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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::hybridization::HybridizeFoldtreeDynamic Class Reference

#include <HybridizeFoldtreeDynamic.hh>

Public Member Functions

 HybridizeFoldtreeDynamic ()
 
void initialize (core::pose::Pose &pose, protocols::loops::Loops const &core_chunks, utility::vector1< std::pair< core::Size, core::Size > > const &strand_pairs, std::set< core::Size > const &strand_pair_library_positions)
 
void reset (core::pose::Pose &pose)
 
utility::vector1< core::Sizeget_anchors ()
 

Private Member Functions

core::Size choose_anchor_position (const protocols::loops::Loop &chunk) const
 
void update (core::pose::Pose &pose)
 
void set_core_chunks (const protocols::loops::Loops &chunks)
 
void jumps_and_cuts_from_foldtree (core::kinematics::FoldTree &foldtree, utility::vector1< std::pair< core::Size, core::Size > > &jumps, utility::vector1< core::Size > &cuts)
 
utility::vector1< core::Sizedecide_cuts (core::pose::Pose &pose, core::Size n_residues)
 
void choose_anchors ()
 
void make_complete_chunks (utility::vector1< core::Size > cut_positions, core::Size n_residues)
 
void get_pair_core_chunks (core::Size const chunk_index, utility::vector1< core::Size > &pair_chunks, utility::vector1< std::pair< core::Size, core::Size > > &pair_chunks_pairs)
 
void get_core_chunk_index_from_position (core::Size const position, core::Size &index)
 
void add_overlapping_pair_chunks (core::Size const index, utility::vector1< core::Size > &cuts, utility::vector1< std::pair< core::Size, core::Size > > &jumps, std::set< core::Size > &rooted_chunk_indices)
 
void remove_cut (core::Size const cut, utility::vector1< core::Size > &cuts)
 

Private Attributes

protocols::loops::Loops chunks_
 
protocols::loops::Loops core_chunks_
 
utility::vector1< core::Sizeanchor_positions_
 
int virtual_res_
 index of the virtual residue we added to the pose in set_up() More...
 
core::Size num_nonvirt_residues_ = 0
 
core::Size num_polymer_residues_ = 0
 
core::kinematics::FoldTree initial_asymm_foldtree_
 
core::kinematics::FoldTree saved_ft_
 
core::Size saved_n_residue_
 
utility::vector1< std::pair
< core::Size, core::Size > > 
strand_pairs_
 
std::set< core::Sizestrand_pair_library_positions_
 
std::set< core::Sizetemplate_core_chunk_indices_
 
std::set< core::Sizerooted_chunk_indices_
 

Constructor & Destructor Documentation

protocols::hybridization::HybridizeFoldtreeDynamic::HybridizeFoldtreeDynamic ( )

Member Function Documentation

void protocols::hybridization::HybridizeFoldtreeDynamic::add_overlapping_pair_chunks ( core::Size const  index,
utility::vector1< core::Size > &  cuts,
utility::vector1< std::pair< core::Size, core::Size > > &  jumps,
std::set< core::Size > &  rooted_chunk_indices 
)
private
core::Size protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchor_position ( const protocols::loops::Loop chunk) const
private
void protocols::hybridization::HybridizeFoldtreeDynamic::choose_anchors ( )
private
utility::vector1< core::Size > protocols::hybridization::HybridizeFoldtreeDynamic::decide_cuts ( core::pose::Pose pose,
core::Size  n_residues 
)
private
utility::vector1< core::Size > protocols::hybridization::HybridizeFoldtreeDynamic::get_anchors ( )
inline
void protocols::hybridization::HybridizeFoldtreeDynamic::get_core_chunk_index_from_position ( core::Size const  position,
core::Size index 
)
private
void protocols::hybridization::HybridizeFoldtreeDynamic::get_pair_core_chunks ( core::Size const  chunk_index,
utility::vector1< core::Size > &  pair_chunks,
utility::vector1< std::pair< core::Size, core::Size > > &  pair_chunks_pairs 
)
private
void protocols::hybridization::HybridizeFoldtreeDynamic::initialize ( core::pose::Pose pose,
protocols::loops::Loops const &  core_chunks,
utility::vector1< std::pair< core::Size, core::Size > > const &  strand_pairs,
std::set< core::Size > const &  strand_pair_library_positions 
)
void protocols::hybridization::HybridizeFoldtreeDynamic::jumps_and_cuts_from_foldtree ( core::kinematics::FoldTree foldtree,
utility::vector1< std::pair< core::Size, core::Size > > &  jumps,
utility::vector1< core::Size > &  cuts 
)
private
void protocols::hybridization::HybridizeFoldtreeDynamic::make_complete_chunks ( utility::vector1< core::Size cut_positions,
core::Size  n_residues 
)
private
void protocols::hybridization::HybridizeFoldtreeDynamic::remove_cut ( core::Size const  cut,
utility::vector1< core::Size > &  cuts 
)
private

Referenced by update().

void protocols::hybridization::HybridizeFoldtreeDynamic::reset ( core::pose::Pose pose)
void protocols::hybridization::HybridizeFoldtreeDynamic::set_core_chunks ( const protocols::loops::Loops chunks)
private

References core_chunks_.

Referenced by initialize().

void protocols::hybridization::HybridizeFoldtreeDynamic::update ( core::pose::Pose pose)
private

Member Data Documentation

utility::vector1< core::Size > protocols::hybridization::HybridizeFoldtreeDynamic::anchor_positions_
private

Referenced by choose_anchors(), get_anchors(), and update().

protocols::loops::Loops protocols::hybridization::HybridizeFoldtreeDynamic::chunks_
private
protocols::loops::Loops protocols::hybridization::HybridizeFoldtreeDynamic::core_chunks_
private
core::kinematics::FoldTree protocols::hybridization::HybridizeFoldtreeDynamic::initial_asymm_foldtree_
private

Referenced by decide_cuts(), initialize(), and update().

core::Size protocols::hybridization::HybridizeFoldtreeDynamic::num_nonvirt_residues_ = 0
private

Referenced by initialize(), and update().

core::Size protocols::hybridization::HybridizeFoldtreeDynamic::num_polymer_residues_ = 0
private

Referenced by initialize().

std::set<core::Size> protocols::hybridization::HybridizeFoldtreeDynamic::rooted_chunk_indices_
private
core::kinematics::FoldTree protocols::hybridization::HybridizeFoldtreeDynamic::saved_ft_
private

Referenced by initialize(), and reset().

core::Size protocols::hybridization::HybridizeFoldtreeDynamic::saved_n_residue_
private

Referenced by initialize(), and reset().

std::set<core::Size> protocols::hybridization::HybridizeFoldtreeDynamic::strand_pair_library_positions_
private

Referenced by initialize().

utility::vector1< std::pair< core::Size, core::Size > > protocols::hybridization::HybridizeFoldtreeDynamic::strand_pairs_
private
std::set<core::Size> protocols::hybridization::HybridizeFoldtreeDynamic::template_core_chunk_indices_
private

Referenced by initialize(), and update().

int protocols::hybridization::HybridizeFoldtreeDynamic::virtual_res_
private

index of the virtual residue we added to the pose in set_up()

Referenced by initialize().


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