Rosetta  2021.07
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Namespaces | Functions
util.cc File Reference
#include <core/chemical/rna/util.hh>
#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>
#include <core/types.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/rna/RNA_Info.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AA.hh>
#include <core/kinematics/Stub.hh>
#include <numeric/constants.hh>
#include <numeric/angle.functions.hh>
#include <utility/vector1.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <ObjexxFCL/string.functions.hh>

Namespaces

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

Functions

static basic::Tracer core::chemical::rna::TR ("core.chemical.rna")
 
Size core::chemical::rna::convert_acgu_to_1234 (char const c)
 
char core::chemical::rna::get_edge_from_num (Size const num)
 
std::string core::chemical::rna::get_full_edge_from_num (Size const num)
 
BaseEdge core::chemical::rna::get_edge_from_char (char const e)
 
char core::chemical::rna::get_orientation_from_num (Size const num)
 
std::string core::chemical::rna::get_full_orientation_from_num (Size const num)
 
char core::chemical::rna::get_side_from_num (Size const num)
 
std::string core::chemical::rna::get_full_side_from_num (Size const num)
 
BaseDoubletOrientation core::chemical::rna::get_orientation_from_char (char const o)
 
LW_BaseDoubletOrientation core::chemical::rna::get_LW_orientation_from_char (char const o)
 
std::string core::chemical::rna::get_full_LW_orientation_from_num (Size const num)
 
char core::chemical::rna::get_LW_orientation_from_num (Size const num)
 
std::string const core::chemical::rna::first_base_atom (chemical::ResidueType const &rsd)
 
Size core::chemical::rna::first_base_atom_index (chemical::ResidueType const &rsd)
 
std::string const core::chemical::rna::chi1_torsion_atom (chemical::ResidueType const &rsd)
 
Size core::chemical::rna::chi1_torsion_atom_index (chemical::ResidueType const &rsd)
 
std::string const core::chemical::rna::default_jump_atom (chemical::ResidueType const &rsd)
 
bool core::chemical::rna::possibly_canonical (chemical::AA const &aa1, chemical::AA const &aa2)
 
bool core::chemical::rna::possibly_canonical_strict (chemical::AA const &aa1, chemical::AA const &aa2)
 
std::string core::chemical::rna::get_WC_atom (core::chemical::AA const &res_type)
 
void core::chemical::rna::get_watson_crick_base_pair_atoms (chemical::ResidueType const &rsd_type1, chemical::ResidueType const &rsd_type2, std::string &atom1, std::string &atom2)
 
void core::chemical::rna::get_base_pair_atoms (chemical::ResidueType const &rsd_type1, chemical::ResidueType const &rsd_type2, utility::vector1< std::string > &atom_ids1, utility::vector1< std::string > &atom_ids2, chemical::rna::BaseEdge const edge1, chemical::rna::BaseEdge const edge2, chemical::rna::LW_BaseDoubletOrientation const orientation)
 
Vector core::chemical::rna::get_rna_base_centroid (conformation::Residue const &rsd, bool verbose)
 
numeric::xyzMatrix< core::Realcore::chemical::rna::get_rna_base_coordinate_system (conformation::Residue const &rsd, Vector const &centroid)
 
core::kinematics::Stub core::chemical::rna::get_rna_base_coordinate_system_stub (core::conformation::Residue const &rsd)
 wrapper around get_rna_base_centroid & get_rna_base_coordinate_system More...
 
bool core::chemical::rna::is_base_phosphate_atom_pair (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const atomno_1, Size const atomno_2)
 
ChiState core::chemical::rna::get_residue_base_state (conformation::Residue const &rsd)
 
PuckerState core::chemical::rna::get_residue_pucker_state (conformation::Residue const &rsd)
 
bool core::chemical::rna::rna_dna_match (core::chemical::AA const &aa1, core::chemical::AA const &aa2)