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

#include <RNA_ChunkLibrary.hh>

Public Member Functions

 RNA_ChunkLibrary ()
 
 RNA_ChunkLibrary (utility::vector1< std::string > const &pdb_files, utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)
 
 RNA_ChunkLibrary (utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)
 
 ~RNA_ChunkLibrary ()
 
void initialize_rna_chunk_library (utility::vector1< std::string > const &pdb_files, utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, utility::vector1< core::Size > const &input_res)
 
Size num_chunk_sets () const
 
Size num_chunks (Size const n) const
 
ChunkSetOP chunk_set (Size const n) const
 
void add_chunk_set (std::string const &silent_file, core::pose::ResMap const &res_map, core::pose::Pose const &big_pose)
 
void insert_chunk_into_pose (core::pose::Pose &pose, Size const &chunk_list_index, Size const &chunk_pose_index) const
 
utility::vector1< Sizeget_indices_of_moving_chunks () const
 
Size num_moving_chunks () const
 
bool random_chunk_insertion (core::pose::Pose &pose) const
 
void initialize_random_chunks (core::pose::Pose &pose, bool const dump_pdb=false) const
 
toolbox::AllowInsertOP allow_insert ()
 
void set_allow_insert (toolbox::AllowInsertOP allow_insert)
 
core::Real const & chunk_coverage () const
 
void superimpose_to_first_chunk (core::pose::Pose &pose) const
 
bool check_fold_tree_OK (core::pose::Pose const &pose)
 
void setup_base_pair_step_chunks (core::pose::Pose const &pose, utility::vector1< BasePairStep > base_pair_steps)
 

Private Member Functions

void update_allow_insert (core::pose::ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &scratch_pose, Size const domain_num)
 
bool check_fold_tree_OK (core::pose::ResMap const &res_map, core::pose::Pose const &pose, core::pose::Pose const &scratch_pose)
 
void figure_out_chunk_coverage ()
 
bool check_res_map (core::pose::ResMap const &res_map, core::pose::Pose const &scratch_pose, std::string const &sequence) const
 
void align_to_chunk (core::pose::Pose &pose, ChunkSet const &chunk_set, core::Size const chunk_index) const
 

Private Attributes

utility::vector1< ChunkSetOPchunk_sets_
 
toolbox::AllowInsertOP allow_insert_
 
ObjexxFCL::FArray1D< boolcovered_by_chunk_
 
core::Real chunk_coverage_
 
bool coarse_rna_
 
BasePairStepLibraryOP base_pair_step_library_
 

Constructor & Destructor Documentation

protocols::farna::RNA_ChunkLibrary::RNA_ChunkLibrary ( )
protocols::farna::RNA_ChunkLibrary::RNA_ChunkLibrary ( utility::vector1< std::string > const &  pdb_files,
utility::vector1< std::string > const &  silent_files,
core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  input_res 
)
protocols::farna::RNA_ChunkLibrary::RNA_ChunkLibrary ( utility::vector1< std::string > const &  silent_files,
core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  input_res 
)
protocols::farna::RNA_ChunkLibrary::~RNA_ChunkLibrary ( )

Member Function Documentation

void protocols::farna::RNA_ChunkLibrary::add_chunk_set ( std::string const &  silent_file,
core::pose::ResMap const &  res_map,
core::pose::Pose const &  big_pose 
)
void protocols::farna::RNA_ChunkLibrary::align_to_chunk ( core::pose::Pose pose,
ChunkSet const &  chunk_set,
core::Size const  chunk_index 
) const
private
toolbox::AllowInsertOP protocols::farna::RNA_ChunkLibrary::allow_insert ( )
inline
bool protocols::farna::RNA_ChunkLibrary::check_fold_tree_OK ( core::pose::Pose const &  pose)
bool protocols::farna::RNA_ChunkLibrary::check_fold_tree_OK ( core::pose::ResMap const &  res_map,
core::pose::Pose const &  pose,
core::pose::Pose const &  scratch_pose 
)
private
bool protocols::farna::RNA_ChunkLibrary::check_res_map ( core::pose::ResMap const &  res_map,
core::pose::Pose const &  scratch_pose,
std::string const &  sequence 
) const
private
core::Real const& protocols::farna::RNA_ChunkLibrary::chunk_coverage ( ) const
inline
ChunkSetOP protocols::farna::RNA_ChunkLibrary::chunk_set ( Size const  n) const
inline

References chunk_sets_.

void protocols::farna::RNA_ChunkLibrary::figure_out_chunk_coverage ( )
private
utility::vector1< Size > protocols::farna::RNA_ChunkLibrary::get_indices_of_moving_chunks ( ) const
void protocols::farna::RNA_ChunkLibrary::initialize_random_chunks ( core::pose::Pose pose,
bool const  dump_pdb = false 
) const
void protocols::farna::RNA_ChunkLibrary::initialize_rna_chunk_library ( utility::vector1< std::string > const &  pdb_files,
utility::vector1< std::string > const &  silent_files,
core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  input_res 
)
void protocols::farna::RNA_ChunkLibrary::insert_chunk_into_pose ( core::pose::Pose pose,
Size const &  chunk_list_index,
Size const &  chunk_pose_index 
) const
Size protocols::farna::RNA_ChunkLibrary::num_chunk_sets ( ) const
inline

References chunk_sets_.

Size protocols::farna::RNA_ChunkLibrary::num_chunks ( Size const  n) const
inline

References chunk_sets_.

Size protocols::farna::RNA_ChunkLibrary::num_moving_chunks ( ) const
bool protocols::farna::RNA_ChunkLibrary::random_chunk_insertion ( core::pose::Pose pose) const
void protocols::farna::RNA_ChunkLibrary::set_allow_insert ( toolbox::AllowInsertOP  allow_insert)
void protocols::farna::RNA_ChunkLibrary::setup_base_pair_step_chunks ( core::pose::Pose const &  pose,
utility::vector1< BasePairStep base_pair_steps 
)
void protocols::farna::RNA_ChunkLibrary::superimpose_to_first_chunk ( core::pose::Pose pose) const
void protocols::farna::RNA_ChunkLibrary::update_allow_insert ( core::pose::ResMap const &  res_map,
core::pose::Pose const &  pose,
core::pose::Pose const &  scratch_pose,
Size const  domain_num 
)
private

Member Data Documentation

toolbox::AllowInsertOP protocols::farna::RNA_ChunkLibrary::allow_insert_
private

Referenced by allow_insert().

BasePairStepLibraryOP protocols::farna::RNA_ChunkLibrary::base_pair_step_library_
private
core::Real protocols::farna::RNA_ChunkLibrary::chunk_coverage_
private

Referenced by chunk_coverage().

utility::vector1< ChunkSetOP > protocols::farna::RNA_ChunkLibrary::chunk_sets_
private
bool protocols::farna::RNA_ChunkLibrary::coarse_rna_
private
ObjexxFCL::FArray1D<bool> protocols::farna::RNA_ChunkLibrary::covered_by_chunk_
private

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