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util.hh File Reference
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/kinematics/Stub.fwd.hh>
#include <numeric/xyzMatrix.fwd.hh>
#include <numeric/xyzVector.fwd.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector1.hh>

Namespaces

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

Enumerations

enum  core::chemical::rna::BaseEdge {
  core::chemical::rna::ANY_BASE_EDGE, core::chemical::rna::WATSON_CRICK, core::chemical::rna::HOOGSTEEN, core::chemical::rna::SUGAR,
  core::chemical::rna::O2PRIME, core::chemical::rna::PHOSPHATE
}
 
enum  core::chemical::rna::RNA_Torsion {
  core::chemical::rna::ANY_TORSION, core::chemical::rna::ALPHA, core::chemical::rna::BETA, core::chemical::rna::GAMMA,
  core::chemical::rna::DELTA, core::chemical::rna::EPSILON, core::chemical::rna::ZETA, core::chemical::rna::CHI,
  core::chemical::rna::NU2, core::chemical::rna::NU1, core::chemical::rna::O2H
}
 
enum  core::chemical::rna::ChiState { core::chemical::rna::ANY_CHI, core::chemical::rna::ANTI, core::chemical::rna::SYN, core::chemical::rna::NO_CHI }
 
enum  core::chemical::rna::PuckerState { core::chemical::rna::ANY_PUCKER, core::chemical::rna::NORTH, core::chemical::rna::SOUTH, core::chemical::rna::NO_PUCKER }
 
enum  core::chemical::rna::BaseDoubletOrientation { core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION, core::chemical::rna::ANTIPARALLEL, core::chemical::rna::PARALLEL }
 
enum  core::chemical::rna::LW_BaseDoubletOrientation { core::chemical::rna::ANY_LW_BASE_DOUBLET_ORIENTATION, core::chemical::rna::CIS, core::chemical::rna::TRANS }
 
enum  core::chemical::rna::BaseStackWhichSide { core::chemical::rna::ANY_BASE_STACK_SIDE, core::chemical::rna::ABOVE, core::chemical::rna::BELOW }
 

Functions

std::string const core::chemical::rna::rna_nts ("acgu")
 
Size const core::chemical::rna::NUM_EDGES (3)
 
Size const core::chemical::rna::NUM_RNA_TORSIONS (10)
 
Size const core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS (6)
 
Size const core::chemical::rna::NUM_RNA_CHI_TORSIONS (NUM_RNA_TORSIONS-NUM_RNA_MAINCHAIN_TORSIONS)
 
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)
 
std::string core::chemical::rna::get_full_LW_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)
 
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 (core::conformation::Residue const &rsd, numeric::xyzVector< core::Real > 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)
 

Variables

utility::vector1< std::string >
const 
core::chemical::rna::non_main_chain_sugar_atoms = utility::tools::make_vector1( " C2'", " C1'", " O4'" )
 
utility::vector1< std::string >
const 
core::chemical::rna::atoms_involved_in_phosphate_torsion = utility::tools::make_vector1( " P ", " OP2", " OP1", " O5'", " H5'", "H5''" )
 
utility::vector1< std::string >
const 
core::chemical::rna::non_base_atoms
 
utility::vector1< std::string >
const 
core::chemical::rna::sugar_atoms = utility::tools::make_vector1( " C1'", " C2'", " C3'", " C4'", " C5'", " O2'", " O3'", " O4'", " O5'" )
 

Detailed Description

Author
Rhiju