protocols::farna::RNA_StructureParameters Class Reference

#include <RNA_StructureParameters.hh>

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

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	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(), fold_tree, protocols::abinitio::abscript::I, core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), o, 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_, core::pose::Pose::set_jump(), and utility_exit_with_message.

Referenced by insert_base_pair_jumps(), and random_jump_change().

toolbox::AllowInsertOP protocols::farna::RNA_StructureParameters::allow_insert

(

)

References allow_insert_.

Referenced by protocols::farna::RNA_DeNovoProtocol::apply(), protocols::farna::RNA_DeNovoProtocol::get_moving_res(), and protocols::farna::RNA_DeNovoProtocol::initialize_movers().

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, utility::pointer::owning_ptr< T >::get(), is_cutpoint_open(), core::conformation::Residue::is_RNA(), j, 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.

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

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::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_.

Referenced by protocols::farna::RNA_DeNovoProtocol::apply(), and protocols::farna::RNA_DeNovoProtocol::apply_chem_shift_data().

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

private

References 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, utility::vector1< T, class >::has_value(), j, protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, and rna_pairing_list_.

Referenced by protocols::farna::RNA_DeNovoProtocol::initialize_movers(), and setup_jumps().

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

private

References protocols::match::upstream::b, check_in_pairing_sets(), protocols::farna::RNA_Pairing::edge1, protocols::farna::RNA_Pairing::edge2, protocols::abinitio::abscript::I, o, obligate_pairing_sets_, protocols::farna::RNA_Pairing::orientation, protocols::farna::RNA_Pairing::pos1, protocols::farna::RNA_Pairing::pos2, rna_pairing_list_, stem_pairing_sets_, tag, and utility_exit_with_message.

Referenced by read_parameters_from_file().

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_.

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

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_.

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

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(), utility::pointer::owning_ptr< T >::get(), 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_, default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), utility::pointer::owning_ptr< T >::get(), core::pose::Pose::num_jump(), core::pose::Pose::residue(), protocols::farna::RG, sample_alternative_chain_connection(), numeric::random::RandomGenerator::uniform(), and core::kinematics::FoldTree::upstream_jump_residue().

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

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

private

References chain_connections_, runtime_assert, tag, and utility_exit_with_message.

Referenced by read_parameters_from_file().

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

private

References allow_insert_res_, utility::io::izstream::close(), cutpoints_closed_, cutpoints_open_, get_pairings_from_line(), getline(), read_chain_connection(), rna_secstruct_, runtime_assert, secstruct_defined_, tag, protocols::farna::tr, utility_exit_with_message, 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(), fold_tree, protocols::abinitio::abscript::I, protocols::farna::RG, core::pose::Pose::total_residue(), numeric::random::RandomGenerator::uniform(), and utility_exit_with_message.

Referenced by random_jump_change().

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_.

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

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_.

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

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

inline

References suppress_bp_constraint_.

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

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, utility::pointer::owning_ptr< T >::get(), protocols::abinitio::abscript::I, core::conformation::Residue::is_RNA(), j, named_atom_id_to_atom_id(), protocols::farna::RNA_Pairing::orientation, pairings, 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.

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

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

private

References allow_insert_, core::pose::rna::correctly_position_cutpoint_phosphate_torsions(), cutpoints_open_, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), j, 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().

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

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(), utility::pointer::owning_ptr< T >::get(), get_base_pair_steps(), protocols::farna::get_rigid_body_jumps(), protocols::farna::get_rna_secstruct(), utility::vector1< T, class >::has_value(), protocols::abinitio::abscript::I, protocols::farna::BasePairStep::i(), protocols::farna::BasePairStep::i_next(), insert_base_pair_jumps(), core::conformation::Residue::is_RNA(), protocols::farna::BasePairStep::j(), protocols::farna::BasePairStep::j_next(), utility::tools::make_vector1(), named_atom_id_to_atom_id(), nres, obligate_pairing_sets_, core::kinematics::FoldTree::possible_root(), q, numeric::random::RandomGenerator::random_range(), core::kinematics::FoldTree::random_tree_from_jump_points(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), protocols::farna::RG, rna_pairing_list_, root_at_first_rigid_body_, runtime_assert, stem_pairing_sets_, core::pose::Pose::total_residue(), numeric::random::RandomGenerator::uniform(), core::kinematics::FoldTree::upstream_jump_residue(), utility_exit_with_message, 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 allow_insert_, chemical, CUTPOINT_LOWER, 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(), utility_exit_with_message, and VIRTUAL_PHOSPHATE.

Referenced by initialize(), and protocols::farna::RNA_DeNovoProtocol::initialize_movers().

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(), and setup_jumps().

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

private

Referenced by read_parameters_from_file(), and setup_jumps().

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

private

Referenced by append_virtual_anchor(), get_base_pair_steps(), read_parameters_from_file(), setup_chainbreak_variants(), setup_jumps(), and setup_virtual_phosphate_variants().

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

private

Referenced by append_virtual_anchor(), get_pairings_from_line(), and setup_jumps().

RNA_JumpLibraryOP protocols::farna::RNA_StructureParameters::rna_jump_library_

private

Referenced by add_new_RNA_jump(), initialize(), and set_jump_library().

RNA_PairingList protocols::farna::RNA_StructureParameters::rna_pairing_list_

private

Referenced by add_new_RNA_jump(), append_virtual_anchor(), check_base_pairs(), check_in_pairing_sets(), connections(), get_base_pair_steps(), get_pairings_from_line(), get_stem_residues(), initialize(), initialize_secstruct(), setup_base_pair_constraints(), and setup_jumps().

std::string protocols::farna::RNA_StructureParameters::rna_secstruct_

private

Referenced by initialize_secstruct(), override_secstruct(), and read_parameters_from_file().

bool protocols::farna::RNA_StructureParameters::root_at_first_rigid_body_

private

Referenced by set_root_at_first_rigid_body(), and setup_jumps().

bool protocols::farna::RNA_StructureParameters::secstruct_defined_

private

Referenced by initialize_secstruct(), and read_parameters_from_file().

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

private

Referenced by get_pairings_from_line(), and setup_jumps().

core::Real protocols::farna::RNA_StructureParameters::suppress_bp_constraint_

private

Referenced by set_suppress_bp_constraint(), and setup_base_pair_constraints().

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

private

Referenced by append_virtual_anchor(), initialize(), read_parameters_from_file(), and setup_jumps().

---

The documentation for this class was generated from the following files:

• symlinks/rosetta/src/protocols/farna/RNA_StructureParameters.hh
• symlinks/rosetta/src/protocols/farna/RNA_StructureParameters.cc