Factory class for the creation and initialization of PackerTask objects. More...
#include <TaskFactory.hh>
Public Types | |
| typedef utility::VirtualBase | 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 | n_task_operations () const |
| How many TaskOperations does this TaskFactory contain? More... | |
| bool | has_task_operations () const |
| Does this TaskFactory contain TaskOperations? 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
◆ const_iterator
| typedef OperationList::const_iterator core::pack::task::TaskFactory::const_iterator |
◆ DefaultPackerPalette
| typedef core::pack::palette::DefaultPackerPalette core::pack::task::TaskFactory::DefaultPackerPalette |
◆ DefaultPackerPaletteOP
| typedef core::pack::palette::DefaultPackerPaletteOP core::pack::task::TaskFactory::DefaultPackerPaletteOP |
◆ OperationList
| typedef std::list< TaskOperationOP > core::pack::task::TaskFactory::OperationList |
◆ PackerPalette
◆ PackerPaletteCOP
◆ PackerPaletteOP
◆ parent
| typedef utility::VirtualBase core::pack::task::TaskFactory::parent |
◆ TaskOperation
◆ TaskOperationCOP
◆ TaskOperationOP
Constructor & Destructor Documentation
◆ TaskFactory() [1/2]
| core::pack::task::TaskFactory::TaskFactory | ( | ) |
Default constructor.
Defaults to storing a DefaultPackerPalette; the operations_ list starts out empty.
◆ TaskFactory() [2/2]
| core::pack::task::TaskFactory::TaskFactory | ( | TaskFactory const & | src | ) |
Copy constructor.
References copy_operations(), and packer_palette_.
◆ ~TaskFactory()
|
overridedefault |
Member Function Documentation
◆ begin()
| TaskFactory::const_iterator core::pack::task::TaskFactory::begin | ( | ) | const |
begin iterator of operations_
References operations_.
◆ clear()
| 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_.
◆ clone()
|
virtual |
◆ copy_operations()
|
private |
References operations_.
Referenced by operator=(), and TaskFactory().
◆ create_packer_task() [1/2]
|
static |
Static construction of a task.
Returns a new PackerTask with NO TaskOperations, and with a supplied PackerPalette (used directly – not cloned on input).
◆ create_packer_task() [2/2]
|
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::abinitio::ResolutionSwitcher::apply(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::apply(), protocols::protein_interface_design::movers::BestHotspotCstMover::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::relax::CentroidRelax::apply(), protocols::relax::LocalRelax::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::task_operations::StoreCompoundTaskMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::minimization_packing::RepackSidechainsMover::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::quantum_annealing::InteractionGraphSummaryMetric::calculate(), protocols::simple_ddg::ddG::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_solvate(), protocols::protein_interface_design::movers::finalize_stub_set(), 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::enzdes::EnzdesFlexBBProtocol::modified_task(), 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::drug_design::place_new_restype_rotamer_align(), 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::enzdes::enzutil::recreate_task(), protocols::relax::RangeRelaxMover::repack_all(), protocols::relax::RangeRelaxMover::repack_sequence_window(), protocols::relax::RangeRelaxMover::repack_spherical_range(), core::pack::guidance_scoreterms::sap::rotamer_sets_from_pose(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), protocols::hydrate::set_task_and_movemap(), protocols::hydrate::set_task_with_de_novo_water_using_resfile(), protocols::minimization_packing::PackRotamersMover::setup(), protocols::minimization_packing::RotamerizeMover::setup(), 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().
◆ create_task_and_apply_taskoperations()
| 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(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task(), protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_packing_task(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), protocols::docking::DockingHighResLegacy::define_loops(), protocols::match::TaskOperationMPM::modified_match_positions(), and core::pack::task::residue_selector::task_from_bool_mask().
◆ end()
| TaskFactory::const_iterator core::pack::task::TaskFactory::end | ( | ) | const |
end iterator of operations_
References operations_.
◆ has_packer_palette()
|
inline |
Has a PackerPalette been set for this TaskFactory?
References packer_palette_.
◆ has_task_operations()
| bool core::pack::task::TaskFactory::has_task_operations | ( | ) | const |
Does this TaskFactory contain TaskOperations?
Returns true if and only if the number of task operations is greater than or equal to one.
References operations_.
◆ modify_task()
| 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().
◆ n_task_operations()
| core::Size core::pack::task::TaskFactory::n_task_operations | ( | ) | const |
How many TaskOperations does this TaskFactory contain?
References operations_.
◆ operator=()
| TaskFactory & core::pack::task::TaskFactory::operator= | ( | TaskFactory const & | rhs | ) |
References copy_operations().
◆ packer_palette()
|
inline |
Access the PackerPalette (const-access only).
References packer_palette_.
Referenced by create_task_and_apply_taskoperations().
◆ push_back()
| 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::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task(), protocols::hotspot_hashing::movers::PlaceProbeMover::create_refinement_packing_task(), protocols::protein_interface_design::movers::MapHotspot::create_rotamer_set(), protocols::docking::DockingHighResLegacy::define_loops(), protocols::match::TaskOperationMPM::modified_match_positions(), and core::pack::task::residue_selector::task_from_bool_mask().
◆ set_packer_palette()
| 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.
References packer_palette_.
◆ size()
| core::Size core::pack::task::TaskFactory::size | ( | ) | const |
return the size of the operations_ list
References operations_.
Member Data Documentation
◆ operations_
|
private |
The list of TaskOperations to apply.
Referenced by begin(), clear(), copy_operations(), end(), has_task_operations(), n_task_operations(), push_back(), and size().
◆ packer_palette_
|
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.
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:
- src/core/pack/task/TaskFactory.hh
- src/core/pack/task/TaskFactory.cc
