#include <RNA_StructureParameters.hh>

Inheritance diagram for protocols::farna::RNA_StructureParameters:

Public Member Functions
	RNA_StructureParameters ()

virtual	~RNA_StructureParameters ()

void	initialize (core::pose::Pose &pose, std::string const rna_params_file, std::string const jump_library_file, bool const ignore_secstruct)

void	setup_fold_tree_and_jumps_and_variants (core::pose::Pose &pose)

bool	random_jump_change (core::pose::Pose &pose) const

toolbox::AllowInsertOP	allow_insert ()

void	set_allow_insert (toolbox::AllowInsertOP allow_insert)

void	set_root_at_first_rigid_body (bool const setting)

void	set_suppress_bp_constraint (core::Real const setting)

void	set_bps_moves (Size const setting)

bool	check_base_pairs (core::pose::Pose &pose) const

std::map< Size, Size >	connections () const

std::list< Size >	get_stem_residues (core::pose::Pose const &pose) const

void	setup_base_pair_constraints (core::pose::Pose &pose)

void	setup_virtual_phosphate_variants (core::pose::Pose &pose)

utility::vector1< BasePairStep >	get_base_pair_steps () const

utility::vector1 < utility::vector1< core::Size > >	get_obligate_pairing_sets ()

RNA_PairingList	get_rna_pairing_list ()

Private Member Functions
void	initialize_secstruct (core::pose::Pose &pose)

void	override_secstruct (core::pose::Pose &pose)

void	append_virtual_anchor (core::pose::Pose &pose)

void	initialize_allow_insert (core::pose::Pose &pose)

void	get_pairings_from_line (std::istringstream &line_stream, bool const in_stem)

void	save_res_lists_to_chain_connections_and_clear (utility::vector1< Size > &res_list1, utility::vector1< Size > &res_list2)

void	read_chain_connection (std::istringstream &line_stream)

void	read_parameters_from_file (std::string const &pairing_file)

void	setup_jumps (core::pose::Pose &pose)

void	setup_chainbreak_variants (core::pose::Pose &pose)

void	set_jump_library (RNA_JumpLibraryOP rna_jump_library)

std::string const	read_secstruct_from_file (std::string const &rna_secstruct_file)

core::Size	check_in_chain_connections (core::Size const &pos1, core::Size const &pos2) const

bool	check_forward_backward (core::pose::Pose &pose, core::Size const jump_pos) const

void	add_new_RNA_jump (core::pose::Pose &pose, core::Size const &which_jump, bool &success) const

void	sample_alternative_chain_connection (core::pose::Pose &pose, core::Size const &which_jump) const

void	insert_base_pair_jumps (core::pose::Pose &pose, bool &success) const

void	fill_in_default_jump_atoms (core::kinematics::FoldTree &f, core::pose::Pose const &pose) const

Size	check_in_pairing_sets (utility::vector1< utility::vector1< core::Size > > pairing_sets, RNA_Pairing const &rna_pairing_check) const

Private Attributes
RNA_JumpLibraryOP	rna_jump_library_

RNA_PairingList	rna_pairing_list_

utility::vector1 < utility::vector1< core::Size > >	obligate_pairing_sets_

utility::vector1 < utility::vector1< core::Size > >	stem_pairing_sets_

utility::vector1< std::pair < utility::vector1< core::Size > , utility::vector1< core::Size > > >	chain_connections_

utility::vector1< core::Size >	cutpoints_open_

utility::vector1< core::Size >	cutpoints_closed_

utility::vector1< core::Size >	virtual_anchor_attachment_points_

bool	secstruct_defined_

std::string	rna_secstruct_

bool	assume_non_stem_is_loop

bool	bps_moves_

bool	allow_cuts_inside_base_pair_steps_

bool	add_virtual_anchor_

bool	root_at_first_rigid_body_

core::Real	suppress_bp_constraint_

utility::vector1< core::Size >	allow_insert_res_

toolbox::AllowInsertOP	allow_insert_

Constructor & Destructor Documentation

protocols::farna::RNA_StructureParameters::RNA_StructureParameters ( )

protocols::farna::RNA_StructureParameters::~RNA_StructureParameters ( )

virtual

Member Function Documentation

void protocols::farna::RNA_StructureParameters::add_new_RNA_jump	(	core::pose::Pose &	pose,
		core::Size const &	which_jump,
		bool &	success
	)		const

private

References check_forward_backward(), check_in_chain_connections(), protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, core::pose::Pose::fold_tree(), core::chemical::element::I, core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, core::pose::Pose::residue(), rna_jump_library_, rna_pairing_list_, and core::pose::Pose::set_jump().

Referenced by insert_base_pair_jumps(), and random_jump_change().

toolbox::AllowInsertOP protocols::farna::RNA_StructureParameters::allow_insert ( )

References allow_insert_.

void protocols::farna::RNA_StructureParameters::append_virtual_anchor ( core::pose::Pose & pose )

private

References allow_insert_, core::pose::Pose::annotated_sequence(), core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), cutpoints_open_, protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, core::chemical::ResidueTypeSet::name3_map(), obligate_pairing_sets_, protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), rna_pairing_list_, core::pose::Pose::total_residue(), and virtual_anchor_attachment_points_.

Referenced by initialize().

bool protocols::farna::RNA_StructureParameters::check_base_pairs ( core::pose::Pose & pose ) const

References allow_insert_, protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, core::pose::rna::is_cutpoint_open(), core::conformation::Residue::is_RNA(), core::conformation::named_atom_id_to_atom_id(), protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, core::pose::Pose::residue(), rna_pairing_list_, and protocols::farna::TR().

bool protocols::farna::RNA_StructureParameters::check_forward_backward	(	core::pose::Pose &	pose,
		core::Size const	jump_pos
	)		const

private

References core::kinematics::AtomTree::atom(), core::conformation::Residue::atom_index(), core::pose::Pose::atom_tree(), core::kinematics::tree::Atom::get_self_ptr(), core::conformation::Residue::is_coarse(), core::conformation::Residue::is_RNA(), and core::pose::Pose::residue().

Referenced by add_new_RNA_jump().

Size protocols::farna::RNA_StructureParameters::check_in_chain_connections	(	core::Size const &	pos1,
		core::Size const &	pos2
	)		const

private

References chain_connections_, and protocols::farna::in_list().

Referenced by add_new_RNA_jump(), and sample_alternative_chain_connection().

Size protocols::farna::RNA_StructureParameters::check_in_pairing_sets	(	utility::vector1< utility::vector1< core::Size > >	pairing_sets,
		RNA_Pairing const &	rna_pairing_check
	)		const

private

References protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, and rna_pairing_list_.

Referenced by get_pairings_from_line(), and setup_jumps().

std::map< Size, Size > protocols::farna::RNA_StructureParameters::connections ( ) const

References protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, and rna_pairing_list_.

void protocols::farna::RNA_StructureParameters::fill_in_default_jump_atoms	(	core::kinematics::FoldTree &	f,
		core::pose::Pose const &	pose
	)		const

private

References core::chemical::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by sample_alternative_chain_connection(), and setup_jumps().

utility::vector1< BasePairStep > protocols::farna::RNA_StructureParameters::get_base_pair_steps ( ) const

References cutpoints_open_, protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, core::sequence::end, protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, and rna_pairing_list_.

Referenced by setup_jumps().

utility::vector1< utility::vector1 <core::Size > > protocols::farna::RNA_StructureParameters::get_obligate_pairing_sets ( )

inline

References obligate_pairing_sets_.

void protocols::farna::RNA_StructureParameters::get_pairings_from_line	(	std::istringstream &	line_stream,
		bool const	in_stem
	)

private

References core::pose::motif::a(), protocols::match::upstream::b, check_in_pairing_sets(), protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, core::chemical::element::I, obligate_pairing_sets_, protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, rna_pairing_list_, and stem_pairing_sets_.

Referenced by read_parameters_from_file().

RNA_PairingList protocols::farna::RNA_StructureParameters::get_rna_pairing_list ( )

inline

References rna_pairing_list_.

std::list< Size > protocols::farna::RNA_StructureParameters::get_stem_residues ( core::pose::Pose const & pose ) const

References core::conformation::Residue::aa(), protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, core::chemical::rna::possibly_canonical(), core::pose::Pose::residue(), and rna_pairing_list_.

void protocols::farna::RNA_StructureParameters::initialize	(	core::pose::Pose &	pose,
		std::string const	rna_params_file,
		std::string const	jump_library_file,
		bool const	ignore_secstruct
	)

References append_virtual_anchor(), chain_connections_, initialize_allow_insert(), initialize_secstruct(), override_secstruct(), read_parameters_from_file(), rna_jump_library_, rna_pairing_list_, setup_virtual_phosphate_variants(), and virtual_anchor_attachment_points_.

void protocols::farna::RNA_StructureParameters::initialize_allow_insert ( core::pose::Pose & pose )

private

References allow_insert_, allow_insert_res_, and core::pose::Pose::total_residue().

Referenced by initialize().

void protocols::farna::RNA_StructureParameters::initialize_secstruct ( core::pose::Pose & pose )

private

References core::conformation::Residue::aa(), assume_non_stem_is_loop, protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, core::chemical::rna::possibly_canonical(), core::pose::Pose::residue(), rna_pairing_list_, rna_secstruct_, secstruct_defined_, protocols::farna::set_rna_secstruct(), and core::pose::Pose::total_residue().

Referenced by initialize().

void protocols::farna::RNA_StructureParameters::insert_base_pair_jumps	(	core::pose::Pose &	pose,
		bool &	success
	)		const

private

References add_new_RNA_jump(), allow_insert_, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), protocols::farna::moveable_jump(), core::pose::Pose::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by setup_jumps().

void protocols::farna::RNA_StructureParameters::override_secstruct ( core::pose::Pose & pose )

private

References rna_secstruct_, protocols::farna::set_rna_secstruct(), and core::pose::Pose::total_residue().

Referenced by initialize().

bool protocols::farna::RNA_StructureParameters::random_jump_change ( core::pose::Pose & pose ) const

References add_new_RNA_jump(), allow_insert_, core::chemical::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), protocols::farna::moveable_jump(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), core::scoring::rg, sample_alternative_chain_connection(), and core::kinematics::FoldTree::upstream_jump_residue().

void protocols::farna::RNA_StructureParameters::read_chain_connection ( std::istringstream & line_stream )

private

References chain_connections_, and save_res_lists_to_chain_connections_and_clear().

Referenced by read_parameters_from_file().

void protocols::farna::RNA_StructureParameters::read_parameters_from_file ( std::string const & pairing_file )

private

References core::pose::motif::a(), allow_insert_res_, cutpoints_closed_, cutpoints_open_, get_pairings_from_line(), read_chain_connection(), rna_secstruct_, secstruct_defined_, protocols::farna::TR(), and virtual_anchor_attachment_points_.

Referenced by initialize().

std::string const protocols::farna::RNA_StructureParameters::read_secstruct_from_file ( std::string const & rna_secstruct_file )

private

void protocols::farna::RNA_StructureParameters::sample_alternative_chain_connection	(	core::pose::Pose &	pose,
		core::Size const &	which_jump
	)		const

private

References chain_connections_, check_in_chain_connections(), fill_in_default_jump_atoms(), core::pose::Pose::fold_tree(), core::chemical::element::I, core::scoring::rg, and core::pose::Pose::total_residue().

Referenced by random_jump_change().

void protocols::farna::RNA_StructureParameters::save_res_lists_to_chain_connections_and_clear	(	utility::vector1< Size > &	res_list1,
		utility::vector1< Size > &	res_list2
	)

private

References chain_connections_.

Referenced by read_chain_connection().

void protocols::farna::RNA_StructureParameters::set_allow_insert ( toolbox::AllowInsertOP allow_insert )

References allow_insert_.

void protocols::farna::RNA_StructureParameters::set_bps_moves ( Size const setting )

inline

References bps_moves_.

void protocols::farna::RNA_StructureParameters::set_jump_library ( RNA_JumpLibraryOP rna_jump_library )

private

References rna_jump_library_.

void protocols::farna::RNA_StructureParameters::set_root_at_first_rigid_body ( bool const setting )

inline

References root_at_first_rigid_body_.

void protocols::farna::RNA_StructureParameters::set_suppress_bp_constraint ( core::Real const setting )

inline

References suppress_bp_constraint_.

void protocols::farna::RNA_StructureParameters::setup_base_pair_constraints ( core::pose::Pose & pose )

References allow_insert_, bps_moves_, protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, core::chemical::element::I, core::conformation::Residue::is_RNA(), core::conformation::named_atom_id_to_atom_id(), protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, core::pose::Pose::residue(), rna_pairing_list_, protocols::farna::setup_base_pair_constraints(), suppress_bp_constraint_, and protocols::farna::TR().

void protocols::farna::RNA_StructureParameters::setup_chainbreak_variants ( core::pose::Pose & pose )

private

References allow_insert_, core::id::BB, core::pose::correctly_add_cutpoint_variants(), cutpoints_open_, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::mainchain_torsions(), core::pose::Pose::residue(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::pose::Pose::total_residue().

Referenced by setup_fold_tree_and_jumps_and_variants().

void protocols::farna::RNA_StructureParameters::setup_fold_tree_and_jumps_and_variants ( core::pose::Pose & pose )

References setup_chainbreak_variants(), and setup_jumps().

void protocols::farna::RNA_StructureParameters::setup_jumps ( core::pose::Pose & pose )

private

References allow_insert_, bps_moves_, chain_connections_, check_in_pairing_sets(), cutpoints_closed_, cutpoints_open_, fill_in_default_jump_atoms(), core::pose::Pose::fold_tree(), get_base_pair_steps(), protocols::farna::get_rigid_body_jumps(), protocols::farna::get_rna_secstruct(), protocols::farna::BasePairStep::i(), core::chemical::element::I, protocols::farna::BasePairStep::i_next(), insert_base_pair_jumps(), core::conformation::Residue::is_RNA(), protocols::farna::BasePairStep::j(), protocols::farna::BasePairStep::j_next(), core::conformation::named_atom_id_to_atom_id(), obligate_pairing_sets_, core::kinematics::FoldTree::possible_root(), core::chemical::q, core::kinematics::FoldTree::random_tree_from_jump_points(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::scoring::rg, rna_pairing_list_, root_at_first_rigid_body_, core::io::serialization::size(), stem_pairing_sets_, core::pose::Pose::total_residue(), core::kinematics::FoldTree::upstream_jump_residue(), and virtual_anchor_attachment_points_.

Referenced by setup_fold_tree_and_jumps_and_variants().

void protocols::farna::RNA_StructureParameters::setup_virtual_phosphate_variants ( core::pose::Pose & pose )

References core::pose::add_variant_type_to_pose_residue(), allow_insert_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, cutpoints_open_, core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_RNA(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by initialize().

Member Data Documentation

bool protocols::farna::RNA_StructureParameters::add_virtual_anchor_

private

bool protocols::farna::RNA_StructureParameters::allow_cuts_inside_base_pair_steps_

private

toolbox::AllowInsertOP protocols::farna::RNA_StructureParameters::allow_insert_

private

Referenced by allow_insert(), append_virtual_anchor(), check_base_pairs(), initialize_allow_insert(), insert_base_pair_jumps(), random_jump_change(), set_allow_insert(), setup_base_pair_constraints(), setup_chainbreak_variants(), setup_jumps(), and setup_virtual_phosphate_variants().

utility::vector1< core::Size > protocols::farna::RNA_StructureParameters::allow_insert_res_

private

Referenced by initialize_allow_insert(), and read_parameters_from_file().

bool protocols::farna::RNA_StructureParameters::assume_non_stem_is_loop

private

Referenced by initialize_secstruct().

bool protocols::farna::RNA_StructureParameters::bps_moves_

private

Referenced by set_bps_moves(), setup_base_pair_constraints(), and setup_jumps().

utility::vector1< std::pair< utility::vector1 <core::Size >, utility::vector1 <core::Size > > > protocols::farna::RNA_StructureParameters::chain_connections_

private

Referenced by check_in_chain_connections(), initialize(), read_chain_connection(), sample_alternative_chain_connection(), save_res_lists_to_chain_connections_and_clear(), and setup_jumps().