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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

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
using protocols::nonlocal::Normal = typedef boost::math::normal
typedef utility::pointer::shared_ptr<Policy const> protocols::nonlocal::PolicyCOP
typedef utility::pointer::shared_ptr<Policy> protocols::nonlocal::PolicyOP
using protocols::nonlocal::Probabilities = typedef utility::vector1<core::Real>
typedef utility::pointer::shared_ptr<Region const> protocols::nonlocal::RegionCOP
typedef utility::pointer::shared_ptr<Region> protocols::nonlocal::RegionOP
using protocols::nonlocal::ScoreList = typedef utility::vector1<core::Real>
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< core::Real > *  point 
)
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().

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().

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().

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().

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, 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 
)
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().

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.

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

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