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protocols::rna::RNA_ChunkLibrary Class Reference

#include <RNA_ChunkLibrary.hh>

Inheritance diagram for protocols::rna::RNA_ChunkLibrary:
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Collaboration diagram for protocols::rna::RNA_ChunkLibrary:
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Public Member Functions

 RNA_ChunkLibrary ()
 
 RNA_ChunkLibrary (utility::vector1< std::string > const &silent_files, core::pose::Pose const &pose, std::map< Size, Size > const &connections_in_big_pose)
 
 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
 
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)
 

Private Member Functions

void zero_out_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 ()
 
void get_component_sequences (core::pose::Pose const &pose, utility::vector1< std::string > &sequences, utility::vector1< core::Size > &chain_id, utility::vector1< core::Size > &sequence_start) const
 
void process_input_file (std::string const &silent_file, utility::vector1< core::pose::PoseOP > &pose_list, bool is_pdb=false) const
 
void figure_out_possible_res_maps (utility::vector1< core::pose::ResMap > &res_maps, core::pose::Pose const &scratch_pose, std::string const &sequence_of_big_pose, std::map< Size, Size > const &connections_in_big_pose) const
 
void find_res_maps (utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const
 
void get_sequence_matches (utility::vector1< utility::vector1< Size > > &matches_to_each_scratch_sequence, utility::vector1< std::string > const &scratch_sequences, std::string const &sequence_of_big_pose) const
 
void check_connections (Size const &num_chain, core::pose::ResMap &res_map, utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const
 
bool fill_res_map (core::pose::ResMap &res_map, Size const &match_pos, Size const &scratch_start_pos, Size const &scratch_sequence_length) const
 
void test_matches (Size const &res1, Size const &res2, core::pose::ResMap &res_map, utility::vector1< Size > const &chain_id, utility::vector1< Size > const &scratch_sequence_start, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::pose::ResMap > &res_maps) const
 
bool check_res_map (core::pose::ResMap const &res_map, core::pose::Pose const &scratch_pose, std::string const &sequence) const
 
void check_res_map_recursively (core::pose::ResMap const &res_map_old, utility::vector1< std::string > const &scratch_sequences, utility::vector1< utility::vector1< Size > > const &matches_to_each_scratch_sequence, core::pose::Pose const &scratch_pose, std::map< Size, Size > const &connections_in_big_pose, utility::vector1< core::Size > const &chain_id, core::Size const &num_sequence, core::Size const &num_match, utility::vector1< core::pose::ResMap > &res_maps) const
 
bool check_jump_match (core::pose::Pose const &scratch_pose, std::map< core::Size, core::Size > const &connections_in_big_pose, core::pose::ResMap const &res_map, utility::vector1< Size > const &chain_id) 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_
 

Constructor & Destructor Documentation

protocols::rna::RNA_ChunkLibrary::RNA_ChunkLibrary ( )
protocols::rna::RNA_ChunkLibrary::RNA_ChunkLibrary ( utility::vector1< std::string > const &  silent_files,
core::pose::Pose const &  pose,
std::map< Size, Size > const &  connections_in_big_pose 
)
protocols::rna::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::rna::RNA_ChunkLibrary::RNA_ChunkLibrary ( utility::vector1< std::string > const &  silent_files,
core::pose::Pose const &  pose,
utility::vector1< core::Size > const &  input_res 
)
protocols::rna::RNA_ChunkLibrary::~RNA_ChunkLibrary ( )
inline

Member Function Documentation

void protocols::rna::RNA_ChunkLibrary::add_chunk_set ( std::string const &  silent_file,
core::pose::ResMap const &  res_map,
core::pose::Pose const &  big_pose 
)
void protocols::rna::RNA_ChunkLibrary::align_to_chunk ( core::pose::Pose pose,
ChunkSet const &  chunk_set,
core::Size const  chunk_index 
) const
private
toolbox::AllowInsertOP protocols::rna::RNA_ChunkLibrary::allow_insert ( )
inline

References allow_insert_.

void protocols::rna::RNA_ChunkLibrary::check_connections ( Size const &  num_chain,
core::pose::ResMap res_map,
utility::vector1< Size > const &  chain_id,
utility::vector1< Size > const &  scratch_sequence_start,
utility::vector1< std::string > const &  scratch_sequences,
utility::vector1< utility::vector1< Size > > const &  matches_to_each_scratch_sequence,
core::pose::Pose const &  scratch_pose,
std::map< Size, Size > const &  connections_in_big_pose,
utility::vector1< core::pose::ResMap > &  res_maps 
) const
private
bool protocols::rna::RNA_ChunkLibrary::check_fold_tree_OK ( core::pose::Pose const &  pose)
bool protocols::rna::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::rna::RNA_ChunkLibrary::check_jump_match ( core::pose::Pose const &  scratch_pose,
std::map< core::Size, core::Size > const &  connections_in_big_pose,
core::pose::ResMap const &  res_map,
utility::vector1< Size > const &  chain_id 
) const
private
bool protocols::rna::RNA_ChunkLibrary::check_res_map ( core::pose::ResMap const &  res_map,
core::pose::Pose const &  scratch_pose,
std::string const &  sequence 
) const
private
void protocols::rna::RNA_ChunkLibrary::check_res_map_recursively ( core::pose::ResMap const &  res_map_old,
utility::vector1< std::string > const &  scratch_sequences,
utility::vector1< utility::vector1< Size > > const &  matches_to_each_scratch_sequence,
core::pose::Pose const &  scratch_pose,
std::map< Size, Size > const &  connections_in_big_pose,
utility::vector1< core::Size > const &  chain_id,
core::Size const &  num_sequence,
core::Size const &  num_match,
utility::vector1< core::pose::ResMap > &  res_maps 
) const
private
core::Real const& protocols::rna::RNA_ChunkLibrary::chunk_coverage ( ) const
inline

References chunk_coverage_.

ChunkSetOP protocols::rna::RNA_ChunkLibrary::chunk_set ( Size const  n) const
inline

References chunk_sets_.

void protocols::rna::RNA_ChunkLibrary::figure_out_chunk_coverage ( )
private
void protocols::rna::RNA_ChunkLibrary::figure_out_possible_res_maps ( utility::vector1< core::pose::ResMap > &  res_maps,
core::pose::Pose const &  scratch_pose,
std::string const &  sequence_of_big_pose,
std::map< Size, Size > const &  connections_in_big_pose 
) const
private
bool protocols::rna::RNA_ChunkLibrary::fill_res_map ( core::pose::ResMap res_map,
Size const &  match_pos,
Size const &  scratch_start_pos,
Size const &  scratch_sequence_length 
) const
private

References protocols::rna::TR().

void protocols::rna::RNA_ChunkLibrary::find_res_maps ( utility::vector1< Size > const &  chain_id,
utility::vector1< Size > const &  scratch_sequence_start,
utility::vector1< std::string > const &  scratch_sequences,
utility::vector1< utility::vector1< Size > > const &  matches_to_each_scratch_sequence,
core::pose::Pose const &  scratch_pose,
std::map< Size, Size > const &  connections_in_big_pose,
utility::vector1< core::pose::ResMap > &  res_maps 
) const
private
void protocols::rna::RNA_ChunkLibrary::get_component_sequences ( core::pose::Pose const &  pose,
utility::vector1< std::string > &  sequences,
utility::vector1< core::Size > &  chain_id,
utility::vector1< core::Size > &  sequence_start 
) const
private
void protocols::rna::RNA_ChunkLibrary::get_sequence_matches ( utility::vector1< utility::vector1< Size > > &  matches_to_each_scratch_sequence,
utility::vector1< std::string > const &  scratch_sequences,
std::string const &  sequence_of_big_pose 
) const
private

References protocols::rna::TR().

void protocols::rna::RNA_ChunkLibrary::initialize_random_chunks ( core::pose::Pose pose,
bool const  dump_pdb = false 
) const
void protocols::rna::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::rna::RNA_ChunkLibrary::insert_chunk_into_pose ( core::pose::Pose pose,
Size const &  chunk_list_index,
Size const &  chunk_pose_index 
) const
Size protocols::rna::RNA_ChunkLibrary::num_chunk_sets ( ) const
inline

References chunk_sets_.

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

References chunk_sets_.

void protocols::rna::RNA_ChunkLibrary::process_input_file ( std::string const &  silent_file,
utility::vector1< core::pose::PoseOP > &  pose_list,
bool  is_pdb = false 
) const
private
bool protocols::rna::RNA_ChunkLibrary::random_chunk_insertion ( core::pose::Pose pose) const

References protocols::rna::RG().

void protocols::rna::RNA_ChunkLibrary::set_allow_insert ( toolbox::AllowInsertOP  allow_insert)
void protocols::rna::RNA_ChunkLibrary::superimpose_to_first_chunk ( core::pose::Pose pose) const
void protocols::rna::RNA_ChunkLibrary::test_matches ( Size const &  res1,
Size const &  res2,
core::pose::ResMap res_map,
utility::vector1< Size > const &  chain_id,
utility::vector1< Size > const &  scratch_sequence_start,
utility::vector1< std::string > const &  scratch_sequences,
utility::vector1< utility::vector1< Size > > const &  matches_to_each_scratch_sequence,
core::pose::Pose const &  scratch_pose,
std::map< Size, Size > const &  connections_in_big_pose,
utility::vector1< core::pose::ResMap > &  res_maps 
) const
private
void protocols::rna::RNA_ChunkLibrary::zero_out_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::rna::RNA_ChunkLibrary::allow_insert_
private

Referenced by allow_insert().

core::Real protocols::rna::RNA_ChunkLibrary::chunk_coverage_
private

Referenced by chunk_coverage().

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

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