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< Real >	get_full_torsions (Real const bin_size)
utility::vector1< Real >	get_epsilon_torsions (Real const delta, bool const extra_epsilon, Real const bin_size)
utility::vector1< Real >	get_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::Real >	get_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::Real >	get_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

typedef utility::pointer::owning_ptr< RNA_FittedTorsionInfo > core::chemical::rna::RNA_FittedTorsionInfoOP

typedef utility::pointer::access_ptr< RNA_ResidueType > core::chemical::rna::RNA_ResidueTypeAP

typedef utility::pointer::access_ptr< RNA_ResidueType const > core::chemical::rna::RNA_ResidueTypeCAP

typedef utility::pointer::owning_ptr< RNA_ResidueType const > core::chemical::rna::RNA_ResidueTypeCOP

typedef utility::pointer::owning_ptr< RNA_ResidueType > core::chemical::rna::RNA_ResidueTypeOP

Enumeration Type Documentation

enum core::chemical::rna::BaseEdge

Enumerator
ANY_BASE_EDGE
WATSON_CRICK
HOOGSTEEN
SUGAR
O2PRIME
PHOSPHATE

enum core::chemical::rna::ChiState

Enumerator
ANY_CHI
ANTI
SYN
NO_CHI

enum core::chemical::rna::PuckerState

Enumerator
ANY_PUCKER
NORTH
SOUTH
NO_PUCKER

enum core::chemical::rna::RNA_Torsion

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

)

References core::conformation::Residue::atom_name(), and chi1_torsion_atom_index().

Referenced by default_jump_atom(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), and core::pose::pdbslice().

Size core::chemical::rna::chi1_torsion_atom_index

(

conformation::Residue const &

rsd

)

References core::conformation::Residue::chi_atoms().

Referenced by chi1_torsion_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), and core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone().

Size core::chemical::rna::convert_acgu_to_1234

(

char const

c

)

Referenced by core::scoring::rna::RNA_LowResolutionPotential::get_rna_base_backbone_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_zeta_cutoff(), and core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs().

std::string const core::chemical::rna::default_jump_atom

(

conformation::Residue const &

rsd

)

References chi1_torsion_atom(), core::conformation::Residue::is_coarse(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name3(), and utility_exit_with_message.

std::string const core::chemical::rna::first_base_atom

(

conformation::Residue const &

rsd

)

References core::conformation::Residue::atom_name(), and first_base_atom_index().

Size core::chemical::rna::first_base_atom_index

(

conformation::Residue const &

rsd

)

References core::conformation::Residue::chi_atoms().

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), first_base_atom(), and core::pose::rna::initialize_atoms_for_which_we_need_new_dofs().

char core::chemical::rna::get_edge_from_num

(

Size const

num

)

References HOOGSTEEN, O2PRIME, PHOSPHATE, SUGAR, and WATSON_CRICK.

Referenced by core::pose::rna::classify_base_pairs(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score().

utility::vector1< Real > core::chemical::rna::get_epsilon_torsions	(	Real const	delta,
		bool const	extra_epsilon,
		Real const	bin_size
	)

References core::chemical::rna::RNA_FittedTorsionInfo::delta_cutoff(), numeric::principal_angle_degrees(), and torsion_info.

Referenced by core::pack::rotamer_set::build_three_prime_phosphate_rotamers().

utility::vector1< Real > core::chemical::rna::get_epsilon_torsions	(	bool const	north_pucker,
		bool const	extra_epsilon,
		Real	const
	)

References add_values_from_center(), core::conformation::membrane::center, and torsion_info.

std::string core::chemical::rna::get_full_edge_from_num

(

Size const

num

)

References HOOGSTEEN, O2PRIME, PHOSPHATE, SUGAR, utility_exit_with_message, and WATSON_CRICK.

Referenced by core::pose::rna::BasePair::print_info().

std::string core::chemical::rna::get_full_LW_orientation_from_num

(

Size const

num

)

References utility_exit_with_message.

Referenced by core::pose::rna::BasePair::print_info().

std::string core::chemical::rna::get_full_orientation_from_num

(

Size const

num

)

References utility_exit_with_message.

Referenced by core::pose::rna::BasePair::print_info().

utility::vector1< Real > core::chemical::rna::get_full_torsions

(

Real const

bin_size

)

References add_values_from_center().

Referenced by core::pack::rotamer_set::build_five_prime_phosphate_rotamers(), and core::pack::rotamer_set::build_three_prime_phosphate_rotamers().

char core::chemical::rna::get_orientation_from_num

(

Size const

num

)

Referenced by core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score().

numeric::xyzVector< core::Real > core::chemical::rna::get_rna_base_centroid	(	conformation::Residue const &	rsd,
		bool	verbose
	)

References core::chemical::rna::RNA_ResidueType::atom_is_virtual(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atomic_charge(), centroid, core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::is_RNA(), core::chemical::AtomType::name(), core::conformation::Residue::nheavyatoms(), core::chemical::rna::RNA_ResidueType::o2prime_index(), basic::options::option, basic::options::OptionKeys::rna::rna_prot_erraser, core::conformation::Residue::RNA_type(), core::conformation::Residue::type(), utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::RNA_CentroidInfo::get_base_centroid().

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
	)

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::chemical::aa_unp, chemical, numeric::xyzMatrix< class >::cols(), cross(), core::conformation::Residue::first_sidechain_atom(), numeric::xyzMatrix< class >::identity(), core::conformation::Residue::is_RNA(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, numeric::xyzVector< class >::normalize(), basic::options::option, basic::options::OptionKeys::rna::rna_prot_erraser, utility_exit_with_message, and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system().

void core::chemical::rna::get_watson_crick_base_pair_atoms	(	chemical::AA const &	aa1,
		chemical::AA const &	aa2,
		std::string &	atom1,
		std::string &	atom2
	)

References core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.

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
	)

References chemical, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.

std::string core::chemical::rna::get_WC_atom

(

core::chemical::AA const &

res_type

)

References core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.

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
	)

References core::chemical::rna::RNA_ResidueType::atom_is_phosphate(), core::chemical::rna::RNA_ResidueType::is_RNA_base_atom(), core::conformation::Residue::path_distance(), core::conformation::Residue::RNA_type(), core::conformation::Residue::seqpos(), and utility_exit_with_message.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_RNA_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_RNA_intra(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), and core::scoring::methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra().

bool core::chemical::rna::is_purine

(

conformation::Residue const &

rsd

)

References core::conformation::Residue::name1().

Size const core::chemical::rna::NUM_EDGES

(

3

)

Referenced by core::scoring::rna::RNA_RawBaseBaseInfo::copy_values(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy(), and core::scoring::rna::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy().

Size const core::chemical::rna::NUM_RNA_CHI_TORSIONS

(

NUM_RNA_TORSIONS-

NUM_RNA_MAINCHAIN_TORSIONS

)

Referenced by core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::init_from_lines(), and core::io::silent::RNA_SilentStruct::print_conformation().

Size const core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS

(

6

)

Referenced by core::pose::rna::apply_non_main_chain_sugar_coords(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::init_from_lines(), and core::io::silent::RNA_SilentStruct::print_conformation().

Size const core::chemical::rna::NUM_RNA_TORSIONS

(

10

)

Referenced by core::pose::rna::apply_non_main_chain_sugar_coords().

bool core::chemical::rna::possibly_canonical	(	chemical::AA const &	aa1,
		chemical::AA const &	aa2
	)

References core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.

bool core::chemical::rna::possibly_canonical_strict	(	chemical::AA const &	aa1,
		chemical::AA const &	aa2
	)

References core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.

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:

= utility::tools::make_vector1(
  " P  ", " OP2", " OP1", " O5'", " C4'", " O4'", " C3'", " O3'", " C1'",
  " C2'", " O2'", " H5'", "H5''", " H4'", " H3'", " H2'", "HO2'", " H1'" )

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'" )

Referenced by core::io::silent::RNA_SilentStruct::fill_struct(), core::pose::rna::fix_sugar_coords_WORKS_BUT_SLOW(), and core::pose::rna::prepare_scratch_residue().

basic::Tracer core::chemical::rna::TR("core.chemical.rna.RNA_ResidueType")

static

Referenced by core::pose::rna::apply_virtual_rna_residue_variant_type(), core::pose::rna::has_virtual_rna_residue_variant_type(), core::pose::rna::is_torsion_valid(), core::pose::rna::output_boolean(), and core::pose::rna::print_torsion_info().