core::pose::rna Namespace Reference

Classes
class	RNA_IdealCoord
class	RNA_SuiteAssignment
class	RNA_SuiteInfo
class	RNA_SuiteName

Typedefs
typedef utility::pointer::owning_ptr < RNA_IdealCoord >	RNA_IdealCoordOP
typedef utility::pointer::owning_ptr < RNA_SuiteName >	RNA_SuiteNameOP

Functions
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)

Typedef Documentation

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(), j, 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().

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().

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, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), runtime_assert, core::pose::Pose::total_residue(), core::chemical::UPPER_TERMINUS, 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::ChemicalManager::get_instance(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), core::chemical::ChemicalManager::residue_type_set(), core::chemical::RNA, and core::pose::Pose::set_torsion().

Referenced by correctly_add_cutpoint_variants().

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_RNA(), is_rna_chainbreak(), core::kinematics::FoldTree::new_jump(), nres, 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(), j, 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(), j, core::chemical::rna::non_main_chain_sugar_atoms, core::pose::Pose::residue(), core::pose::Pose::set_dof(), and core::pose::Pose::set_xyz().

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_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().

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 core::scoring::rna::RNA_TorsionPotential::should_score_torsion().

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::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::pose::Pose::conformation(), j, core::chemical::rna::non_main_chain_sugar_atoms, and core::conformation::Residue::xyz().

Referenced by fix_sugar_coords().

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().