protocols::indexed_structure_store Namespace Reference

Namespaces
	filters
	movers
	search

Classes
struct	_map_string_vector_Real
struct	_map_string_vector_Size
struct	_map_string_vector_vector_Real
class	BinaryFragmentStoreBackend
struct	DirectSegmentLookup
struct	DirectSegmentLookupConfig
struct	DirectSegmentLookupResult
class	DirStructureStoreBackend
class	FragmentLookup
class	FragmentLookupResult
struct	FragmentSpecification
class	FragmentStore
class	FragmentStoreManager
class	FragmentStoreProvider
class	JSONStructureStoreBackend
class	PoseUtilityPlaceholder
struct	ResidueBackboneEntry
struct	ResidueEntry
struct	ResidueOrientEntry
struct	ResidueSidechainEntry
struct	SegmentSequenceProfile
struct	SegmentSequenceProfileConfig
struct	SegmentSequenceProfileResult
class	SilentStructureStoreBackend
class	SSHashedFragmentStore
struct	StructureEntry
struct	StructureRecord
class	StructureStore
class	StructureStoreManager
class	StructureStoreProvider

Typedefs
typedef utility::pointer::shared_ptr < FragmentLookup >	FragmentLookupOP
typedef utility::pointer::shared_ptr < FragmentLookup const >	FragmentLookupCOP
typedef utility::pointer::weak_ptr < FragmentLookup >	FragmentLookupAP
typedef utility::pointer::weak_ptr < FragmentLookup const >	FragmentLookupCAP
typedef utility::pointer::shared_ptr < FragmentStore >	FragmentStoreOP
typedef utility::pointer::shared_ptr < FragmentStore const >	FragmentStoreCOP
typedef utility::pointer::shared_ptr < FragmentStoreProvider >	FragmentStoreProviderOP
typedef utility::pointer::shared_ptr < FragmentStoreProvider const >	FragmentStoreProviderCOP
typedef utility::pointer::shared_ptr < StructureStore >	StructureStoreOP
typedef utility::pointer::shared_ptr < StructureStore const >	StructureStoreCOP
typedef utility::pointer::weak_ptr < StructureStore >	StructureStoreAP
typedef utility::pointer::shared_ptr < StructureStoreProvider >	StructureStoreProviderOP
typedef utility::pointer::shared_ptr < StructureStoreProvider const >	StructureStoreProviderCOP

Enumerations
enum	OverlapDeleteMode { DELETE_UPSTREAM, DELETE_DOWNSTREAM }

Functions
static basic::Tracer	TR ("core.indexed_structure_store.BinaryFragmentStoreBackend")
void	to_json (nlohmann::json &j, const ResidueBackboneEntry &i)
void	from_json (const nlohmann::json &j, ResidueBackboneEntry &i)
void	to_json (nlohmann::json &j, const ResidueSidechainEntry &i)
void	from_json (const nlohmann::json &j, ResidueSidechainEntry &i)
void	to_json (nlohmann::json &j, const ResidueOrientEntry &i)
void	from_json (const nlohmann::json &j, ResidueOrientEntry &i)
void	to_json (nlohmann::json &j, const ResidueEntry &i)
void	from_json (const nlohmann::json &j, ResidueEntry &i)
void	to_json (nlohmann::json &j, const StructureEntry &i)
void	from_json (const nlohmann::json &j, StructureEntry &i)
ndarray::Array< ResidueEntry, 1, 1 >	_pose_res (core::pose::Pose &pose, core::Size start_res, core::Size end_res)
void	to_json (nlohmann::json &j, const DirectSegmentLookupConfig &c)
void	from_json (const nlohmann::json &j, DirectSegmentLookupConfig &c)
static basic::Tracer	TR ("core.indexed_structure_store.DirStructureStoreBackend")
std::ostream &	operator<< (std::ostream &os, const FragmentSpecification &s)
static basic::Tracer	TR ("core.indexed_structure_store.FragmentStoreManager")
static basic::Tracer	TR ("core.indexed_structure_store.JSONStructureStoreBackend")
void	to_json (json &j, const StructureRecord &i)
void	from_json (const json &j, StructureRecord &i)
ndarray::ArrayRef< float, 4, 1 >	orient_array (ndarray::Array< ResidueEntry, 2 > res)
ndarray::ArrayRef< float, 3, 1 >	orient_array (ndarray::Array< ResidueEntry, 1 > res)
ndarray::ArrayRef< float, 2, 1 >	orient_array (ResidueEntry &src)
ResidueEntry	extract_residue_entry (core::conformation::Residue const &res)
ndarray::Array< ResidueEntry, 1 >	extract_residue_entries (core::pose::Pose const &pose, bool ignore_non_protein)
void	apply_residue_entries_to_pose (ndarray::Array< ResidueEntry, 1 > residue_entries, core::pose::Pose &pose, core::Size start_residue, bool apply_bb, bool apply_sidechain, bool apply_orient)
core::pose::PoseOP	residue_entries_to_pose (ndarray::Array< protocols::indexed_structure_store::ResidueEntry, 1 > residue_entries, std::string residue_type, bool auto_termini)
template<typename Range >
std::string	to_str (Range range)
template<typename Range , typename Op >
std::vector< size_t >	index_if (Range const &r, Op &pred)
core::pose::PoseOP	initial_pose_for_residues (ndarray::Array< protocols::indexed_structure_store::ResidueEntry, 1 > residue_entries, std::string residue_type, bool auto_termini)
core::pose::PoseOP	residue_entries_to_pose (ndarray::Array< ResidueEntry, 1 > residue_entries, std::string residue_type="fa_standard", bool auto_termini=true)
template<typename ResidueRange >
core::pose::PoseOP	residue_entries_to_pose (ResidueRange residue_entries, std::string residue_type="fa_standard", bool auto_termini=true)
core::pose::PoseOP	initial_pose_for_residues (ndarray::Array< ResidueEntry, 1 > residue_entries, std::string residue_type="fa_standard", bool auto_termini=true)
core::pose::PoseOP	pose_from_store (StructureStore &store, uint32_t structure_id)
template<typename Module >
void	bind_pose_utility (Module &m)
void	to_json (nlohmann::json &j, const SegmentSequenceProfileConfig &c)
void	from_json (const nlohmann::json &j, SegmentSequenceProfileConfig &c)
static basic::Tracer	TR ("core.indexed_structure_store.SilentStructureStoreBackend")
template<typename Module >
void	bind_StructureStore (Module &m)
static basic::Tracer	TR ("core.indexed_structure_store.StructureStoreManager")
core::pose::PoseOP	append_pose_by_bond (core::pose::Pose &upstream_pose, core::pose::Pose &downstream_pose)
core::pose::PoseOP	append_pose_with_overlap (core::pose::Pose &upstream_pose, core::pose::Pose &downstream_pose, core::Size overlap, OverlapDeleteMode delete_overlap)

Typedef Documentation

typedef utility::pointer::weak_ptr<FragmentLookup> protocols::indexed_structure_store::FragmentLookupAP

typedef utility::pointer::weak_ptr<FragmentLookup const> protocols::indexed_structure_store::FragmentLookupCAP

typedef utility::pointer::shared_ptr<FragmentLookup const> protocols::indexed_structure_store::FragmentLookupCOP

typedef utility::pointer::shared_ptr<FragmentLookup> protocols::indexed_structure_store::FragmentLookupOP

typedef utility::pointer::shared_ptr<FragmentStore const> protocols::indexed_structure_store::FragmentStoreCOP

typedef utility::pointer::shared_ptr<FragmentStore> protocols::indexed_structure_store::FragmentStoreOP

typedef utility::pointer::shared_ptr<FragmentStoreProvider const> protocols::indexed_structure_store::FragmentStoreProviderCOP

typedef utility::pointer::shared_ptr<FragmentStoreProvider> protocols::indexed_structure_store::FragmentStoreProviderOP

typedef utility::pointer::weak_ptr<StructureStore> protocols::indexed_structure_store::StructureStoreAP

typedef utility::pointer::shared_ptr<StructureStore const> protocols::indexed_structure_store::StructureStoreCOP

typedef utility::pointer::shared_ptr<StructureStore> protocols::indexed_structure_store::StructureStoreOP

typedef utility::pointer::shared_ptr<StructureStoreProvider const> protocols::indexed_structure_store::StructureStoreProviderCOP

typedef utility::pointer::shared_ptr<StructureStoreProvider> protocols::indexed_structure_store::StructureStoreProviderOP

Enumeration Type Documentation

enum protocols::indexed_structure_store::OverlapDeleteMode

Enumerator
DELETE_UPSTREAM
DELETE_DOWNSTREAM

Function Documentation

ndarray::Array<ResidueEntry, 1, 1> protocols::indexed_structure_store::_pose_res	(	core::pose::Pose &	pose,
		core::Size	start_res,
		core::Size	end_res
	)

References extract_residue_entry(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup().

core::pose::PoseOP protocols::indexed_structure_store::append_pose_by_bond	(	core::pose::Pose &	upstream_pose,
		core::pose::Pose &	downstream_pose
	)

References append_pose_with_overlap(), and DELETE_UPSTREAM.

core::pose::PoseOP protocols::indexed_structure_store::append_pose_with_overlap	(	core::pose::Pose &	upstream_pose,
		core::pose::Pose &	downstream_pose,
		core::Size	overlap,
		OverlapDeleteMode	delete_overlap
	)

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint(), DELETE_UPSTREAM, core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::num_jump(), core::scoring::packstat::overlap(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::size(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by append_pose_by_bond(), and protocols::indexed_structure_store::movers::DirectSegmentLookupMover::generate_result_pose().

void protocols::indexed_structure_store::apply_residue_entries_to_pose	(	ndarray::Array< ResidueEntry, 1 >	residue_entries,
		core::pose::Pose &	pose,
		core::Size	start_residue,
		bool	apply_bb,
		bool	apply_sidechain,
		bool	apply_orient
	)

References core::chemical::aa_from_oneletter_code(), core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::fill_missing_atoms(), core::pose::get_restype_for_pose(), core::chemical::ResidueTypeBase::mode(), core::conformation::Residue::name1(), core::chemical::name_from_aa(), core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), core::conformation::Residue::orient_onto_location(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::AtomID_Map< T >::resize(), core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

Referenced by bind_pose_utility(), and residue_entries_to_pose().

template<typename Module >

void protocols::indexed_structure_store::bind_pose_utility

(

Module &

m

)

References apply_residue_entries_to_pose(), extract_residue_entries(), extract_residue_entry(), initial_pose_for_residues(), pose_from_store(), and residue_entries_to_pose().

template<typename Module >

void protocols::indexed_structure_store::bind_StructureStore

(

Module &

m

)

References protocols::cluster::calibur::aa, core::chemical::element::C, protocols::frag_picker::CA, protocols::indexed_structure_store::StructureStore::check_entries(), core::energy_methods::eval(), protocols::indexed_structure_store::StructureStore::get_residues(), protocols::indexed_structure_store::StructureStore::get_structure(), core::chemical::element::N, core::chemical::element::O, core::scoring::omega, protocols::indexed_structure_store::StructureStore::residue_entries, protocols::indexed_structure_store::StructureStore::resize(), and protocols::indexed_structure_store::StructureStore::structure_entries.

ndarray::Array< ResidueEntry, 1 > protocols::indexed_structure_store::extract_residue_entries	(	core::pose::Pose const &	pose,
		bool	ignore_non_protein
	)

References core::pack::dunbrack::c, core::conformation::Conformation::chain_end(), core::chemical::combine(), core::pose::Pose::conformation(), extract_residue_entry(), core::conformation::Residue::is_protein(), core::conformation::Conformation::num_chains(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::kinmatch::str(), and protocols::hybridization::t.

Referenced by bind_pose_utility(), protocols::indexed_structure_store::SilentStructureStoreBackend::load_store(), and protocols::indexed_structure_store::DirStructureStoreBackend::load_store().

ResidueEntry protocols::indexed_structure_store::extract_residue_entry

(

core::conformation::Residue const &

res

)

References core::conformation::Residue::chi(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::name1(), core::conformation::Residue::nchi(), core::id::omega_torsion(), core::conformation::membrane::out, core::id::phi_torsion(), core::id::psi_torsion(), and core::conformation::Residue::xyz().

Referenced by _pose_res(), bind_pose_utility(), extract_residue_entries(), and protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile().

void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j, SegmentSequenceProfileConfig &  c  )

inline

References protocols::indexed_structure_store::SegmentSequenceProfileConfig::pseudocount, and protocols::indexed_structure_store::SegmentSequenceProfileConfig::rmsd_tolerance.

void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j, DirectSegmentLookupConfig &  c  )

inline

References protocols::indexed_structure_store::DirectSegmentLookupConfig::max_insertion_length, protocols::indexed_structure_store::DirectSegmentLookupConfig::rmsd_tolerance, and protocols::indexed_structure_store::DirectSegmentLookupConfig::segment_cluster_tolerance.

void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j, ResidueBackboneEntry &  i  )

inline

References protocols::indexed_structure_store::ResidueBackboneEntry::omega, protocols::indexed_structure_store::ResidueBackboneEntry::phi, and protocols::indexed_structure_store::ResidueBackboneEntry::psi.

void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j, ResidueSidechainEntry &  i  )

inline

References protocols::indexed_structure_store::ResidueSidechainEntry::aa, protocols::indexed_structure_store::ResidueSidechainEntry::chi1, protocols::indexed_structure_store::ResidueSidechainEntry::chi2, protocols::indexed_structure_store::ResidueSidechainEntry::chi3, and protocols::indexed_structure_store::ResidueSidechainEntry::chi4.

void protocols::indexed_structure_store::from_json ( const json &  j, StructureRecord &  i  )

inline

References protocols::indexed_structure_store::StructureRecord::residues, and protocols::indexed_structure_store::StructureRecord::structure.

void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j, ResidueOrientEntry &  i  )

inline

References protocols::indexed_structure_store::ResidueOrientEntry::C, protocols::indexed_structure_store::ResidueOrientEntry::CA, protocols::indexed_structure_store::ResidueOrientEntry::N, and protocols::indexed_structure_store::ResidueOrientEntry::O.

void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j, ResidueEntry &  i  )

inline

References protocols::indexed_structure_store::ResidueEntry::bb, protocols::indexed_structure_store::ResidueEntry::chain_ending, protocols::indexed_structure_store::ResidueEntry::orient, protocols::indexed_structure_store::ResidueEntry::residue_id, protocols::indexed_structure_store::ResidueEntry::sc, and protocols::indexed_structure_store::ResidueEntry::structure_id.

void protocols::indexed_structure_store::from_json ( const nlohmann::json &  j, StructureEntry &  i  )

inline

References protocols::indexed_structure_store::StructureEntry::id, and protocols::indexed_structure_store::StructureEntry::name.

template<typename Range , typename Op >

std::vector<size_t> protocols::indexed_structure_store::index_if	(	Range const &	r,
		Op &	pred
	)

References core::scoring::pair.

core::pose::PoseOP protocols::indexed_structure_store::initial_pose_for_residues	(	ndarray::Array< ResidueEntry, 1 >	residue_entries,
		std::string	residue_type = "fa_standard",
		bool	auto_termini = true
	)

core::pose::PoseOP protocols::indexed_structure_store::initial_pose_for_residues	(	ndarray::Array< protocols::indexed_structure_store::ResidueEntry, 1 >	residue_entries,
		std::string	residue_type,
		bool	auto_termini
	)

References core::pose::make_pose_from_sequence(), and protocols::loops::start.

Referenced by bind_pose_utility(), and residue_entries_to_pose().

std::ostream& protocols::indexed_structure_store::operator<<	(	std::ostream &	os,
		const FragmentSpecification &	s
	)

References protocols::indexed_structure_store::FragmentSpecification::fragment_atoms, and protocols::indexed_structure_store::FragmentSpecification::fragment_length.

ndarray::ArrayRef<float, 4, 1> protocols::indexed_structure_store::orient_array ( ndarray::Array< ResidueEntry, 2 >  res )

inline

Referenced by protocols::indexed_structure_store::search::StructureDatabase::initialize(), protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup(), and protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile().

ndarray::ArrayRef<float, 3, 1> protocols::indexed_structure_store::orient_array ( ndarray::Array< ResidueEntry, 1 >  res )

inline

ndarray::ArrayRef<float, 2, 1> protocols::indexed_structure_store::orient_array ( ResidueEntry &  src )

inline

References protocols::indexed_structure_store::ResidueOrientEntry::N, and protocols::indexed_structure_store::ResidueEntry::orient.

core::pose::PoseOP protocols::indexed_structure_store::pose_from_store	(	StructureStore &	store,
		uint32_t	structure_id
	)

References protocols::indexed_structure_store::StructureStore::get_residues(), protocols::indexed_structure_store::StructureStore::get_structure(), protocols::indexed_structure_store::StructureEntry::id, and residue_entries_to_pose().

Referenced by bind_pose_utility().

core::pose::PoseOP protocols::indexed_structure_store::residue_entries_to_pose	(	ndarray::Array< ResidueEntry, 1 >	residue_entries,
		std::string	residue_type = "fa_standard",
		bool	auto_termini = true
	)

template<typename ResidueRange >

core::pose::PoseOP protocols::indexed_structure_store::residue_entries_to_pose	(	ResidueRange	residue_entries,
		std::string	residue_type = "fa_standard",
		bool	auto_termini = true
	)

References core::sequence::end, and residue_entries_to_pose().

core::pose::PoseOP protocols::indexed_structure_store::residue_entries_to_pose	(	ndarray::Array< protocols::indexed_structure_store::ResidueEntry, 1 >	residue_entries,
		std::string	residue_type,
		bool	auto_termini
	)

References apply_residue_entries_to_pose(), and initial_pose_for_residues().

Referenced by bind_pose_utility(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::generate_result_pose(), pose_from_store(), and residue_entries_to_pose().

void protocols::indexed_structure_store::to_json ( nlohmann::json &  j, const DirectSegmentLookupConfig &  c  )

inline

References protocols::indexed_structure_store::DirectSegmentLookupConfig::max_insertion_length, protocols::indexed_structure_store::DirectSegmentLookupConfig::rmsd_tolerance, and protocols::indexed_structure_store::DirectSegmentLookupConfig::segment_cluster_tolerance.

void protocols::indexed_structure_store::to_json ( nlohmann::json &  j, const SegmentSequenceProfileConfig &  c  )

inline

References protocols::indexed_structure_store::SegmentSequenceProfileConfig::pseudocount, and protocols::indexed_structure_store::SegmentSequenceProfileConfig::rmsd_tolerance.

void protocols::indexed_structure_store::to_json ( nlohmann::json &  j, const ResidueBackboneEntry &  i  )

inline

References protocols::indexed_structure_store::ResidueBackboneEntry::omega, protocols::indexed_structure_store::ResidueBackboneEntry::phi, and protocols::indexed_structure_store::ResidueBackboneEntry::psi.

void protocols::indexed_structure_store::to_json ( nlohmann::json &  j, const ResidueSidechainEntry &  i  )

inline

References protocols::indexed_structure_store::ResidueSidechainEntry::aa, protocols::indexed_structure_store::ResidueSidechainEntry::chi1, protocols::indexed_structure_store::ResidueSidechainEntry::chi2, protocols::indexed_structure_store::ResidueSidechainEntry::chi3, and protocols::indexed_structure_store::ResidueSidechainEntry::chi4.

void protocols::indexed_structure_store::to_json ( json &  j, const StructureRecord &  i  )

inline

References protocols::indexed_structure_store::StructureRecord::residues, and protocols::indexed_structure_store::StructureRecord::structure.

void protocols::indexed_structure_store::to_json ( nlohmann::json &  j, const ResidueOrientEntry &  i  )

inline

References protocols::indexed_structure_store::ResidueOrientEntry::C, protocols::indexed_structure_store::ResidueOrientEntry::CA, protocols::indexed_structure_store::ResidueOrientEntry::N, and protocols::indexed_structure_store::ResidueOrientEntry::O.

void protocols::indexed_structure_store::to_json ( nlohmann::json &  j, const ResidueEntry &  i  )

inline

References protocols::indexed_structure_store::ResidueEntry::bb, protocols::indexed_structure_store::ResidueEntry::chain_ending, protocols::indexed_structure_store::ResidueEntry::orient, protocols::indexed_structure_store::ResidueEntry::residue_id, protocols::indexed_structure_store::ResidueEntry::sc, and protocols::indexed_structure_store::ResidueEntry::structure_id.

void protocols::indexed_structure_store::to_json ( nlohmann::json &  j, const StructureEntry &  i  )

inline

References protocols::indexed_structure_store::StructureEntry::id, and protocols::indexed_structure_store::StructureEntry::name.

template<typename Range >

std::string protocols::indexed_structure_store::to_str

(

Range

range

)

References core::sequence::end.

static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.BinaryFragmentStoreBackend"  )

static

Referenced by protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::apply(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::generate_result_pose(), protocols::indexed_structure_store::SSHashedFragmentStore::get_valid_resid(), protocols::indexed_structure_store::FragmentStoreManager::load_fragment_lookup(), protocols::indexed_structure_store::FragmentStoreManager::load_fragment_store(), protocols::indexed_structure_store::SilentStructureStoreBackend::load_store(), protocols::indexed_structure_store::JSONStructureStoreBackend::load_store(), protocols::indexed_structure_store::DirStructureStoreBackend::load_store(), protocols::indexed_structure_store::StructureStoreManager::load_structure_store(), protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup(), protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), protocols::indexed_structure_store::JSONStructureStoreBackend::write_store(), and protocols::indexed_structure_store::StructureStoreManager::write_structure_store().

static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.FragmentStoreManager"  )

static

static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.DirStructureStoreBackend"  )

static

static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.SilentStructureStoreBackend"  )

static

static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.JSONStructureStoreBackend"  )

static

static basic::Tracer protocols::indexed_structure_store::TR ( "core.indexed_structure_store.StructureStoreManager"  )

static