_out_base_pair_orientation (core::pose::Pose &pose, Size const &i, Size const &j)
bool	core::pose::rna::residue_is_bulge (pose::Pose const &pose, Size const i)
Size	core::pose::rna::bases_form_a_hydrogen_bond (core::scoring::hbonds::HBondSetOP const &hbond_set, core::pose::Pose &pose, Size const i, Size const j)
bool	core::pose::rna::bases_are_coplanar (core::pose::Pose &pose, Size const i, Size const j)
utility::vector1 < core::pose::rna::BasePair >	core::pose::rna::classify_base_pairs (core::pose::Pose const &pose_input)
void	core::pose::rna::classify_base_pairs (core::pose::Pose const &pose_input, utility::vector1< core::pose::rna::BasePair > &base_pair_list, utility::vector1< bool > &is_bulged)
Size	core::pose::rna::get_number_base_stacks (core::pose::Pose const &pose_input)
EnergyBaseStackList	core::pose::rna::get_scored_base_stack_list (core::pose::Pose const &pose_input)

Function Documentation

static basic::Tracer TR ( "core.pose.rna.RNA_BasePairClassifier"  )

static