protocols::indexed_structure_store::FragmentLookup Class Reference

#include <FragmentLookup.hh>

Inheritance diagram for protocols::indexed_structure_store::FragmentLookup:

Public Member Functions
	FragmentLookup (FragmentStoreOP store)
template<class xyzVectorIterator >
FragmentLookupResult	lookup_fragment (xyzVectorIterator input)
template<class xyzVectorIterator >
FragmentLookupResult	lookup_closest_fragment (xyzVectorIterator input)
template<class xyzVectorIterator >
FragmentLookupResult	lookup_closest_fragment_subset (xyzVectorIterator input, std::vector< bool > subset)
template<class xyzVectorIterator >
std::vector< FragmentLookupResult >	lookup_close_fragments (xyzVectorIterator input, numeric::Real rms_threshold)
template<class FragmentLookupOutputIterator , class ResidueNumberOutputIterator >
void	lookup_pose_fragments (core::pose::Pose const &pose, FragmentLookupOutputIterator result_out, ResidueNumberOutputIterator fragment_start_out)
template<class FragmentLookupOutputIterator , class ResidueNumberOutputIterator >
void	lookup_closest_pose_fragments (core::pose::Pose const &pose, FragmentLookupOutputIterator result_out, ResidueNumberOutputIterator fragment_start_out)
FragmentStoreCOP	store ()
FragmentSpecification const &	fragment_specification ()

Protected Types
typedef std::pair< core::Size, core::Size >	ResidueSpan

Protected Member Functions
std::vector< ResidueSpan >	get_fragment_residue_spans (core::pose::Pose const &target_pose)
FragmentLookupResult	lookup_fragment_v (std::vector< numeric::xyzVector< numeric::Real > > &query_coordinates)
FragmentLookupResult	lookup_closest_fragment_v (std::vector< numeric::xyzVector< numeric::Real > > &query_coordinates)
FragmentLookupResult	lookup_closest_fragment_subset_v (std::vector< numeric::xyzVector< numeric::Real > > &query_coordinates, std::vector< bool > subset)
std::vector< FragmentLookupResult >	lookup_close_fragments_v (std::vector< numeric::xyzVector< numeric::Real > > &query_coordinates, numeric::Real rms_threshold, numeric::Size max_matches=99999999)

Private Attributes
FragmentStoreOP	store_
numeric::coordinate_fitting::CoordinateArray_RMSD_FlatLookup< numeric::Real >	lookup_

Member Typedef Documentation

ResidueSpan

typedef std::pair<core::Size, core::Size> protocols::indexed_structure_store::FragmentLookup::ResidueSpan

protected

Constructor & Destructor Documentation

FragmentLookup()

protocols::indexed_structure_store::FragmentLookup::FragmentLookup

(

FragmentStoreOP

store

)

Member Function Documentation

fragment_specification()

FragmentSpecification const& protocols::indexed_structure_store::FragmentLookup::fragment_specification ( )

inline

References store_.

get_fragment_residue_spans()

std::vector< std::pair< numeric::Size, numeric::Size > > protocols::indexed_structure_store::FragmentLookup::get_fragment_residue_spans ( core::pose::Pose const &  target_pose )

protected

References core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::symmetry::symmetry_info().

Referenced by lookup_closest_pose_fragments(), and lookup_pose_fragments().

lookup_close_fragments()

template<class xyzVectorIterator >

std::vector<FragmentLookupResult> protocols::indexed_structure_store::FragmentLookup::lookup_close_fragments ( xyzVectorIterator  input, numeric::Real  rms_threshold  )

inline

References lookup_close_fragments_v(), and store_.

lookup_close_fragments_v()

std::vector< FragmentLookupResult > protocols::indexed_structure_store::FragmentLookup::lookup_close_fragments_v ( std::vector< numeric::xyzVector< numeric::Real > > &  query_coordinates, numeric::Real  rms_threshold, numeric::Size  max_matches = 99999999  )

protected

References protocols::indexed_structure_store::FragmentLookupResult::found_match, lookup_, protocols::indexed_structure_store::FragmentLookupResult::match_index, and protocols::indexed_structure_store::FragmentLookupResult::match_rmsd.

Referenced by lookup_close_fragments().

lookup_closest_fragment()

template<class xyzVectorIterator >

FragmentLookupResult protocols::indexed_structure_store::FragmentLookup::lookup_closest_fragment ( xyzVectorIterator  input )

inline

References lookup_closest_fragment_v(), and store_.

Referenced by lookup_closest_pose_fragments().

lookup_closest_fragment_subset()

template<class xyzVectorIterator >

FragmentLookupResult protocols::indexed_structure_store::FragmentLookup::lookup_closest_fragment_subset ( xyzVectorIterator  input, std::vector< bool >  subset  )

inline

References lookup_closest_fragment_subset_v(), and store_.

lookup_closest_fragment_subset_v()

FragmentLookupResult protocols::indexed_structure_store::FragmentLookup::lookup_closest_fragment_subset_v ( std::vector< numeric::xyzVector< numeric::Real > > &  query_coordinates, std::vector< bool >  subset  )

protected

References protocols::indexed_structure_store::FragmentLookupResult::found_match, lookup_, protocols::indexed_structure_store::FragmentLookupResult::match_index, protocols::indexed_structure_store::FragmentLookupResult::match_rmsd, protocols::indexed_structure_store::FragmentLookupResult::match_rmsd_threshold, protocols::indexed_structure_store::FragmentLookupResult::match_score, and store_.

Referenced by lookup_closest_fragment_subset().

lookup_closest_fragment_v()

FragmentLookupResult protocols::indexed_structure_store::FragmentLookup::lookup_closest_fragment_v ( std::vector< numeric::xyzVector< numeric::Real > > &  query_coordinates )

protected

References protocols::indexed_structure_store::FragmentLookupResult::found_match, lookup_, protocols::indexed_structure_store::FragmentLookupResult::match_index, protocols::indexed_structure_store::FragmentLookupResult::match_rmsd, protocols::indexed_structure_store::FragmentLookupResult::match_rmsd_threshold, protocols::indexed_structure_store::FragmentLookupResult::match_score, and store_.

Referenced by lookup_closest_fragment().

lookup_closest_pose_fragments()

template<class FragmentLookupOutputIterator , class ResidueNumberOutputIterator >

void protocols::indexed_structure_store::FragmentLookup::lookup_closest_pose_fragments ( core::pose::Pose const &  pose, FragmentLookupOutputIterator  result_out, ResidueNumberOutputIterator  fragment_start_out  )

inline

References get_fragment_residue_spans(), lookup_closest_fragment(), core::pose::Pose::residue(), store_, and core::conformation::Residue::xyz().

lookup_fragment()

template<class xyzVectorIterator >

FragmentLookupResult protocols::indexed_structure_store::FragmentLookup::lookup_fragment ( xyzVectorIterator  input )

inline

References lookup_fragment_v(), and store_.

Referenced by lookup_pose_fragments().

lookup_fragment_v()

FragmentLookupResult protocols::indexed_structure_store::FragmentLookup::lookup_fragment_v ( std::vector< numeric::xyzVector< numeric::Real > > &  query_coordinates )

protected

References protocols::indexed_structure_store::FragmentLookupResult::found_match, lookup_, protocols::indexed_structure_store::FragmentLookupResult::match_index, protocols::indexed_structure_store::FragmentLookupResult::match_rmsd, protocols::indexed_structure_store::FragmentLookupResult::match_rmsd_threshold, protocols::indexed_structure_store::FragmentLookupResult::match_score, and store_.

Referenced by lookup_fragment().

lookup_pose_fragments()

template<class FragmentLookupOutputIterator , class ResidueNumberOutputIterator >

void protocols::indexed_structure_store::FragmentLookup::lookup_pose_fragments ( core::pose::Pose const &  pose, FragmentLookupOutputIterator  result_out, ResidueNumberOutputIterator  fragment_start_out  )

inline

References get_fragment_residue_spans(), lookup_fragment(), core::pose::Pose::residue(), store_, and core::conformation::Residue::xyz().

store()

FragmentStoreCOP protocols::indexed_structure_store::FragmentLookup::store ( )

inline

References store_.

Member Data Documentation

lookup_

numeric::coordinate_fitting::CoordinateArray_RMSD_FlatLookup<numeric::Real> protocols::indexed_structure_store::FragmentLookup::lookup_

private

Referenced by lookup_close_fragments_v(), lookup_closest_fragment_subset_v(), lookup_closest_fragment_v(), and lookup_fragment_v().

store_

FragmentStoreOP protocols::indexed_structure_store::FragmentLookup::store_

private

Referenced by fragment_specification(), lookup_close_fragments(), lookup_closest_fragment(), lookup_closest_fragment_subset(), lookup_closest_fragment_subset_v(), lookup_closest_fragment_v(), lookup_closest_pose_fragments(), lookup_fragment(), lookup_fragment_v(), lookup_pose_fragments(), and store().

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

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