Classes
class	BasePairStep

class	BasePairStepLibrary

class	BasePairStepSequence

class	BasePairType

class	ChunkSet

class	FragmentLibrary

class	FullAtomRNA_Fragments

class	MultipleDomainMover
	The RNA de novo structure modeling protocol. More...

class	RNA_ChunkLibrary

class	RNA_DataReader

class	RNA_DeNovoProtocol
	The RNA de novo structure modeling protocol. More...

class	RNA_FragmentMover
	The RNA de novo structure modeling protocol. More...

class	RNA_Fragments

class	RNA_JumpLibrary

class	RNA_LoopCloser
	The RNA de novo structure modeling protocol. More...

class	RNA_Minimizer
	The RNA de novo structure modeling protocol. More...

class	RNA_Pairing

class	RNA_PairingTemplate

class	RNA_Relaxer
	The RNA de novo structure modeling protocol. More...

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

class	RNA_StructureParameters

class	TorsionSet

Typedefs
typedef utility::pointer::owning_ptr < BasePairStep >	BasePairStepOP

typedef utility::pointer::owning_ptr < BasePairStep const >	BasePairStepCOP

typedef utility::pointer::owning_ptr < BasePairStepLibrary >	BasePairStepLibraryOP

typedef utility::pointer::owning_ptr < BasePairStepLibrary const >	BasePairStepLibraryCOP

typedef utility::pointer::owning_ptr < FragmentLibrary >	FragmentLibraryOP

typedef std::pair< std::string, std::string >	SequenceSecStructPair

typedef std::map < SequenceSecStructPair, FragmentLibraryOP >	FragmentLibraryPointerMap

typedef utility::pointer::owning_ptr < MultipleDomainMover >	MultipleDomainMoverOP

typedef numeric::xyzMatrix< Real >	Matrix

typedef utility::pointer::owning_ptr < RNA_ChunkLibrary >	RNA_ChunkLibraryOP

typedef utility::pointer::owning_ptr < ChunkSet >	ChunkSetOP

typedef utility::pointer::owning_ptr < RNA_DataReader >	RNA_DataReaderOP

typedef utility::pointer::owning_ptr < RNA_FragmentMover >	RNA_FragmentMoverOP

typedef utility::pointer::owning_ptr < RNA_Fragments >	RNA_FragmentsOP

typedef utility::pointer::owning_ptr < RNA_JumpLibrary >	RNA_JumpLibraryOP

typedef utility::pointer::owning_ptr < RNA_PairingTemplate >	RNA_PairingTemplateOP

typedef utility::vector1 < RNA_PairingTemplateOP >	RNA_PairingTemplateList

typedef std::map< BasePairType, RNA_PairingTemplateList >	RNA_PairingTemplateMap

typedef utility::pointer::owning_ptr < RNA_LoopCloser >	RNA_LoopCloserOP

typedef utility::pointer::owning_ptr < RNA_Minimizer >	RNA_MinimizerOP

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

typedef utility::pointer::owning_ptr < RNA_Relaxer >	RNA_RelaxerOP

typedef utility::pointer::owning_ptr < RNA_SecStructInfo >	RNA_SecStructInfoOP

typedef utility::pointer::owning_ptr < RNA_StructureParameters >	RNA_StructureParametersOP

typedef utility::vector1 < RNA_Pairing >	RNA_PairingList

Enumerations
enum	MATCH_ENUM { MATCH_ALL, MATCH_YR, MATCH_EXACT }
	name MATCH_ENUM added for PyRosetta compatability More...

enum	_RNA_MatchType_ { MATCH_ALL, MATCH_YR, MATCH_EXACT }

Functions
void	update_edge_hbond_numbers (conformation::Residue const &rsd, Size const &atm, Size &N_W, Size &N_H, Size &N_S)

void	update_edge_hbond_numbers_careful_hydrogen (conformation::Residue const &rsd, Size const &atm, conformation::Residue const &other_rsd, Size const &other_atm, Size &N_W, Size &N_H, Size &N_S)

bool	atom_is_polar (core::conformation::Residue const &rsd, Size const &atm)

bool	heavy_atom_is_polar (core::conformation::Residue const &rsd, Size const &atm)

bool	atom_is_acceptor (core::conformation::Residue const &rsd, Size const &atm)

void	figure_out_number_base_contacts (conformation::Residue const &rsd_i, conformation::Residue const &rsd_j, Size &edge_classification)

Size	figure_out_base_pair_orientation (core::pose::Pose &pose, Size const &i, Size const &j)

bool	residue_is_bulge (pose::Pose const &pose, Size const i)

Size	bases_form_a_hydrogen_bond (core::scoring::hbonds::HBondSetOP const &hbond_set, core::pose::Pose &pose, Size const &i, Size const &j)

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

void	classify_base_pairs (core::pose::Pose const &pose_input, utility::vector1< core::scoring::rna::Base_pair > &base_pair_list, utility::vector1< bool > &is_bulged)

Size	get_number_base_stacks (core::pose::Pose const &pose_input)

bool	check_in_base_pair_list (scoring::rna::Base_pair const &base_pair, utility::vector1< core::scoring::rna::Base_pair > const &base_pair_list)

std::ostream &	operator<< (std::ostream &os, RNA_DeNovoProtocol const &mover)

std::ostream &	operator<< (std::ostream &os, RNA_Minimizer const &mover)

void	get_base_pairing_info (pose::Pose const &pose, Size const &seqpos, char &secstruct, FArray1D< bool > &edge_is_base_pairing)

void	get_base_pairing_list (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > &base_pairing_list)

void	figure_out_secstruct (pose::Pose &pose)

void	create_rna_vall_torsions (pose::Pose &pose, utility::io::ozstream &torsions_out, utility::vector1< Size > const &exclude_res_list)

void	create_rna_vall_torsions (pose::Pose &pose, std::string const outfile, utility::vector1< Size > const &exclude_res_list)

Real	get_op2_op1_sign (pose::Pose const &pose)

Real	get_op2_op1_sign (pose::Pose const &pose, Size res_num)

void	assert_phosphate_nomenclature_matches_mini (pose::Pose const &pose)

void	ensure_phosphate_nomenclature_matches_mini (pose::Pose &pose)

void	make_phosphate_nomenclature_matches_mini (pose::Pose &pose)

void	export_packer_results (utility::vector1< std::pair< Real, std::string > > &results, utility::vector1< pose::PoseOP > pose_list, scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dump)

void	check_base_pair (pose::Pose &pose, FArray1D_int &struct_type)

void	setup_base_pair_constraints (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > const &pairings, Real const suppress_factor)

void	setup_coarse_chainbreak_constraints (pose::Pose &pose, Size const &n)

std::string const	convert_based_on_match_type (std::string const RNA_string, Size const type)

bool	compare_RNA_char (char const char1, char const char2)

bool	compare_RNA_secstruct (char const char1, char const char2)

Vector	get_sugar_centroid (core::conformation::Residue const &rsd)

void	make_extended_coarse_pose (pose::Pose &coarse_pose, std::string const &full_sequence)

void	make_coarse_pose (pose::Pose const &pose, pose::Pose &coarse_pose)

void	remove_cutpoint_closed (pose::Pose &pose, Size const i)

void	remove_cutpoints_closed (pose::Pose &pose)

void	print_internal_coords (core::pose::Pose const &pose)

bool	possible_root (core::kinematics::FoldTree const &f, core::Size const &n)

utility::vector1< Size >	get_rigid_body_jumps (core::pose::Pose const &pose)

bool	let_rigid_body_jumps_move (core::kinematics::MoveMap &movemap, pose::Pose const &pose, bool const move_first_rigid_body)

void	translate_virtual_anchor_to_first_rigid_body (pose::Pose &pose)

bool	involved_in_phosphate_torsion (std::string atomname)

void	set_output_res_num (pose::Pose &extended_pose, utility::vector1< Size > const &output_res_num)

void	figure_out_base_pair_partner (pose::Pose &pose, std::map< Size, Size > &partner, bool const strict)

void	process_input_file (std::string const &input_file, utility::vector1< pose::PoseOP > &pose_list, bool is_pdb, bool coarse_rna)

void	print_hbonds (pose::Pose &pose)

void	get_base_pairing_info (core::pose::Pose const &pose, core::Size const &seqpos, char &secstruct, ObjexxFCL::FArray1D< bool > &edge_is_base_pairing)

void	get_base_pairing_list (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &base_pairing_list)

void	export_packer_results (utility::vector1< std::pair< core::Real, std::string > > &results, utility::vector1< core::pose::PoseOP > pose_list, core::scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dumo=false)

void	check_base_pair (core::pose::Pose &pose, ObjexxFCL::FArray1D_int &struct_type)

void	setup_base_pair_constraints (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const &pairings, core::Real const suppress_factor=1.0)

bool	is_num_in_list (core::Size const i, utility::vector1< core::Size > const &list)

std::string const &	get_rna_secstruct (core::pose::Pose &pose)

void	set_rna_secstruct (core::pose::Pose &pose, std::string const rna_secstruct_string)

bool	in_list (Size const &pos, utility::vector1< Size > const &res_list)

Variables
static basic::Tracer	tr ("protocols.rna.RNA_DataReader")

static numeric::random::RandomGenerator	RG (12320)

static basic::Tracer	TR ("protocols.rna.RNA_DeNovoProtocol")

static numeric::random::RandomGenerator	RG (144621)

static basic::Tracer	tr ("protocols.rna.RNA_JumpLibrary")

static numeric::random::RandomGenerator	RG (144620)

static basic::Tracer	tr ("protocols.rna.RNA_StructureParameters")

Typedef Documentation

typedef utility::pointer::owning_ptr< BasePairStep const > protocols::farna::BasePairStepCOP

typedef utility::pointer::owning_ptr< BasePairStepLibrary const > protocols::farna::BasePairStepLibraryCOP

typedef utility::pointer::owning_ptr< BasePairStepLibrary > protocols::farna::BasePairStepLibraryOP

typedef utility::pointer::owning_ptr< BasePairStep > protocols::farna::BasePairStepOP

typedef utility::pointer::owning_ptr< ChunkSet > protocols::farna::ChunkSetOP

typedef utility::pointer::owning_ptr< FragmentLibrary > protocols::farna::FragmentLibraryOP

typedef std::map< SequenceSecStructPair, FragmentLibraryOP > protocols::farna::FragmentLibraryPointerMap

typedef numeric::xyzMatrix< Real > protocols::farna::Matrix

typedef utility::pointer::owning_ptr< MultipleDomainMover > protocols::farna::MultipleDomainMoverOP

typedef utility::pointer::owning_ptr< RNA_ChunkLibrary > protocols::farna::RNA_ChunkLibraryOP

typedef utility::pointer::owning_ptr< RNA_DataReader > protocols::farna::RNA_DataReaderOP

typedef utility::pointer::owning_ptr< RNA_FragmentMover > protocols::farna::RNA_FragmentMoverOP

typedef utility::pointer::owning_ptr< RNA_Fragments > protocols::farna::RNA_FragmentsOP

typedef utility::pointer::owning_ptr< RNA_JumpLibrary > protocols::farna::RNA_JumpLibraryOP

typedef utility::pointer::owning_ptr< RNA_LoopCloser > protocols::farna::RNA_LoopCloserOP

typedef utility::pointer::owning_ptr< RNA_Minimizer > protocols::farna::RNA_MinimizerOP

typedef utility::vector1< RNA_Pairing > protocols::farna::RNA_PairingList

typedef utility::vector1< RNA_PairingTemplateOP > protocols::farna::RNA_PairingTemplateList

typedef std::map< BasePairType, RNA_PairingTemplateList > protocols::farna::RNA_PairingTemplateMap

typedef utility::pointer::owning_ptr< RNA_PairingTemplate > protocols::farna::RNA_PairingTemplateOP

typedef utility::pointer::owning_ptr< RNA_Relaxer > protocols::farna::RNA_RelaxerOP

typedef utility::pointer::owning_ptr< RNA_SecStructInfo > protocols::farna::RNA_SecStructInfoOP

typedef utility::pointer::owning_ptr< RNA_StructureParameters > protocols::farna::RNA_StructureParametersOP

typedef std::pair< std::string, std::string > protocols::farna::SequenceSecStructPair

typedef numeric::xyzVector< core::Length > protocols::farna::Vector

Enumeration Type Documentation

enum protocols::farna::_RNA_MatchType_

Enumerator
MATCH_ALL
MATCH_YR
MATCH_EXACT

enum protocols::farna::MATCH_ENUM

name MATCH_ENUM added for PyRosetta compatability

Enumerator
MATCH_ALL
MATCH_YR
MATCH_EXACT

Function Documentation

void protocols::farna::assert_phosphate_nomenclature_matches_mini ( pose::Pose const & pose )

References get_op2_op1_sign(), make_pose_from_sequence(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), runtime_assert, core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

bool protocols::farna::atom_is_acceptor	(	core::conformation::Residue const &	rsd,
		Size const &	atm
	)

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

Referenced by figure_out_number_base_contacts().

bool protocols::farna::atom_is_polar	(	core::conformation::Residue const &	rsd,
		Size const &	atm
	)

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

bool protocols::farna::bases_are_coplanar	(	core::pose::Pose &	pose,
		Size const &	i,
		Size const &	j
	)

References numeric::xyzMatrix< class >::col_z(), dot_product(), core::kinematics::Stub::M, nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().

Referenced by classify_base_pairs().

Size protocols::farna::bases_form_a_hydrogen_bond	(	core::scoring::hbonds::HBondSetOP const &	hbond_set,
		core::pose::Pose &	pose,
		Size const &	i,
		Size const &	j
	)

References core::conformation::Residue::atom_base(), core::scoring::hbonds::HBond::don_res(), core::conformation::Residue::first_sidechain_atom(), length, num_hbonds, and core::pose::Pose::residue().

Referenced by classify_base_pairs().

void protocols::farna::check_base_pair	(	core::pose::Pose &	pose,
		ObjexxFCL::FArray1D_int &	struct_type
	)

void protocols::farna::check_base_pair	(	pose::Pose &	pose,
		FArray1D_int &	struct_type
	)

References core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, protocols::abinitio::abscript::I, j, nres, core::scoring::rna::Base_pair::orientation, possibly_canonical(), core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, core::pose::Pose::residue(), RNA_LORES_WTS, rna_scoring_info_from_pose(), core::pose::Pose::total_residue(), and WATSON_CRICK.

bool protocols::farna::check_in_base_pair_list	(	scoring::rna::Base_pair const &	base_pair,
		utility::vector1< core::scoring::rna::Base_pair > const &	base_pair_list
	)

References core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, in_list(), core::scoring::rna::Base_pair::orientation, core::scoring::rna::Base_pair::res1, and core::scoring::rna::Base_pair::res2.

Referenced by protocols::farna::RNA_DeNovoProtocol::add_number_native_base_pairs().

void protocols::farna::classify_base_pairs	(	core::pose::Pose const &	pose_input,
		utility::vector1< core::scoring::rna::Base_pair > &	base_pair_list,
		utility::vector1< bool > &	is_bulged
	)

References bases_are_coplanar(), bases_form_a_hydrogen_bond(), figure_out_base_pair_orientation(), figure_out_number_base_contacts(), core::chemical::rna::get_edge_from_num(), hbond_sc, j, num_hbonds, and residue_is_bulge().

Referenced by protocols::farna::RNA_DeNovoProtocol::add_number_base_pairs(), protocols::farna::RNA_DeNovoProtocol::add_number_native_base_pairs(), and protocols::stepwise::sampling::legacy::RigidBodySampler::assign_WC_edges_to_base_pair12().

bool protocols::farna::compare_RNA_char	(	char const	char1,
		char const	char2
	)

Referenced by protocols::farna::RNA_Fragments::pick_fragment_library().

bool protocols::farna::compare_RNA_secstruct	(	char const	char1,
		char const	char2
	)

Referenced by protocols::farna::RNA_Fragments::pick_fragment_library().

std::string const protocols::farna::convert_based_on_match_type	(	std::string const	RNA_string,
		Size const	type
	)

References MATCH_ALL, MATCH_YR, runtime_assert, and size().

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::pick_random_fragment(), and protocols::farna::RNA_Fragments::pick_random_fragment().

void protocols::farna::create_rna_vall_torsions	(	pose::Pose &	pose,
		utility::io::ozstream &	torsions_out,
		utility::vector1< Size > const &	exclude_res_list
	)

void protocols::farna::create_rna_vall_torsions	(	pose::Pose &	pose,
		std::string const	outfile,
		utility::vector1< Size > const &	exclude_res_list
	)

void protocols::farna::ensure_phosphate_nomenclature_matches_mini ( pose::Pose & pose )

References get_op2_op1_sign(), make_pose_from_sequence(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), runtime_assert, core::pose::Pose::set_xyz(), and core::pose::Pose::total_residue().

void protocols::farna::export_packer_results	(	utility::vector1< std::pair< core::Real, std::string > > &	results,
		utility::vector1< core::pose::PoseOP >	pose_list,
		core::scoring::ScoreFunctionOP &	scorefxn,
		std::string const &	outfile,
		bool const	dumo = `false`
	)

void protocols::farna::export_packer_results	(	utility::vector1< std::pair< Real, std::string > > &	results,
		utility::vector1< pose::PoseOP >	pose_list,
		scoring::ScoreFunctionOP &	scorefxn,
		std::string const &	outfile,
		bool const	dump
	)

References utility::io::ozstream::close(), core::pose::Pose::dump_pdb(), out, s, and tag.

Size protocols::farna::figure_out_base_pair_orientation	(	core::pose::Pose &	pose,
		Size const &	i,
		Size const &	j
	)

References numeric::xyzMatrix< class >::col_z(), dot_product(), core::kinematics::Stub::M, nonconst_rna_scoring_info_from_pose(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), and core::scoring::rna::RNA_CentroidInfo::update().

Referenced by classify_base_pairs().

void protocols::farna::figure_out_base_pair_partner	(	pose::Pose &	pose,
		std::map< Size, Size > &	partner,
		bool const	strict
	)

References core::id::CHI, core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, get_watson_crick_base_pair_atoms(), j, length, core::scoring::rna::Base_pair::orientation, possibly_canonical(), possibly_canonical_strict(), core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), RNA_LORES_WTS, rna_scoring_info_from_pose(), core::pose::Pose::torsion(), and WATSON_CRICK.

void protocols::farna::figure_out_number_base_contacts	(	conformation::Residue const &	rsd_i,
		conformation::Residue const &	rsd_j,
		Size &	edge_classification
	)

References atom_is_acceptor(), core::conformation::Residue::first_sidechain_atom(), heavy_atom_is_polar(), core::chemical::rna::HOOGSTEEN, length, core::conformation::Residue::nheavyatoms(), core::chemical::rna::SUGAR, update_edge_hbond_numbers(), update_edge_hbond_numbers_careful_hydrogen(), core::chemical::rna::WATSON_CRICK, and core::conformation::Residue::xyz().

Referenced by classify_base_pairs().

void protocols::farna::figure_out_secstruct ( pose::Pose & pose )

References get_base_pairing_info(), rna_base_pair, set_rna_secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::initialize_frag_source_pose().

void protocols::farna::get_base_pairing_info	(	core::pose::Pose const &	pose,
		core::Size const &	seqpos,
		char &	secstruct,
		ObjexxFCL::FArray1D< bool > &	edge_is_base_pairing
	)

void protocols::farna::get_base_pairing_info	(	pose::Pose const &	pose,
		Size const &	seqpos,
		char &	secstruct,
		FArray1D< bool > &	edge_is_base_pairing
	)

References core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, get_watson_crick_base_pair_atoms(), j, length, core::scoring::rna::Base_pair::orientation, possibly_canonical(), core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), rna_scoring_info_from_pose(), and WATSON_CRICK.

Referenced by create_rna_vall_torsions(), and figure_out_secstruct().

void protocols::farna::get_base_pairing_list	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > &	base_pairing_list
	)

void protocols::farna::get_base_pairing_list	(	pose::Pose &	pose,
		utility::vector1< std::pair< Size, Size > > &	base_pairing_list
	)

References core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, get_watson_crick_base_pair_atoms(), j, length, core::scoring::rna::Base_pair::orientation, possibly_canonical(), core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, core::pose::Pose::residue(), rna_base_pair, rna_scoring_info_from_pose(), and WATSON_CRICK.

core::Size protocols::farna::get_number_base_stacks ( core::pose::Pose const & pose_input )

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::RNA_LORES_WTS, rna_scoring_info_from_pose(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::size().

Referenced by protocols::farna::RNA_DeNovoProtocol::add_number_base_pairs().

core::Real protocols::farna::get_op2_op1_sign ( pose::Pose const & pose )

References cross(), dot(), core::pose::Pose::residue(), sign(), core::pose::Pose::total_residue(), and utility_exit_with_message.

core::Real protocols::farna::get_op2_op1_sign	(	pose::Pose const &	pose,
		Size	res_num
	)

References cross(), dot(), basic::options::option, core::pose::Pose::residue(), basic::options::OptionKeys::rna::rna_prot_erraser, sign(), core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by assert_phosphate_nomenclature_matches_mini(), ensure_phosphate_nomenclature_matches_mini(), and make_phosphate_nomenclature_matches_mini().

utility::vector1< core::Size > protocols::farna::get_rigid_body_jumps ( core::pose::Pose const & pose )

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), TR, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by let_rigid_body_jumps_move(), protocols::farna::RNA_DeNovoProtocol::randomize_rigid_body_orientations(), protocols::farna::RNA_StructureParameters::setup_jumps(), protocols::farna::RNA_DeNovoProtocol::setup_monte_carlo_cycles(), and translate_virtual_anchor_to_first_rigid_body().

std::string const & protocols::farna::get_rna_secstruct ( core::pose::Pose & pose )

Pose must already contain a core::pose::datacache::CacheableDataType::RNA_SCORING_INFO object or this method will fail.

References core::pose::Pose::data(), basic::datacache::BasicDataCache::get_const_ptr(), basic::datacache::BasicDataCache::has(), core::pose::datacache::CacheableDataType::RNA_SECSTRUCT_INFO, set_rna_secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::initialize_frag_source_pose(), protocols::coarse_rna::CoarseRNA_Fragments::pick_random_fragment(), protocols::farna::RNA_Fragments::pick_random_fragment(), protocols::farna::FullAtomRNA_Fragments::pick_random_fragment(), and protocols::farna::RNA_StructureParameters::setup_jumps().

Vector protocols::farna::get_sugar_centroid ( core::conformation::Residue const & rsd )

References core::conformation::Residue::atom_index(), and core::conformation::Residue::xyz().

Referenced by make_coarse_pose().

bool protocols::farna::heavy_atom_is_polar	(	core::conformation::Residue const &	rsd,
		Size const &	atm
	)

References core::conformation::Residue::atom_base(), and core::conformation::Residue::Hpos_polar().

Referenced by figure_out_number_base_contacts().

bool protocols::farna::in_list	(	Size const &	pos,
		utility::vector1< Size > const &	res_list
	)

Referenced by check_in_base_pair_list(), and protocols::farna::RNA_StructureParameters::check_in_chain_connections().

bool protocols::farna::involved_in_phosphate_torsion ( std::string atomname )

References core::chemical::rna::atoms_involved_in_phosphate_torsion.

Referenced by protocols::farna::RNA_ChunkLibrary::update_allow_insert().

bool protocols::farna::is_num_in_list	(	core::Size const	i,
		utility::vector1< core::Size > const &	list
	)

inline

Referenced by create_rna_vall_torsions().

bool protocols::farna::let_rigid_body_jumps_move	(	core::kinematics::MoveMap &	movemap,
		pose::Pose const &	pose,
		bool const	move_first_rigid_body
	)

References get_rigid_body_jumps(), core::kinematics::MoveMap::set_jump(), and protocols::loops::start.

Referenced by protocols::farna::RNA_Minimizer::setup_movemap(), and protocols::farna::RNA_DeNovoProtocol::setup_rigid_body_mover().

void protocols::farna::make_coarse_pose	(	pose::Pose const &	pose,
		pose::Pose &	coarse_pose
	)

References COARSE_RNA, numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), core::pose::Pose::fold_tree(), get_sugar_centroid(), core::kinematics::Stub::M, make_extended_coarse_pose(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::kinematics::FoldTree::set_jump_atoms(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by process_input_file().

void protocols::farna::make_extended_coarse_pose	(	pose::Pose &	coarse_pose,
		std::string const &	full_sequence
	)

References BB, COARSE_RNA, make_pose_from_sequence(), core::pose::Pose::set_torsion(), and core::pose::Pose::total_residue().

Referenced by make_coarse_pose().

void protocols::farna::make_phosphate_nomenclature_matches_mini ( pose::Pose & pose )

References get_op2_op1_sign(), core::conformation::Residue::is_RNA(), make_pose_from_sequence(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::protein::InputStreamWithResidueInfo::cleanup_pose(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::create_VDW_rep_screen_pose(), protocols::stepwise::sampling::protein::StepWisePoseSetup::get_working_pose(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::Import_pose(), protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::sampling::rna::legacy::setup_pose_setup_class(), and protocols::stepwise::sampling::rna::legacy::setup_simple_full_length_rna_job_parameters().

std::ostream & protocols::farna::operator<<	(	std::ostream &	os,
		RNA_Minimizer const &	mover
	)

References protocols::farna::RNA_Minimizer::show().

std::ostream & protocols::farna::operator<<	(	std::ostream &	os,
		RNA_DeNovoProtocol const &	mover
	)

References protocols::farna::RNA_DeNovoProtocol::show().

bool protocols::farna::possible_root	(	core::kinematics::FoldTree const &	f,
		core::Size const &	n
	)

References core::kinematics::FoldTree::possible_root().

Referenced by protocols::stepwise::reroot_based_on_full_model_info().

void protocols::farna::print_hbonds ( pose::Pose & pose )

References core::conformation::Residue::atom_name(), core::scoring::hbonds::HBond::don_res(), core::conformation::Residue::name1(), and core::pose::Pose::residue().

void protocols::farna::print_internal_coords ( core::pose::Pose const & pose )

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), core::id::D, degrees(), numeric::conversions::degrees(), core::kinematics::AtomTree::dof(), j, core::conformation::Residue::name3(), core::id::PHI, core::pose::Pose::residue(), core::id::THETA, and core::pose::Pose::total_residue().

Referenced by protocols::coarse_rna::CoarseRNA_DeNovoProtocol::apply().

void protocols::farna::process_input_file	(	std::string const &	input_file,
		utility::vector1< pose::PoseOP > &	pose_list,
		bool	is_pdb,
		bool	coarse_rna
	)

References core::io::silent::SilentFileData::begin(), end, core::io::silent::SilentFileData::end(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), core::chemical::ChemicalManager::get_instance(), make_coarse_pose(), core::import_pose::pose_from_pdb(), core::io::silent::SilentFileData::read_file(), remove_cutpoints_closed(), core::chemical::ChemicalManager::residue_type_set(), core::chemical::RNA, utility_exit_with_message, and core::pose::rna::virtualize_5prime_phosphates().

Referenced by protocols::farna::RNA_ChunkLibrary::add_chunk_set(), protocols::farna::BasePairStepLibrary::initialize(), and protocols::farna::RNA_ChunkLibrary::initialize_rna_chunk_library().

void protocols::farna::remove_cutpoint_closed	(	pose::Pose &	pose,
		Size const	i
	)

References CUTPOINT_LOWER, CUTPOINT_UPPER, core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), nres, core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::partition_by_jump(), remove_variant_type_from_pose_residue(), core::pose::Pose::total_residue(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), core::kinematics::FoldTree::upstream_jump_residue(), and utility_exit_with_message.

Referenced by remove_cutpoints_closed().

void protocols::farna::remove_cutpoints_closed ( pose::Pose & pose )

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), remove_cutpoint_closed(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by process_input_file().

bool protocols::farna::residue_is_bulge	(	pose::Pose const &	pose,
		Size const	i
	)

References j, length, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by classify_base_pairs().

void protocols::farna::set_output_res_num	(	pose::Pose &	extended_pose,
		utility::vector1< Size > const &	output_res_num
	)

References core::pose::Pose::pdb_info(), runtime_assert, and core::pose::Pose::total_residue().

void protocols::farna::set_rna_secstruct	(	core::pose::Pose &	pose,
		std::string const	rna_secstruct_string
	)

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.

References core::pose::Pose::data(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), core::pose::datacache::CacheableDataType::RNA_SECSTRUCT_INFO, and basic::datacache::BasicDataCache::set().

Referenced by figure_out_secstruct(), get_rna_secstruct(), protocols::farna::RNA_StructureParameters::initialize_secstruct(), and protocols::farna::RNA_StructureParameters::override_secstruct().

void protocols::farna::setup_base_pair_constraints	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	pairings,
		core::Real const	suppress_factor = `1.0`
	)

void protocols::farna::setup_base_pair_constraints	(	pose::Pose &	pose,
		utility::vector1< std::pair< Size, Size > > const &	pairings,
		Real const	suppress_factor
	)

References core::conformation::Residue::aa(), core::pose::Pose::add_constraint(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::atom_index(), get_watson_crick_base_pair_atoms(), protocols::abinitio::abscript::I, core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), j, core::conformation::Residue::name1(), pairings, core::pose::Pose::residue(), TR, and core::conformation::Residue::type().

Referenced by protocols::stepwise::sampling::rna::helix::RNA_HelixAssembler::put_constraints_on_base_step(), and protocols::farna::RNA_StructureParameters::setup_base_pair_constraints().

void protocols::farna::setup_coarse_chainbreak_constraints	(	pose::Pose &	pose,
		Size const &	n
	)

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

void protocols::farna::translate_virtual_anchor_to_first_rigid_body ( pose::Pose & pose )

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), get_rigid_body_jumps(), j, core::conformation::Residue::natoms(), nres, core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), core::kinematics::FoldTree::upstream_jump_residue(), and core::pose::Pose::xyz().

Referenced by protocols::farna::RNA_DeNovoProtocol::do_random_moves().

void protocols::farna::update_edge_hbond_numbers	(	conformation::Residue const &	rsd,
		Size const &	atm,
		Size &	N_W,
		Size &	N_H,
		Size &	N_S
	)

References core::conformation::Residue::aa(), core::conformation::Residue::atom_name(), na_rad, na_rcy, na_rgu, na_ura, and utility_exit_with_message.

Referenced by figure_out_number_base_contacts().

void protocols::farna::update_edge_hbond_numbers_careful_hydrogen	(	conformation::Residue const &	rsd,
		Size const &	atm,
		conformation::Residue const &	other_rsd,
		Size const &	other_atm,
		Size &	N_W,
		Size &	N_H,
		Size &	N_S
	)