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

#include <RNA_ResidueType.hh>

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

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< boolIs_RNA_base_atom_list_
 
utility::vector1< boolIs_phosphate_atom_list_
 
utility::vector1< boolIs_virtual_atom_list_
 
ResidueTypeCOP residue_type_
 

Private Member Functions

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

Constructor & Destructor Documentation

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

Member Function Documentation

bool core::chemical::rna::RNA_ResidueType::atom_is_phosphate ( Size const  atomno) const
bool core::chemical::rna::RNA_ResidueType::atom_is_virtual ( Size const  atomno) const
Size core::chemical::rna::RNA_ResidueType::c1star_atom_index ( ) const
Size core::chemical::rna::RNA_ResidueType::c2star_atom_index ( ) const
Size core::chemical::rna::RNA_ResidueType::c4star_atom_index ( ) const
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
bool core::chemical::rna::RNA_ResidueType::is_RNA_base_atom ( Size const  atomno) const
utility::vector1< bool > const & core::chemical::rna::RNA_ResidueType::Is_RNA_base_atom_list ( ) const
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
Size core::chemical::rna::RNA_ResidueType::o3star_atom_index ( ) const

References o3star_index_.

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

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!

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)

Member Data Documentation

AtomIndices core::chemical::rna::RNA_ResidueType::base_atom_list_
core::Size core::chemical::rna::RNA_ResidueType::c1star_index_
core::Size core::chemical::rna::RNA_ResidueType::c2star_index_
core::Size core::chemical::rna::RNA_ResidueType::c4star_index_
core::Size core::chemical::rna::RNA_ResidueType::ho2star_index_
utility::vector1< bool > core::chemical::rna::RNA_ResidueType::Is_phosphate_atom_list_
utility::vector1< bool > core::chemical::rna::RNA_ResidueType::Is_RNA_base_atom_list_
utility::vector1< bool > core::chemical::rna::RNA_ResidueType::Is_virtual_atom_list_
core::Size core::chemical::rna::RNA_ResidueType::o1p_atom_index_
core::Size core::chemical::rna::RNA_ResidueType::o2p_atom_index_
core::Size core::chemical::rna::RNA_ResidueType::o2star_index_
core::Size core::chemical::rna::RNA_ResidueType::o3star_index_
core::Size core::chemical::rna::RNA_ResidueType::o4star_index_
core::Size core::chemical::rna::RNA_ResidueType::o5star_index_
core::Size core::chemical::rna::RNA_ResidueType::p_atom_index_
ResidueTypeCOP core::chemical::rna::RNA_ResidueType::residue_type_

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