#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 ()

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_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? More...

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

Private Member Functions
void	rna_note_chi_controls_atom (core::Size const chi, core::Size const atomno, utility::vector1< core::Size > &last_controlling_chi)

Detailed Description

Definition at line 43 of file RNA_ResidueType.hh.

Constructor & Destructor Documentation

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

Definition at line 51 of file RNA_ResidueType.cc.

References base_atom_list_, Is_phosphate_atom_list_, and Is_RNA_base_atom_list_.

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

virtual

Definition at line 71 of file RNA_ResidueType.cc.

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?

Definition at line 303 of file RNA_ResidueType.cc.

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

Definition at line 284 of file RNA_ResidueType.cc.

References Is_virtual_atom_list_.

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

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

Definition at line 450 of file RNA_ResidueType.cc.

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

Definition at line 459 of file RNA_ResidueType.cc.

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

Definition at line 468 of file RNA_ResidueType.cc.

References c4star_index_.

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

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

Definition at line 355 of file RNA_ResidueType.cc.

References ho2star_index_.

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

Definition at line 294 of file RNA_ResidueType.cc.

References Is_phosphate_atom_list_.

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

Definition at line 323 of file RNA_ResidueType.cc.

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

Definition at line 313 of file RNA_ResidueType.cc.

References Is_RNA_base_atom_list_.

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

Definition at line 275 of file RNA_ResidueType.cc.

References Is_virtual_atom_list_.

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

Definition at line 400 of file RNA_ResidueType.cc.

References o1p_atom_index_.

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

Definition at line 411 of file RNA_ResidueType.cc.

References o2p_atom_index_.

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

Definition at line 367 of file RNA_ResidueType.cc.

References o2star_index_.

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

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

Definition at line 431 of file RNA_ResidueType.cc.

References o3star_index_.

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

Definition at line 441 of file RNA_ResidueType.cc.

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

Definition at line 421 of file RNA_ResidueType.cc.

References o5star_index_.

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

Definition at line 389 of file RNA_ResidueType.cc.

References p_atom_index_.

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

Definition at line 337 of file RNA_ResidueType.cc.

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
	)

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!

Definition at line 161 of file RNA_ResidueType.cc.

References residue_type_.

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!

Definition at line 214 of file RNA_ResidueType.cc.

References residue_type_, and rna_note_chi_controls_atom().

Referenced by core::chemical::ResidueType::update_derived_data().

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

Definition at line 77 of file RNA_ResidueType.cc.

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_.

Referenced by core::chemical::ResidueType::update_derived_data().

Member Data Documentation

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

Definition at line 147 of file RNA_ResidueType.hh.

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

core::Size core::chemical::rna::RNA_ResidueType::c1star_index_

Definition at line 143 of file RNA_ResidueType.hh.

Referenced by c1star_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::c2star_index_

Definition at line 144 of file RNA_ResidueType.hh.

Referenced by c2star_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::c4star_index_

Definition at line 145 of file RNA_ResidueType.hh.

Referenced by c4star_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::ho2star_index_

Definition at line 132 of file RNA_ResidueType.hh.

Referenced by ho2star_index(), and update_derived_rna_data().

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

Definition at line 150 of file RNA_ResidueType.hh.

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

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

Definition at line 149 of file RNA_ResidueType.hh.

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

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

Definition at line 152 of file RNA_ResidueType.hh.

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

core::Size core::chemical::rna::RNA_ResidueType::o1p_atom_index_

Definition at line 136 of file RNA_ResidueType.hh.

Referenced by o1p_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::o2p_atom_index_

Definition at line 137 of file RNA_ResidueType.hh.

Referenced by o2p_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::o2star_index_

Definition at line 131 of file RNA_ResidueType.hh.

Referenced by o2star_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::o3star_index_

Definition at line 139 of file RNA_ResidueType.hh.

Referenced by o3star_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::o4star_index_

Definition at line 142 of file RNA_ResidueType.hh.

Referenced by o4star_atom_index(), and update_derived_rna_data().

core::Size core::chemical::rna::RNA_ResidueType::o5star_index_

Definition at line 138 of file RNA_ResidueType.hh.

Referenced by o5star_atom_index(), and update_derived_rna_data().

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

Definition at line 135 of file RNA_ResidueType.hh.

Referenced by p_atom_index(), and update_derived_rna_data().

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

Definition at line 156 of file RNA_ResidueType.hh.

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

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

src/core/chemical/rna/RNA_ResidueType.hh
src/core/chemical/rna/RNA_ResidueType.cc

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_

Public Member Functions

Public Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation