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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::indexed_structure_store::SSHashedFragmentStore Class Reference

#include <SSHashedFragmentStore.hh>

Public Member Functions

 SSHashedFragmentStore (std::string const &fragment_store_path="", std::string const &fragment_store_format="hashed", std::string const &fragment_store_compression="all")
 
void load_prehashed_fragmentStore (std::string const &fragment_store_path)
 
void set_threshold_distance (numeric::Real threshold_distance)
 
numeric::Size get_valid_resid (core::pose::Pose const &pose, int resid)
 
std::set< std::string > potential_valid_ss_strings (std::string frag_ss)
 
numeric::Real max_rmsd_in_region (core::pose::Pose const &pose, utility::vector1< numeric::Size > resids)
 
numeric::Real lookback_account_for_dssp_inaccuracy (core::pose::Pose const &pose, numeric::Size resid, bool find_closest, numeric::Real rms_threshold)
 
numeric::Real lookback_account_for_dssp_inaccuracy (core::pose::Pose const &pose, numeric::Size resid, std::string frags_ss, bool find_closest, numeric::Real rms_threshold)
 
numeric::Real lookback_account_for_dssp_inaccuracy (core::pose::Pose const &pose, numeric::Size resid, std::string frag_ss, numeric::Real &match_rmsd, numeric::Size &match_index, numeric::Size &match_ss_index)
 
numeric::Real lookback (core::pose::Pose const &pose, numeric::Size resid)
 
numeric::Real lookback (core::pose::Pose const &pose, numeric::Size resid, std::string frag_ss, bool find_closest)
 
void lookback_stub (std::vector< numeric::xyzVector< numeric::Real > > coordinates, char resTypeBeforeLoop, char resTypeAfterLoop, numeric::Size loop_length, numeric::Real &top_match_rmsd, utility::vector1< BackboneStub > &stubVector, numeric::Real stubRmsdThreshold)
 
std::vector< numeric::xyzVector< numeric::Real > > get_fragment_coordinates (numeric::Size db_index, numeric::Size match_index)
 
void get_hits_below_rms (core::pose::Pose const &pose, numeric::Size resid, numeric::Real rms_threshold, utility::vector1< std::vector< numeric::Real > > &hits_cen, utility::vector1< numeric::Real > &hits_rms, utility::vector1< std::string > &hits_aa)
 
protocols::indexed_structure_store::FragmentStoreOP get_fragment_store (numeric::Size db_index)
 
protocols::indexed_structure_store::FragmentStoreOP get_fragment_store ()
 
std::map< numeric::Size, protocols::indexed_structure_store::FragmentStoreOPget_hashed_fragment_store ()
 
numeric::Size get_fragment_length ()
 

Private Member Functions

void init_SS_stub_HashedFragmentStore ()
 
std::vector< bool > generate_subset_residues_to_compare (numeric::Size loop_length, numeric::Size fragment_length)
 

Private Attributes

std::map< numeric::Size, protocols::indexed_structure_store::FragmentStoreOPSSHashedFragmentStore_
 
std::map< std::string, utility::vector1< numeric::Size > > SS_stub_HashedFragmentStoreIndex_
 

Constructor & Destructor Documentation

◆ SSHashedFragmentStore()

protocols::indexed_structure_store::SSHashedFragmentStore::SSHashedFragmentStore ( std::string const &  fragment_store_path = "",
std::string const &  fragment_store_format = "hashed",
std::string const &  fragment_store_compression = "all" 
)

Member Function Documentation

◆ generate_subset_residues_to_compare()

vector< bool > protocols::indexed_structure_store::SSHashedFragmentStore::generate_subset_residues_to_compare ( numeric::Size  loop_length,
numeric::Size  fragment_length 
)
private

◆ get_fragment_coordinates()

std::vector< xyzVector< Real > > protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_coordinates ( numeric::Size  db_index,
numeric::Size  match_index 
)

◆ get_fragment_length()

Size protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_length ( )

◆ get_fragment_store() [1/2]

FragmentStoreOP protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_store ( )

◆ get_fragment_store() [2/2]

protocols::indexed_structure_store::FragmentStoreOP protocols::indexed_structure_store::SSHashedFragmentStore::get_fragment_store ( numeric::Size  db_index)

◆ get_hashed_fragment_store()

std::map< core::Size, protocols::indexed_structure_store::FragmentStoreOP > protocols::indexed_structure_store::SSHashedFragmentStore::get_hashed_fragment_store ( )

◆ get_hits_below_rms()

void protocols::indexed_structure_store::SSHashedFragmentStore::get_hits_below_rms ( core::pose::Pose const &  pose,
numeric::Size  resid,
numeric::Real  rms_threshold,
utility::vector1< std::vector< numeric::Real > > &  hits_cen,
utility::vector1< numeric::Real > &  hits_rms,
utility::vector1< std::string > &  hits_aa 
)

◆ get_valid_resid()

Size protocols::indexed_structure_store::SSHashedFragmentStore::get_valid_resid ( core::pose::Pose const &  pose,
int  resid 
)

◆ init_SS_stub_HashedFragmentStore()

void protocols::indexed_structure_store::SSHashedFragmentStore::init_SS_stub_HashedFragmentStore ( )
private

◆ load_prehashed_fragmentStore()

void protocols::indexed_structure_store::SSHashedFragmentStore::load_prehashed_fragmentStore ( std::string const &  fragment_store_path)

◆ lookback() [1/2]

numeric::Real protocols::indexed_structure_store::SSHashedFragmentStore::lookback ( core::pose::Pose const &  pose,
numeric::Size  resid 
)

◆ lookback() [2/2]

numeric::Real protocols::indexed_structure_store::SSHashedFragmentStore::lookback ( core::pose::Pose const &  pose,
numeric::Size  resid,
std::string  frag_ss,
bool  find_closest 
)

◆ lookback_account_for_dssp_inaccuracy() [1/3]

numeric::Real protocols::indexed_structure_store::SSHashedFragmentStore::lookback_account_for_dssp_inaccuracy ( core::pose::Pose const &  pose,
numeric::Size  resid,
bool  find_closest,
numeric::Real  rms_threshold 
)

◆ lookback_account_for_dssp_inaccuracy() [2/3]

numeric::Real protocols::indexed_structure_store::SSHashedFragmentStore::lookback_account_for_dssp_inaccuracy ( core::pose::Pose const &  pose,
numeric::Size  resid,
std::string  frag_ss,
numeric::Real &  match_rmsd,
numeric::Size &  match_index,
numeric::Size &  match_ss_index 
)

◆ lookback_account_for_dssp_inaccuracy() [3/3]

numeric::Real protocols::indexed_structure_store::SSHashedFragmentStore::lookback_account_for_dssp_inaccuracy ( core::pose::Pose const &  pose,
numeric::Size  resid,
std::string  frags_ss,
bool  find_closest,
numeric::Real  rms_threshold 
)

◆ lookback_stub()

void protocols::indexed_structure_store::SSHashedFragmentStore::lookback_stub ( std::vector< numeric::xyzVector< numeric::Real > >  coordinates,
char  resTypeBeforeLoop,
char  resTypeAfterLoop,
numeric::Size  loop_length,
numeric::Real &  top_match_rmsd,
utility::vector1< BackboneStub > &  stubVector,
numeric::Real  stubRmsdThreshold 
)

◆ max_rmsd_in_region()

Real protocols::indexed_structure_store::SSHashedFragmentStore::max_rmsd_in_region ( core::pose::Pose const &  pose,
utility::vector1< numeric::Size >  resids 
)

◆ potential_valid_ss_strings()

set< std::string > protocols::indexed_structure_store::SSHashedFragmentStore::potential_valid_ss_strings ( std::string  frag_ss)

◆ set_threshold_distance()

void protocols::indexed_structure_store::SSHashedFragmentStore::set_threshold_distance ( numeric::Real  threshold_distance)

Member Data Documentation

◆ SS_stub_HashedFragmentStoreIndex_

std::map<std::string, utility::vector1<numeric::Size> > protocols::indexed_structure_store::SSHashedFragmentStore::SS_stub_HashedFragmentStoreIndex_
private

◆ SSHashedFragmentStore_

std::map<numeric::Size, protocols::indexed_structure_store::FragmentStoreOP> protocols::indexed_structure_store::SSHashedFragmentStore::SSHashedFragmentStore_
private

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