Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::coarse_rna::CoarseRNA_Fragments Class Reference

#include <CoarseRNA_Fragments.hh>

Public Member Functions

 CoarseRNA_Fragments (std::string const &filename)
 
virtual ~CoarseRNA_Fragments ()
 
virtual void apply_random_fragment (core::pose::Pose &pose, core::Size const position, core::Size const size, core::Size const type, protocols::toolbox::AllowInsertOP allow_insert)
 
virtual bool is_fullatom ()
 
- Public Member Functions inherited from protocols::farna::RNA_Fragments
 RNA_Fragments ()
 
virtual ~RNA_Fragments ()
 
 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 insert_fragment (core::pose::Pose &pose, Size const &insert_res, Size const &source_res, Size const &frag_size, protocols::toolbox::AllowInsertOP allow_insert)
 
void find_source_positions (SequenceSecStructPair const &key)
 
Size pick_random_fragment (std::string const RNA_string, std::string const RNA_secstruct_string, Size const type)
 
Size pick_random_fragment (core::pose::Pose &pose, Size const position, Size const size, Size const type)
 
void initialize_frag_source_pose ()
 

Private Attributes

std::string frag_source_secstruct_
 
std::string const frag_source_file_
 
core::pose::MiniPoseOP frag_source_pose_
 
std::map
< SequenceSecStructPair,
SourcePositionsOP
source_positions_map_
 
std::map< std::string, Sizecoarse_rna_name_to_num_
 

Constructor & Destructor Documentation

protocols::coarse_rna::CoarseRNA_Fragments::CoarseRNA_Fragments ( std::string const &  filename)
protocols::coarse_rna::CoarseRNA_Fragments::~CoarseRNA_Fragments ( )
virtual

Member Function Documentation

void protocols::coarse_rna::CoarseRNA_Fragments::apply_random_fragment ( core::pose::Pose pose,
core::Size const  position,
core::Size const  size,
core::Size const  type,
protocols::toolbox::AllowInsertOP  allow_insert 
)
virtual
void protocols::coarse_rna::CoarseRNA_Fragments::find_source_positions ( SequenceSecStructPair const &  key)
private
void protocols::coarse_rna::CoarseRNA_Fragments::initialize_frag_source_pose ( )
private
void protocols::coarse_rna::CoarseRNA_Fragments::insert_fragment ( core::pose::Pose pose,
Size const &  insert_res,
Size const &  source_res,
Size const &  frag_size,
protocols::toolbox::AllowInsertOP  allow_insert 
)
private
bool protocols::coarse_rna::CoarseRNA_Fragments::is_fullatom ( )
virtual

Reimplemented from protocols::farna::RNA_Fragments.

Size protocols::coarse_rna::CoarseRNA_Fragments::pick_random_fragment ( std::string const  RNA_string,
std::string const  RNA_secstruct_string,
Size const  type 
)
private
Size protocols::coarse_rna::CoarseRNA_Fragments::pick_random_fragment ( core::pose::Pose pose,
Size const  position,
Size const  size,
Size const  type 
)
private

Member Data Documentation

std::map< std::string, Size > protocols::coarse_rna::CoarseRNA_Fragments::coarse_rna_name_to_num_
private
std::string const protocols::coarse_rna::CoarseRNA_Fragments::frag_source_file_
private
core::pose::MiniPoseOP protocols::coarse_rna::CoarseRNA_Fragments::frag_source_pose_
private
std::string protocols::coarse_rna::CoarseRNA_Fragments::frag_source_secstruct_
private
std::map< SequenceSecStructPair, SourcePositionsOP > protocols::coarse_rna::CoarseRNA_Fragments::source_positions_map_
private

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