core::pose::rna Namespace Reference

Classes
class	BasePair
class	BaseStack
class	RNA_IdealCoord
class	RNA_SuiteAssignment
class	RNA_SuiteInfo
class	RNA_SuiteName

Typedefs
typedef std::pair< Real, BasePair >	EnergyBasePair
typedef std::list< EnergyBasePair >	EnergyBasePairList
typedef std::pair< Real, BaseStack >	EnergyBaseStack
typedef std::list < EnergyBaseStack >	EnergyBaseStackList
typedef numeric::xyzMatrix< Real >	Matrix
typedef utility::pointer::owning_ptr < RNA_IdealCoord >	RNA_IdealCoordOP
typedef utility::pointer::owning_ptr < RNA_SuiteName >	RNA_SuiteNameOP

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::pose::rna::BasePair > &base_pair_list, utility::vector1< bool > &is_bulged)
Size	get_number_base_stacks (core::pose::Pose const &pose_input)
bool	mutate_position (pose::Pose &pose, Size const i, char const &new_seq)
void	figure_out_reasonable_rna_fold_tree (pose::Pose &pose)
void	virtualize_5prime_phosphates (pose::Pose &pose)
bool	is_cutpoint_open (Pose const &pose, Size const i)
bool	is_rna_chainbreak (Pose const &pose, Size const i)
void	fix_sugar_coords_WORKS_BUT_SLOW (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< utility::vector1< id::DOF_Type > > which_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose &pose, Size const i)
void	prepare_scratch_residue (core::conformation::ResidueOP &scratch_rsd, core::conformation::Residue const &start_rsd, utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose const &pose)
void	fix_sugar_coords (utility::vector1< std::string > atoms_for_which_we_need_new_dofs, utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose &pose, Pose const &reference_pose, Size const i)
void	initialize_atoms_for_which_we_need_new_dofs (utility::vector1< std::string > &atoms_for_which_we_need_new_dofs, Pose const &pose, Size const i)
void	apply_non_main_chain_sugar_coords (utility::vector1< Vector > const &non_main_chain_sugar_coords, Pose &pose, Pose const &reference_pose, Size const i)
void	apply_ideal_c2endo_sugar_coords (Pose &pose, Size const i)
PuckerState	assign_pucker (Pose const &pose, Size const rsd_id)
void	apply_pucker (Pose &pose, Size const i, PuckerState pucker_state, bool const skip_same_state, bool const idealize_coord)
void	correctly_position_cutpoint_phosphate_torsions (pose::Pose &current_pose, Size const five_prime_chainbreak)
void	correctly_add_cutpoint_variants (core::pose::Pose &pose, Size const res_to_add, bool const check_fold_tree)
bool	is_torsion_valid (pose::Pose const &pose, id::TorsionID const &torsion_id, bool verbose, bool skip_chainbreak_torsions)
void	print_torsion_info (pose::Pose const &pose, id::TorsionID const &torsion_id)
void	output_boolean (std::string const &tag, bool boolean)
bool	is_cutpoint_closed_atom (core::conformation::Residue const &rsd, id::AtomID const &id)
bool	is_cutpoint_closed_torsion (pose::Pose const &pose, id::TorsionID const &torsion_id)
void	apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, bool const apply_check)
void	apply_virtual_rna_residue_variant_type (core::pose::Pose &pose, core::Size const &seq_num, utility::vector1< core::Size > const &working_cutpoint_closed_list, bool const apply_check)
void	remove_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)
bool	has_virtual_rna_residue_variant_type (pose::Pose &pose, Size const &seq_num)

Typedef Documentation

typedef std::pair< Real, BasePair > core::pose::rna::EnergyBasePair

typedef std::list< EnergyBasePair > core::pose::rna::EnergyBasePairList

typedef std::pair< Real, BaseStack > core::pose::rna::EnergyBaseStack

typedef std::list< EnergyBaseStack > core::pose::rna::EnergyBaseStackList

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

typedef utility::pointer::owning_ptr< RNA_IdealCoord > core::pose::rna::RNA_IdealCoordOP

typedef utility::pointer::owning_ptr< RNA_SuiteName > core::pose::rna::RNA_SuiteNameOP

Function Documentation

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

References apply_non_main_chain_sugar_coords(), apply_pucker(), core::id::BB, core::id::CHI, basic::options::OptionKeys::rna::corrected_geo, basic::options::option, core::pose::Pose::set_torsion(), and core::chemical::rna::SOUTH.

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

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

Referenced by apply_ideal_c2endo_sugar_coords(), and core::io::silent::RNA_SilentStruct::fill_pose().

void core::pose::rna::apply_pucker	(	Pose &	pose,
		Size const	i,
		PuckerState	pucker_state,
		bool const	skip_same_state,
		bool const	idealize_coord
	)

References core::chemical::rna::ANY_PUCKER, core::pose::rna::RNA_IdealCoord::apply_pucker(), assign_pucker(), core::id::BB, core::id::CHI, core::chemical::rna::RNA_FittedTorsionInfo::delta_north(), core::chemical::rna::RNA_FittedTorsionInfo::delta_south(), core::chemical::rna::NORTH, core::chemical::rna::RNA_FittedTorsionInfo::nu1_north(), core::chemical::rna::RNA_FittedTorsionInfo::nu1_south(), core::chemical::rna::RNA_FittedTorsionInfo::nu2_north(), core::chemical::rna::RNA_FittedTorsionInfo::nu2_south(), core::pose::Pose::set_torsion(), and torsion_info.

Referenced by apply_ideal_c2endo_sugar_coords().

void core::pose::rna::apply_virtual_rna_residue_variant_type	(	core::pose::Pose &	pose,
		core::Size const &	seq_num,
		bool const	apply_check
	)

References apply_virtual_rna_residue_variant_type().

void core::pose::rna::apply_virtual_rna_residue_variant_type	(	core::pose::Pose &	pose,
		core::Size const &	seq_num,
		utility::vector1< core::Size > const &	working_cutpoint_closed_list,
		bool const	apply_check
	)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::annotated_sequence(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), is_cutpoint_open(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), runtime_assert, core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by apply_virtual_rna_residue_variant_type().

core::chemical::rna::PuckerState core::pose::rna::assign_pucker	(	Pose const &	pose,
		Size const	rsd_id
	)

References core::id::BB, core::chemical::rna::RNA_FittedTorsionInfo::delta_cutoff(), core::chemical::rna::NORTH, core::chemical::rna::SOUTH, core::pose::Pose::torsion(), and torsion_info.

Referenced by apply_pucker().

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

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

bool core::pose::rna::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, core::scoring::rna::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 core::pose::rna::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::conformation::Residue::first_sidechain_atom(), hbond, length, core::scoring::num_hbonds, and core::pose::Pose::residue().

Referenced by classify_base_pairs().

void core::pose::rna::classify_base_pairs	(	core::pose::Pose const &	pose_input,
		utility::vector1< core::pose::rna::BasePair > &	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::scoring::hbonds::fill_hbond_set(), core::chemical::rna::get_edge_from_num(), core::scoring::hbond_sc, core::scoring::num_hbonds, residue_is_bulge(), and core::scoring::ScoreFunction::set_weight().

Referenced by core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status().

void core::pose::rna::correctly_add_cutpoint_variants	(	core::pose::Pose &	pose,
		Size const	res_to_add,
		bool const	check_fold_tree
	)

References core::pose::add_variant_type_to_pose_residue(), correctly_position_cutpoint_phosphate_torsions(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_RNA(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), runtime_assert, core::pose::Pose::total_residue(), core::chemical::UPPER_TERMINUS_VARIANT, and core::chemical::VIRTUAL_PHOSPHATE.

void core::pose::rna::correctly_position_cutpoint_phosphate_torsions	(	pose::Pose &	current_pose,
		Size const	five_prime_chainbreak
	)

References core::chemical::aa_from_name(), core::id::BB, core::conformation::ResidueFactory::create_residue(), core::pose::Pose::delete_polymer_residue(), core::chemical::FA_RNA, core::chemical::ChemicalManager::get_instance(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), core::chemical::ChemicalManager::residue_type_set(), and core::pose::Pose::set_torsion().

Referenced by correctly_add_cutpoint_variants(), and core::pose::correctly_add_cutpoint_variants().

Size core::pose::rna::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, core::scoring::rna::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 core::pose::rna::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 core::pose::rna::figure_out_reasonable_rna_fold_tree

(

pose::Pose &

pose

)

References core::chemical::rna::chi1_torsion_atom(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), is_rna_chainbreak(), core::kinematics::FoldTree::new_jump(), nres, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::kinematics::FoldTree::set_jump_atoms(), and core::pose::Pose::total_residue().

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

References numeric::angle_radians(), core::kinematics::AtomTree::atom_dont_do_update(), core::pose::Pose::atom_tree(), core::id::D, numeric::dihedral_radians(), core::chemical::PHI, numeric::constants::d::pi, prepare_scratch_residue(), core::pose::Pose::residue(), core::pose::Pose::set_dof(), and core::chemical::THETA.

Referenced by apply_non_main_chain_sugar_coords().

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

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

core::Size core::pose::rna::get_number_base_stacks

(

core::pose::Pose const &

pose_input

)

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

bool core::pose::rna::has_virtual_rna_residue_variant_type	(	pose::Pose &	pose,
		Size const &	seq_num
	)

References core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::chemical::rna::TR, and utility_exit_with_message.

bool core::pose::rna::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().

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

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

Referenced by apply_non_main_chain_sugar_coords().

bool core::pose::rna::is_cutpoint_closed_atom	(	core::conformation::Residue const &	rsd,
		id::AtomID const &	id
	)

References core::chemical::ResidueType::atom_name(), and core::conformation::Residue::type().

Referenced by is_torsion_valid().

bool core::pose::rna::is_cutpoint_closed_torsion	(	pose::Pose const &	pose,
		id::TorsionID const &	torsion_id
	)

References core::chemical::rna::ALPHA, core::id::BB, core::chemical::rna::BETA, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::rna::DELTA, core::chemical::rna::EPSILON, core::chemical::rna::GAMMA, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), core::pose::Pose::total_residue(), core::id::TorsionID::type(), utility_exit_with_message, and core::chemical::rna::ZETA.

Referenced by is_torsion_valid().

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

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

Referenced by apply_virtual_rna_residue_variant_type().

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

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

Referenced by core::pose::rna::RNA_SuiteName::assign(), figure_out_reasonable_rna_fold_tree(), and is_torsion_valid().

bool core::pose::rna::is_torsion_valid	(	pose::Pose const &	pose,
		id::TorsionID const &	torsion_id,
		bool	verbose,
		bool	skip_chainbreak_torsions
	)

References core::id::AtomID::atomno(), core::pose::Pose::conformation(), core::conformation::Conformation::get_torsion_angle_atom_ids(), is_cutpoint_closed_atom(), is_cutpoint_closed_torsion(), core::conformation::Residue::is_RNA(), is_rna_chainbreak(), core::conformation::Residue::is_virtual(), output_boolean(), print_torsion_info(), core::pose::Pose::residue(), core::id::AtomID::rsd(), runtime_assert, core::conformation::Residue::seqpos(), core::chemical::rna::TR, and utility_exit_with_message.

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::scoring::rna::RNA_SuitePotential::eval_score(), core::scoring::rna::RNA_TorsionPotential::get_f1_f2(), core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(), and core::scoring::rna::RNA_JR_SuiteEnergy::residue_pair_energy().

bool core::pose::rna::mutate_position	(	pose::Pose &	pose,
		Size const	i,
		char const &	new_seq
	)

References core::pose::Pose::chi(), core::pose::Pose::conformation(), core::conformation::Residue::is_RNA(), core::chemical::ResidueSelector::match_variants(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::pose::Pose::sequence(), core::pose::Pose::set_chi(), core::chemical::ResidueSelector::set_name1(), core::chemical::ResidueSelector::set_property(), and core::conformation::Residue::type().

void core::pose::rna::output_boolean	(	std::string const &	tag,
		bool	boolean
	)

References core::chemical::rna::TR.

Referenced by is_torsion_valid().

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

References core::conformation::Residue::atom_index(), core::conformation::Residue::build_atom_ideal(), core::pose::Pose::conformation(), core::conformation::Residue::first_sidechain_atom(), core::chemical::rna::non_main_chain_sugar_atoms, core::conformation::Residue::set_xyz(), and core::conformation::Residue::xyz().

Referenced by fix_sugar_coords().

void core::pose::rna::print_torsion_info	(	pose::Pose const &	pose,
		id::TorsionID const &	torsion_id
	)

References core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atomic_charge(), core::id::AtomID::atomno(), core::pose::Pose::conformation(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::chemical::rna::TR, and core::conformation::Residue::type().

Referenced by is_torsion_valid().

void core::pose::rna::remove_virtual_rna_residue_variant_type	(	pose::Pose &	pose,
		Size const &	seq_num
	)

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

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

References 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 core::pose::rna::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(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, and utility_exit_with_message.

Referenced by figure_out_number_base_contacts().

void core::pose::rna::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
	)

References core::conformation::Residue::aa(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), length, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::conformation::Residue::xyz().

Referenced by figure_out_number_base_contacts().

void core::pose::rna::virtualize_5prime_phosphates

(

pose::Pose &

pose

)

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