Rosetta Core  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
core::chemical::rna Namespace Reference

Classes

class  GaussianParameter
 
class  RNA_FittedTorsionInfo
 
class  RNA_ResidueType
 

Typedefs

typedef
utility::pointer::owning_ptr
< RNA_FittedTorsionInfo
RNA_FittedTorsionInfoOP
 
typedef
utility::pointer::access_ptr
< RNA_ResidueType
RNA_ResidueTypeAP
 
typedef
utility::pointer::access_ptr
< RNA_ResidueType const > 
RNA_ResidueTypeCAP
 
typedef
utility::pointer::owning_ptr
< RNA_ResidueType
RNA_ResidueTypeOP
 
typedef
utility::pointer::owning_ptr
< RNA_ResidueType const > 
RNA_ResidueTypeCOP
 

Enumerations

enum  BaseEdge {
  ANY_BASE_EDGE, WATSON_CRICK, HOOGSTEEN, SUGAR,
  O2PRIME, PHOSPHATE
}
 
enum  RNA_Torsion {
  ANY_TORSION, ALPHA, BETA, GAMMA,
  DELTA, EPSILON, ZETA, CHI,
  NU2, NU1, O2H
}
 
enum  ChiState { ANY_CHI, ANTI, SYN, NO_CHI }
 
enum  PuckerState { ANY_PUCKER, NORTH, SOUTH, NO_PUCKER }
 

Functions

void add_values_from_center (utility::vector1< core::Real > &torsions, Real const center, Real const max_range, Real const bin_size)
 
utility::vector1< Realget_full_torsions (Real const bin_size)
 
utility::vector1< Realget_epsilon_torsions (Real const delta, bool const extra_epsilon, Real const bin_size)
 
utility::vector1< Realget_epsilon_torsions (bool const north_pucker, bool const extra_epsilon, Real const )
 
Size convert_acgu_to_1234 (char const c)
 
char get_edge_from_num (Size const num)
 
std::string get_full_edge_from_num (Size const num)
 
char get_orientation_from_num (Size const num)
 
std::string get_full_orientation_from_num (Size const num)
 
std::string get_full_LW_orientation_from_num (Size const num)
 
std::string const first_base_atom (conformation::Residue const &rsd)
 
bool is_purine (conformation::Residue const &rsd)
 
Size first_base_atom_index (conformation::Residue const &rsd)
 
std::string const chi1_torsion_atom (conformation::Residue const &rsd)
 
Size chi1_torsion_atom_index (conformation::Residue const &rsd)
 
std::string const default_jump_atom (conformation::Residue const &rsd)
 
bool possibly_canonical (chemical::AA const &aa1, chemical::AA const &aa2)
 
bool possibly_canonical_strict (chemical::AA const &aa1, chemical::AA const &aa2)
 
std::string get_WC_atom (core::chemical::AA const &res_type)
 
void get_watson_crick_base_pair_atoms (chemical::AA const &aa1, chemical::AA const &aa2, std::string &atom1, std::string &atom2)
 
void get_watson_crick_base_pair_atoms (chemical::AA const &aa1, chemical::AA const &aa2, utility::vector1< std::string > &atom_ids1, utility::vector1< std::string > &atom_ids2)
 
Vector get_rna_base_centroid (conformation::Residue const &rsd, bool verbose)
 
numeric::xyzMatrix< core::Realget_rna_base_coordinate_system (conformation::Residue const &rsd, Vector const &centroid)
 
bool Is_base_phosphate_atom_pair (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const atomno_1, Size const atomno_2)
 
Size const NUM_EDGES (3)
 
Size const NUM_RNA_TORSIONS (10)
 
Size const NUM_RNA_MAINCHAIN_TORSIONS (6)
 
Size const NUM_RNA_CHI_TORSIONS (NUM_RNA_TORSIONS-NUM_RNA_MAINCHAIN_TORSIONS)
 
numeric::xyzMatrix< core::Realget_rna_base_coordinate_system (core::conformation::Residue const &rsd, numeric::xyzVector< core::Real > const &centroid)
 

Variables

static basic::Tracer TR ("core.chemical.rna.RNA_ResidueType")
 
utility::vector1< std::string >
const 
non_main_chain_sugar_atoms = utility::tools::make_vector1( " C2'", " C1'", " O4'" )
 
utility::vector1< std::string >
const 
atoms_involved_in_phosphate_torsion = utility::tools::make_vector1( " P ", " OP2", " OP1", " O5'", " H5'", "H5''" )
 
utility::vector1< std::string >
const 
non_base_atoms
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
ANY_BASE_EDGE 
WATSON_CRICK 
HOOGSTEEN 
SUGAR 
O2PRIME 
PHOSPHATE 
Enumerator
ANY_CHI 
ANTI 
SYN 
NO_CHI 
Enumerator
ANY_PUCKER 
NORTH 
SOUTH 
NO_PUCKER 
Enumerator
ANY_TORSION 
ALPHA 
BETA 
GAMMA 
DELTA 
EPSILON 
ZETA 
CHI 
NU2 
NU1 
O2H 

Function Documentation

void core::chemical::rna::add_values_from_center ( utility::vector1< core::Real > &  torsions,
Real const  center,
Real const  max_range,
Real const  bin_size 
)

References epsilon.

Referenced by get_epsilon_torsions(), and get_full_torsions().

std::string const core::chemical::rna::chi1_torsion_atom ( conformation::Residue const &  rsd)
Size core::chemical::rna::chi1_torsion_atom_index ( conformation::Residue const &  rsd)
Size core::chemical::rna::convert_acgu_to_1234 ( char const  c)
std::string const core::chemical::rna::default_jump_atom ( conformation::Residue const &  rsd)
std::string const core::chemical::rna::first_base_atom ( conformation::Residue const &  rsd)
Size core::chemical::rna::first_base_atom_index ( conformation::Residue const &  rsd)
char core::chemical::rna::get_edge_from_num ( Size const  num)
utility::vector1< Real > core::chemical::rna::get_epsilon_torsions ( Real const  delta,
bool const  extra_epsilon,
Real const  bin_size 
)
utility::vector1< Real > core::chemical::rna::get_epsilon_torsions ( bool const  north_pucker,
bool const  extra_epsilon,
Real  const 
)
std::string core::chemical::rna::get_full_edge_from_num ( Size const  num)
std::string core::chemical::rna::get_full_LW_orientation_from_num ( Size const  num)
std::string core::chemical::rna::get_full_orientation_from_num ( Size const  num)
utility::vector1< Real > core::chemical::rna::get_full_torsions ( Real const  bin_size)
char core::chemical::rna::get_orientation_from_num ( Size const  num)
numeric::xyzVector< core::Real > core::chemical::rna::get_rna_base_centroid ( conformation::Residue const &  rsd,
bool  verbose 
)
numeric::xyzMatrix< core::Real > core::chemical::rna::get_rna_base_coordinate_system ( core::conformation::Residue const &  rsd,
numeric::xyzVector< core::Real > const &  centroid 
)
numeric::xyzMatrix< core::Real > core::chemical::rna::get_rna_base_coordinate_system ( conformation::Residue const &  rsd,
Vector const &  centroid 
)
void core::chemical::rna::get_watson_crick_base_pair_atoms ( chemical::AA const &  aa1,
chemical::AA const &  aa2,
std::string &  atom1,
std::string &  atom2 
)
void core::chemical::rna::get_watson_crick_base_pair_atoms ( chemical::AA const &  aa1,
chemical::AA const &  aa2,
utility::vector1< std::string > &  atom_ids1,
utility::vector1< std::string > &  atom_ids2 
)
std::string core::chemical::rna::get_WC_atom ( core::chemical::AA const &  res_type)
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 
)
bool core::chemical::rna::is_purine ( conformation::Residue const &  rsd)
Size const core::chemical::rna::NUM_EDGES ( )
Size const core::chemical::rna::NUM_RNA_CHI_TORSIONS ( NUM_RNA_TORSIONS-  NUM_RNA_MAINCHAIN_TORSIONS)
Size const core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS ( )
Size const core::chemical::rna::NUM_RNA_TORSIONS ( 10  )
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 
)

Variable Documentation

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
Initial value:
" P ", " OP2", " OP1", " O5'", " C4'", " O4'", " C3'", " O3'", " C1'",
" C2'", " O2'", " H5'", "H5''", " H4'", " H3'", " H2'", "HO2'", " H1'" )
utility::vector1< T > make_vector1(const T i0)

Referenced by core::pose::rna::RNA_IdealCoord::apply_coords().

utility::vector1< std::string > const core::chemical::rna::non_main_chain_sugar_atoms = utility::tools::make_vector1( " C2'", " C1'", " O4'" )
basic::Tracer core::chemical::rna::TR("core.chemical.rna.RNA_ResidueType")
static