core::chemical::rna::RNA_Info Class Reference

#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

core::chemical::rna::RNA_Info::RNA_Info

(

)

References base_atom_list_, is_phosphate_, and is_RNA_base_.

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

overridedefault

Member Function Documentation

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().

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().

Size core::chemical::rna::RNA_Info::c1prime_atom_index

(

)

const

References c1prime_index_.

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

Size core::chemical::rna::RNA_Info::c2prime_atom_index

(

)

const

References c2prime_index_.

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

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().

Size core::chemical::rna::RNA_Info::c4prime_atom_index

(

)

const

References c4prime_index_.

Referenced by core::scoring::rna::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().

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().

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().

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().

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().

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().

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().

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().

Size core::chemical::rna::RNA_Info::ho2prime_index

(

)

const

References ho2prime_index_.

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

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

(

)

const

References is_phosphate_.

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

(

)

const

References is_RNA_base_.

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::scoring::methods::FreeDOF_Energy::get_hbond_energy(), protocols::pockets::GenPharmacophore::get_RNAring_sasa(), and core::chemical::rna::is_base_phosphate_atom_pair().

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

(

)

const

References is_virtual_.

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::scoring::methods::FreeDOF_Energy::get_hbond_energy(), core::chemical::rna::get_rna_base_centroid(), and core::pose::rna::is_tna_chainbreak().

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().

Size core::chemical::rna::RNA_Info::o4prime_atom_index

(

)

const

References o4prime_index_.

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

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().

Size core::chemical::rna::RNA_Info::op1_atom_index

(

)

const

References op1_atom_index_.

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

Size core::chemical::rna::RNA_Info::op2_atom_index

(

)

const

References op2_atom_index_.

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

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(), and protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser::figure_out_dof_ids_and_offsets().

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

(

)

const

References base_atom_list_.

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().

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().

void core::chemical::rna::RNA_Info::update_derived_rna_data

(

ResidueType const &

residue_type_in

)

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atoms_last_controlled_by_chi(), base_atom_list_, c1prime_index_, c2prime_index_, c3prime_index_, c4prime_index_, c5prime_index_, core::chemical::ResidueType::chi_atoms(), chi_number_pseudoalpha_, chi_number_pseudobeta_, chi_number_pseudoepsilon_, chi_number_pseudogamma_, chi_number_pseudozeta_, core::chemical::ResidueType::has(), ho2prime_index_, is_phosphate_, is_RNA_base_, core::chemical::ResidueType::is_TNA(), core::chemical::ResidueType::is_virtual(), is_virtual_, core::chemical::ResidueType::last_controlling_chi(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), o2prime_index_, o3prime_index_, o4prime_index_, o5prime_index_, op1_atom_index_, op2_atom_index_, and p_atom_index_.

Member Data Documentation

AtomIndices core::chemical::rna::RNA_Info::base_atom_list_

Referenced by RNA_base_atoms(), RNA_Info(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::c1prime_index_

Referenced by c1prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::c2prime_index_

Referenced by c2prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::c3prime_index_

Referenced by c3prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::c4prime_index_

Referenced by c4prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::c5prime_index_

Referenced by c5prime_atom_index(), and update_derived_rna_data().

Size core::chemical::rna::RNA_Info::chi_number_pseudoalpha_

Referenced by chi_number_pseudoalpha(), and update_derived_rna_data().

Size core::chemical::rna::RNA_Info::chi_number_pseudobeta_

Referenced by chi_number_pseudobeta(), and update_derived_rna_data().

Size core::chemical::rna::RNA_Info::chi_number_pseudoepsilon_

Referenced by chi_number_pseudoepsilon(), and update_derived_rna_data().

Size core::chemical::rna::RNA_Info::chi_number_pseudogamma_

Referenced by chi_number_pseudogamma(), and update_derived_rna_data().

Size core::chemical::rna::RNA_Info::chi_number_pseudozeta_

Referenced by chi_number_pseudozeta(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::ho2prime_index_

Referenced by ho2prime_index(), and update_derived_rna_data().

utility::vector1< bool > core::chemical::rna::RNA_Info::is_phosphate_

Referenced by atom_is_phosphate(), is_phosphate(), RNA_Info(), and update_derived_rna_data().

utility::vector1< bool > core::chemical::rna::RNA_Info::is_RNA_base_

Referenced by is_RNA_base(), is_RNA_base_atom(), RNA_Info(), and update_derived_rna_data().

utility::vector1< bool > core::chemical::rna::RNA_Info::is_virtual_

Referenced by atom_is_virtual(), is_virtual(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::o2prime_index_

Referenced by o2prime_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::o3prime_index_

Referenced by o3prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::o4prime_index_

Referenced by o4prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::o5prime_index_

Referenced by o5prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::op1_atom_index_

Referenced by op1_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::op2_atom_index_

Referenced by op2_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_Info::p_atom_index_

Referenced by p_atom_index(), and update_derived_rna_data().

---

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

• src/core/chemical/rna/RNA_Info.hh
• src/core/chemical/rna/RNA_Info.cc