protocols::indexed_structure_store::search::StructureData Class Reference

#include <QueryDatabase.hh>

Public Types
typedef Eigen::Matrix< SearchReal, 3, 1 >	Coordinate
typedef Eigen::Matrix< SearchReal, 3, Eigen::Dynamic >	CoordinateMatrix
typedef Eigen::Array< Index, Eigen::Dynamic, 1 >	IndexArray

Public Member Functions
void	initialize (Index src_structure_offset, ndarray::Array< SearchReal, 3, 3 > src_coordinates, IndexArray src_chain_endpoints)
void	prepare_for_query (Index fragment_length)
IndexArray &	get_fragment_indicies (Index fragment_length)
CoordinateMatrix &	get_fragment_centers_of_mass (Index fragment_length)
IndexArray	get_fragment_indicies_copy (Index fragment_length)
CoordinateMatrix	get_fragment_centers_of_mass_copy (Index fragment_length)

Public Attributes
Index	structure_offset
CoordinateMatrix	coordinate_buffer
Index	n_entry
Index	c_per_entry
IndexArray	chain_endpoints
std::map< Index, IndexArray >	fragment_index_cache
std::map< Index, CoordinateMatrix >	fragment_center_of_mass_cache

Member Typedef Documentation

Coordinate

typedef Eigen::Matrix<SearchReal, 3, 1> protocols::indexed_structure_store::search::StructureData::Coordinate

CoordinateMatrix

typedef Eigen::Matrix<SearchReal, 3, Eigen::Dynamic> protocols::indexed_structure_store::search::StructureData::CoordinateMatrix

IndexArray

typedef Eigen::Array<Index, Eigen::Dynamic, 1> protocols::indexed_structure_store::search::StructureData::IndexArray

Member Function Documentation

get_fragment_centers_of_mass()

CoordinateMatrix& protocols::indexed_structure_store::search::StructureData::get_fragment_centers_of_mass ( Index  fragment_length )

inline

References fragment_center_of_mass_cache, and prepare_for_query().

Referenced by protocols::indexed_structure_store::search::PairQueryExecutor::execute_structure(), and protocols::indexed_structure_store::search::SingleQueryExecutor::execute_structure().

get_fragment_centers_of_mass_copy()

CoordinateMatrix protocols::indexed_structure_store::search::StructureData::get_fragment_centers_of_mass_copy ( Index  fragment_length )

inline

References fragment_center_of_mass_cache, and prepare_for_query().

Referenced by protocols::indexed_structure_store::search::bind_QueryDatabase().

get_fragment_indicies()

IndexArray& protocols::indexed_structure_store::search::StructureData::get_fragment_indicies ( Index  fragment_length )

inline

References fragment_index_cache, and prepare_for_query().

Referenced by protocols::indexed_structure_store::search::PairQueryExecutor::execute_structure(), and protocols::indexed_structure_store::search::SingleQueryExecutor::execute_structure().

get_fragment_indicies_copy()

IndexArray protocols::indexed_structure_store::search::StructureData::get_fragment_indicies_copy ( Index  fragment_length )

inline

References fragment_index_cache, and prepare_for_query().

Referenced by protocols::indexed_structure_store::search::bind_QueryDatabase().

initialize()

void protocols::indexed_structure_store::search::StructureData::initialize	(	Index	src_structure_offset,
		ndarray::Array< SearchReal, 3, 3 >	src_coordinates,
		IndexArray	src_chain_endpoints
	)

References c_per_entry, chain_endpoints, coordinate_buffer, n_entry, and structure_offset.

Referenced by protocols::indexed_structure_store::search::StructureDatabase::initialize_structure_data_from_buffer().

prepare_for_query()

void protocols::indexed_structure_store::search::StructureData::prepare_for_query

(

Index

fragment_length

)

References c_per_entry, chain_endpoints, coordinate_buffer, fragment_center_of_mass_cache, and fragment_index_cache.

Referenced by get_fragment_centers_of_mass(), get_fragment_centers_of_mass_copy(), get_fragment_indicies(), and get_fragment_indicies_copy().

Member Data Documentation

c_per_entry

Index protocols::indexed_structure_store::search::StructureData::c_per_entry

Referenced by initialize(), and prepare_for_query().

chain_endpoints

IndexArray protocols::indexed_structure_store::search::StructureData::chain_endpoints

Referenced by protocols::indexed_structure_store::search::bind_QueryDatabase(), initialize(), and prepare_for_query().

coordinate_buffer

CoordinateMatrix protocols::indexed_structure_store::search::StructureData::coordinate_buffer

Referenced by protocols::indexed_structure_store::search::bind_QueryDatabase(), initialize(), protocols::indexed_structure_store::search::SingleQueryExecutor::perform_structure_rmsd(), protocols::indexed_structure_store::search::PairQueryExecutor::perform_structure_rmsd(), and prepare_for_query().

fragment_center_of_mass_cache

std::map<Index, CoordinateMatrix > protocols::indexed_structure_store::search::StructureData::fragment_center_of_mass_cache

Referenced by get_fragment_centers_of_mass(), get_fragment_centers_of_mass_copy(), and prepare_for_query().

fragment_index_cache

std::map<Index, IndexArray > protocols::indexed_structure_store::search::StructureData::fragment_index_cache

Referenced by get_fragment_indicies(), get_fragment_indicies_copy(), and prepare_for_query().

n_entry

Index protocols::indexed_structure_store::search::StructureData::n_entry

Referenced by initialize().

structure_offset

Index protocols::indexed_structure_store::search::StructureData::structure_offset

Referenced by protocols::indexed_structure_store::search::bind_QueryDatabase(), protocols::indexed_structure_store::search::PairQueryExecutor::execute_structure(), protocols::indexed_structure_store::search::SingleQueryExecutor::execute_structure(), and initialize().

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

• src/protocols/indexed_structure_store/search/QueryDatabase.hh
• src/protocols/indexed_structure_store/search/QueryDatabase.cc