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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::rna::RNA_Fragments Class Reference

#include <RNA_FragmentsClasses.hh>

Inheritance diagram for protocols::rna::RNA_Fragments:
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Public Member Functions

 RNA_Fragments ()
 
virtual ~RNA_Fragments ()
 
virtual void apply_random_fragment (core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type, toolbox::AllowInsertOP allow_insert)
 
virtual bool is_fullatom ()
 
 RNA_Fragments (std::string const filename)
 
void read_vall_torsions (std::string const filename)
 
void pick_random_fragment (TorsionSet &torsion_set, core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type=MATCH_YR)
 
core::Real torsions (core::Size const &i, core::Size const &j) const
 
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
 

Private Member Functions

void pick_random_fragment (TorsionSet &torsion_set, std::string const RNA_string, std::string const RNA_secstruct_string, core::Size const type=MATCH_YR)
 
std::string const convert_based_on_match_type (std::string const RNA_string, core::Size const type)
 
bool compare_RNA_char (char const char1, char const char2)
 
bool compare_RNA_secstruct (char const char1, char const char2)
 
void pick_fragment_library (SequenceSecStructPair const &key)
 
void pick_random_fragment (FArray1D< core::Real > &RNA_torsions, std::string const RNA_string)
 

Private Attributes

FArray2D< core::Realvall_torsions_
 
FArray3D< core::Realvall_non_main_chain_sugar_coords_
 
FArray1D< char > vall_sequence_
 
FArray1D< boolvall_is_chainbreak_
 
FArray2D< boolvall_edge_is_base_pairing_
 
FArray1D< boolvall_makes_canonical_base_pair_
 
FArray1D< char > vall_secstruct_
 
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

protocols::rna::RNA_Fragments::RNA_Fragments ( )
protocols::rna::RNA_Fragments::~RNA_Fragments ( )
virtual
protocols::rna::RNA_Fragments::RNA_Fragments ( std::string const  filename)
inline

Member Function Documentation

void protocols::rna::RNA_Fragments::apply_random_fragment ( core::pose::Pose pose,
core::Size const  position,
core::Size const  size,
core::Size const  type,
toolbox::AllowInsertOP  allow_insert 
)
virtual
bool protocols::rna::RNA_Fragments::compare_RNA_char ( char const  char1,
char const  char2 
)
private
bool protocols::rna::RNA_Fragments::compare_RNA_secstruct ( char const  char1,
char const  char2 
)
private
std::string const protocols::rna::RNA_Fragments::convert_based_on_match_type ( std::string const  RNA_string,
core::Size const  type 
)
private
bool protocols::rna::RNA_Fragments::is_fullatom ( )
virtual
std::string protocols::rna::RNA_Fragments::name ( core::Size const &  i) const
inline
core::Real protocols::rna::RNA_Fragments::non_main_chain_sugar_coords ( core::Size const &  i,
core::Size const &  j,
core::Size const &  k 
) const
inline
bool protocols::rna::RNA_Fragments::non_main_chain_sugar_coords_defined ( ) const
inline
void protocols::rna::RNA_Fragments::pick_fragment_library ( SequenceSecStructPair const &  key)
private
void protocols::rna::RNA_Fragments::pick_random_fragment ( TorsionSet torsion_set,
core::pose::Pose pose,
core::Size const  position,
core::Size const  size,
core::Size const  type = MATCH_YR 
)
void protocols::rna::RNA_Fragments::pick_random_fragment ( TorsionSet torsion_set,
std::string const  RNA_string,
std::string const  RNA_secstruct_string,
core::Size const  type = MATCH_YR 
)
private
void protocols::rna::RNA_Fragments::pick_random_fragment ( FArray1D< core::Real > &  RNA_torsions,
std::string const  RNA_string 
)
private
void protocols::rna::RNA_Fragments::read_vall_torsions ( std::string const  filename)
char protocols::rna::RNA_Fragments::secstruct ( core::Size const &  i) const
inline
core::Real protocols::rna::RNA_Fragments::torsions ( core::Size const &  i,
core::Size const &  j 
) const
inline

Member Data Documentation

FragmentLibraryPointerMap protocols::rna::RNA_Fragments::fragment_library_pointer_map
private
FArray2D<bool> protocols::rna::RNA_Fragments::vall_edge_is_base_pairing_
private
FArray1D<bool> protocols::rna::RNA_Fragments::vall_is_chainbreak_
private
FArray1D<bool> protocols::rna::RNA_Fragments::vall_makes_canonical_base_pair_
private
FArray1D<std::string> protocols::rna::RNA_Fragments::vall_name_
private
FArray3D<core::Real> protocols::rna::RNA_Fragments::vall_non_main_chain_sugar_coords_
private
bool protocols::rna::RNA_Fragments::vall_non_main_chain_sugar_coords_defined_
private
FArray1D<char> protocols::rna::RNA_Fragments::vall_secstruct_
private
FArray1D<char> protocols::rna::RNA_Fragments::vall_sequence_
private
core::Size protocols::rna::RNA_Fragments::vall_size_
private
FArray2D<core::Real> protocols::rna::RNA_Fragments::vall_torsions_
private

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