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::FragmentStoreOP >	get_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::FragmentStoreOP >	SSHashedFragmentStore_
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
	)

References protocols::simple_filters::dssp(), protocols::indexed_structure_store::FragmentLookupResult::match_index, protocols::indexed_structure_store::FragmentLookupResult::match_rmsd, core::pose::Pose::residue(), protocols::frag_picker::quota::ss_index(), core::sequence::SSManager::symbolString2index(), and core::conformation::Residue::xyz().

get_valid_resid()

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

References core::pose::Pose::total_residue(), and protocols::indexed_structure_store::TR().

init_SS_stub_HashedFragmentStore()

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

private

References core::sequence::SSManager::index2symbolString(), and core::scoring::pair.

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
	)

References protocols::indexed_structure_store::FragmentLookupResult::match_rmsd.

max_rmsd_in_region()

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

References core::select::resids().

potential_valid_ss_strings()

set< std::string > protocols::indexed_structure_store::SSHashedFragmentStore::potential_valid_ss_strings

(

std::string

frag_ss

)

References protocols::stepwise::modeler::rna::set_union().

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

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

• src/protocols/indexed_structure_store/SSHashedFragmentStore.hh
• src/protocols/indexed_structure_store/SSHashedFragmentStore.cc