RNA_BasePairClassifier.cc File Reference

#include <protocols/farna/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/scoring/rna/RNA_BaseDoubletClasses.hh>
#include <core/chemical/rna/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 <vector>
#include <string>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>

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

Typedefs
typedef numeric::xyzMatrix< Real >	protocols::farna::Matrix

Functions
void	protocols::farna::update_edge_hbond_numbers (conformation::Residue const &rsd, Size const &atm, Size &N_W, Size &N_H, Size &N_S)
void	protocols::farna::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	protocols::farna::atom_is_polar (core::conformation::Residue const &rsd, Size const &atm)
bool	protocols::farna::heavy_atom_is_polar (core::conformation::Residue const &rsd, Size const &atm)
bool	protocols::farna::atom_is_acceptor (core::conformation::Residue const &rsd, Size const &atm)
void	protocols::farna::figure_out_number_base_contacts (conformation::Residue const &rsd_i, conformation::Residue const &rsd_j, Size &edge_classification)
Size	protocols::farna::figure_out_base_pair_orientation (core::pose::Pose &pose, Size const &i, Size const &j)
bool	protocols::farna::residue_is_bulge (pose::Pose const &pose, Size const i)
Size	protocols::farna::bases_form_a_hydrogen_bond (core::scoring::hbonds::HBondSetOP const &hbond_set, core::pose::Pose &pose, Size const &i, Size const &j)
bool	protocols::farna::bases_are_coplanar (core::pose::Pose &pose, Size const &i, Size const &j)
void	protocols::farna::classify_base_pairs (core::pose::Pose const &pose_input, utility::vector1< core::scoring::rna::Base_pair > &base_pair_list, utility::vector1< bool > &is_bulged)
Size	protocols::farna::get_number_base_stacks (core::pose::Pose const &pose_input)

Variables
static basic::Tracer	TR ("protocols.rna.RNA_BasePairClassifier")

Variable Documentation

basic::Tracer TR("protocols.rna.RNA_BasePairClassifier")

static