protocols::nonlocal Namespace Reference

Classes
class	BiasedFragmentMover
class	Chunk
class	HelixRotate
class	Policy
class	PolicyFactory
class	Region
class	SheetTranslate
class	SimpleTreeBuilder
class	SingleFragmentMover
class	SingleFragmentMoverCreator
class	SmoothPolicy
class	StarTreeBuilder
class	TreeBuilder
class	TreeBuilderFactory
class	UniformPolicy

Typedefs
typedef utility::vector1< double >	Probabilities
typedef utility::pointer::owning_ptr < BiasedFragmentMover >	BiasedFragmentMoverOP
typedef utility::pointer::owning_ptr < BiasedFragmentMover const >	BiasedFragmentMoverCOP
typedef boost::math::normal	Normal
typedef utility::pointer::owning_ptr < Chunk >	ChunkOP
typedef utility::pointer::owning_ptr < Chunk const >	ChunkCOP
typedef utility::pointer::owning_ptr < HelixRotate >	HelixRotateOP
typedef utility::pointer::owning_ptr < HelixRotate const >	HelixRotateCOP
typedef utility::pointer::owning_ptr < Policy >	PolicyOP
typedef utility::pointer::owning_ptr < Policy const >	PolicyCOP
typedef utility::pointer::owning_ptr < Region >	RegionOP
typedef utility::pointer::owning_ptr < Region const >	RegionCOP
typedef utility::pointer::owning_ptr < SheetTranslate >	SheetTranslateOP
typedef utility::pointer::owning_ptr < SheetTranslate const >	SheetTranslateCOP
typedef utility::pointer::owning_ptr < SimpleTreeBuilder >	SimpleTreeBuilderOP
typedef utility::pointer::owning_ptr < SimpleTreeBuilder const >	SimpleTreeBuilderCOP
typedef utility::pointer::owning_ptr < SingleFragmentMover >	SingleFragmentMoverOP
typedef utility::pointer::owning_ptr < SingleFragmentMover const >	SingleFragmentMoverCOP
typedef utility::vector1 < core::Real >	ScoreList
typedef utility::pointer::owning_ptr < StarTreeBuilder >	StarTreeBuilderOP
typedef utility::pointer::owning_ptr < StarTreeBuilder const >	StarTreeBuilderCOP
typedef utility::pointer::owning_ptr < TreeBuilder >	TreeBuilderOP
typedef utility::pointer::owning_ptr < TreeBuilder const >	TreeBuilderCOP

Functions
static basic::Tracer	TR ("protocols.nonlocal.HelixRotate")
void	avg_ca_position (const core::pose::Pose &pose, const protocols::loops::Loop &region, numeric::xyzVector< double > *point)
static basic::Tracer	TR ("protocols.nonlocal.SheetTranslate")
static basic::Tracer	TR ("protocols.nonlocal.SingleFragmentMover")
core::Size	make_selection (numeric::random::WeightedReservoirSampler< core::Size > *sampler)
	Convenience method for retrieving the single highest-weighted sample. More...
static numeric::random::RandomGenerator	RG (330)
static basic::Tracer	TR ("protocols.nonlocal.util")
void	chunks_by_CA_CA_distance (const core::pose::Pose &pose, protocols::loops::LoopsOP chunks)
	Computes the distance between consecutive CA atoms. If the distance exceeds a user-specified threshold, creates a new chunk and adds it to <chunks>. CA-CA distance threshold is retrieved from the option system (rigid::max_ca_ca_dist). More...
void	chunks_by_CA_CA_distance (const core::pose::Pose &pose, protocols::loops::LoopsOP chunks, double threshold)
	Computes the distance between consecutive CA atoms. If the distance exceeds <threshold>, creates a new chunk and adds it to <chunks>. More...
protocols::loops::Loops	combine_and_trim (core::Size min_chunk_sz, core::Size num_residues, const protocols::loops::LoopsOP aligned_regions, const protocols::loops::LoopsOP unaligned_regions)
	Combine aligned and unaligned regions, limit size of final loop. More...
void	limit_chunk_size (core::Size min_chunk_sz, core::Size max_chunk_sz, protocols::loops::LoopsOP &regions)
	Best-effort attempt to limit the length of a chunk by recursively decomposing <regions> such that min_chunk_sz <= |chunk| <= max_chunk_sz. More...
void	decompose (core::Size min_chunk_sz, core::Size max_chunk_sz, const protocols::loops::Loop &loop, utility::vector1< protocols::loops::Loop > *pieces)
	Recursively decomposes <loop> into a series of <pieces>, each having length less than or equal to <max_length>. More...
void	find_regions_with_minimum_size (const core::sequence::SequenceAlignment &alignment, const core::Size unaligned_region_min_sz, protocols::loops::LoopsOP &aligned_regions, protocols::loops::LoopsOP &unaligned_regions)
void	emit_intermediate (const core::pose::Pose &pose, const std::string &file)
	If -abinitio:debug is enabled, writes <pose> to <file>. More...
protocols::comparative_modeling::ThreadingJob const *	current_job ()
	Retrieves the current job from the JobDistributor. More...
core::Real	get_per_residue_score (core::Size rsd_idx, core::scoring::ScoreType scoretype, core::pose::Pose const &pose)
	Returns the unweighted score of the ScoreType for the given residue. Assumes that the Pose has recently been scored by ScoreFunction with non-zero weight for the ScoreType. More...

Typedef Documentation

typedef utility::pointer::owning_ptr<BiasedFragmentMover const> protocols::nonlocal::BiasedFragmentMoverCOP

Definition at line 23 of file BiasedFragmentMover.fwd.hh.

typedef utility::pointer::owning_ptr<BiasedFragmentMover> protocols::nonlocal::BiasedFragmentMoverOP

Definition at line 21 of file BiasedFragmentMover.fwd.hh.

typedef utility::pointer::owning_ptr<Chunk const> protocols::nonlocal::ChunkCOP

Definition at line 23 of file Chunk.fwd.hh.

typedef utility::pointer::owning_ptr<Chunk> protocols::nonlocal::ChunkOP

Definition at line 21 of file Chunk.fwd.hh.

typedef utility::pointer::owning_ptr<HelixRotate const> protocols::nonlocal::HelixRotateCOP

Definition at line 23 of file HelixRotate.fwd.hh.

typedef utility::pointer::owning_ptr<HelixRotate> protocols::nonlocal::HelixRotateOP

Definition at line 21 of file HelixRotate.fwd.hh.

typedef boost::math::normal protocols::nonlocal::Normal

Definition at line 49 of file Chunk.cc.

typedef utility::pointer::owning_ptr<Policy const> protocols::nonlocal::PolicyCOP

Definition at line 23 of file Policy.fwd.hh.

typedef utility::pointer::owning_ptr<Policy> protocols::nonlocal::PolicyOP

Definition at line 21 of file Policy.fwd.hh.

typedef utility::vector1<double> protocols::nonlocal::Probabilities

Definition at line 50 of file BiasedFragmentMover.cc.

typedef utility::pointer::owning_ptr<Region const> protocols::nonlocal::RegionCOP

Definition at line 23 of file Region.fwd.hh.

typedef utility::pointer::owning_ptr<Region> protocols::nonlocal::RegionOP

Definition at line 21 of file Region.fwd.hh.

typedef utility::vector1<core::Real> protocols::nonlocal::ScoreList

Definition at line 33 of file SmoothPolicy.cc.

typedef utility::pointer::owning_ptr<SheetTranslate const> protocols::nonlocal::SheetTranslateCOP

Definition at line 23 of file SheetTranslate.fwd.hh.

typedef utility::pointer::owning_ptr<SheetTranslate> protocols::nonlocal::SheetTranslateOP

Definition at line 21 of file SheetTranslate.fwd.hh.

typedef utility::pointer::owning_ptr<SimpleTreeBuilder const> protocols::nonlocal::SimpleTreeBuilderCOP

Definition at line 23 of file SimpleTreeBuilder.fwd.hh.

typedef utility::pointer::owning_ptr<SimpleTreeBuilder> protocols::nonlocal::SimpleTreeBuilderOP

Definition at line 21 of file SimpleTreeBuilder.fwd.hh.

typedef utility::pointer::owning_ptr<SingleFragmentMover const> protocols::nonlocal::SingleFragmentMoverCOP

Definition at line 23 of file SingleFragmentMover.fwd.hh.

typedef utility::pointer::owning_ptr<SingleFragmentMover> protocols::nonlocal::SingleFragmentMoverOP

Definition at line 21 of file SingleFragmentMover.fwd.hh.

typedef utility::pointer::owning_ptr<StarTreeBuilder const> protocols::nonlocal::StarTreeBuilderCOP

Definition at line 23 of file StarTreeBuilder.fwd.hh.

typedef utility::pointer::owning_ptr<StarTreeBuilder> protocols::nonlocal::StarTreeBuilderOP

Definition at line 21 of file StarTreeBuilder.fwd.hh.

typedef utility::pointer::owning_ptr<TreeBuilder const> protocols::nonlocal::TreeBuilderCOP

Definition at line 23 of file TreeBuilder.fwd.hh.

typedef utility::pointer::owning_ptr<TreeBuilder> protocols::nonlocal::TreeBuilderOP

Definition at line 21 of file TreeBuilder.fwd.hh.

Function Documentation

void protocols::nonlocal::avg_ca_position	(	const core::pose::Pose &	pose,
		const protocols::loops::Loop &	region,
		numeric::xyzVector< double > *	point
	)

Definition at line 99 of file HelixRotate.cc.

References protocols::loops::Loop::length(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and core::pose::Pose::xyz().

Referenced by protocols::nonlocal::HelixRotate::get_rotation_parameters().

void protocols::nonlocal::chunks_by_CA_CA_distance	(	const core::pose::Pose &	pose,
		protocols::loops::LoopsOP	chunks
	)

Computes the distance between consecutive CA atoms. If the distance exceeds a user-specified threshold, creates a new chunk and adds it to <chunks>. CA-CA distance threshold is retrieved from the option system (rigid::max_ca_ca_dist).

Definition at line 61 of file util.cc.

Referenced by protocols::medal::MedalMover::decompose_structure().

void protocols::nonlocal::chunks_by_CA_CA_distance	(	const core::pose::Pose &	pose,
		protocols::loops::LoopsOP	chunks,
		double	threshold
	)

Computes the distance between consecutive CA atoms. If the distance exceeds <threshold>, creates a new chunk and adds it to <chunks>.

Definition at line 67 of file util.cc.

References core::kinematics::distance(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), TR(), and core::pose::Pose::xyz().

protocols::loops::Loops protocols::nonlocal::combine_and_trim	(	core::Size	min_chunk_sz,
		core::Size	num_residues,
		const protocols::loops::LoopsOP	aligned_regions,
		const protocols::loops::LoopsOP	unaligned_regions
	)

Combine aligned and unaligned regions, limit size of final loop.

Definition at line 104 of file util.cc.

References protocols::loops::Loops::push_back(), and protocols::loops::Loops::size().

protocols::comparative_modeling::ThreadingJob const * protocols::nonlocal::current_job

(

)

Retrieves the current job from the JobDistributor.

Definition at line 218 of file util.cc.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::qsar::qsarMover::apply(), protocols::RotamerDump::RotamerDumpMover::apply(), protocols::star::StarAbinitio::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::medal::MedalMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::antibody2::GraftCDRLoopsProtocol::apply(), protocols::antibody2::AntibodyModelerProtocol::apply(), protocols::toolbox::task_operations::ReadResfileFromDB::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::simple_moves::ddG::apply(), protocols::contact_map::ContactMap::apply(), protocols::ligand_docking::InterfaceScoreCalculator::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::loops::loops_definers::LoopsDatabaseDefiner::apply(), protocols::ligand_docking::LigandDockMain::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::docking::DockingProtocol::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::hotspot_hashing::movers::PlaceProbeMover::check_and_initialize(), protocols::floppy_tail::create_extra_output(), protocols::anchored_design::debug_dump_pose(), protocols::jobdist::BaseJobDistributor::get_current_output_tag(), protocols::jd2::JD2ResourceManager::get_option(), protocols::features::get_write_delete_pair(), protocols::jd2::JD2ResourceManager::has_option(), protocols::jd2::JD2ResourceManager::has_resource_with_description(), protocols::features::JobDataFeatures::load_string_data(), protocols::features::JobDataFeatures::load_string_real_data(), protocols::features::JobDataFeatures::load_string_string_data(), protocols::features::TopCountOfEachInput::operator()(), protocols::simple_moves::SequenceProfileMover::parse_my_tag(), protocols::protein_interface_design::movers::SubroutineMover::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_interface_residues(), protocols::analysis::InterfaceAnalyzerMover::report_data(), protocols::features::JobDataFeatures::report_features(), protocols::rosetta_scripts::ParsedProtocol::report_filters_to_job(), protocols::simple_filters::ShapeComplementarityFilter::report_sm(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), protocols::features::ProteinSilentReport::write_full_report(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::write_to_pdb(), and protocols::simple_filters::RotamerBoltzmannWeight::write_to_pdb().

void protocols::nonlocal::decompose	(	core::Size	min_chunk_sz,
		core::Size	max_chunk_sz,
		const protocols::loops::Loop &	loop,
		utility::vector1< protocols::loops::Loop > *	pieces
	)

Recursively decomposes <loop> into a series of <pieces>, each having length less than or equal to <max_length>.

Definition at line 144 of file util.cc.

References core::sequence::left, protocols::loops::Loop::length(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by limit_chunk_size().

void protocols::nonlocal::emit_intermediate	(	const core::pose::Pose &	pose,
		const std::string &	filename
	)

If -abinitio:debug is enabled, writes <pose> to <file>.

Definition at line 210 of file util.cc.

References core::pack::interaction_graph::debug, and core::io::pdb::dump_pdb().

void protocols::nonlocal::find_regions_with_minimum_size	(	const core::sequence::SequenceAlignment &	alignment,
		const core::Size	unaligned_region_min_sz,
		protocols::loops::LoopsOP &	aligned_regions,
		protocols::loops::LoopsOP &	unaligned_regions
	)

Definition at line 190 of file util.cc.

References protocols::comparative_modeling::bounded_loops_from_alignment(), core::sequence::SequenceAlignment::length(), and core::sequence::SequenceAlignment::sequence().

core::Real protocols::nonlocal::get_per_residue_score	(	core::Size	rsd_idx,
		core::scoring::ScoreType	scoretype,
		core::pose::Pose const &	pose
	)

Returns the unweighted score of the ScoreType for the given residue. Assumes that the Pose has recently been scored by ScoreFunction with non-zero weight for the ScoreType.

Definition at line 228 of file util.cc.

References core::pose::Pose::energies(), core::scoring::Energies::residue_total_energies(), and core::pose::Pose::total_residue().

void protocols::nonlocal::limit_chunk_size	(	core::Size	min_chunk_sz,
		core::Size	max_chunk_sz,
		protocols::loops::LoopsOP &	regions
	)

Best-effort attempt to limit the length of a chunk by recursively decomposing <regions> such that min_chunk_sz <= |chunk| <= max_chunk_sz.

Definition at line 121 of file util.cc.

References decompose().

core::Size protocols::nonlocal::make_selection

(

numeric::random::WeightedReservoirSampler< core::Size > *

sampler)

Convenience method for retrieving the single highest-weighted sample.

Definition at line 36 of file SmoothPolicy.cc.

Referenced by protocols::nonlocal::SmoothPolicy::choose().

static numeric::random::RandomGenerator protocols::nonlocal::RG ( 330  )

static

Referenced by protocols::nonlocal::UniformPolicy::choose().

static basic::Tracer protocols::nonlocal::TR ( "protocols.nonlocal.HelixRotate"  )

static

Referenced by protocols::nonlocal::SheetTranslate::apply(), protocols::nonlocal::HelixRotate::apply(), and chunks_by_CA_CA_distance().

static basic::Tracer protocols::nonlocal::TR ( "protocols.nonlocal.SheetTranslate"  )

static

static basic::Tracer protocols::nonlocal::TR ( "protocols.nonlocal.SingleFragmentMover"  )

static

static basic::Tracer protocols::nonlocal::TR ( "protocols.nonlocal.util"  )

static