protocols::indexed_structure_store::search::PairQueryExecutor Class Reference

#include <QueryDatabase.hh>

Public Types
typedef PairQuerySummaryStatistics	SummaryStatistics
typedef StructurePairQueryResult	QueryResult
typedef StructurePairQuery	Query

Public Member Functions
	PairQueryExecutor (Query const &query)
void	execute (StructureDatabase &database)
void	execute_structure (Index structure_index, StructureData &target_structure)
SearchReal	perform_structure_rmsd (StructureData &target_structure, StructureData::IndexArray &fragment_indicies_a, StructureData::IndexArray &fragment_indicies_b, StructureData::CoordinateMatrix &fragment_centers_of_mass_a, StructureData::CoordinateMatrix &fragment_centers_of_mass_b, Index fragment_index_a, Index fragment_index_b)

Public Attributes
Query	query
Eigen::Matrix< SearchReal, 3, Eigen::Dynamic >	query_coordinate_buffer
Eigen::Matrix< SearchReal, 3, Eigen::Dynamic >	structure_coordinate_buffer
Eigen::Matrix< SearchReal, 3, 1 >	query_coordinate_com
Eigen::Matrix< SearchReal, 3, 1 >	structure_coordinate_com
std::vector< QueryResult >	query_results
SummaryStatistics	query_stats

Member Typedef Documentation

typedef StructurePairQuery protocols::indexed_structure_store::search::PairQueryExecutor::Query

typedef StructurePairQueryResult protocols::indexed_structure_store::search::PairQueryExecutor::QueryResult

typedef PairQuerySummaryStatistics protocols::indexed_structure_store::search::PairQueryExecutor::SummaryStatistics

Constructor & Destructor Documentation

protocols::indexed_structure_store::search::PairQueryExecutor::PairQueryExecutor

(

Query const &

query

)

References protocols::indexed_structure_store::search::StructurePairQuery::q_buffer_a, protocols::indexed_structure_store::search::StructurePairQuery::q_buffer_b, query_coordinate_buffer, query_coordinate_com, and structure_coordinate_buffer.

Member Function Documentation

void protocols::indexed_structure_store::search::PairQueryExecutor::execute

(

StructureDatabase &

database

)

References execute_structure(), query_results, query_stats, protocols::indexed_structure_store::search::PairQuerySummaryStatistics::result_count, and protocols::indexed_structure_store::search::StructureDatabase::structure_data.

Referenced by protocols::indexed_structure_store::search::bind_QueryDatabase(), and protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup().

void protocols::indexed_structure_store::search::PairQueryExecutor::execute_structure	(	Index	structure_index,
		StructureData &	target_structure
	)

References core::pose::motif::a(), protocols::match::upstream::b, protocols::indexed_structure_store::search::PairQuerySummaryStatistics::fragments_considered, protocols::indexed_structure_store::search::PairQuerySummaryStatistics::fragments_expanded, protocols::indexed_structure_store::search::StructureData::get_fragment_centers_of_mass(), protocols::indexed_structure_store::search::StructureData::get_fragment_indicies(), protocols::indexed_structure_store::search::StructurePairQuery::limit_primary_distance, protocols::indexed_structure_store::search::StructurePairQuery::max_primary_distance, protocols::indexed_structure_store::search::StructurePairQuery::n_entry_a, protocols::indexed_structure_store::search::StructurePairQuery::n_entry_b, protocols::indexed_structure_store::search::PairQuerySummaryStatistics::pairs_considered, perform_structure_rmsd(), query, query_results, query_stats, protocols::indexed_structure_store::search::StructurePairQuery::rmsd_tolerance, protocols::indexed_structure_store::search::StructureData::structure_offset, and protocols::indexed_structure_store::search::PairQuerySummaryStatistics::structures_considered.

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

SearchReal protocols::indexed_structure_store::search::PairQueryExecutor::perform_structure_rmsd	(	StructureData &	target_structure,
		StructureData::IndexArray &	fragment_indicies_a,
		StructureData::IndexArray &	fragment_indicies_b,
		StructureData::CoordinateMatrix &	fragment_centers_of_mass_a,
		StructureData::CoordinateMatrix &	fragment_centers_of_mass_b,
		Index	fragment_index_a,
		Index	fragment_index_b
	)

References core::pose::motif::a(), protocols::match::upstream::b, protocols::indexed_structure_store::search::StructurePairQuery::c_per_entry, protocols::indexed_structure_store::search::StructureData::coordinate_buffer, protocols::indexed_structure_store::search::PairQuerySummaryStatistics::pairs_aligned, protocols::indexed_structure_store::search::StructurePairQuery::q_buffer_a, protocols::indexed_structure_store::search::StructurePairQuery::q_buffer_b, query, query_coordinate_buffer, query_coordinate_com, query_stats, structure_coordinate_buffer, and structure_coordinate_com.

Referenced by execute_structure().

Member Data Documentation

Query protocols::indexed_structure_store::search::PairQueryExecutor::query

Referenced by execute_structure(), and perform_structure_rmsd().

Eigen::Matrix<SearchReal, 3, Eigen::Dynamic> protocols::indexed_structure_store::search::PairQueryExecutor::query_coordinate_buffer

Referenced by PairQueryExecutor(), and perform_structure_rmsd().

Eigen::Matrix<SearchReal, 3, 1> protocols::indexed_structure_store::search::PairQueryExecutor::query_coordinate_com

Referenced by PairQueryExecutor(), and perform_structure_rmsd().

std::vector<QueryResult> protocols::indexed_structure_store::search::PairQueryExecutor::query_results

Referenced by protocols::indexed_structure_store::search::bind_QueryDatabase(), execute(), execute_structure(), and protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup().

SummaryStatistics protocols::indexed_structure_store::search::PairQueryExecutor::query_stats

Referenced by execute(), execute_structure(), perform_structure_rmsd(), and protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup().

Eigen::Matrix<SearchReal, 3, Eigen::Dynamic> protocols::indexed_structure_store::search::PairQueryExecutor::structure_coordinate_buffer

Referenced by PairQueryExecutor(), and perform_structure_rmsd().

Eigen::Matrix<SearchReal, 3, 1> protocols::indexed_structure_store::search::PairQueryExecutor::structure_coordinate_com

Referenced by perform_structure_rmsd().

---

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