#include <RNA_ResidueType.hh>

Inheritance diagram for core::chemical::rna::RNA_ResidueType:

Collaboration diagram for core::chemical::rna::RNA_ResidueType:

Public Member Functions
	RNA_ResidueType ()
	~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_atom_list () const
bool	atom_is_virtual (Size const atomno) const
utility::vector1< bool > const &	Is_phosphate_atom_list () 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?
utility::vector1< bool > const &	Is_RNA_base_atom_list () const
bool	is_RNA_base_atom (Size const atomno) const
AtomIndices const &	RNA_base_atoms () const
Size	ho2star_index () const
Size	o2star_index () const
Size	p_atom_index () const
Size	o1p_atom_index () const
Size	o2p_atom_index () const
Size	o5star_atom_index () const
Size	o3star_atom_index () const
Size	o4star_atom_index () const
Size	c1star_atom_index () const
Size	c2star_atom_index () const
Size	c4star_atom_index () const
Public Attributes
core::Size	o2star_index_
core::Size	ho2star_index_
core::Size	p_atom_index_
core::Size	o1p_atom_index_
core::Size	o2p_atom_index_
core::Size	o5star_index_
core::Size	o3star_index_
core::Size	o4star_index_
core::Size	c1star_index_
core::Size	c2star_index_
core::Size	c4star_index_
AtomIndices	base_atom_list_
utility::vector1< bool >	Is_RNA_base_atom_list_
utility::vector1< bool >	Is_phosphate_atom_list_
utility::vector1< bool >	Is_virtual_atom_list_
ResidueTypeCOP	residue_type_

Constructor & Destructor Documentation

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

References base_atom_list_, Is_phosphate_atom_list_, and Is_RNA_base_atom_list_.

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

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_atom_list_.

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::scoring::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_atom_list_.

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

Size core::chemical::rna::RNA_ResidueType::c1star_atom_index ( ) const

References c1star_index_.

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

Size core::chemical::rna::RNA_ResidueType::c2star_atom_index ( ) const

References c2star_index_.

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

Size core::chemical::rna::RNA_ResidueType::c4star_atom_index ( ) const

References c4star_index_.

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

Size core::chemical::rna::RNA_ResidueType::ho2star_index ( ) const

References ho2star_index_.

utility::vector1< bool > const & core::chemical::rna::RNA_ResidueType::Is_phosphate_atom_list ( ) const

References Is_phosphate_atom_list_.

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

References Is_RNA_base_atom_list_.

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::scoring::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_RNA_base_atom_list ( ) const

References Is_RNA_base_atom_list_.

utility::vector1< bool > const & core::chemical::rna::RNA_ResidueType::Is_virtual_atom_list ( ) const

References Is_virtual_atom_list_.

Size core::chemical::rna::RNA_ResidueType::o1p_atom_index ( ) const

References o1p_atom_index_.

Size core::chemical::rna::RNA_ResidueType::o2p_atom_index ( ) const

References o2p_atom_index_.

Size core::chemical::rna::RNA_ResidueType::o2star_index ( ) const

References o2star_index_.

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

Size core::chemical::rna::RNA_ResidueType::o3star_atom_index ( ) const

References o3star_index_.

Size core::chemical::rna::RNA_ResidueType::o4star_atom_index ( ) const

References o4star_index_.

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

Size core::chemical::rna::RNA_ResidueType::o5star_atom_index ( ) const

References o5star_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_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 residue_type_.

void core::chemical::rna::RNA_ResidueType::update_derived_rna_data ( ResidueTypeCOP const residue_type_in )

References base_atom_list_, c1star_index_, c2star_index_, c4star_index_, ho2star_index_, protocols::swa::rna::Is_phosphate_atom(), Is_phosphate_atom_list_, Is_RNA_base_atom_list_, Is_virtual_atom_list_, o1p_atom_index_, o2p_atom_index_, o2star_index_, o3star_index_, o4star_index_, o5star_index_, p_atom_index_, and residue_type_.