Namespaces
	chemical_shift

Classes
class	Gaussian_parameter

class	RG_Energy_RNA

class	RG_Energy_RNACreator

class	RNA_AtomVDW

class	RNA_BaseBaseEnergy

class	Base_pair

class	Base_stack

class	RNA_BulgeEnergy

class	RNA_BulgeEnergyCreator

class	RNA_CentroidInfo
	Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...

class	RNA_DataBackboneEnergy

class	RNA_DataBackboneEnergyCreator

class	RNA_Datum

class	RNA_DataInfo
	Keep track of RNA centroid information inside the pose. More...

class	RNA_FA_Stack

class	RNA_FilteredBaseBaseInfo
	Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...

class	RNA_FittedTorsionInfo

class	RNA_FullAtomStackingEnergy

class	RNA_FullAtomStackingEnergyCreator

class	RNA_FullAtomVDW_BasePhosphate

class	RNA_FullAtomVDW_BasePhosphateCreator

class	RNA_LJ_BaseEnergy

class	RNA_LJ_BaseEnergyCreator

class	RNA_LowResolutionPotential

class	RNA_Mg_Energy

class	RNA_Mg_EnergyCreator

class	RNA_Mg_KnowledgeBasedPotential

class	RNA_PairwiseLowResolutionEnergy

class	RNA_PairwiseLowResolutionEnergyCreator

class	RNA_RawBaseBaseInfo
	Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! / Also, should probably use EnergyGraph instead of FArrays – much smaller memory footprint (!) /. More...

class	RNA_ScoringInfo
	Keep track of RNA centroid, useful atom, base-base info inside the pose. More...

class	RNA_SugarCloseEnergy

class	RNA_SugarCloseEnergyCreator

class	RNA_TorsionEnergy

class	RNA_TorsionEnergyCreator

class	RNA_TorsionPotential

class	RNA_VDW_Energy

class	RNA_VDW_EnergyCreator

Typedefs
typedef utility::pointer::owning_ptr < RNA_AtomVDW >	RNA_AtomVDWOP

typedef utility::pointer::owning_ptr < RNA_AtomVDW const >	RNA_AtomVDWCOP

typedef std::pair< Real, Base_pair >	Energy_base_pair

typedef std::list < Energy_base_pair >	Energy_base_pair_list

typedef std::pair< Real, Base_stack >	Energy_base_stack

typedef std::list < Energy_base_stack >	Energy_base_stack_list

typedef numeric::xyzMatrix< Real >	Matrix

typedef utility::pointer::owning_ptr < RNA_CentroidInfo >	RNA_CentroidInfoOP

typedef numeric::xyzVector < core::Real >	Vector

typedef utility::pointer::owning_ptr < RNA_DataInfo >	RNA_DataInfoOP

typedef utility::pointer::access_ptr < RNA_DataInfo >	RNA_DataInfoAP

typedef utility::vector1 < RNA_Datum >	RNA_Data

typedef utility::pointer::owning_ptr < RNA_FilteredBaseBaseInfo >	RNA_FilteredBaseBaseInfoOP

typedef utility::vector1 < Gaussian_parameter >	Gaussian_parameter_set

typedef utility::pointer::owning_ptr < RNA_FullAtomVDW_BasePhosphate >	RNA_FullAtomVDW_BasePhosphateOP

typedef utility::pointer::owning_ptr < RNA_FullAtomVDW_BasePhosphate const >	RNA_FullAtomVDW_BasePhosphateCOP

typedef utility::pointer::owning_ptr < RNA_LowResolutionPotential >	RNA_LowResolutionPotentialOP

typedef utility::pointer::owning_ptr < RNA_Mg_KnowledgeBasedPotential >	RNA_Mg_KnowledgeBasedPotentialOP

typedef utility::pointer::owning_ptr < RNA_Mg_KnowledgeBasedPotential const >	RNA_Mg_KnowledgeBasedPotentialCOP

typedef utility::pointer::owning_ptr < RNA_RawBaseBaseInfo >	RNA_RawBaseBaseInfoOP

typedef utility::pointer::access_ptr < RNA_RawBaseBaseInfo >	RNA_RawBaseBaseInfoAP

typedef utility::pointer::owning_ptr < RNA_ScoringInfo >	RNA_ScoringInfoOP

typedef utility::pointer::owning_ptr < RNA_SugarCloseEnergy >	RNA_SugarCloseEnergyOP

typedef utility::pointer::owning_ptr < RNA_SugarCloseEnergy const >	RNA_SugarCloseEnergyCOP

typedef utility::pointer::owning_ptr < RNA_TorsionEnergy >	RNA_TorsionEnergyOP

typedef utility::pointer::owning_ptr < RNA_TorsionEnergy const >	RNA_TorsionEnergyCOP

typedef utility::pointer::owning_ptr < RNA_TorsionPotential >	RNA_TorsionPotentialOP

typedef utility::pointer::owning_ptr < RNA_TorsionPotential const >	RNA_TorsionPotentialCOP

Enumerations
enum	_RNA_FittedTorsionInfo_ { WHATEVER, ALPHA, BETA, GAMMA, DELTA, EPSILON, ZETA, CHI, NU2, NU1, O2H }

enum	__RNA_UTIL__ { X, WATSON_CRICK, HOOGSTEEN, SUGAR, O2STAR, PHOSPHATE }

Functions
Size	rna_residue_name_to_num (char const c)

Size	get_position_in_vector (utility::vector1< std::string > &vec, std::string const element)

RNA_ScoringInfo const &	rna_scoring_info_from_pose (pose::Pose const &pose)

RNA_ScoringInfo &	nonconst_rna_scoring_info_from_pose (pose::Pose &pose)

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)

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)

bool	is_cutpoint_open (core::pose::Pose const &pose, Size const i)

bool	is_rna_chainbreak (core::pose::Pose const &pose, Size const i)

void	initialize_non_main_chain_sugar_atoms ()

void	fix_sugar_coords_WORKS_BUT_SLOW (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< utility::vector1< id::DOF_Type > > which_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::Size const &i)

void	prepare_scratch_residue (core::conformation::ResidueOP &scratch_rsd, core::conformation::Residue const &start_rsd, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose const &pose)

void	fix_sugar_coords (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::pose::Pose const &reference_pose, core::Size const &i)

void	initialize_atoms_for_which_we_need_new_dofs (utility::vector1< std::string > &atoms_for_which_we_need_new_dofs, pose::Pose const &pose, Size const &i)

void	apply_non_main_chain_sugar_coords (utility::vector1< Vector > const &non_main_chain_sugar_coords, core::pose::Pose &pose, core::pose::Pose const &reference_pose, core::Size const &i)

void	apply_ideal_c2endo_sugar_coords (core::pose::Pose &pose, core::Size const &i)

void	get_fade_correction (Real const z, Real const cutoff_lower, Real const cutoff_upper, Real const fade_zone, Real &fade_value, Real &fade_deriv)

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
utility::vector1< std::string >	non_main_chain_sugar_atoms

Typedef Documentation

typedef std::pair<Real, Base_pair> core::scoring::rna::Energy_base_pair

Definition at line 128 of file RNA_BaseDoubletClasses.hh.

typedef std::list<Energy_base_pair> core::scoring::rna::Energy_base_pair_list

Definition at line 129 of file RNA_BaseDoubletClasses.hh.

typedef std::pair<Real, Base_stack> core::scoring::rna::Energy_base_stack

Definition at line 179 of file RNA_BaseDoubletClasses.hh.

typedef std::list<Energy_base_stack> core::scoring::rna::Energy_base_stack_list

Definition at line 180 of file RNA_BaseDoubletClasses.hh.

typedef utility::vector1< Gaussian_parameter > core::scoring::rna::Gaussian_parameter_set

Definition at line 31 of file RNA_FittedTorsionInfo.hh.

typedef numeric::xyzMatrix< Real > core::scoring::rna::Matrix

Definition at line 55 of file RNA_CentroidInfo.cc.

typedef utility::pointer::owning_ptr< RNA_AtomVDW const > core::scoring::rna::RNA_AtomVDWCOP

Definition at line 34 of file RNA_AtomVDW.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_AtomVDW > core::scoring::rna::RNA_AtomVDWOP

Definition at line 31 of file RNA_AtomVDW.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_CentroidInfo > core::scoring::rna::RNA_CentroidInfoOP

Definition at line 36 of file RNA_CentroidInfo.fwd.hh.

typedef utility::vector1< RNA_Datum > core::scoring::rna::RNA_Data

Definition at line 54 of file RNA_DataInfo.hh.

typedef utility::pointer::access_ptr< RNA_DataInfo > core::scoring::rna::RNA_DataInfoAP

Definition at line 33 of file RNA_DataInfo.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_DataInfo > core::scoring::rna::RNA_DataInfoOP

Definition at line 31 of file RNA_DataInfo.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_FilteredBaseBaseInfo > core::scoring::rna::RNA_FilteredBaseBaseInfoOP

Definition at line 25 of file RNA_FilteredBaseBaseInfo.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_FullAtomVDW_BasePhosphate const > core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCOP

Definition at line 27 of file RNA_FullAtomVDW_BasePhosphate.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_FullAtomVDW_BasePhosphate > core::scoring::rna::RNA_FullAtomVDW_BasePhosphateOP

Definition at line 24 of file RNA_FullAtomVDW_BasePhosphate.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_LowResolutionPotential > core::scoring::rna::RNA_LowResolutionPotentialOP

Definition at line 35 of file RNA_LowResolutionPotential.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_Mg_KnowledgeBasedPotential const > core::scoring::rna::RNA_Mg_KnowledgeBasedPotentialCOP

Definition at line 34 of file RNA_Mg_KnowledgeBasedPotential.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_Mg_KnowledgeBasedPotential > core::scoring::rna::RNA_Mg_KnowledgeBasedPotentialOP

Definition at line 31 of file RNA_Mg_KnowledgeBasedPotential.fwd.hh.

typedef utility::pointer::access_ptr< RNA_RawBaseBaseInfo > core::scoring::rna::RNA_RawBaseBaseInfoAP

Definition at line 30 of file RNA_RawBaseBaseInfo.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_RawBaseBaseInfo > core::scoring::rna::RNA_RawBaseBaseInfoOP

Definition at line 28 of file RNA_RawBaseBaseInfo.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_ScoringInfo > core::scoring::rna::RNA_ScoringInfoOP

Definition at line 36 of file RNA_ScoringInfo.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_SugarCloseEnergy const > core::scoring::rna::RNA_SugarCloseEnergyCOP

Definition at line 29 of file RNA_SugarCloseEnergy.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_SugarCloseEnergy > core::scoring::rna::RNA_SugarCloseEnergyOP

Definition at line 26 of file RNA_SugarCloseEnergy.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_TorsionEnergy const > core::scoring::rna::RNA_TorsionEnergyCOP

Definition at line 29 of file RNA_TorsionEnergy.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_TorsionEnergy > core::scoring::rna::RNA_TorsionEnergyOP

Definition at line 26 of file RNA_TorsionEnergy.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_TorsionPotential const > core::scoring::rna::RNA_TorsionPotentialCOP

Definition at line 26 of file RNA_TorsionPotential.fwd.hh.

typedef utility::pointer::owning_ptr< RNA_TorsionPotential > core::scoring::rna::RNA_TorsionPotentialOP

Definition at line 23 of file RNA_TorsionPotential.fwd.hh.

typedef numeric::xyzVector< core::Real > core::scoring::rna::Vector

Definition at line 57 of file RNA_DataBackboneEnergy.cc.

Enumeration Type Documentation

enum core::scoring::rna::__RNA_UTIL__

Enumerator
X
WATSON_CRICK
HOOGSTEEN
SUGAR
O2STAR
PHOSPHATE

Definition at line 34 of file RNA_Util.hh.

enum core::scoring::rna::_RNA_FittedTorsionInfo_

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

Definition at line 29 of file RNA_FittedTorsionInfo.hh.

Function Documentation

void core::scoring::rna::apply_ideal_c2endo_sugar_coords	(	core::pose::Pose &	pose,
		core::Size const &	i
	)

Definition at line 610 of file RNA_Util.cc.

References apply_non_main_chain_sugar_coords(), core::id::BB, core::id::CHI, and core::pose::Pose::set_torsion().

Referenced by protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker().

void core::scoring::rna::apply_non_main_chain_sugar_coords	(	utility::vector1< Vector > const &	non_main_chain_sugar_coords,
		core::pose::Pose &	pose,
		core::pose::Pose const &	reference_pose,
		core::Size const &	i
	)

Definition at line 569 of file RNA_Util.cc.

References core::id::BB, core::id::CHI, fix_sugar_coords(), initialize_atoms_for_which_we_need_new_dofs(), initialize_non_main_chain_sugar_atoms(), NUM_RNA_MAINCHAIN_TORSIONS(), NUM_RNA_TORSIONS(), core::pose::Pose::set_torsion(), and core::pose::Pose::torsion().

Referenced by apply_ideal_c2endo_sugar_coords(), core::io::silent::RNA_SilentStruct::fill_pose(), and protocols::rna::FullAtomRNA_Fragments::insert_fragment().

std::string const core::scoring::rna::chi1_torsion_atom ( conformation::Residue const & rsd)

Definition at line 141 of file RNA_Util.cc.

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

Referenced by protocols::rna::RNA_HelixAssembler::apply(), default_jump_atom(), protocols::rna::figure_out_reasonable_rna_fold_tree(), protocols::rna::RNA_HelixAssembler::get_rid_of_capping_base_pairs(), protocols::swa::pdbslice(), and protocols::rna::RNA_LoopCloser::rna_ccd_close().

Size core::scoring::rna::chi1_torsion_atom_index ( conformation::Residue const & rsd)

Definition at line 149 of file RNA_Util.cc.

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::scoring::rna::convert_acgu_to_1234 ( char const c)

Definition at line 52 of file RNA_Util.cc.

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::scoring::rna::default_jump_atom ( conformation::Residue const & rsd)

Definition at line 157 of file RNA_Util.cc.

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

Referenced by protocols::rna::RNA_StructureParameters::fill_in_default_jump_atoms(), and protocols::rna::RNA_StructureParameters::random_jump_change().

std::string const core::scoring::rna::first_base_atom ( conformation::Residue const & rsd)

Definition at line 120 of file RNA_Util.cc.

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

Size core::scoring::rna::first_base_atom_index ( conformation::Residue const & rsd)

Definition at line 134 of file RNA_Util.cc.

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

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::swa::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion(), protocols::swa::StepWisePoseSetup::add_terminal_res_repulsion(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), first_base_atom(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), and initialize_atoms_for_which_we_need_new_dofs().

void core::scoring::rna::fix_sugar_coords	(	utility::vector1< std::string >	atoms_for_which_we_need_new_dofs,
		utility::vector1< Vector > const &	non_main_chain_sugar_coords,
		core::pose::Pose &	pose,
		core::pose::Pose const &	reference_pose,
		core::Size const &	i
	)

Definition at line 440 of file RNA_Util.cc.

References core::kinematics::AtomTree::atom_dont_do_update(), core::pose::Pose::atom_tree(), core::id::D, core::scoring::PHI, protocols::swa::phi(), prepare_scratch_residue(), core::pose::Pose::residue(), core::pose::Pose::set_dof(), and core::id::THETA.

Referenced by apply_non_main_chain_sugar_coords().

void core::scoring::rna::fix_sugar_coords_WORKS_BUT_SLOW	(	utility::vector1< std::string >	atoms_for_which_we_need_new_dofs,
		utility::vector1< utility::vector1< id::DOF_Type > >	which_dofs,
		utility::vector1< Vector > const &	non_main_chain_sugar_coords,
		core::pose::Pose &	pose,
		core::Size const &	i
	)

Definition at line 352 of file RNA_Util.cc.

References core::pose::Pose::atom_tree(), core::kinematics::AtomTree::dof(), core::pose::Pose::residue(), core::pose::Pose::set_dof(), and core::pose::Pose::set_xyz().

char core::scoring::rna::get_edge_from_num ( Size const num)

Definition at line 63 of file RNA_Util.cc.

References HOOGSTEEN, O2STAR, PHOSPHATE, SUGAR, and WATSON_CRICK.

Referenced by protocols::rna::RNA_DeNovoProtocol::add_number_native_base_pairs(), protocols::rna::classify_base_pairs(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score().

void core::scoring::rna::get_fade_correction	(	Real const	z,
		Real const	cutoff_lower,
		Real const	cutoff_upper,
		Real const	fade_zone,
		Real &	fade_value,
		Real &	fade_deriv
	)

Definition at line 641 of file RNA_Util.cc.

References protocols::match::upstream::b.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential(), core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential_RNA(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_base_backbone_xy(), core::scoring::rna::RNA_LowResolutionPotential::get_rna_basepair_xy(), and core::scoring::rna::RNA_LowResolutionPotential::get_rna_stack_score().

std::string core::scoring::rna::get_full_edge_from_num ( Size const num)

Definition at line 74 of file RNA_Util.cc.

References HOOGSTEEN, O2STAR, PHOSPHATE, SUGAR, and WATSON_CRICK.

Referenced by core::scoring::rna::Base_pair::print_info().

std::string core::scoring::rna::get_full_LW_orientation_from_num ( Size const num)

Definition at line 109 of file RNA_Util.cc.

Referenced by core::scoring::rna::Base_pair::print_info().

std::string core::scoring::rna::get_full_orientation_from_num ( Size const num)

Definition at line 98 of file RNA_Util.cc.

Referenced by core::scoring::rna::Base_pair::print_info().

char core::scoring::rna::get_orientation_from_num ( Size const num)

Definition at line 89 of file RNA_Util.cc.

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

Size core::scoring::rna::get_position_in_vector	(	utility::vector1< std::string > &	vec,
		std::string const	element
	)

Definition at line 56 of file RNA_AtomVDW.cc.

Referenced by core::scoring::rna::RNA_AtomVDW::RNA_AtomVDW().

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

Definition at line 682 of file RNA_Util.cc.

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), core::scoring::rna::RNA_CentroidInfo::get_base_centroid(), protocols::swa::rna::get_max_centroid_to_atom_distance(), protocols::swa::rna::StepWiseRNA_ResidueSampler::get_reference_stub(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), protocols::swa::rna::set_to_origin(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_user_input_VDW_pose(), and protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::setup_using_working_pose().

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

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

Definition at line 731 of file RNA_Util.cc.

References core::conformation::Residue::aa(), core::conformation::Residue::is_RNA(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, and core::conformation::Residue::xyz().

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(), protocols::swa::rna::StepWiseRNA_ResidueSampler::get_reference_stub(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), and protocols::swa::rna::set_to_origin().

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

Definition at line 199 of file RNA_Util.cc.

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

Referenced by protocols::rna::get_base_pairing_info(), protocols::rna::get_base_pairing_list(), and protocols::rna::setup_base_pair_constraints().

void core::scoring::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
	)

Definition at line 245 of file RNA_Util.cc.

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

void core::scoring::rna::initialize_atoms_for_which_we_need_new_dofs	(	utility::vector1< std::string > &	atoms_for_which_we_need_new_dofs,
		pose::Pose const &	pose,
		Size const &	i
	)

Definition at line 512 of file RNA_Util.cc.

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), first_base_atom_index(), and core::pose::Pose::residue().

Referenced by apply_non_main_chain_sugar_coords().

void core::scoring::rna::initialize_non_main_chain_sugar_atoms ( )

Definition at line 336 of file RNA_Util.cc.

References core::init().

Referenced by apply_non_main_chain_sugar_coords(), protocols::rna::create_rna_vall_torsions(), core::io::silent::RNA_SilentStruct::fill_struct(), and protocols::rna::FullAtomRNA_Fragments::insert_fragment().

bool core::scoring::rna::Is_base_phosphate_atom_pair	(	conformation::Residue const &	rsd_1,
		conformation::Residue const &	rsd_2,
		Size const	atomno_1,
		Size const	atomno_2
	)

Definition at line 777 of file RNA_Util.cc.

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(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::acceptorRes_occludingRes_geometric_sol_RNA_intra(), core::scoring::geometric_solvation::GeometricSolEnergy::acceptorRes_occludingRes_geometric_sol_RNA_intra(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::donorRes_occludingRes_geometric_sol_RNA_intra(), core::scoring::geometric_solvation::GeometricSolEnergy::donorRes_occludingRes_geometric_sol_RNA_intra(), core::scoring::methods::LK_CosThetaEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative_intra_RNA(), and core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative_intra_RNA().

bool core::scoring::rna::is_cutpoint_open	(	core::pose::Pose const &	pose,
		Size const	i
	)

Definition at line 290 of file RNA_Util.cc.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::rna::RNA_StructureParameters::check_base_pairs().

bool core::scoring::rna::is_purine ( conformation::Residue const & rsd)

Definition at line 127 of file RNA_Util.cc.

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

Referenced by protocols::swa::monte_carlo::RNA_TorsionMover::apply_random_nucleoside_torsion(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_sample_base_states(), protocols::swa::rna::FloatingBaseChainClosureJobParameter::set_base_and_pucker_state(), protocols::swa::rna::setup_residue_at_origin_list(), and protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::standard_sampling().

bool core::scoring::rna::is_rna_chainbreak	(	core::pose::Pose const &	pose,
		Size const	i
	)

Definition at line 306 of file RNA_Util.cc.

References core::conformation::Residue::atom_index(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::rna::figure_out_reasonable_rna_fold_tree(), and core::scoring::rna::RNA_TorsionPotential::Should_score_torsion().

RNA_ScoringInfo & core::scoring::rna::nonconst_rna_scoring_info_from_pose ( pose::Pose & pose)

Either returns a non-const reference to the rna_scoring object already stored in the pose, or creates a new rna scoring info object, places it in the pose, and returns a non-const reference to it.

Definition at line 82 of file RNA_ScoringInfo.cc.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::RNA_SCORING_INFO, and core::pose::Pose::total_residue().

Size const core::scoring::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(), protocols::rna::RNA_Fragments::read_vall_torsions(), protocols::rna::FullAtomRNA_Fragments::read_vall_torsions(), 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::scoring::rna::NUM_RNA_CHI_TORSIONS ( NUM_RNA_TORSIONS- NUM_RNA_MAINCHAIN_TORSIONS)

Referenced by protocols::rna::create_rna_vall_torsions(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), 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::scoring::rna::NUM_RNA_MAINCHAIN_TORSIONS ( 6 )

Referenced by protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), apply_non_main_chain_sugar_coords(), protocols::swa::rna::copy_torsions_FROM_TO(), protocols::rna::create_rna_vall_torsions(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), core::io::silent::RNA_SilentStruct::fill_pose(), protocols::swa::rna::Get_residue_base_state(), core::io::silent::RNA_SilentStruct::init_from_lines(), protocols::rna::FullAtomRNA_Fragments::insert_fragment(), core::io::silent::RNA_SilentStruct::print_conformation(), protocols::rna::RNA_LoopCloser::remove_variants_at_extra_cutpoints(), protocols::rna::RNA_Minimizer::setup_movemap(), and protocols::rna::RNA_LoopCloser::setup_variants_at_extra_cutpoints().

Size const core::scoring::rna::NUM_RNA_TORSIONS ( 10 )

Referenced by protocols::rna::FragmentLibrary::add_torsion(), apply_non_main_chain_sugar_coords(), protocols::rna::FullAtomRNA_Fragments::insert_fragment(), protocols::rna::TorsionSet::operator=(), protocols::rna::RNA_Fragments::read_vall_torsions(), protocols::rna::FullAtomRNA_Fragments::read_vall_torsions(), protocols::rna::RNA_Minimizer::setup_movemap(), and protocols::rna::TorsionSet::TorsionSet().

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

Definition at line 176 of file RNA_Util.cc.

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

Referenced by protocols::rna::RNA_DeNovoProtocol::add_number_base_pairs(), protocols::rna::RNA_DeNovoProtocol::add_number_native_base_pairs(), protocols::rna::check_base_pair(), protocols::rna::get_base_pairing_info(), protocols::rna::get_base_pairing_list(), protocols::rna::RNA_StructureParameters::get_stem_residues(), and protocols::rna::RNA_StructureParameters::initialize_secstruct().

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

Definition at line 189 of file RNA_Util.cc.

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

void core::scoring::rna::prepare_scratch_residue	(	core::conformation::ResidueOP &	scratch_rsd,
		core::conformation::Residue const &	start_rsd,
		utility::vector1< Vector > const &	non_main_chain_sugar_coords,
		core::pose::Pose const &	pose
	)