Rosetta 3.4
Classes | Typedefs | Functions
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.
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).
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>.
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.
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.
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>.
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>.
protocols::comparative_modeling::ThreadingJob
const *const 
current_job ()
 Retrieves the current job from the JobDistributor.
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.

Typedef Documentation

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

Function Documentation

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

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

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.

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

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

Retrieves the current job from the JobDistributor.

Referenced by protocols::toolbox::task_operations::ReadResfileFromDB::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::star::StarAbinitio::apply(), protocols::simple_moves::GreedyOptMutationMover::apply(), protocols::simple_moves::ddG::apply(), protocols::RotamerDump::RotamerDumpMover::apply(), protocols::qsar::qsarMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::medal::MedalMover::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::StartFrom::apply(), protocols::ligand_docking::LigandDockMain::apply(), protocols::ligand_docking::InterfaceScoreCalculator::apply(), protocols::docking::DockingProtocol::apply(), protocols::contact_map::ContactMap::apply(), protocols::antibody2::Ab_ModelCDRH3::apply(), protocols::antibody2::Ab_Assemble_Templates::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), JDtestmover::apply(), protocols::anchored_design::debug_dump_pose(), protocols::anchored_design::AnchoredDesignMover::forget_initial_loops(), protocols::jobdist::BaseJobDistributor::get_current_output_tag(), protocols::features::get_write_delete_pair(), protocols::features::TopCountOfEachInput::operator()(), protocols::simple_moves::SequenceProfileMover::parse_my_tag(), protocols::protein_interface_design::movers::SubroutineMover::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::report_data(), protocols::features::JobDataFeatures::report_features(), protocols::rosetta_scripts::ParsedProtocol::report_filters_to_job(), and protocols::analysis::InterfaceAnalyzerMover::set_pose_info().

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::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.

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

static numeric::random::RandomGenerator protocols::nonlocal::RG ( 330  ) [static]
static basic::Tracer protocols::nonlocal::TR ( "protocols.nonlocal.util"  ) [static]
static basic::Tracer protocols::nonlocal::TR ( "protocols.nonlocal.SingleFragmentMover"  ) [static]
static basic::Tracer protocols::nonlocal::TR ( "protocols.nonlocal.SheetTranslate"  ) [static]
static basic::Tracer protocols::nonlocal::TR ( "protocols.nonlocal.HelixRotate"  ) [static]
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