protocols::farna Namespace Reference

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_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::shared_ptr < BasePairStep >	BasePairStepOP
typedef utility::pointer::shared_ptr < BasePairStep const >	BasePairStepCOP
typedef utility::pointer::shared_ptr < BasePairStepLibrary >	BasePairStepLibraryOP
typedef utility::pointer::shared_ptr < BasePairStepLibrary const >	BasePairStepLibraryCOP
typedef utility::pointer::shared_ptr < FragmentLibrary >	FragmentLibraryOP
typedef std::pair< std::string, std::string >	SequenceSecStructPair
typedef std::map < SequenceSecStructPair, FragmentLibraryOP >	FragmentLibraryPointerMap
typedef utility::pointer::shared_ptr < MultipleDomainMover >	MultipleDomainMoverOP
typedef utility::pointer::shared_ptr < RNA_ChunkLibrary >	RNA_ChunkLibraryOP
typedef utility::pointer::shared_ptr < ChunkSet >	ChunkSetOP
typedef utility::pointer::shared_ptr < RNA_FragmentMover >	RNA_FragmentMoverOP
typedef utility::pointer::shared_ptr < RNA_Fragments >	RNA_FragmentsOP
typedef utility::pointer::shared_ptr < RNA_JumpLibrary >	RNA_JumpLibraryOP
typedef utility::pointer::shared_ptr < RNA_PairingTemplate >	RNA_PairingTemplateOP
typedef utility::vector1 < RNA_PairingTemplateOP >	RNA_PairingTemplateList
typedef std::map< BasePairType, RNA_PairingTemplateList >	RNA_PairingTemplateMap
typedef utility::pointer::shared_ptr < RNA_LoopCloser >	RNA_LoopCloserOP
typedef utility::pointer::shared_ptr < RNA_Minimizer >	RNA_MinimizerOP
typedef utility::pointer::shared_ptr < RNA_Relaxer >	RNA_RelaxerOP
typedef utility::pointer::shared_ptr < RNA_SecStructInfo >	RNA_SecStructInfoOP
typedef utility::pointer::shared_ptr < RNA_StructureParameters >	RNA_StructureParametersOP
typedef utility::vector1 < RNA_Pairing >	RNA_PairingList
typedef numeric::xyzVector < core::Length >	Vector

Enumerations
enum	_RNA_MatchType_ { MATCH_ALL, MATCH_YR, MATCH_EXACT }

Functions
static thread_local basic::Tracer	TR ("protocols.rna.RNA_DeNovoProtocol")
bool	check_in_base_pair_list (pose::rna::BasePair const &base_pair, utility::vector1< core::pose::rna::BasePair > const &base_pair_list)
std::ostream &	operator<< (std::ostream &os, RNA_DeNovoProtocol const &mover)
static thread_local basic::Tracer	tr ("protocols.rna.RNA_JumpLibrary")
std::ostream &	operator<< (std::ostream &os, RNA_Minimizer const &mover)
std::string const &	get_rna_secstruct (core::pose::Pose &pose)
void	set_rna_secstruct (core::pose::Pose &pose, std::string const rna_secstruct_string)
static thread_local basic::Tracer	TR ("protocols.farna.RNA_StructureParameters")
bool	in_list (Size const &pos, utility::vector1< Size > const &res_list)
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)
bool	moveable_jump (id::AtomID const &jump_atom_id1, id::AtomID const &jump_atom_id2, protocols::toolbox::AllowInsert const &allow_insert)
bool	moveable_jump (Size const jump_pos1, Size const jump_pos2, protocols::toolbox::AllowInsert const &allow_insert)
void	get_default_allowed_bulge_res (utility::vector1< core::Size > &allow_bulge_res_list, core::pose::Pose const &pose, bool const verbose)
core::Size	virtualize_bulges (core::pose::Pose &input_pose, utility::vector1< core::Size > const &in_allow_bulge_res_list, core::scoring::ScoreFunctionCOP const &scorefxn, std::string const &tag, bool const allow_pre_virtualize, bool const allow_consecutive_bulges, bool const verbose)
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)

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::shared_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::shared_ptr< RNA_PairingTemplate > protocols::farna::RNA_PairingTemplateOP

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

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

typedef utility::pointer::shared_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

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::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs().

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::pose::rna::BasePair::edge1, core::pose::rna::BasePair::edge2, F, I, core::pose::rna::BasePair::orientation, possibly_canonical(), core::pose::rna::BasePair::res1, core::pose::rna::BasePair::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	(	pose::rna::BasePair const &	base_pair,
		utility::vector1< core::pose::rna::BasePair > const &	base_pair_list
	)

References core::pose::rna::BasePair::edge1, core::pose::rna::BasePair::edge2, in_list(), core::pose::rna::BasePair::orientation, core::pose::rna::BasePair::res1, and core::pose::rna::BasePair::res2.

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

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

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::find_source_positions(), and protocols::farna::FullAtomRNA_Fragments::pick_fragment_library().

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

Referenced by protocols::coarse_rna::CoarseRNA_Fragments::find_source_positions(), and protocols::farna::FullAtomRNA_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::FullAtomRNA_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
	)

References core::pose::Pose::append_residue_by_bond(), core::id::BB, core::id::CHI, F, protocols::idealize::IdealizeMover::fast(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), core::pose::Pose::fold_tree(), get_base_pairing_info(), I, core::kinematics::FoldTree::is_cutpoint(), is_num_in_list(), core::conformation::Residue::name1(), non_main_chain_sugar_atoms, core::chemical::rna::NUM_RNA_CHI_TORSIONS(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::pose::Pose::residue(), rna_base_pair, core::pose::Pose::torsion(), core::pose::Pose::total_residue(), numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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(), and F.

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

References core::id::CHI, core::pose::rna::BasePair::edge1, core::pose::rna::BasePair::edge2, get_watson_crick_base_pair_atoms(), core::pose::rna::BasePair::orientation, possibly_canonical(), possibly_canonical_strict(), core::pose::rna::BasePair::res1, core::pose::rna::BasePair::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_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::pose::rna::BasePair::edge1, core::pose::rna::BasePair::edge2, get_watson_crick_base_pair_atoms(), core::pose::rna::BasePair::orientation, possibly_canonical(), core::pose::rna::BasePair::res1, core::pose::rna::BasePair::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::pose::rna::BasePair::edge1, core::pose::rna::BasePair::edge2, get_watson_crick_base_pair_atoms(), core::pose::rna::BasePair::orientation, possibly_canonical(), core::pose::rna::BasePair::res1, core::pose::rna::BasePair::res2, core::pose::Pose::residue(), rna_base_pair, rna_scoring_info_from_pose(), and WATSON_CRICK.

void protocols::farna::get_default_allowed_bulge_res	(	utility::vector1< core::Size > &	allow_bulge_res_list,
		core::pose::Pose const &	pose,
		bool const	verbose
	)

References core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), TR(), and utility_exit_with_message.

Referenced by virtualize_bulges().

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(), 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::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::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::modeler::protein::InputStreamWithResidueInfo::cleanup_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_rep_screen_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::Import_pose(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class(), and protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters().

bool protocols::farna::moveable_jump	(	id::AtomID const &	jump_atom_id1,
		id::AtomID const &	jump_atom_id2,
		protocols::toolbox::AllowInsert const &	allow_insert
	)

References protocols::toolbox::AllowInsert::get(), and protocols::toolbox::AllowInsert::get_domain().

Referenced by protocols::farna::RNA_StructureParameters::insert_base_pair_jumps(), protocols::farna::RNA_StructureParameters::random_jump_change(), and protocols::farna::RNA_Minimizer::setup_movemap().

bool protocols::farna::moveable_jump	(	Size const	jump_pos1,
		Size const	jump_pos2,
		protocols::toolbox::AllowInsert const &	allow_insert
	)

References protocols::toolbox::AllowInsert::get(), and protocols::toolbox::AllowInsert::get_domain().

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().

void protocols::farna::print_hbonds

(

pose::Pose &

pose

)

References core::conformation::Residue::atom_name(), hbond, 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, numeric::conversions::degrees(), degrees(), core::kinematics::AtomTree::dof(), F, core::kinematics::tree::Atom::get_self_ptr(), 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::chemical::FA_RNA, core::pose::rna::figure_out_reasonable_rna_fold_tree(), make_coarse_pose(), core::import_pose::pose_from_pdb(), core::io::silent::SilentFileData::read_file(), remove_cutpoints_closed(), 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 core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), 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::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().

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::pose::Pose::add_constraint(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), get_watson_crick_base_pair_atoms(), I, core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), core::pose::Pose::residue(), TR(), and core::conformation::Residue::type().

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

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

static

Referenced by protocols::farna::RNA_JumpLibrary::read_jumps_from_file().

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

static

Referenced by protocols::farna::RNA_DeNovoProtocol::align_and_output_to_silent_file(), protocols::farna::RNA_Minimizer::apply(), protocols::farna::RNA_LoopCloser::apply(), protocols::farna::RNA_Relaxer::apply(), protocols::farna::RNA_DeNovoProtocol::apply(), protocols::farna::RNA_DeNovoProtocol::calc_rmsds(), protocols::farna::RNA_StructureParameters::check_base_pairs(), protocols::farna::RNA_DeNovoProtocol::check_score_filter(), protocols::farna::RNA_DeNovoProtocol::do_random_moves(), protocols::farna::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff(), protocols::farna::BasePairStepLibrary::initialize(), protocols::farna::RNA_LoopCloser::local_minimize_at_chainbreaks(), protocols::farna::RNA_Relaxer::lores_monte_carlo(), protocols::farna::RNA_Minimizer::o2prime_trials(), protocols::farna::RNA_DeNovoProtocol::output_silent_struct(), protocols::farna::RNA_DeNovoProtocol::output_to_silent_file(), protocols::farna::RNA_LoopCloser::passes_fast_scan(), protocols::farna::RNA_StructureParameters::read_parameters_from_file(), protocols::farna::RNA_LoopCloser::rna_ccd_close(), protocols::farna::RNA_StructureParameters::setup_base_pair_constraints(), protocols::farna::RNA_DeNovoProtocol::setup_monte_carlo_cycles(), protocols::farna::RNA_DeNovoProtocol::setup_rigid_body_mover(), protocols::farna::RNA_DeNovoProtocol::update_frag_size(), and protocols::farna::RNA_DeNovoProtocol::update_pose_constraints().

static thread_local basic::Tracer protocols::farna::TR ( "protocols.farna.RNA_StructureParameters"  )

static

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(), core::conformation::Residue::natoms(), 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().

core::Size protocols::farna::virtualize_bulges	(	core::pose::Pose &	input_pose,
		utility::vector1< core::Size > const &	in_allow_bulge_res_list,
		core::scoring::ScoreFunctionCOP const &	scorefxn,
		std::string const &	tag,
		bool const	allow_pre_virtualize,
		bool const	allow_consecutive_bulges,
		bool const	verbose
	)

References core::pose::rna::apply_virtual_rna_residue_variant_type(), get_default_allowed_bulge_res(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), rna_bulge, core::pose::Pose::total_residue(), TR(), and utility_exit_with_message.

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