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Public Member Functions | Static Public Member Functions | Public Attributes | Static Private Member Functions | List of all members
core::chemical::rna::RNA_Info Class Reference

#include <RNA_Info.hh>

Inheritance diagram for core::chemical::rna::RNA_Info:
Inheritance graph
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Public Member Functions

 RNA_Info ()
 
 ~RNA_Info () override
 
void update_derived_rna_data (ResidueType const &residue_type_in)
 
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 c3prime_atom_index () const
 
Size c5prime_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
 

Static Public Member Functions

static void rna_update_last_controlling_chi (ResidueType const &residue_type_in, utility::vector1< core::Size > &last_controlling_chi, utility::vector1< AtomIndices > &atoms_last_controlled_by_chi)
 This is used for setting up the two passed vectors on the ResidueType. This can/will be called before this RNA_Info object is complete, so it's static. More...
 

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_
 
core::Size c3prime_index_
 
core::Size c5prime_index_
 
AtomIndices base_atom_list_
 
utility::vector1< boolis_RNA_base_
 
utility::vector1< boolis_phosphate_
 
utility::vector1< boolis_virtual_
 
Size chi_number_pseudoalpha_
 
Size chi_number_pseudobeta_
 
Size chi_number_pseudogamma_
 
Size chi_number_pseudoepsilon_
 
Size chi_number_pseudozeta_
 

Static Private Member Functions

static utility::vector1< Size >
const 
figure_out_chi_order (ResidueType const &residue_type)
 
static void rna_note_chi_controls_atom (ResidueType const &residue_type_in, 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_Info::RNA_Info ( )
core::chemical::rna::RNA_Info::~RNA_Info ( )
overridedefault

Member Function Documentation

bool core::chemical::rna::RNA_Info::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::chemical::rna::is_base_phosphate_atom_pair().

bool core::chemical::rna::RNA_Info::atom_is_virtual ( Size const  atomno) const
Size core::chemical::rna::RNA_Info::c1prime_atom_index ( ) const
Size core::chemical::rna::RNA_Info::c2prime_atom_index ( ) const
Size core::chemical::rna::RNA_Info::c3prime_atom_index ( ) const
inline
Size core::chemical::rna::RNA_Info::c4prime_atom_index ( ) const
Size core::chemical::rna::RNA_Info::c5prime_atom_index ( ) const
inline
Size core::chemical::rna::RNA_Info::chi_number_pseudoalpha ( ) const
inline
Size core::chemical::rna::RNA_Info::chi_number_pseudobeta ( ) const
inline
Size core::chemical::rna::RNA_Info::chi_number_pseudoepsilon ( ) const
inline
Size core::chemical::rna::RNA_Info::chi_number_pseudogamma ( ) const
inline
Size core::chemical::rna::RNA_Info::chi_number_pseudozeta ( ) const
inline
utility::vector1< Size > const core::chemical::rna::RNA_Info::figure_out_chi_order ( ResidueType const &  residue_type)
staticprivate
Size core::chemical::rna::RNA_Info::ho2prime_index ( ) const
utility::vector1< bool > const & core::chemical::rna::RNA_Info::is_phosphate ( ) const

References is_phosphate_.

utility::vector1< bool > const & core::chemical::rna::RNA_Info::is_RNA_base ( ) const

References is_RNA_base_.

bool core::chemical::rna::RNA_Info::is_RNA_base_atom ( Size const  atomno) const
utility::vector1< bool > const & core::chemical::rna::RNA_Info::is_virtual ( ) const

References is_virtual_.

Size core::chemical::rna::RNA_Info::o2prime_index ( ) const
Size core::chemical::rna::RNA_Info::o3prime_atom_index ( ) const
Size core::chemical::rna::RNA_Info::o4prime_atom_index ( ) const
Size core::chemical::rna::RNA_Info::o5prime_atom_index ( ) const
Size core::chemical::rna::RNA_Info::op1_atom_index ( ) const
Size core::chemical::rna::RNA_Info::op2_atom_index ( ) const
Size core::chemical::rna::RNA_Info::p_atom_index ( ) const
AtomIndices const & core::chemical::rna::RNA_Info::RNA_base_atoms ( ) const

References base_atom_list_.

void core::chemical::rna::RNA_Info::rna_note_chi_controls_atom ( ResidueType const &  residue_type_in,
core::Size const  chi,
core::Size const  atomno,
utility::vector1< core::Size > &  last_controlling_chi,
utility::vector1< core::Size > const &  chi_order 
)
staticprivate
void core::chemical::rna::RNA_Info::rna_update_last_controlling_chi ( ResidueType const &  residue_type_in,
utility::vector1< core::Size > &  last_controlling_chi,
utility::vector1< AtomIndices > &  atoms_last_controlled_by_chi 
)
static
void core::chemical::rna::RNA_Info::update_derived_rna_data ( ResidueType const &  residue_type_in)

Member Data Documentation

AtomIndices core::chemical::rna::RNA_Info::base_atom_list_
core::Size core::chemical::rna::RNA_Info::c1prime_index_
core::Size core::chemical::rna::RNA_Info::c2prime_index_
core::Size core::chemical::rna::RNA_Info::c3prime_index_
core::Size core::chemical::rna::RNA_Info::c4prime_index_
core::Size core::chemical::rna::RNA_Info::c5prime_index_
Size core::chemical::rna::RNA_Info::chi_number_pseudoalpha_
Size core::chemical::rna::RNA_Info::chi_number_pseudobeta_
Size core::chemical::rna::RNA_Info::chi_number_pseudoepsilon_
Size core::chemical::rna::RNA_Info::chi_number_pseudogamma_
Size core::chemical::rna::RNA_Info::chi_number_pseudozeta_
core::Size core::chemical::rna::RNA_Info::ho2prime_index_
utility::vector1< bool > core::chemical::rna::RNA_Info::is_phosphate_
utility::vector1< bool > core::chemical::rna::RNA_Info::is_RNA_base_
utility::vector1< bool > core::chemical::rna::RNA_Info::is_virtual_
core::Size core::chemical::rna::RNA_Info::o2prime_index_
core::Size core::chemical::rna::RNA_Info::o3prime_index_
core::Size core::chemical::rna::RNA_Info::o4prime_index_
core::Size core::chemical::rna::RNA_Info::o5prime_index_
core::Size core::chemical::rna::RNA_Info::op1_atom_index_
core::Size core::chemical::rna::RNA_Info::op2_atom_index_
core::Size core::chemical::rna::RNA_Info::p_atom_index_

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