Singleton for creating StructureData objects. More...

#include <StructureDataFactory.hh>

Inheritance diagram for protocols::denovo_design::components::StructureDataFactory:

Public Types
typedef std::map< std::string, std::set< basic::datacache::WriteableCacheableDataOP > >	WriteableCacheableDataMap

Public Member Functions
void	save_into_pose (core::pose::Pose &pose, StructureData const &sd) const
	stores the data of this permutation into a pose for later retrieval StructureData stored in a pose this way can be retrieved by calling get_from_pose(), or get_from_const_pose() More...

void	clear_from_pose (core::pose::Pose &pose) const
	clears all structuredata information (including cached xml) from this pose. More...

StructureData const &	get_from_pose (core::pose::Pose &pose) const
	retrieves a StructureData object from the pose observable cache creates one if necessary More...

StructureData const &	get_from_const_pose (core::pose::Pose const &pose) const
	retrieves a StructureData object from the pose observable cache Creates a StructureData using the pose (but doesn't attach it) if the cached StructureData could not be retrieved properly More...

StructureData	create_from_pose (core::pose::Pose const &pose) const
	retrieves a StructureData object from the pose data cache Creates a StructureData using the pose (but doesn't store it) if the cached StructureData is not present More...

StructureData	create_from_pose (core::pose::Pose const &pose, SegmentName const &prefix) const
	retrieves a StructureData object from the pose data cache Creates a StructureData using the pose (but doesn't store it) if the cached StructureData is not present. Adds id_val as a prefix for all new segments More...

StructureData	create_from_cacheable_data (std::istream &raw_stream) const
	creates from CacheableData stream More...

StructureData	create_from_xml (std::istream &xmltag) const
	creates a StructureData from an xml stringstream More...

StructureData	create_from_remarks (core::io::Remarks const &rem) const
	creates SD from description stored in PDB remarks More...

StructureData	create_from_motifs (std::string const &motif_str) const
	creates a StructureData from a motif string More...

StructureData	create_from_motifs (std::string const &motif_str, SegmentName const &prefix) const
	creates a StructureData from a motif string, optionally prefixing a string to the name of each segment More...

bool	observer_attached (core::pose::Pose const &pose) const
	checks for a StructureData in the pose observer cache Returns true if one is found, false otherwise More...

StructureDataObserverCOP	retrieve_observer (core::pose::Pose const &pose) const
	returns observer pointer if the pose has one cached pointer returned can be null if no StructureData is present in the cache More...

void	attach_observer (core::pose::Pose &pose) const
	attaches cacheable observer. Sets up cached SD if there isn't one More...

void	detach_observer (core::pose::Pose &pose) const
	detaches cacheable observer and removes from observable cache More...

bool	has_cached_data (core::pose::Pose const &pose) const
	checks whether StructureData is stored in the pose's datacache More...

Static Public Attributes
static int const	REMARK_NUM = 994

Private Member Functions
	StructureDataFactory ()
	Private constructor for singleton. More...

StructureData	infer_from_pose (core::pose::Pose const &pose, SegmentName const &prefix) const
	sets data from a given pose's information, not taking into account PDB remarks More...

StructureDataOP	retrieve_cached_data_ptr (core::pose::Pose &pose) const

StructureData const &	retrieve_cached_data (core::pose::Pose const &pose) const
	retrieves a StructureData object from the pose's datacache More...

void	set_cached_data (core::pose::Pose &pose, StructureData const &sd) const
	stores a StructureData in the pose's datacache More...

void	clear_cached_data (core::pose::Pose &pose) const
	clears stored StructureData from the pose's datacache More...

void	add_perm_remark (core::io::Remarks &remarks, std::string const &rem_value) const
	adds a remark to remarks object More...

Friends
class	utility::SingletonBase< StructureDataFactory >

Detailed Description

Singleton for creating StructureData objects.

Member Typedef Documentation

◆ WriteableCacheableDataMap

typedef std::map< std::string, std::set< basic::datacache::WriteableCacheableDataOP > > protocols::denovo_design::components::StructureDataFactory::WriteableCacheableDataMap

Constructor & Destructor Documentation

◆ StructureDataFactory()

protocols::denovo_design::components::StructureDataFactory::StructureDataFactory ( )

private

Private constructor for singleton.

Member Function Documentation

◆ add_perm_remark()

void protocols::denovo_design::components::StructureDataFactory::add_perm_remark	(	core::io::Remarks &	remarks,
		std::string const &	rem_value
	)		const

private

adds a remark to remarks object

References protocols::denovo_design::add_remark(), and REMARK_NUM.

Referenced by save_into_pose().

◆ attach_observer()

void protocols::denovo_design::components::StructureDataFactory::attach_observer ( core::pose::Pose & pose ) const

attaches cacheable observer. Sets up cached SD if there isn't one

attaches cacheable observer. Overwrites whatever was there before

References core::pose::Pose::observer_cache(), retrieve_cached_data_ptr(), core::pose::datacache::ObserverCache::set(), core::pose::datacache::STRUCTUREDATA_OBSERVER, and protocols::TR().

Referenced by protocols::denovo_design::movers::AlignResiduesMover::apply().

◆ clear_cached_data()

void protocols::denovo_design::components::StructureDataFactory::clear_cached_data ( core::pose::Pose & pose ) const

private

clears stored StructureData from the pose's datacache

References protocols::denovo_design::components::StructureData::class_name(), and core::pose::Pose::data().

Referenced by clear_from_pose().

◆ clear_from_pose()

void protocols::denovo_design::components::StructureDataFactory::clear_from_pose ( core::pose::Pose & pose ) const

clears all structuredata information (including cached xml) from this pose.

References clear_cached_data(), detach_observer(), and core::pose::Pose::pdb_info().

◆ create_from_cacheable_data()

StructureData protocols::denovo_design::components::StructureDataFactory::create_from_cacheable_data ( std::istream & raw_stream ) const

creates from CacheableData stream

References protocols::denovo_design::components::clean_from_storage(), create_from_xml(), and protocols::TR().

Referenced by protocols::denovo_design::components::StructureDataCreator::create_data().

◆ create_from_motifs() [1/2]

StructureData protocols::denovo_design::components::StructureDataFactory::create_from_motifs ( std::string const & motif_str ) const

creates a StructureData from a motif string

Parameters

[in] motifs String of secstruct/abego motifs (e.g. "1LX-5EB-2LG-5EB-1LA-1LB-1LG-10HA-1LX" )

Returns: StructureData containing one segment per motif with the specified secondary structure and abego. Each motif is connected to the previous and next motifs. Segments are named by their secondary structure (e.g. L01, E01, L02, E02, L03, H01, L04 )

◆ create_from_motifs() [2/2]

StructureData protocols::denovo_design::components::StructureDataFactory::create_from_motifs	(	std::string const &	motif_str,
		SegmentName const &	prefix
	)		const

creates a StructureData from a motif string, optionally prefixing a string to the name of each segment

Parameters

[in]	motifs	String of secstruct/abego motifs (e.g. "1LX-5EB-2LG-5EB-1LA-1LB-1LG-10HA-1LX" )
[in]	prefix	Name to be prepended before the segment names. If empty, names will be as [ L01, E01, L02, ... ]. If set to "myprefix", names will be as [ myprefix.L01, myprefix.E01, ... ]

Returns: StructureData containing one segment per motif with the specified secondary structure and abego. Each motif is connected to the previous and next motifs. Segments are named by their secondary structure (e.g. L01, E01, L02, E02, L03, H01, L04 )

References protocols::denovo_design::components::add_segments_for_chain(), and protocols::denovo_design::parse_motif_string().

◆ create_from_pose() [1/2]

StructureData protocols::denovo_design::components::StructureDataFactory::create_from_pose ( core::pose::Pose const & pose ) const

retrieves a StructureData object from the pose data cache Creates a StructureData using the pose (but doesn't store it) if the cached StructureData is not present

retrieves a StructureData object from the pose observable cache Creates a StructureData using the pose (but doesn't attach it) if the cached StructureData could not be retrieved properly

Parameters

[in] pose The input pose

Referenced by protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), get_from_pose(), and retrieve_cached_data_ptr().

◆ create_from_pose() [2/2]

StructureData protocols::denovo_design::components::StructureDataFactory::create_from_pose	(	core::pose::Pose const &	pose,
		SegmentName const &	prefix
	)		const

retrieves a StructureData object from the pose data cache Creates a StructureData using the pose (but doesn't store it) if the cached StructureData is not present. Adds id_val as a prefix for all new segments

Parameters

[in]	pose	The input pose
[in]	prefix	A prefix to be added to the segments in the pose. For example, if prefix is empty, the first helix would be named 'H01', but if prefix is set to 'pose1', the first helix will be named 'pose.H01'

References protocols::denovo_design::components::StructureData::check_pose_consistency(), create_from_remarks(), has_cached_data(), infer_from_pose(), core::pose::Pose::pdb_info(), retrieve_cached_data(), protocols::denovo_design::components::StructureData::save_remarks(), and protocols::TR().

◆ create_from_remarks()

StructureData protocols::denovo_design::components::StructureDataFactory::create_from_remarks ( core::io::Remarks const & rem ) const

creates SD from description stored in PDB remarks

References create_from_xml(), protocols::denovo_design::get_remark_line(), REMARK_NUM, and protocols::TR().

Referenced by protocols::denovo_design::movers::MakeAsymmetricStructureDataMover::apply(), and create_from_pose().

◆ create_from_xml()

StructureData protocols::denovo_design::components::StructureDataFactory::create_from_xml ( std::istream & xmltag ) const

creates a StructureData from an xml stringstream

References protocols::denovo_design::components::StructureData::parse_tag().

Referenced by create_from_cacheable_data(), and create_from_remarks().

◆ detach_observer()

void protocols::denovo_design::components::StructureDataFactory::detach_observer ( core::pose::Pose & pose ) const

detaches cacheable observer and removes from observable cache

References core::pose::datacache::ObserverCache::clear(), core::pose::Pose::observer_cache(), and core::pose::datacache::STRUCTUREDATA_OBSERVER.

Referenced by clear_from_pose().

◆ get_from_const_pose()

StructureData const & protocols::denovo_design::components::StructureDataFactory::get_from_const_pose ( core::pose::Pose const & pose ) const

retrieves a StructureData object from the pose observable cache Creates a StructureData using the pose (but doesn't attach it) if the cached StructureData could not be retrieved properly

retrieves a StructureData object from the pose observable cache utility_exit() if no StructureData object is found

References retrieve_cached_data().

Referenced by protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), protocols::denovo_design::constraints::FileConstraintGenerator::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::denovo_design::movers::FoldArchitectMover::create_loops(), protocols::fldsgn::filters::SecondaryStructureFilter::get_filtered_secstruct(), protocols::fldsgn::filters::SheetTopologyFilter::get_filtered_sheet_topology(), get_from_pose(), protocols::fldsgn::filters::HSSTripletFilter::get_hss3s(), and protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_sheet_topology().

◆ get_from_pose()

StructureData const & protocols::denovo_design::components::StructureDataFactory::get_from_pose ( core::pose::Pose & pose ) const

retrieves a StructureData object from the pose observable cache creates one if necessary

References create_from_pose(), get_from_const_pose(), has_cached_data(), and save_into_pose().

Referenced by protocols::denovo_design::movers::AlignResiduesMover::align_residues(), and protocols::denovo_design::movers::FoldArchitectMover::fold_attempt().

◆ has_cached_data()

bool protocols::denovo_design::components::StructureDataFactory::has_cached_data ( core::pose::Pose const & pose ) const

checks whether StructureData is stored in the pose's datacache

checks whether a pose contains a structuredata in its datacache

References protocols::denovo_design::components::StructureData::class_name(), core::pose::Pose::data(), and protocols::denovo_design::components::get_writeable_cacheable_map().

Referenced by protocols::denovo_design::movers::FoldTreeFromFoldGraphMover::apply(), protocols::denovo_design::constraints::FileConstraintGenerator::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), create_from_pose(), protocols::denovo_design::movers::FoldArchitectMover::fold_attempt(), protocols::fldsgn::SheetConstraintGenerator::get_abego(), protocols::fldsgn::filters::SecondaryStructureFilter::get_filtered_secstruct(), protocols::fldsgn::filters::SheetTopologyFilter::get_filtered_sheet_topology(), get_from_pose(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::get_sheet_topology(), and retrieve_cached_data_ptr().

◆ infer_from_pose()

StructureData protocols::denovo_design::components::StructureDataFactory::infer_from_pose	(	core::pose::Pose const &	pose,
		SegmentName const &	prefix
	)		const

private

sets data from a given pose's information, not taking into account PDB remarks

Parameters

[in]	pose	The input pose
[in]	prefix	A prefix to be added to the segments in the pose. For example, if prefix is empty, the first helix would be named 'H01', but if prefix is set to 'pose1', the first helix will be named 'pose.H01'

References core::scoring::abego, protocols::denovo_design::abego_str(), protocols::denovo_design::components::StructureData::add_covalent_bond(), protocols::denovo_design::components::add_segments_for_chain(), core::chemical::ResidueType::atom_name(), core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), core::conformation::Residue::connected_residue_at_resconn(), protocols::simple_filters::dssp(), core::conformation::Residue::is_polymer(), core::conformation::Residue::n_non_polymeric_residue_connections(), core::pose::Pose::residue(), core::conformation::Residue::residue_connect_atom_index(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Residue::type().

Referenced by create_from_pose().

◆ observer_attached()

bool protocols::denovo_design::components::StructureDataFactory::observer_attached ( core::pose::Pose const & pose ) const

checks for a StructureData in the pose observer cache Returns true if one is found, false otherwise

References core::pose::datacache::ObserverCache::is_attached(), core::pose::Pose::observer_cache(), and core::pose::datacache::STRUCTUREDATA_OBSERVER.

Referenced by retrieve_observer().

◆ retrieve_cached_data()

StructureData const & protocols::denovo_design::components::StructureDataFactory::retrieve_cached_data ( core::pose::Pose const & pose ) const

private

retrieves a StructureData object from the pose's datacache

References protocols::denovo_design::components::StructureData::class_name(), core::pose::Pose::data(), and protocols::denovo_design::components::get_writeable_cacheable_map().

Referenced by create_from_pose(), and get_from_const_pose().

◆ retrieve_cached_data_ptr()

StructureDataOP protocols::denovo_design::components::StructureDataFactory::retrieve_cached_data_ptr ( core::pose::Pose & pose ) const

private

References protocols::denovo_design::components::StructureData::class_name(), create_from_pose(), core::pose::Pose::data(), protocols::denovo_design::components::get_writeable_cacheable_map(), has_cached_data(), and save_into_pose().

Referenced by attach_observer().

◆ retrieve_observer()

StructureDataObserverCOP protocols::denovo_design::components::StructureDataFactory::retrieve_observer ( core::pose::Pose const & pose ) const

returns observer pointer if the pose has one cached pointer returned can be null if no StructureData is present in the cache

References observer_attached(), core::pose::Pose::observer_cache(), and core::pose::datacache::STRUCTUREDATA_OBSERVER.

◆ save_into_pose()

void protocols::denovo_design::components::StructureDataFactory::save_into_pose	(	core::pose::Pose &	pose,
		StructureData const &	sd
	)		const

stores the data of this permutation into a pose for later retrieval StructureData stored in a pose this way can be retrieved by calling get_from_pose(), or get_from_const_pose()

References add_perm_remark(), protocols::denovo_design::components::StructureData::check_pose_consistency(), core::pose::Pose::pdb_info(), protocols::denovo_design::components::StructureData::retrieve_remarks(), and set_cached_data().

Referenced by protocols::denovo_design::movers::AlignResiduesMover::align_residues(), get_from_pose(), and retrieve_cached_data_ptr().

◆ set_cached_data()

void protocols::denovo_design::components::StructureDataFactory::set_cached_data	(	core::pose::Pose &	pose,
		StructureData const &	sd
	)		const

private

stores a StructureData in the pose's datacache

References protocols::denovo_design::components::StructureData::class_name(), and core::pose::Pose::data().

Referenced by save_into_pose().

Friends And Related Function Documentation

◆ utility::SingletonBase< StructureDataFactory >

friend class utility::SingletonBase< StructureDataFactory >

friend

Member Data Documentation

◆ REMARK_NUM

int const protocols::denovo_design::components::StructureDataFactory::REMARK_NUM = 994

static

Referenced by add_perm_remark(), create_from_remarks(), and protocols::denovo_design::components::StructureData::save_remarks().

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

src/protocols/denovo_design/components/StructureDataFactory.hh
src/protocols/denovo_design/components/StructureDataFactory.cc

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Friends

Detailed Description

Member Typedef Documentation

◆ WriteableCacheableDataMap

Constructor & Destructor Documentation

◆ StructureDataFactory()

Member Function Documentation

◆ add_perm_remark()

◆ attach_observer()

◆ clear_cached_data()

◆ clear_from_pose()

◆ create_from_cacheable_data()

◆ create_from_motifs() [1/2]

◆ create_from_motifs() [2/2]

◆ create_from_pose() [1/2]

◆ create_from_pose() [2/2]

◆ create_from_remarks()

◆ create_from_xml()

◆ detach_observer()

◆ get_from_const_pose()

◆ get_from_pose()

◆ has_cached_data()

◆ infer_from_pose()

◆ observer_attached()

◆ retrieve_cached_data()

◆ retrieve_cached_data_ptr()

◆ retrieve_observer()

◆ save_into_pose()

◆ set_cached_data()

Friends And Related Function Documentation

◆ utility::SingletonBase< StructureDataFactory >

Member Data Documentation

◆ REMARK_NUM