core::chemical::rna::RNA_ResidueType Class Reference

#include <RNA_ResidueType.hh>

Public Member Functions
	RNA_ResidueType ()
virtual	~RNA_ResidueType ()
void	update_derived_rna_data (ResidueTypeCOP const residue_type_in)
void	rna_update_last_controlling_chi (ResidueTypeCOP const residue_type_in, utility::vector1< core::Size > &last_controlling_chi, utility::vector1< AtomIndices > &atoms_last_controlled_by_chi)
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	chi_number_pseudoalpha () const
Size	chi_number_pseudobeta () const
Size	chi_number_pseudogamma () const
Size	chi_number_pseudoepsilon () const
Size	chi_number_pseudozeta () const

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_
AtomIndices	base_atom_list_
utility::vector1< bool >	is_RNA_base_
utility::vector1< bool >	is_phosphate_
utility::vector1< bool >	is_virtual_
ResidueTypeCOP	residue_type_
Size	chi_number_pseudoalpha_
Size	chi_number_pseudobeta_
Size	chi_number_pseudogamma_
Size	chi_number_pseudoepsilon_
Size	chi_number_pseudozeta_

Private Member Functions
utility::vector1< Size > const	figure_out_chi_order () const
void	rna_note_chi_controls_atom (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_ResidueType::RNA_ResidueType

(

)

References base_atom_list_, is_phosphate_, and is_RNA_base_.

core::chemical::rna::RNA_ResidueType::~RNA_ResidueType ( )

virtual

Member Function Documentation

bool core::chemical::rna::RNA_ResidueType::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::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), core::chemical::rna::Is_base_phosphate_atom_pair(), and core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().

bool core::chemical::rna::RNA_ResidueType::atom_is_virtual

(

Size const

atomno

)

const

References is_virtual_.

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

Size core::chemical::rna::RNA_ResidueType::c1prime_atom_index

(

)

const

References c1prime_index_.

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

Size core::chemical::rna::RNA_ResidueType::c2prime_atom_index

(

)

const

References c2prime_index_.

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

Size core::chemical::rna::RNA_ResidueType::c4prime_atom_index

(

)

const

References c4prime_index_.

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

Size core::chemical::rna::RNA_ResidueType::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_ResidueType::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_ResidueType::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_ResidueType::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_ResidueType::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_ResidueType::figure_out_chi_order ( ) const

private

Referenced by rna_update_last_controlling_chi().

Size core::chemical::rna::RNA_ResidueType::ho2prime_index

(

)

const

References ho2prime_index_.

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

(

)

const

References is_phosphate_.

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

(

)

const

References is_RNA_base_.

bool core::chemical::rna::RNA_ResidueType::is_RNA_base_atom

(

Size const

atomno

)

const

References is_RNA_base_.

Referenced by core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::eval_atom_derivative(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), core::chemical::rna::Is_base_phosphate_atom_pair(), and core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy().

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

(

)

const

References is_virtual_.

Size core::chemical::rna::RNA_ResidueType::o2prime_index

(

)

const

References o2prime_index_.

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

Size core::chemical::rna::RNA_ResidueType::o3prime_atom_index

(

)

const

References o3prime_index_.

Size core::chemical::rna::RNA_ResidueType::o4prime_atom_index

(

)

const

References o4prime_index_.

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

Size core::chemical::rna::RNA_ResidueType::o5prime_atom_index

(

)

const

References o5prime_index_.

Size core::chemical::rna::RNA_ResidueType::op1_atom_index

(

)

const

References op1_atom_index_.

Size core::chemical::rna::RNA_ResidueType::op2_atom_index

(

)

const

References op2_atom_index_.

Size core::chemical::rna::RNA_ResidueType::p_atom_index

(

)

const

References p_atom_index_.

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

(

)

const

References base_atom_list_.

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

private

WARNING THIS FUNCTION SHOULD NOT ACCESS ANY DATA of the RNA_ResidueType object itself since at this point it is not yet updated! ALSO SHOULD MAKE THIS FUNCTION A CONST FUNCTION!

References residue_type_, and runtime_assert.

Referenced by rna_update_last_controlling_chi().

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

WARNING THIS FUNCTION SHOULD NOT ACCESS ANY DATA of the RNA_ResidueType object itself since at this point it is not yet updated! ALSO SHOULD MAKE THIS FUNCTION A CONST FUNCTION!

References figure_out_chi_order(), residue_type_, and rna_note_chi_controls_atom().

void core::chemical::rna::RNA_ResidueType::update_derived_rna_data

(

ResidueTypeCOP const

residue_type_in

)

References base_atom_list_, c1prime_index_, c2prime_index_, c4prime_index_, chi_number_pseudoalpha_, chi_number_pseudobeta_, chi_number_pseudoepsilon_, chi_number_pseudogamma_, chi_number_pseudozeta_, ho2prime_index_, is_phosphate_, is_RNA_base_, is_virtual_, o2prime_index_, o3prime_index_, o4prime_index_, o5prime_index_, op1_atom_index_, op2_atom_index_, p_atom_index_, residue_type_, runtime_assert, and utility_exit_with_message.

Member Data Documentation

AtomIndices core::chemical::rna::RNA_ResidueType::base_atom_list_

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

core::Size core::chemical::rna::RNA_ResidueType::c1prime_index_

Referenced by c1prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::c2prime_index_

Referenced by c2prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::c4prime_index_

Referenced by c4prime_atom_index(), and update_derived_rna_data().

Size core::chemical::rna::RNA_ResidueType::chi_number_pseudoalpha_

Referenced by chi_number_pseudoalpha(), and update_derived_rna_data().

Size core::chemical::rna::RNA_ResidueType::chi_number_pseudobeta_

Referenced by chi_number_pseudobeta(), and update_derived_rna_data().

Size core::chemical::rna::RNA_ResidueType::chi_number_pseudoepsilon_

Referenced by chi_number_pseudoepsilon(), and update_derived_rna_data().

Size core::chemical::rna::RNA_ResidueType::chi_number_pseudogamma_

Referenced by chi_number_pseudogamma(), and update_derived_rna_data().

Size core::chemical::rna::RNA_ResidueType::chi_number_pseudozeta_

Referenced by chi_number_pseudozeta(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::ho2prime_index_

Referenced by ho2prime_index(), and update_derived_rna_data().

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

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

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

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

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

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

core::Size core::chemical::rna::RNA_ResidueType::o2prime_index_

Referenced by o2prime_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::o3prime_index_

Referenced by o3prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::o4prime_index_

Referenced by o4prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::o5prime_index_

Referenced by o5prime_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::op1_atom_index_

Referenced by op1_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::op2_atom_index_

Referenced by op2_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::p_atom_index_

Referenced by p_atom_index(), and update_derived_rna_data().

ResidueTypeCOP core::chemical::rna::RNA_ResidueType::residue_type_

Referenced by rna_note_chi_controls_atom(), rna_update_last_controlling_chi(), and update_derived_rna_data().

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

• symlinks/rosetta/src/core/chemical/rna/RNA_ResidueType.hh
• symlinks/rosetta/src/core/chemical/rna/RNA_ResidueType.cc