core::chemical::rna Namespace Reference

Classes
class	GaussianParameter
class	RNA_FittedTorsionInfo
class	RNA_Info

Typedefs
typedef utility::pointer::shared_ptr< RNA_FittedTorsionInfo >	RNA_FittedTorsionInfoOP
typedef utility::pointer::weak_ptr< RNA_Info >	RNA_InfoAP
typedef utility::pointer::weak_ptr< RNA_Info const >	RNA_InfoCAP
typedef utility::pointer::shared_ptr< RNA_Info >	RNA_InfoOP
typedef utility::pointer::shared_ptr< RNA_Info const >	RNA_InfoCOP

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 }
enum	BaseDoubletOrientation { ANY_BASE_DOUBLET_ORIENTATION , ANTIPARALLEL , PARALLEL }
enum	LW_BaseDoubletOrientation { ANY_LW_BASE_DOUBLET_ORIENTATION , CIS , TRANS }
enum	BaseStackWhichSide { ANY_BASE_STACK_SIDE , ABOVE , BELOW }

Functions
static basic::Tracer	TR ("core.chemical.rna.RNA_Info")
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)
static basic::Tracer	TR ("core.chemical.rna")
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)
BaseEdge	get_edge_from_char (char const e)
char	get_orientation_from_num (Size const num)
std::string	get_full_orientation_from_num (Size const num)
char	get_side_from_num (Size const num)
std::string	get_full_side_from_num (Size const num)
BaseDoubletOrientation	get_orientation_from_char (char const o)
LW_BaseDoubletOrientation	get_LW_orientation_from_char (char const o)
std::string	get_full_LW_orientation_from_num (Size const num)
char	get_LW_orientation_from_num (Size const num)
std::string const	first_base_atom (chemical::ResidueType const &rsd)
Size	first_base_atom_index (chemical::ResidueType const &rsd)
std::string const	chi1_torsion_atom (chemical::ResidueType const &rsd)
Size	chi1_torsion_atom_index (chemical::ResidueType const &rsd)
std::string const	default_jump_atom (chemical::ResidueType 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::ResidueType const &rsd_type1, chemical::ResidueType const &rsd_type2, std::string &atom1, std::string &atom2)
void	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	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)
core::kinematics::Stub	get_rna_base_coordinate_system_stub (core::conformation::Residue const &rsd)
	wrapper around get_rna_base_centroid & get_rna_base_coordinate_system More...
bool	is_base_phosphate_atom_pair (conformation::Residue const &rsd_1, conformation::Residue const &rsd_2, Size const atomno_1, Size const atomno_2)
ChiState	get_residue_base_state (conformation::Residue const &rsd)
PuckerState	get_residue_pucker_state (conformation::Residue const &rsd)
bool	rna_dna_match (core::chemical::AA const &aa1, core::chemical::AA const &aa2)
std::string const	rna_nts ("acgu")
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
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
utility::vector1< std::string > const	sugar_atoms = utility::tools::make_vector1( " C1'", " C2'", " C3'", " C4'", " C5'", " O2'", " O3'", " O4'", " O5'" )

Typedef Documentation

RNA_FittedTorsionInfoOP

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

RNA_InfoAP

typedef utility::pointer::weak_ptr< RNA_Info > core::chemical::rna::RNA_InfoAP

RNA_InfoCAP

typedef utility::pointer::weak_ptr< RNA_Info const > core::chemical::rna::RNA_InfoCAP

RNA_InfoCOP

typedef utility::pointer::shared_ptr< RNA_Info const > core::chemical::rna::RNA_InfoCOP

RNA_InfoOP

typedef utility::pointer::shared_ptr< RNA_Info > core::chemical::rna::RNA_InfoOP

Enumeration Type Documentation

BaseDoubletOrientation

enum core::chemical::rna::BaseDoubletOrientation

Enumerator
ANY_BASE_DOUBLET_ORIENTATION
ANTIPARALLEL
PARALLEL

BaseEdge

enum core::chemical::rna::BaseEdge

Enumerator
ANY_BASE_EDGE
WATSON_CRICK
HOOGSTEEN
SUGAR
O2PRIME
PHOSPHATE

BaseStackWhichSide

enum core::chemical::rna::BaseStackWhichSide

Enumerator
ANY_BASE_STACK_SIDE
ABOVE
BELOW

ChiState

enum core::chemical::rna::ChiState

Enumerator
ANY_CHI
ANTI
SYN
NO_CHI

LW_BaseDoubletOrientation

enum core::chemical::rna::LW_BaseDoubletOrientation

Enumerator
ANY_LW_BASE_DOUBLET_ORIENTATION
CIS
TRANS

PuckerState

enum core::chemical::rna::PuckerState

Enumerator
ANY_PUCKER
NORTH
SOUTH
NO_PUCKER

RNA_Torsion

enum core::chemical::rna::RNA_Torsion

Enumerator
ANY_TORSION
ALPHA
BETA
GAMMA
DELTA
EPSILON
ZETA
CHI
NU2
NU1
O2H

Function Documentation

add_values_from_center()

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 core::conformation::membrane::center.

Referenced by get_epsilon_torsions(), get_full_torsions(), protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::init(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::init(), and protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard().

chi1_torsion_atom()

std::string const core::chemical::rna::chi1_torsion_atom

(

chemical::ResidueType const &

rsd

)

References core::chemical::ResidueType::atom_name(), and chi1_torsion_atom_index().

Referenced by core::import_pose::RNA_HelixAssembler::build_init_pose(), default_jump_atom(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), core::import_pose::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), core::pose::pdbslice(), and protocols::rna::movers::RNA_LoopCloser::rna_ccd_close().

chi1_torsion_atom_index()

Size core::chemical::rna::chi1_torsion_atom_index

(

chemical::ResidueType const &

rsd

)

References core::chemical::ResidueType::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().

convert_acgu_to_1234()

Size core::chemical::rna::convert_acgu_to_1234

(

char const

c

)

References rna_nts().

Referenced by core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), core::scoring::rna::get_bin(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_base_pair(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_pair(), and core::scoring::rna::RNP_LowResStackData::initialize_rnp_stack_xy().

default_jump_atom()

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

(

chemical::ResidueType const &

rsd

)

References core::chemical::ResidueType::atom_name(), chi1_torsion_atom(), core::chemical::ResidueType::is_aramid(), core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueType::is_coarse(), core::chemical::ResidueTypeBase::is_DNA(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_TNA(), core::chemical::ResidueTypeBase::name1(), and core::chemical::ResidueTypeBase::name3().

Referenced by core::import_pose::RNA_JumpMover::add_new_RNA_jump(), protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), core::pose::rna::fill_in_default_jump_atoms(), protocols::stepwise::monte_carlo::mover::filter_for_proximity(), core::import_pose::get_tree(), protocols::stepwise::modeler::merge_two_poses(), protocols::recces::pose_setup_from_file(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::prepare_fold_tree_for_erraser(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), core::import_pose::put_in_cutpoint(), core::import_pose::RNA_JumpMover::random_jump_change(), protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly(), and protocols::magnesium::update_mg_hoh_fold_tree().

first_base_atom()

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

(

chemical::ResidueType const &

rsd

)

References core::chemical::ResidueType::atom_name(), and first_base_atom_index().

Referenced by core::chemical::MutableResidueType::autodetermine_chi_bonds().

first_base_atom_index()

Size core::chemical::rna::first_base_atom_index

(

chemical::ResidueType const &

rsd

)

References core::chemical::ResidueType::chi_atoms().

Referenced by protocols::rna::movers::ErraserMinimizerMover::add_fixed_res_constraints(), core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_terminal_res_repulsion(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), core::energy_methods::RG_Energy_RNA::eval_atom_derivative(), first_base_atom(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), and core::pose::rna::initialize_atoms_for_which_we_need_new_dofs().

get_base_pair_atoms()

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
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_unk, core::chemical::aa_unp, core::chemical::ResidueTypeBase::base_analogue(), CIS, HOOGSTEEN, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, core::chemical::ResidueTypeBase::name3(), SUGAR, TR(), and WATSON_CRICK.

Referenced by core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), and core::pose::rna::setup_base_pair_constraints().

get_edge_from_char()

BaseEdge core::chemical::rna::get_edge_from_char

(

char const

e

)

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

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), core::import_pose::RNA_DeNovoParameters::get_pairings_from_line(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::refine_working_obligate_pairs(), and core::import_pose::libraries::RNA_JumpLibrary::save_in_jump_library().

get_edge_from_num()

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(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::get_number_native_base_pairs(), core::pose::rna::output_base_pairs(), and core::import_pose::libraries::BasePairType::tag().

get_epsilon_torsions() [1/2]

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.

get_epsilon_torsions() [2/2]

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(), and torsion_info.

Referenced by core::pack::rotamer_set::build_three_prime_phosphate_rotamers(), protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard(), and protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate().

get_full_edge_from_num()

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

(

Size const

num

)

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

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

get_full_LW_orientation_from_num()

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

(

Size const

num

)

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

get_full_orientation_from_num()

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

(

Size const

num

)

References ANTIPARALLEL, ANY_BASE_DOUBLET_ORIENTATION, and PARALLEL.

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

get_full_side_from_num()

std::string core::chemical::rna::get_full_side_from_num

(

Size const

num

)

for stacking

References ABOVE, ANY_BASE_STACK_SIDE, and BELOW.

get_full_torsions()

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(), core::pack::rotamer_set::build_three_prime_phosphate_rotamers(), protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler::init(), protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::init_standard(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_five_prime_phosphate(), and protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate().

get_LW_orientation_from_char()

LW_BaseDoubletOrientation core::chemical::rna::get_LW_orientation_from_char

(

char const

o

)

References ANY_LW_BASE_DOUBLET_ORIENTATION, CIS, and TRANS.

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), core::import_pose::RNA_DeNovoParameters::get_pairings_from_line(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::refine_working_obligate_pairs().

get_LW_orientation_from_num()

char core::chemical::rna::get_LW_orientation_from_num

(

Size const

num

)

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

get_orientation_from_char()

BaseDoubletOrientation core::chemical::rna::get_orientation_from_char

(

char const

o

)

References ANTIPARALLEL, ANY_BASE_DOUBLET_ORIENTATION, and PARALLEL.

Referenced by core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), core::import_pose::RNA_DeNovoParameters::get_pairings_from_line(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::refine_working_obligate_pairs(), and core::import_pose::libraries::RNA_JumpLibrary::save_in_jump_library().

get_orientation_from_num()

char core::chemical::rna::get_orientation_from_num

(

Size const

num

)

Referenced by core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), core::pose::rna::output_base_stacks(), and core::import_pose::libraries::BasePairType::tag().

get_residue_base_state()

ChiState core::chemical::rna::get_residue_base_state

(

conformation::Residue const &

rsd

)

References ANTI, CHI, core::conformation::Residue::chi(), NUM_RNA_MAINCHAIN_TORSIONS(), and SYN.

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

get_residue_pucker_state()

PuckerState core::chemical::rna::get_residue_pucker_state

(

conformation::Residue const &

rsd

)

References DELTA, core::chemical::rna::RNA_FittedTorsionInfo::delta_cutoff(), core::conformation::Residue::mainchain_torsion(), NORTH, and SOUTH.

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

get_rna_base_centroid()

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

References core::chemical::rna::RNA_Info::atom_is_virtual(), core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atomic_charge(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_NA(), core::conformation::Residue::is_polymer(), core::chemical::AtomType::is_repulsive(), core::conformation::Residue::is_RNA(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name(), core::chemical::AtomType::name(), core::conformation::Residue::nheavyatoms(), core::chemical::rna::RNA_Info::o2prime_index(), core::conformation::Residue::RNA_info(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::toolbox::sample_around::centroid_dist(), protocols::stepwise::screener::CentroidDistanceScreener::check_screen(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::scoring::rna::RNA_CentroidInfo::get_base_centroid(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz(), get_rna_base_coordinate_system_stub(), core::scoring::rna::get_rna_motifs(), core::energy_methods::RNP_LowResStackEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), protocols::toolbox::rigid_body::set_to_origin(), core::energy_methods::RNP_LowResEnergy::setup_for_scoring(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker(), and protocols::recces::sampler::rna::MC_RNA_OneJump::update().

get_rna_base_coordinate_system() [1/2]

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, core::chemical::ResidueTypeBase::base_analogue(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::is_carbohydrate(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_NA(), core::conformation::Residue::is_polymer(), core::chemical::na_ade, core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_lra, core::chemical::na_lrc, core::chemical::na_lrg, core::chemical::na_lur, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_thy, core::chemical::na_ura, core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name3(), core::id::to_string(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(), get_rna_base_coordinate_system_stub(), core::energy_methods::RNP_LowResStackEnergy::residue_pair_energy(), core::energy_methods::RNP_LowResEnergy::residue_pair_energy(), protocols::toolbox::rigid_body::set_to_origin(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker().

get_rna_base_coordinate_system() [2/2]

numeric::xyzMatrix< core::Real > core::chemical::rna::get_rna_base_coordinate_system	(	core::conformation::Residue const &	rsd,
		numeric::xyzVector< core::Real > const &	centroid
	)

get_rna_base_coordinate_system_stub()

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

References get_rna_base_centroid(), and get_rna_base_coordinate_system().

Referenced by core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), core::pose::rna::get_stub_stub(), and protocols::toolbox::sample_around::rotate_into_nucleobase_frame().

get_side_from_num()

char core::chemical::rna::get_side_from_num

(

Size const

num

)

References ABOVE, ANY_BASE_STACK_SIDE, and BELOW.

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

get_watson_crick_base_pair_atoms()

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
	)

References core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.

Referenced by protocols::rna::denovo::figure_out_base_pair_partner(), core::pose::rna::get_base_pairing_info(), and core::pose::rna::get_base_pairing_list().

get_WC_atom()

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.

is_base_phosphate_atom_pair()

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_Info::atom_is_phosphate(), core::conformation::Residue::is_RNA(), core::chemical::rna::RNA_Info::is_RNA_base_atom(), core::conformation::Residue::path_distance(), core::conformation::Residue::RNA_info(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra(), core::energy_methods::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_energy_RNA_intra(), and core::energy_methods::RNA_FullAtomVDW_BasePhosphate::residue_energy().

NUM_EDGES()

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

(

3

)

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

NUM_RNA_CHI_TORSIONS()

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

(

NUM_RNA_TORSIONS -

NUM_RNA_MAINCHAIN_TORSIONS

)

Referenced by protocols::rna::denovo::create_rna_vall_torsions(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::init_from_lines(), and core::io::silent::RNA_SilentStruct::print_conformation().

NUM_RNA_MAINCHAIN_TORSIONS()

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

(

6

)

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), core::pose::rna::apply_non_main_chain_sugar_coords(), protocols::rna::denovo::create_rna_vall_torsions(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::io::silent::RNA_SilentStruct::fill_pose(), get_residue_base_state(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::fragment::rna::FullAtomRNA_Fragments::insert_fragment(), core::io::silent::RNA_SilentStruct::print_conformation(), and protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap().

NUM_RNA_TORSIONS()

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

(

10

)

Referenced by core::fragment::rna::FragmentLibrary::add_torsion(), core::pose::rna::apply_non_main_chain_sugar_coords(), core::fragment::rna::FullAtomRNA_Fragments::insert_fragment(), core::fragment::rna::FullAtomRNA_Fragments::read_vall_torsions(), and core::fragment::rna::TorsionSet::TorsionSet().

possibly_canonical()

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.

Referenced by protocols::rna::denovo::check_base_pair(), protocols::rna::denovo::figure_out_base_pair_partner(), core::pose::rna::get_base_pairing_info(), core::pose::rna::get_base_pairing_list(), core::pose::rna::get_number_base_pairs(), core::pose::rna::get_number_native_base_pairs(), core::import_pose::RNA_BasePairHandler::get_stem_residues(), and protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct().

possibly_canonical_strict()

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.

Referenced by protocols::rna::denovo::figure_out_base_pair_partner().

rna_dna_match()

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

References core::chemical::na_ade, core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_thy, and core::chemical::na_ura.

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::add_to_atom_id_map_after_checks().

rna_nts()

std::string const core::chemical::rna::rna_nts

(

"acgu"

)

Referenced by convert_acgu_to_1234(), core::import_pose::libraries::BasePairStepLibrary::initialize(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library(), and core::import_pose::libraries::remove_terminus_variant_types_for_rna().

TR() [1/2]

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

static

TR() [2/2]

static basic::Tracer core::chemical::rna::TR ( "core.chemical.rna.RNA_Info"  )

static

Referenced by protocols::stepwise::modeler::rna::align_poses(), protocols::stepwise::modeler::rna::rigid_body::analyze_base_bin_map(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::stepwise::modeler::rna::apply_protonated_H1_adenosine_variant_type(), core::pose::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::rna::atom_square_deviation(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::stepwise::modeler::rna::check_for_messed_up_structure(), protocols::stepwise::modeler::rna::choose_random_if_unspecified_nucleotide(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::cluster(), core::scoring::rna::RNP_LowResPairDistPotential::convert_aa_to_index(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_silent_file_and_tag_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_tags_map(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_tag(), core::pose::rna::detect_base_contacts(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::do_some_clustering(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), core::pose::rna::figure_out_secstruct(), protocols::stepwise::modeler::rna::freeze_sugar_torsions(), get_base_pair_atoms(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), core::pose::rna::get_rigid_body_jumps(), protocols::stepwise::modeler::rna::get_surrounding_O2prime_hydrogen(), core::pose::rna::has_virtual_rna_residue_variant_type(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initial_pose_setup(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_max_memory_pose_num(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_quick_alignment_pose(), core::scoring::rna::RNP_LowResPairDistPotential::initialize_rnp_pair_dist(), core::scoring::rna::RNP_LowResStackData::initialize_rnp_stack_xy(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_sequence_information(), protocols::stepwise::modeler::rna::rigid_body::initialize_xyz_parameters(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_initialization_pdb_numbering_setup(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_pdb_numbering_setup(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_silent_numbering_setup(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_old_individual_suite_cluster(), protocols::stepwise::modeler::rna::is_residues_in_contact(), core::pose::rna::is_rna_chainbreak(), core::pose::rna::is_tna_chainbreak(), core::pose::rna::is_torsion_valid(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::stepwise::modeler::rna::o2prime_trials(), core::pose::rna::output_boolean(), protocols::stepwise::modeler::rna::output_rotamer(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::pass_FARFAR_no_auto_bulge_filter(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_rmsd(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_heavy_atoms(), protocols::stepwise::modeler::rna::print_individual_atom_info(), core::pose::rna::print_torsion_info(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::stepwise::modeler::rna::rescale_scorefxn(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::setup(), core::pose::rna::setup_base_pair_constraints(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_final_res_lists(), protocols::stepwise::modeler::rna::show_scorefxn_weight_lines(), protocols::stepwise::modeler::rna::suite_rmsd(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::two_stage_clustering(), and core::pose::rna::virtualize_free_rna_moieties().

Variable Documentation

atoms_involved_in_phosphate_torsion

utility::vector1< std::string > const core::chemical::rna::atoms_involved_in_phosphate_torsion = utility::tools::make_vector1( " P ", " OP2", " OP1", " O5'", " H5'", "H5''" )

Referenced by core::import_pose::involved_in_phosphate_torsion(), protocols::rna::denovo::involved_in_phosphate_torsion(), and core::pose::toolbox::AtomLevelDomainMap::set_phosphate_domain().

non_base_atoms

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().

non_main_chain_sugar_atoms

utility::vector1< std::string > const core::chemical::rna::non_main_chain_sugar_atoms = utility::tools::make_vector1( " C2'", " C1'", " O4'" )

Referenced by protocols::rna::denovo::create_rna_vall_torsions(), core::io::silent::RNA_SilentStruct::fill_struct(), core::fragment::rna::FullAtomRNA_Fragments::insert_fragment(), and core::pose::rna::prepare_scratch_residue().

sugar_atoms

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

Referenced by core::pose::toolbox::AtomLevelDomainMap::set_sugar_domain(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map().