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core::fragment::rna::FullAtomRNA_Fragments Class Reference

#include <FullAtomRNA_Fragments.hh>

Inheritance diagram for core::fragment::rna::FullAtomRNA_Fragments:
Inheritance graph
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Public Member Functions

 FullAtomRNA_Fragments (std::string const &filename)
 
 ~FullAtomRNA_Fragments () override
 
void apply_random_fragment (core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, core::Size const symm_hack_arity) const override
 
void apply_best_fragment (core::scoring::ScoreFunctionOP sfxn, core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, core::Size const symm_hack_arity, core::Size const exhaustive) const override
 
bool is_fullatom () override
 
std::string name (core::Size const &i) const
 
char secstruct (core::Size const &i) const
 
bool non_main_chain_sugar_coords_defined () const
 
core::Real non_main_chain_sugar_coords (core::Size const &i, core::Size const &j, core::Size const &k) const
 
core::Real torsions (core::Size const &i, core::Size const &j) const
 
FragmentLibraryOP get_fragment_library_pointer (std::string const &RNA_string, std::string const &RNA_secstruct_string, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, utility::vector1< SYN_ANTI_RESTRICTION > const &restriction=utility::vector1< SYN_ANTI_RESTRICTION >(), Size const type=MATCH_YR) const override
 
void insert_fragment (core::pose::Pose &pose, Size const position, TorsionSet const &torsion_set, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map) const override
 
- Public Member Functions inherited from core::fragment::rna::RNA_Fragments
 RNA_Fragments ()
 
 ~RNA_Fragments () override
 

Private Member Functions

void read_vall_torsions (std::string const &filename)
 
void pick_random_fragment (TorsionSet &torsion_set, std::string const &RNA_string, std::string const &RNA_secstruct_string, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, utility::vector1< SYN_ANTI_RESTRICTION > const &restriction=utility::vector1< SYN_ANTI_RESTRICTION >(), core::Size const type=MATCH_YR) const
 
void pick_random_fragment (TorsionSet &torsion_set, core::pose::Pose &pose, core::Size const position, core::Size const size, RNA_FragmentHomologyExclusionCOP const &homology_exclusion, core::Size const type=MATCH_YR) const
 
void pick_fragment_library (FragmentLibraryPointerKey const &key) const
 

Private Attributes

ObjexxFCL::FArray2D< core::Realvall_torsions_
 
ObjexxFCL::FArray3D< core::Realvall_non_main_chain_sugar_coords_
 
ObjexxFCL::FArray1D< char > vall_sequence_
 
ObjexxFCL::FArray1D< boolvall_is_chainbreak_
 
ObjexxFCL::FArray2D< boolvall_edge_is_base_pairing_
 
ObjexxFCL::FArray1D< boolvall_makes_canonical_base_pair_
 
ObjexxFCL::FArray1D< char > vall_secstruct_
 
ObjexxFCL::FArray1D< std::string > vall_name_
 
core::Size vall_size_
 
bool vall_non_main_chain_sugar_coords_defined_
 
FragmentLibraryPointerMap fragment_library_pointer_map
 

Constructor & Destructor Documentation

core::fragment::rna::FullAtomRNA_Fragments::FullAtomRNA_Fragments ( std::string const &  filename)

References read_vall_torsions().

core::fragment::rna::FullAtomRNA_Fragments::~FullAtomRNA_Fragments ( )
inlineoverride

Member Function Documentation

void core::fragment::rna::FullAtomRNA_Fragments::apply_best_fragment ( core::scoring::ScoreFunctionOP  sfxn,
core::pose::Pose pose,
core::Size const  position,
core::Size const  size,
core::Size const  type,
RNA_FragmentHomologyExclusionCOP const &  homology_exclusion,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map,
core::Size const  symm_hack_arity,
core::Size const  exhaustive 
) const
overridevirtual
void core::fragment::rna::FullAtomRNA_Fragments::apply_random_fragment ( core::pose::Pose pose,
core::Size const  position,
core::Size const  size,
core::Size const  type,
RNA_FragmentHomologyExclusionCOP const &  homology_exclusion,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map,
core::Size const  symm_hack_arity 
) const
overridevirtual
FragmentLibraryOP core::fragment::rna::FullAtomRNA_Fragments::get_fragment_library_pointer ( std::string const &  RNA_string,
std::string const &  RNA_secstruct_string,
RNA_FragmentHomologyExclusionCOP const &  homology_exclusion,
utility::vector1< SYN_ANTI_RESTRICTION > const &  restriction = utility::vector1< SYN_ANTI_RESTRICTION >(),
Size const  type = MATCH_YR 
) const
overridevirtual
void core::fragment::rna::FullAtomRNA_Fragments::insert_fragment ( core::pose::Pose pose,
Size const  position,
TorsionSet const &  torsion_set,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map 
) const
overridevirtual
bool core::fragment::rna::FullAtomRNA_Fragments::is_fullatom ( )
overridevirtual
std::string core::fragment::rna::FullAtomRNA_Fragments::name ( core::Size const &  i) const
inline
core::Real core::fragment::rna::FullAtomRNA_Fragments::non_main_chain_sugar_coords ( core::Size const &  i,
core::Size const &  j,
core::Size const &  k 
) const
inline
bool core::fragment::rna::FullAtomRNA_Fragments::non_main_chain_sugar_coords_defined ( ) const
inline
void core::fragment::rna::FullAtomRNA_Fragments::pick_fragment_library ( FragmentLibraryPointerKey const &  key) const
private
void core::fragment::rna::FullAtomRNA_Fragments::pick_random_fragment ( TorsionSet torsion_set,
std::string const &  RNA_string,
std::string const &  RNA_secstruct_string,
RNA_FragmentHomologyExclusionCOP const &  homology_exclusion,
utility::vector1< SYN_ANTI_RESTRICTION > const &  restriction = utility::vector1< SYN_ANTI_RESTRICTION >(),
core::Size const  type = MATCH_YR 
) const
private
void core::fragment::rna::FullAtomRNA_Fragments::pick_random_fragment ( TorsionSet torsion_set,
core::pose::Pose pose,
core::Size const  position,
core::Size const  size,
RNA_FragmentHomologyExclusionCOP const &  homology_exclusion,
core::Size const  type = MATCH_YR 
) const
private
void core::fragment::rna::FullAtomRNA_Fragments::read_vall_torsions ( std::string const &  filename)
private
char core::fragment::rna::FullAtomRNA_Fragments::secstruct ( core::Size const &  i) const
inline
core::Real core::fragment::rna::FullAtomRNA_Fragments::torsions ( core::Size const &  i,
core::Size const &  j 
) const
inline

Member Data Documentation

FragmentLibraryPointerMap core::fragment::rna::FullAtomRNA_Fragments::fragment_library_pointer_map
mutableprivate
ObjexxFCL::FArray2D<bool> core::fragment::rna::FullAtomRNA_Fragments::vall_edge_is_base_pairing_
private

Referenced by read_vall_torsions().

ObjexxFCL::FArray1D<bool> core::fragment::rna::FullAtomRNA_Fragments::vall_is_chainbreak_
private

Referenced by read_vall_torsions().

ObjexxFCL::FArray1D<bool> core::fragment::rna::FullAtomRNA_Fragments::vall_makes_canonical_base_pair_
private
ObjexxFCL::FArray1D<std::string> core::fragment::rna::FullAtomRNA_Fragments::vall_name_
private

Referenced by name(), and read_vall_torsions().

ObjexxFCL::FArray3D<core::Real> core::fragment::rna::FullAtomRNA_Fragments::vall_non_main_chain_sugar_coords_
private
bool core::fragment::rna::FullAtomRNA_Fragments::vall_non_main_chain_sugar_coords_defined_
private
ObjexxFCL::FArray1D<char> core::fragment::rna::FullAtomRNA_Fragments::vall_secstruct_
private
ObjexxFCL::FArray1D<char> core::fragment::rna::FullAtomRNA_Fragments::vall_sequence_
private
core::Size core::fragment::rna::FullAtomRNA_Fragments::vall_size_
private
ObjexxFCL::FArray2D<core::Real> core::fragment::rna::FullAtomRNA_Fragments::vall_torsions_
private

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