Rosetta Core  2014.35
Public Member Functions | Public Attributes | Private Member Functions | List of all members
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< boolis_RNA_base_
 
utility::vector1< boolis_phosphate_
 
utility::vector1< boolis_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 ( )
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::c1prime_atom_index ( ) const
Size core::chemical::rna::RNA_ResidueType::c2prime_atom_index ( ) const
Size core::chemical::rna::RNA_ResidueType::c4prime_atom_index ( ) const
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudoalpha ( ) const
inline
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudobeta ( ) const
inline
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudoepsilon ( ) const
inline
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudogamma ( ) const
inline
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudozeta ( ) const
inline
utility::vector1< Size > const core::chemical::rna::RNA_ResidueType::figure_out_chi_order ( ) const
private
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
utility::vector1< bool > const & core::chemical::rna::RNA_ResidueType::is_virtual ( ) const

References is_virtual_.

Size core::chemical::rna::RNA_ResidueType::o2prime_index ( ) const
Size core::chemical::rna::RNA_ResidueType::o3prime_atom_index ( ) const

References o3prime_index_.

Size core::chemical::rna::RNA_ResidueType::o4prime_atom_index ( ) const
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)

Member Data Documentation

AtomIndices core::chemical::rna::RNA_ResidueType::base_atom_list_
core::Size core::chemical::rna::RNA_ResidueType::c1prime_index_
core::Size core::chemical::rna::RNA_ResidueType::c2prime_index_
core::Size core::chemical::rna::RNA_ResidueType::c4prime_index_
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudoalpha_
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudobeta_
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudoepsilon_
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudogamma_
Size core::chemical::rna::RNA_ResidueType::chi_number_pseudozeta_
core::Size core::chemical::rna::RNA_ResidueType::ho2prime_index_
utility::vector1< bool > core::chemical::rna::RNA_ResidueType::is_phosphate_
utility::vector1< bool > core::chemical::rna::RNA_ResidueType::is_RNA_base_
utility::vector1< bool > core::chemical::rna::RNA_ResidueType::is_virtual_
core::Size core::chemical::rna::RNA_ResidueType::o2prime_index_
core::Size core::chemical::rna::RNA_ResidueType::o3prime_index_
core::Size core::chemical::rna::RNA_ResidueType::o4prime_index_
core::Size core::chemical::rna::RNA_ResidueType::o5prime_index_
core::Size core::chemical::rna::RNA_ResidueType::op1_atom_index_
core::Size core::chemical::rna::RNA_ResidueType::op2_atom_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: