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
using	Probabilities = utility::vector1< core::Real >
typedef utility::pointer::shared_ptr< BiasedFragmentMover >	BiasedFragmentMoverOP
typedef utility::pointer::shared_ptr< BiasedFragmentMover const >	BiasedFragmentMoverCOP
using	Normal = boost::math::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
using	ScoreList = utility::vector1< core::Real >
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 basic::Tracer	TR ("protocols.nonlocal.HelixRotate")
void	avg_ca_position (const core::pose::Pose &pose, const protocols::loops::Loop &region, numeric::xyzVector< core::Real > *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 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, core::Real 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...
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

BiasedFragmentMoverCOP

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

BiasedFragmentMoverOP

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

ChunkCOP

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

ChunkOP

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

HelixRotateCOP

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

HelixRotateOP

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

Normal

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

PolicyCOP

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

PolicyOP

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

Probabilities

using protocols::nonlocal::Probabilities = typedef utility::vector1<core::Real>

RegionCOP

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

RegionOP

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

ScoreList

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

SheetTranslateCOP

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

SheetTranslateOP

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

SimpleTreeBuilderCOP

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

SimpleTreeBuilderOP

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

SingleFragmentMoverCOP

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

SingleFragmentMoverOP

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

StarTreeBuilderCOP

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

StarTreeBuilderOP

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

TreeBuilderCOP

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

TreeBuilderOP

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

Function Documentation

avg_ca_position()

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

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().

chunks_by_CA_CA_distance() [1/2]

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).

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

chunks_by_CA_CA_distance() [2/2]

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

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

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

combine_and_trim()

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().

decompose()

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

Referenced by limit_chunk_size().

emit_intermediate()

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::pack::interaction_graph::debug, core::io::pdb::dump_pdb(), and protocols::abinitio::filename().

find_regions_with_minimum_size()

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 core::scoring::alignment, protocols::comparative_modeling::bounded_loops_from_alignment(), and protocols::mean_field::max().

get_per_residue_score()

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::size().

limit_chunk_size()

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().

make_selection()

core::Size protocols::nonlocal::make_selection

(

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

sampler

)

Convenience method for retrieving the single highest-weighted sample.

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

TR() [1/4]

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

static

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

TR() [2/4]

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

static

TR() [3/4]

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

static

TR() [4/4]

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

static