#include <RNA_Info.hh>

Inheritance diagram for core::chemical::rna::RNA_Info:

Public Member Functions
	RNA_Info ()

	~RNA_Info () override

void	update_derived_rna_data (ResidueType const &residue_type_in)

utility::vector1< bool > const &	is_virtual () const

bool	atom_is_virtual (Size const atomno) const

utility::vector1< bool > const &	is_phosphate () const

bool	atom_is_phosphate (Size const atomno) const
	quick lookup: is the atom with the given index is part of the RNA phosphate or not? More...

utility::vector1< bool > const &	is_RNA_base () const

bool	is_RNA_base_atom (Size const atomno) const

AtomIndices const &	RNA_base_atoms () const

Size	ho2prime_index () const

Size	o2prime_index () const

Size	p_atom_index () const

Size	op2_atom_index () const

Size	op1_atom_index () const

Size	o5prime_atom_index () const

Size	o3prime_atom_index () const

Size	o4prime_atom_index () const

Size	c1prime_atom_index () const

Size	c2prime_atom_index () const

Size	c4prime_atom_index () const

Size	c3prime_atom_index () const

Size	c5prime_atom_index () const

Size	chi_number_pseudoalpha () const

Size	chi_number_pseudobeta () const

Size	chi_number_pseudogamma () const

Size	chi_number_pseudoepsilon () const

Size	chi_number_pseudozeta () const

Static Public Member Functions
static void	rna_update_last_controlling_chi (ResidueType const &residue_type_in, utility::vector1< core::Size > &last_controlling_chi, utility::vector1< AtomIndices > &atoms_last_controlled_by_chi)
	This is used for setting up the two passed vectors on the ResidueType. This can/will be called before this RNA_Info object is complete, so it's static. More...

Public Attributes
core::Size	o2prime_index_

core::Size	ho2prime_index_

core::Size	p_atom_index_

core::Size	op2_atom_index_

core::Size	op1_atom_index_

core::Size	o5prime_index_

core::Size	o3prime_index_

core::Size	o4prime_index_

core::Size	c1prime_index_

core::Size	c2prime_index_

core::Size	c4prime_index_

core::Size	c3prime_index_

core::Size	c5prime_index_

AtomIndices	base_atom_list_

utility::vector1< bool >	is_RNA_base_

utility::vector1< bool >	is_phosphate_

utility::vector1< bool >	is_virtual_

Size	chi_number_pseudoalpha_

Size	chi_number_pseudobeta_

Size	chi_number_pseudogamma_

Size	chi_number_pseudoepsilon_

Size	chi_number_pseudozeta_

Static Private Member Functions
static utility::vector1< Size > const	figure_out_chi_order (ResidueType const &residue_type)

static void	rna_note_chi_controls_atom (ResidueType const &residue_type_in, core::Size const chi, core::Size const atomno, utility::vector1< core::Size > &last_controlling_chi, utility::vector1< core::Size > const &chi_order)

Constructor & Destructor Documentation

◆ RNA_Info()

core::chemical::rna::RNA_Info::RNA_Info ( )

References base_atom_list_, is_phosphate_, and is_RNA_base_.

◆ ~RNA_Info()

core::chemical::rna::RNA_Info::~RNA_Info ( )

overridedefault

Member Function Documentation

◆ atom_is_phosphate()

bool core::chemical::rna::RNA_Info::atom_is_phosphate ( Size const atomno ) const

quick lookup: is the atom with the given index is part of the RNA phosphate or not?

References is_phosphate_.

Referenced by core::chemical::rna::is_base_phosphate_atom_pair().

◆ atom_is_virtual()

bool core::chemical::rna::RNA_Info::atom_is_virtual ( Size const atomno ) const

References is_virtual_.

Referenced by core::chemical::rna::get_rna_base_centroid().

◆ c1prime_atom_index()

Size core::chemical::rna::RNA_Info::c1prime_atom_index ( ) const

References c1prime_index_.

Referenced by core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::pose::rna::get_sugar_centroid(), core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), core::pose::rna::initialize_atoms_for_which_we_need_new_dofs(), and core::pose::rna::setup_base_pair_constraints().

◆ c2prime_atom_index()

Size core::chemical::rna::RNA_Info::c2prime_atom_index ( ) const

References c2prime_index_.

Referenced by core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), core::pose::rna::get_sugar_centroid(), and core::pose::rna::initialize_atoms_for_which_we_need_new_dofs().

◆ c3prime_atom_index()

Size core::chemical::rna::RNA_Info::c3prime_atom_index ( ) const

inline

References c3prime_index_.

Referenced by protocols::rna::denovo::create_rna_vall_torsions(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), and core::pose::rna::get_sugar_centroid().

◆ c4prime_atom_index()

Size core::chemical::rna::RNA_Info::c4prime_atom_index ( ) const

References c4prime_index_.

Referenced by core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::rna::denovo::create_rna_vall_torsions(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), and core::pose::rna::get_sugar_centroid().

◆ c5prime_atom_index()

Size core::chemical::rna::RNA_Info::c5prime_atom_index ( ) const

inline

References c5prime_index_.

Referenced by protocols::rna::denovo::create_rna_vall_torsions(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), and protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets().

◆ chi_number_pseudoalpha()

Size core::chemical::rna::RNA_Info::chi_number_pseudoalpha ( ) const

inline

References chi_number_pseudoalpha_.

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), and core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy().

◆ chi_number_pseudobeta()

Size core::chemical::rna::RNA_Info::chi_number_pseudobeta ( ) const

inline

References chi_number_pseudobeta_.

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), and core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy().

◆ chi_number_pseudoepsilon()

Size core::chemical::rna::RNA_Info::chi_number_pseudoepsilon ( ) const

inline

References chi_number_pseudoepsilon_.

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), and core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy().

◆ chi_number_pseudogamma()

Size core::chemical::rna::RNA_Info::chi_number_pseudogamma ( ) const

inline

References chi_number_pseudogamma_.

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), and core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy().

◆ chi_number_pseudozeta()

Size core::chemical::rna::RNA_Info::chi_number_pseudozeta ( ) const

inline

References chi_number_pseudozeta_.

Referenced by core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), and core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy().

◆ figure_out_chi_order()

utility::vector1< Size > const core::chemical::rna::RNA_Info::figure_out_chi_order ( ResidueType const & residue_type )

staticprivate

References core::chemical::ResidueType::nchi().

Referenced by rna_update_last_controlling_chi().

◆ ho2prime_index()

Size core::chemical::rna::RNA_Info::ho2prime_index ( ) const

References ho2prime_index_.

Referenced by core::energy_methods::FreeDOF_Energy::get_hbond_energy(), and protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::virtualize_poor_scoring_o2prime_hydrogens().

◆ is_phosphate()

utility::vector1< bool > const & core::chemical::rna::RNA_Info::is_phosphate ( ) const

References is_phosphate_.

◆ is_RNA_base()

utility::vector1< bool > const & core::chemical::rna::RNA_Info::is_RNA_base ( ) const

References is_RNA_base_.

◆ is_RNA_base_atom()

bool core::chemical::rna::RNA_Info::is_RNA_base_atom ( Size const atomno ) const

References is_RNA_base_.

Referenced by protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), core::energy_methods::FreeDOF_Energy::get_hbond_energy(), protocols::pockets::GenPharmacophore::get_RNAring_sasa(), and core::chemical::rna::is_base_phosphate_atom_pair().

◆ is_virtual()

utility::vector1< bool > const & core::chemical::rna::RNA_Info::is_virtual ( ) const

References is_virtual_.

◆ o2prime_index()

Size core::chemical::rna::RNA_Info::o2prime_index ( ) const

References o2prime_index_.

Referenced by protocols::stepwise::modeler::packer::check_o2prime_contact(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), core::scoring::hbonds::get_hb_acc_chem_type(), core::energy_methods::FreeDOF_Energy::get_hbond_energy(), core::chemical::rna::get_rna_base_centroid(), core::pose::rna::initialize_atoms_for_which_we_need_new_dofs(), and core::pose::rna::is_tna_chainbreak().

◆ o3prime_atom_index()

Size core::chemical::rna::RNA_Info::o3prime_atom_index ( ) const

References o3prime_index_.

Referenced by protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), core::scoring::hbonds::get_hb_acc_chem_type(), and core::pose::rna::is_rna_chainbreak().

◆ o4prime_atom_index()

Size core::chemical::rna::RNA_Info::o4prime_atom_index ( ) const

References o4prime_index_.

Referenced by core::energy_methods::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::scoring::hbonds::get_hb_acc_chem_type(), core::pose::rna::get_sugar_centroid(), and core::pose::rna::initialize_atoms_for_which_we_need_new_dofs().

◆ o5prime_atom_index()

Size core::chemical::rna::RNA_Info::o5prime_atom_index ( ) const

References o5prime_index_.

Referenced by protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), and core::scoring::hbonds::get_hb_acc_chem_type().

◆ op1_atom_index()

Size core::chemical::rna::RNA_Info::op1_atom_index ( ) const

References op1_atom_index_.

Referenced by core::scoring::hbonds::get_hb_acc_chem_type().

◆ op2_atom_index()

Size core::chemical::rna::RNA_Info::op2_atom_index ( ) const

References op2_atom_index_.

Referenced by core::scoring::hbonds::get_hb_acc_chem_type().

◆ p_atom_index()

Size core::chemical::rna::RNA_Info::p_atom_index ( ) const

References p_atom_index_.

Referenced by protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets(), core::pose::rna::is_rna_chainbreak(), and core::pose::rna::is_tna_chainbreak().

◆ RNA_base_atoms()

AtomIndices const & core::chemical::rna::RNA_Info::RNA_base_atoms ( ) const

References base_atom_list_.

◆ rna_note_chi_controls_atom()

void core::chemical::rna::RNA_Info::rna_note_chi_controls_atom	(	ResidueType const &	residue_type_in,
		core::Size const	chi,
		core::Size const	atomno,
		utility::vector1< core::Size > &	last_controlling_chi,
		utility::vector1< core::Size > const &	chi_order
	)

staticprivate

References core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::bonded_neighbor(), and core::chemical::ResidueType::nchi().

Referenced by rna_update_last_controlling_chi().

◆ rna_update_last_controlling_chi()

void core::chemical::rna::RNA_Info::rna_update_last_controlling_chi	(	ResidueType const &	residue_type_in,
		utility::vector1< core::Size > &	last_controlling_chi,
		utility::vector1< AtomIndices > &	atoms_last_controlled_by_chi
	)

static

This is used for setting up the two passed vectors on the ResidueType. This can/will be called before this RNA_Info object is complete, so it's static.

References core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::chi_atoms(), figure_out_chi_order(), core::chemical::ResidueType::is_canonical_nucleic(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), and rna_note_chi_controls_atom().