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core::pack::task::TaskFactory Class Reference

Factory class for the creation and initialization of PackerTask objects. More...

#include <TaskFactory.hh>

Inheritance diagram for core::pack::task::TaskFactory:
Inheritance graph
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Public Types

typedef
utility::pointer::ReferenceCount 		parent
 
typedef operation::TaskOperation TaskOperation
 
typedef operation::TaskOperationOP TaskOperationOP
 
typedef operation::TaskOperationCOP TaskOperationCOP
 
typedef std::list
< TaskOperationOP > 		OperationList
 
typedef
OperationList::const_iterator 		const_iterator
 
typedef
core::pack::palette::PackerPalette 		PackerPalette
 
typedef
core::pack::palette::PackerPaletteOP 		PackerPaletteOP
 
typedef
core::pack::palette::PackerPaletteCOP 		PackerPaletteCOP
 
typedef
core::pack::palette::DefaultPackerPalette 		DefaultPackerPalette
 
typedef
core::pack::palette::DefaultPackerPaletteOP 		DefaultPackerPaletteOP
 

Public Member Functions

 TaskFactory ()
 Default constructor. More...
 
 TaskFactory (TaskFactory const &)
 Copy constructor. More...
 
 ~TaskFactory () override
 
TaskFactory & operator= (TaskFactory const &)
 
virtual TaskFactoryOP clone () const
 
PackerTaskOP create_task_and_apply_taskoperations (pose::Pose const &pose, core::Size const ig_threads_to_request=0) const
 Non static version. More...
 
void modify_task (core::pose::Pose const &pose, PackerTaskOP task) const
 Apply each of the TaskOperations in the TaskFactory list to the PackerTask to set it up. More...
 
void push_back (TaskOperationCOP)
 clones the input task, and pushes it back into the list More...
 
void set_packer_palette (PackerPaletteCOP packer_palette_in)
 Clones the input PackerPalette, and sets it as the PackerPalette for this TaskFactory. More...
 
bool has_packer_palette () const
 Has a PackerPalette been set for this TaskFactory? More...
 
PackerPaletteCOP packer_palette () const
 Access the PackerPalette (const-access only). More...
 
const_iterator begin () const
 begin iterator of operations_ More...
 
const_iterator end () const
 end iterator of operations_ More...
 
void clear ()
 Empties the list of TaskOperations and clears the PackerPalette, replacing it with a new DefaultPackerPalette. More...
 
core::Size size () const
 return the size of the operations_ list More...
 

Static Public Member Functions

static PackerTaskOP create_packer_task (pose::Pose const &pose, core::Size const ig_threads_to_request=0)
 Static construction of a task. More...
 
static PackerTaskOP create_packer_task (pose::Pose const &pose, core::pack::palette::PackerPaletteCOP palette, core::Size const ig_threads_to_request=0)
 Static construction of a task. More...
 

Private Member Functions

void copy_operations (TaskFactory const &src)
 

Private Attributes

PackerPaletteOP packer_palette_ = nullptr
 The PackerPalette, defining the default packer behaviour in the absence of any TaskOperations. More...
 
OperationList operations_
 The list of TaskOperations to apply. More...
 

Detailed Description

Factory class for the creation and initialization of PackerTask objects.

Member Typedef Documentation

typedef OperationList::const_iterator core::pack::task::TaskFactory::const_iterator
typedef core::pack::palette::DefaultPackerPalette core::pack::task::TaskFactory::DefaultPackerPalette
typedef core::pack::palette::DefaultPackerPaletteOP core::pack::task::TaskFactory::DefaultPackerPaletteOP
typedef std::list< TaskOperationOP > core::pack::task::TaskFactory::OperationList
typedef core::pack::palette::PackerPalette core::pack::task::TaskFactory::PackerPalette
typedef core::pack::palette::PackerPaletteCOP core::pack::task::TaskFactory::PackerPaletteCOP
typedef core::pack::palette::PackerPaletteOP core::pack::task::TaskFactory::PackerPaletteOP
typedef utility::pointer::ReferenceCount core::pack::task::TaskFactory::parent
typedef operation::TaskOperation core::pack::task::TaskFactory::TaskOperation
typedef operation::TaskOperationCOP core::pack::task::TaskFactory::TaskOperationCOP
typedef operation::TaskOperationOP core::pack::task::TaskFactory::TaskOperationOP

Constructor & Destructor Documentation

core::pack::task::TaskFactory::TaskFactory ( )

Default constructor.

Defaults to storing a DefaultPackerPalette; the operations_ list starts out empty.

core::pack::task::TaskFactory::TaskFactory ( TaskFactory const &  src)

Copy constructor.

References copy_operations(), and packer_palette_.

core::pack::task::TaskFactory::~TaskFactory ( )
overridedefault

Member Function Documentation

TaskFactory::const_iterator core::pack::task::TaskFactory::begin ( ) const

begin iterator of operations_

References operations_.

void core::pack::task::TaskFactory::clear ( )

Empties the list of TaskOperations and clears the PackerPalette, replacing it with a new DefaultPackerPalette.

References operations_, and packer_palette_.

TaskFactoryOP core::pack::task::TaskFactory::clone ( ) const
virtual
void core::pack::task::TaskFactory::copy_operations ( TaskFactory const &  src)
private

References operations_.

Referenced by operator=(), and TaskFactory().

PackerTaskOP core::pack::task::TaskFactory::create_packer_task ( pose::Pose const &  pose,
core::Size const  ig_threads_to_request = 0 
)
static

Static construction of a task.

Returns a new PackerTask with NO TaskOperations or PackerPalette applied.

Returns a new PackerTask with NO TaskOperations, and a default PackerPalette applied.

Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::add_bb_csts_to_loop(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::protein_interface_design::movers::PlaceOnLoop::ala_pose_loop(), protocols::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::task_operations::StoreCompoundTaskMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::apply(), protocols::minimization_packing::RepackSidechainsMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::relax::LocalRelax::apply(), protocols::relax::CentroidRelax::apply(), protocols::dna::argrot_dna_dis2(), protocols::relax::FastRelax::batch_apply(), core::pack::rotamer_set::bb_independent_rotamers(), protocols::minimization_packing::DisulfideOptimizationMover::break_repack_reform(), protocols::motifs::Motif::build_rotamers(), protocols::motifs::build_rotamers_lite(), protocols::jumping::ResiduePairJump::build_sidechain_rotamers(), protocols::simple_ddg::ddG::calculate(), protocols::quantum_annealing::InteractionGraphSummaryMetric::calculate(), protocols::simple_ddg::DdGScan::calculate(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::ligand_docking::Rotate::create_random_rotation(), protocols::stepwise::modeler::rna::create_standard_o2prime_pack_task(), protocols::ddG_main(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::pockets::PocketGrid::get_connolly_surfacePoints(), protocols::ligand_docking::get_ligand_torsion_constraints(), core::pack::hbonds::hbond_graph_from_partial_rotsets(), protocols::hydrate::hydrate_hyfile(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), core::pack::interaction_graph::SimpleInteractionGraph::initialize(), protocols::ligand_docking::ProtLigEnsemble::make_packer_task(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), protocols::analysis::InterfaceAnalyzerMover::mut_to_gly(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::frag_picker::FragmentCandidate::output_silent(), core::pack::pack_missing_sidechains(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), protocols::protein_interface_design::point_mutation(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), core::util::rebuild_disulfide(), core::util::rebuild_fa_disulfides(), protocols::relax::RangeRelaxMover::repack_all(), protocols::relax::RangeRelaxMover::repack_sequence_window(), protocols::relax::RangeRelaxMover::repack_spherical_range(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::hydrate::set_task_and_movemap(), protocols::hydrate::set_task_with_de_novo_water_using_resfile(), protocols::ligand_docking::Transform::setup_conformers(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::setup_for_scoring(), protocols::simple_moves::ExplicitWaterMover::setup_pack(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), protocols::protein_interface_design::movers::TryRotamers::setup_rotamer_set(), protocols::simple_ddg::ddG::setup_solvated_task(), protocols::simple_ddg::ddG::setup_task(), protocols::hotspot_hashing::SurfaceSearchPattern::SurfaceSearchPattern(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and protocols::vip::VIP_Mover::try_point_mutants().

PackerTaskOP core::pack::task::TaskFactory::create_packer_task ( pose::Pose const &  pose,
core::pack::palette::PackerPaletteCOP  palette,
core::Size const  ig_threads_to_request = 0 
)
static

Static construction of a task.

Returns a new PackerTask with NO TaskOperations, and with a supplied PackerPalette (used directly – not cloned on input).

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).
PackerTaskOP core::pack::task::TaskFactory::create_task_and_apply_taskoperations ( pose::Pose const &  pose,
core::Size const  ig_threads_to_request = 0 
) const

Non static version.

References modify_task(), packer_palette(), packer_palette_, and core::pack::task::TR().

Referenced by protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), and protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_packing_task().

TaskFactory::const_iterator core::pack::task::TaskFactory::end ( ) const

end iterator of operations_

References operations_.

bool core::pack::task::TaskFactory::has_packer_palette ( ) const
inline

Has a PackerPalette been set for this TaskFactory?

References packer_palette_.

void core::pack::task::TaskFactory::modify_task ( core::pose::Pose const &  pose,
PackerTaskOP  task 
) const

Apply each of the TaskOperations in the TaskFactory list to the PackerTask to set it up.

Must be called AFTER PackerTask initialization. An uninitialized PackerTask that is modified will throw an error.

Referenced by create_task_and_apply_taskoperations().

TaskFactory & core::pack::task::TaskFactory::operator= ( TaskFactory const &  rhs)

References copy_operations().

PackerPaletteCOP core::pack::task::TaskFactory::packer_palette ( ) const
inline

Access the PackerPalette (const-access only).

References packer_palette_.

Referenced by create_task_and_apply_taskoperations().

void core::pack::task::TaskFactory::push_back ( TaskOperationCOP  taskop)

clones the input task, and pushes it back into the list

References operations_.

Referenced by protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::anchored_design::AnchoredRefineMover::apply(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task(), protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_packing_task(), protocols::docking::DockingHighResLegacy::define_loops(), protocols::match::TaskOperationMPM::modified_match_positions(), and core::pack::task::residue_selector::task_from_bool_mask().

void core::pack::task::TaskFactory::set_packer_palette ( PackerPaletteCOP  packer_palette_in)

Clones the input PackerPalette, and sets it as the PackerPalette for this TaskFactory.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References packer_palette_.

core::Size core::pack::task::TaskFactory::size ( ) const

return the size of the operations_ list

References operations_.

Member Data Documentation

OperationList core::pack::task::TaskFactory::operations_
private

The list of TaskOperations to apply.

Referenced by begin(), clear(), copy_operations(), end(), push_back(), and size().

PackerPaletteOP core::pack::task::TaskFactory::packer_palette_ = nullptr
private

The PackerPalette, defining the default packer behaviour in the absence of any TaskOperations.

Added as part of the 2016 Rosetta Chemical XRW (eXtreme Rosetta Workshop), New Brunswick, NJ.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by clear(), create_task_and_apply_taskoperations(), has_packer_palette(), packer_palette(), set_packer_palette(), and TaskFactory().

The documentation for this class was generated from the following files:
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