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

Functions
static thread_local 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 thread_local basic::Tracer	TR ("protocols.nonlocal.SheetTranslate")
static thread_local 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 thread_local 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::shared_ptr<BiasedFragmentMover const> protocols::nonlocal::BiasedFragmentMoverCOP

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Function Documentation

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

References protocols::loops::Loop::length(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::xyz(), and numeric::xyzVector< class >::zero().

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).

References option.

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>.

References 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.

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.

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::simple_moves::AddJobPairData::apply(), protocols::qsar::qsarMover::apply(), protocols::RotamerDump::RotamerDumpMover::apply(), protocols::star::StarAbinitio::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::ligand_docking::ComputeLigandRDF::apply(), protocols::medal::MedalMover::apply(), protocols::make_rot_lib::MakeRotLibMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::simple_moves::ddG::apply(), protocols::anchored_design::AnchoredDesignMover::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::GraftCDRLoopsProtocol::apply(), protocols::toolbox::task_operations::ReadResfileFromDB::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::ligand_docking::InterfaceScoreCalculator::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::loops::loops_definers::LoopsDatabaseDefiner::apply(), protocols::ligand_docking::LigandDockMain::apply(), protocols::helical_bundle::BundleGridSampler::apply(), protocols::docking::DockingProtocol::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::rosetta_scripts::ParsedProtocol::apply_filter(), protocols::make_rot_lib::MakeRotLibMover::calc_final_rotamers(), protocols::hotspot_hashing::movers::PlaceProbeMover::check_and_initialize(), protocols::floppy_tail::create_extra_output(), protocols::jd2::FileSystemJobDistributor::current_job_finished(), protocols::anchored_design::debug_dump_pose(), protocols::jd2::ScreeningJobInputter::fill_jobs(), protocols::rosetta_scripts::ParsedProtocol::finish_protocol(), protocols::features::ScreeningFeatures::get_desriptor_data(), protocols::jd2::JD2ResourceManager::get_option(), protocols::features::get_write_delete_pair(), protocols::jd2::JD2ResourceManager::has_option(), protocols::jd2::JD2ResourceManager::has_resource_with_description(), protocols::jd2::FileSystemJobDistributor::job_failed(), protocols::features::JobDataFeatures::load_string_data(), protocols::features::JobDataFeatures::load_string_real_data(), protocols::features::JobDataFeatures::load_string_string_data(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), protocols::features::TopCountOfEachInput::operator()(), protocols::antibody::design::AntibodyDesignMover::output_ensemble(), protocols::analysis::PeptideDeriverPoseOutputter::output_pose(), 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::jd2::FileSystemJobDistributor::remove_bad_inputs_from_job_list(), protocols::analysis::InterfaceAnalyzerMover::report_data(), protocols::features::ScreeningFeatures::report_features(), protocols::features::JobDataFeatures::report_features(), protocols::rosetta_scripts::ParsedProtocol::report_filters_to_job(), protocols::simple_filters::Operator::report_sm(), protocols::simple_filters::ShapeComplementarityFilter::report_sm(), protocols::analysis::InterfaceAnalyzerMover::set_pose_info(), protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics(), protocols::features::ProteinSilentReport::write_full_report(), protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb(), protocols::matdes::ClashCheckFilter::write_pymol_string_to_pdb(), protocols::simple_filters::MutationsFilter::write_to_pdb(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::write_to_pdb(), protocols::simple_filters::TaskAwareScoreTypeFilter::write_to_pdb(), protocols::simple_filters::RotamerBoltzmannWeight::write_to_pdb(), protocols::simple_filters::DdGScan::write_to_pdb(), protocols::matdes::SymUnsatHbondFilter::write_to_pdb(), protocols::matdes::ClashCheckFilter::write_to_pdb(), and protocols::matdes::OligomericAverageDegreeFilter::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>.

References left, protocols::loops::Loop::length(), midpoint(), numeric::random::random_range(), 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>.

References core::io::pdb::dump_pdb(), and option.

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
	)

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.

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.

References decompose().

core::Size protocols::nonlocal::make_selection

(

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

sampler

)

Convenience method for retrieving the single highest-weighted sample.

References numeric::random::WeightedReservoirSampler< class >::samples().

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

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

static

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

static

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

static