core::pack::task::PackerTask Class Reference

Task class that gives instructions to the packer. More...

#include <PackerTask.hh>

Inheritance diagram for core::pack::task::PackerTask:

Public Types
typedef chemical::AA	AA
typedef rotamer_set::RotamerCouplingsCOP	RotamerCouplingsCOP
typedef rotamer_set::RotamerLinksCOP	RotamerLinksCOP

Public Member Functions
virtual PackerTaskOP	clone () const =0
PackerTaskCOP	get_self_ptr () const
	self pointers More...
PackerTaskOP	get_self_ptr ()
virtual void	clean_residue_task (conformation::Residue const &original_residue, Size const seqpos, core::pose::Pose const &pose)=0
virtual Size	total_residue () const =0
virtual void	temporarily_fix_everything ()=0
virtual void	temporarily_set_pack_residue (int resid, bool setting)=0
virtual bool	pack_residue (int resid) const =0
virtual bool	being_packed (Size resid) const =0
virtual Size	num_to_be_packed () const =0
virtual bool	design_residue (int resid) const =0
virtual bool	being_designed (Size resid) const =0
virtual bool	design_any () const =0
virtual void	set_bump_check (bool setting)=0
virtual bool	bump_check () const =0
virtual void	and_max_rotbump_energy (Real setting)=0
virtual Real	max_rotbump_energy () const =0
virtual void	or_include_current (bool setting)=0
virtual void	or_include_current (bool setting, Size resid)=0
virtual bool	include_current (Size resid) const =0
virtual void	add_behavior (std::string const &behavior)=0
virtual void	add_behavior (std::string const &behavior, Size resid)=0
virtual bool	has_behavior (std::string const &behavior, Size resid) const =0
virtual bool	has_behavior (Size resid) const =0
virtual void	or_adducts (bool setting)=0
virtual void	or_adducts (bool setting, Size resid)=0
virtual bool	adducts (Size resid) const =0
virtual void	or_optimize_h_mode (bool setting)=0
virtual void	or_preserve_c_beta (bool setting)=0
virtual void	or_flip_HNQ (bool setting)=0
virtual void	or_fix_his_tautomer (utility::vector1< int > const &positions, bool setting)=0
virtual void	or_linmem_ig (bool setting)=0
	Activate a LinearMemoryInteraction graph that uses 95% less memory in design runs and runs twice as fast. (Not faster for fixed-sequence repackings). More...
virtual void	and_linmem_ig (bool setting)=0
virtual bool	linmem_ig () const =0
virtual void	decrease_linmem_ig_history_size (Size setting)=0
virtual Size	linmem_ig_history_size () const =0
virtual void	or_lazy_ig (bool setting)=0
	Activate a LazyInteractionGraph that computes rotamer pair energies at most once. More...
virtual bool	lazy_ig () const =0
virtual void	or_double_lazy_ig (bool setting)=0
	Activates the DoubleLazyInteractionGraph, which computes rotamer pair energies at most once, and delays allocating memory to hold them until needed. Used for multistate design. More...
virtual bool	double_lazy_ig () const =0
virtual void	decrease_double_lazy_ig_memlimit (Size nbytes_for_rpes)=0
virtual Size	double_lazy_ig_memlimit () const =0
virtual void	or_multi_cool_annealer (bool setting)=0
virtual bool	multi_cool_annealer () const =0
virtual void	increase_multi_cool_annealer_history_size (Size setting)=0
virtual Size	multi_cool_annealer_history_size () const =0
virtual void	show (std::ostream &out) const =0
virtual void	show () const =0
virtual void	show_residue_task (std::ostream &out, Size resid) const =0
virtual void	show_residue_task (Size resid) const =0
virtual void	show_all_residue_tasks (std::ostream &out) const =0
virtual void	show_all_residue_tasks () const =0
virtual bool	is_initialized () const =0
	Has this PackerTask been initialized with a PackerPalette? More...
virtual PackerTask &	initialize_from_command_line ()=0
virtual PackerTask &	initialize_extra_rotamer_flags_from_command_line ()=0
virtual PackerTask &	initialize_from_options (utility::options::OptionCollection const &options)=0
virtual PackerTask &	initialize_extra_rotamer_flags_from_options (utility::options::OptionCollection const &options)=0
virtual PackerTask &	restrict_to_residues (utility::vector1< bool > const &residues_allowed_to_be_packed)=0
virtual PackerTask &	restrict_to_repacking ()=0
virtual ResidueLevelTask const &	residue_task (Size resid) const =0
virtual ResidueLevelTask &	nonconst_residue_task (Size resid)=0
virtual utility::vector1< bool >	repacking_residues () const =0
virtual utility::vector1< bool >	designing_residues () const =0
virtual bool	keep_sequence_symmetry () const =0
virtual void	keep_sequence_symmetry (bool const setting)=0
virtual bool	rotamer_couplings_exist () const =0
virtual RotamerCouplingsCOP	rotamer_couplings () const =0
virtual void	rotamer_couplings (RotamerCouplingsCOP setting)=0
virtual bool	rotamer_links_exist () const =0
virtual RotamerLinksCOP	rotamer_links () const =0
virtual void	rotamer_links (RotamerLinksCOP setting)=0
virtual IGEdgeReweightContainerCOP	IGEdgeReweights () const =0
virtual IGEdgeReweightContainerOP	set_IGEdgeReweights ()=0
virtual void	append_rotamer_operation (rotamer_set::RotamerOperationOP rotop)=0
virtual void	append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop)=0
virtual rotamer_set::RotSetsOperationListIterator	rotamer_sets_operation_begin () const =0
virtual rotamer_set::RotSetsOperationListIterator	rotamer_sets_operation_end () const =0
virtual void	append_rotamersets_operation (rotamer_set::RotamerSetsOperationOP rotsetsop)=0
virtual void	low_temp (Real const &low_temp)=0
virtual void	high_temp (Real const &high_temp)=0
virtual void	disallow_quench (bool const &disallow_quench)=0
virtual Real	low_temp () const =0
virtual Real	high_temp () const =0
virtual bool	disallow_quench () const =0
virtual std::string	task_string (pose::Pose const &pose) const =0
virtual void	remap_residue_level_tasks (core::id::SequenceMappingCOP seqmap, core::pose::Pose const &pose)=0
virtual void	update_commutative (PackerTask const &to_copy)=0
virtual void	request_symmetrize_by_intersection ()=0
virtual void	request_symmetrize_by_union ()=0
virtual bool	symmetrize_by_union () const =0
virtual bool	symmetrize_by_intersection () const =0
virtual core::Size	ig_threads_to_request () const =0
	How many threads should the packer request for interaction graph precomputation? More...
virtual void	limit_ig_setup_threads (core::Size const setting)=0
	Limit the interaction graph setup threads. More...

Static Public Member Functions
static void	list_options_read (utility::options::OptionKeyList &read_options)

Friends
std::ostream &	operator<< (std::ostream &os, PackerTask const &t)
	output operator More...

Detailed Description

Task class that gives instructions to the packer.

Member Typedef Documentation

typedef chemical::AA core::pack::task::PackerTask::AA

typedef rotamer_set::RotamerCouplingsCOP core::pack::task::PackerTask::RotamerCouplingsCOP

typedef rotamer_set::RotamerLinksCOP core::pack::task::PackerTask::RotamerLinksCOP

Member Function Documentation

virtual void core::pack::task::PackerTask::add_behavior ( std::string const &  behavior )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::add_behavior ( std::string const &  behavior, Size  resid  )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::adducts ( Size  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::and_linmem_ig ( bool  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::and_max_rotbump_energy ( Real  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::append_rotamer_operation ( rotamer_set::RotamerOperationOP  rotop )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::AppendRotamer::apply().

virtual void core::pack::task::PackerTask::append_rotamerset_operation ( rotamer_set::RotamerSetOperationOP  rotsetop )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::JointSequenceOperation::apply(), protocols::task_operations::ImportUnboundRotamersOperation::apply(), protocols::task_operations::LimitAromaChi2Operation::apply(), protocols::splice::SampleRotamersFromPDB::apply(), and core::pack::task::operation::AppendRotamerSet::apply().

virtual void core::pack::task::PackerTask::append_rotamersets_operation ( rotamer_set::RotamerSetsOperationOP  rotsetsop )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::PruneBuriedUnsatsOperation::apply().

virtual bool core::pack::task::PackerTask::being_designed ( Size  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::motifs::LigandMotifSearch::run(), protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache(), and protocols::task_operations::ConservativeDesignOperation::skip_resid().

virtual bool core::pack::task::PackerTask::being_packed ( Size  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::hotspot_hashing::AddSearchPatternRotSetOp::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), core::pack::rotamer_set::ContinuousRotamerSets::ContinuousRotamerSets(), core::pack::create_minimization_graph(), and core::pack::setup_bgres_cops().

virtual bool core::pack::task::PackerTask::bump_check ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), and core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter().

virtual void core::pack::task::PackerTask::clean_residue_task ( conformation::Residue const &  original_residue, Size const  seqpos, core::pose::Pose const &  pose  )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual PackerTaskOP core::pack::task::PackerTask::clone ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), protocols::minimization_packing::RotamerTrialsMinMover::RotamerTrialsMinMover(), protocols::minimization_packing::RotamerTrialsMover::RotamerTrialsMover(), protocols::rotamer_recovery::RRProtocolPackRotamers::run(), protocols::rotamer_recovery::RRProtocolRotamerTrials::run(), protocols::rotamer_recovery::RRProtocolRTMin::run(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_packer_task(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_packer_task(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_packer_task(), and protocols::pack_daemon::PackDaemon::set_pose_and_task().

virtual void core::pack::task::PackerTask::decrease_double_lazy_ig_memlimit ( Size  nbytes_for_rpes )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::decrease_linmem_ig_history_size ( Size  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::design_any ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph().

virtual bool core::pack::task::PackerTask::design_residue ( int  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::ProteinLigandInterfaceUpweighter::apply(), protocols::toolbox::IGLigandDesignEdgeUpweighter::get_edge_reweight(), and protocols::enzdes::EnzdesFlexBBProtocol::modified_task().

virtual utility::vector1< bool > core::pack::task::PackerTask::designing_residues ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::ResidueProbDesignOperation::apply().

virtual void core::pack::task::PackerTask::disallow_quench ( bool const &  disallow_quench )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::ModifyAnnealer::apply().

virtual bool core::pack::task::PackerTask::disallow_quench ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::double_lazy_ig ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph().

virtual Size core::pack::task::PackerTask::double_lazy_ig_memlimit ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph().

PackerTaskCOP core::pack::task::PackerTask::get_self_ptr ( ) const

inline

self pointers

Referenced by protocols::symmetric_docking::SymRestrictTaskForDocking::apply(), and protocols::rotamer_recovery::RRProtocolMinPack::run().

PackerTaskOP core::pack::task::PackerTask::get_self_ptr ( )

inline

virtual bool core::pack::task::PackerTask::has_behavior ( std::string const &  behavior, Size  resid  ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::has_behavior ( Size  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::high_temp ( Real const &  high_temp )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::ModifyAnnealer::apply(), and protocols::optimize_weights::ScaleAnnealerTemperatureOperation::apply().

virtual Real core::pack::task::PackerTask::high_temp ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual core::Size core::pack::task::PackerTask::ig_threads_to_request ( ) const

pure virtual

How many threads should the packer request for interaction graph precomputation?

Must be implemented by derived class.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_and_initialize_two_body_interaction_graph().

virtual IGEdgeReweightContainerCOP core::pack::task::PackerTask::IGEdgeReweights ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::enzdes::enzutil::recreate_task(), and core::pack::interaction_graph::InteractionGraphFactory::setup_IG_res_res_weights().

virtual bool core::pack::task::PackerTask::include_current ( Size  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), core::pack::rotamer_set::build_rna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers(), core::pack::rotamer_set::RotamerSet_::build_virtualizable_rotatable_water_rotamers(), core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(), protocols::rotamer_recovery::RRProtocolRotamerTrials::run(), and protocols::rotamer_recovery::RRProtocolRTMin::run().

virtual void core::pack::task::PackerTask::increase_multi_cool_annealer_history_size ( Size  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::EnableMultiCoolAnnealer::apply(), and core::pack::task::operation::UseMultiCoolAnnealer::apply().

virtual PackerTask& core::pack::task::PackerTask::initialize_extra_rotamer_flags_from_command_line ( )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::InitializeExtraRotsFromCommandline::apply().

virtual PackerTask& core::pack::task::PackerTask::initialize_extra_rotamer_flags_from_options ( utility::options::OptionCollection const &  options )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual PackerTask& core::pack::task::PackerTask::initialize_from_command_line ( )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::symmetric_docking::SymRestrictTaskForDocking::apply(), core::pack::task::operation::OptH::apply(), and core::pack::task::operation::InitializeFromCommandline::apply().

virtual PackerTask& core::pack::task::PackerTask::initialize_from_options ( utility::options::OptionCollection const &  options )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::InitializeFromOptionCollection::apply().

virtual bool core::pack::task::PackerTask::is_initialized ( ) const

pure virtual

Has this PackerTask been initialized with a PackerPalette?

PackerTasks must be initialized with PackerPalettes before being modified with TaskOperations. The TaskFactory will initialize the PackerTask with a DefaultPackerPalette if no custom PackerPalette is provided.

Author

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

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::keep_sequence_symmetry ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::KeepSequenceSymmetry::apply().

virtual void core::pack::task::PackerTask::keep_sequence_symmetry ( bool const  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::lazy_ig ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph().

virtual void core::pack::task::PackerTask::limit_ig_setup_threads ( core::Size const  setting )

pure virtual

Limit the interaction graph setup threads.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tue..nosp@m.org)

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::RestrictInteractionGraphThreadsOperation::apply().

virtual bool core::pack::task::PackerTask::linmem_ig ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph().

virtual Size core::pack::task::PackerTask::linmem_ig_history_size ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph().

void core::pack::task::PackerTask::list_options_read ( utility::options::OptionKeyList &  read_options )

static

References core::pack::task::ResidueLevelTask::list_options_read().

virtual void core::pack::task::PackerTask::low_temp ( Real const &  low_temp )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::ModifyAnnealer::apply(), and protocols::optimize_weights::ScaleAnnealerTemperatureOperation::apply().

virtual Real core::pack::task::PackerTask::low_temp ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual Real core::pack::task::PackerTask::max_rotbump_energy ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::rotamer_set::build_rotated_water_rotamers(), and core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter().

virtual bool core::pack::task::PackerTask::multi_cool_annealer ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual Size core::pack::task::PackerTask::multi_cool_annealer_history_size ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual ResidueLevelTask& core::pack::task::PackerTask::nonconst_residue_task ( Size  resid )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::task_operations::RestrictNonSurfaceToRepackingOperation::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), core::pack::task::operation::FillAUTOTaskOperation::apply(), protocols::task_operations::pHVariantTaskOperation::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::task_operations::ConservativeDesignOperation::apply(), protocols::task_operations::RestrictIdentitiesOperation::apply(), core::pack::task::operation::ReplicateTask::apply(), protocols::task_operations::RestrictToTerminiOperation::apply(), core::pack::task::operation::OperateOnCertainResidues::apply(), protocols::task_operations::ResidueProbDesignOperation::apply(), protocols::task_operations::MutationSetDesignOperation::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), core::pack::task::operation::OperateOnResidueSubset::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::task_operations::JointSequenceOperation::apply(), core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes::apply(), core::pack::task::operation::ClashBasedRepackShell::apply(), core::pack::task::operation::OptH::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::simple_task_operations::DockingNoRepack1::apply(), protocols::hotspot_hashing::AddSearchPatternRotSetOp::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::simple_task_operations::DockingNoRepack2::apply(), core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::apply(), core::pack::task::operation::DesignRestrictions::apply(), protocols::task_operations::DsspDesignOperation::apply(), core::pack::task::operation::RestrictToResidueProperties::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::task_operations::RestrictConservedLowDdgOperation::apply(), core::pack::task::operation::ProhibitResidueProperties::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::pack::task::operation::RestrictResidueToRepacking::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), core::pack::task::operation::DisallowIfNonnative::apply(), core::pack::task::operation::RotamerExplosion::apply(), core::pack::task::operation::ExtraRotamersGeneric::apply(), core::pack::task::operation::AppendResidueRotamerSet::apply(), core::pack::task::operation::PreventRepacking::apply(), core::pack::task::operation::RestrictYSDesign::apply(), core::pack::task::operation::ExtraRotamers::apply(), core::pack::task::operation::ExtraChiCutoff::apply(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::disallow_aas(), core::pack::task::NATRO::residue_action(), core::pack::task::NATAA::residue_action(), core::pack::task::ALLAAxc::residue_action(), core::pack::task::PIKAA::residue_action(), core::pack::task::PIKNA::residue_action(), core::pack::task::NOTAA::residue_action(), core::pack::task::PROPERTY::residue_action(), core::pack::task::POLAR::residue_action(), core::pack::task::APOLAR::residue_action(), core::pack::task::CHARGED::residue_action(), core::pack::task::AROMATIC::residue_action(), core::pack::task::EX::residue_action(), core::pack::task::EX_CUTOFF::residue_action(), core::pack::task::USE_INPUT_SC::residue_action(), core::pack::task::AUTO::residue_action(), core::pack::task::SCAN::residue_action(), core::pack::task::TARGET::residue_action(), core::pack::task::NO_ADDUCTS::residue_action(), core::pack::task::FIX_HIS_TAUTOMER::residue_action(), protocols::motifs::LigandMotifSearch::run(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::setup_energycut_task(), and protocols::simple_task_operations::RestrictToInterface::symmetric_task().

virtual Size core::pack::task::PackerTask::num_to_be_packed ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::rotamer_set::ContinuousRotamerSets::ContinuousRotamerSets(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::pack::repackable_residues(), and core::pack::repackable_residues_dup().

virtual void core::pack::task::PackerTask::or_adducts ( bool  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::or_adducts ( bool  setting, Size  resid  )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::or_double_lazy_ig ( bool  setting )

pure virtual

Activates the DoubleLazyInteractionGraph, which computes rotamer pair energies at most once, and delays allocating memory to hold them until needed. Used for multistate design.

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::SetIGTypeOperation::apply().

virtual void core::pack::task::PackerTask::or_fix_his_tautomer ( utility::vector1< int > const &  positions, bool  setting  )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::or_flip_HNQ ( bool  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::OptH::apply().

virtual void core::pack::task::PackerTask::or_include_current ( bool  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::symmetric_docking::SymRestrictTaskForDocking::apply(), core::pack::task::operation::OptH::apply(), and core::pack::task::operation::IncludeCurrent::apply().

virtual void core::pack::task::PackerTask::or_include_current ( bool  setting, Size  resid  )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::or_lazy_ig ( bool  setting )

pure virtual

Activate a LazyInteractionGraph that computes rotamer pair energies at most once.

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::SetIGTypeOperation::apply().

virtual void core::pack::task::PackerTask::or_linmem_ig ( bool  setting )

pure virtual

Activate a LinearMemoryInteraction graph that uses 95% less memory in design runs and runs twice as fast. (Not faster for fixed-sequence repackings).

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::SetIGTypeOperation::apply().

virtual void core::pack::task::PackerTask::or_multi_cool_annealer ( bool  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::EnableMultiCoolAnnealer::apply(), core::pack::task::operation::OptH::apply(), and core::pack::task::operation::UseMultiCoolAnnealer::apply().

virtual void core::pack::task::PackerTask::or_optimize_h_mode ( bool  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::OptH::apply().

virtual void core::pack::task::PackerTask::or_preserve_c_beta ( bool  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::task::operation::PreserveCBeta::apply().

virtual bool core::pack::task::PackerTask::pack_residue ( int  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), core::pack::rotamer_set::build_dna_rotamers(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check(), core::pack::rotamer_set::bump_check(), protocols::nmr::bump_check(), core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(), core::pack::rotamer_set::RotamerSet_::bump_check(), core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), protocols::hbnet::hbnet_symm_one_body_energies(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::backrub::positions_incompatible_with_task(), core::pack::rotamer_set::pre_bump_check(), core::pack::repackable_residues(), core::pack::repackable_residues_dup(), protocols::rotamer_recovery::RRProtocolMinPack::run(), protocols::rotamer_recovery::RRProtocolPackRotamers::run(), protocols::rotamer_recovery::RRProtocolRotamerTrials::run(), protocols::rotamer_recovery::RRProtocolMover::run(), protocols::rotamer_recovery::RRProtocolRelax::run(), protocols::rotamer_recovery::RRProtocolRTMin::run(), protocols::rotamer_recovery::RRProtocolReferenceStructure::run(), and core::pack::symmetric_repackable_residues().

virtual void core::pack::task::PackerTask::remap_residue_level_tasks ( core::id::SequenceMappingCOP  seqmap, core::pose::Pose const &  pose  )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual utility::vector1< bool > core::pack::task::PackerTask::repacking_residues ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::request_symmetrize_by_intersection ( )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::request_symmetrize_by_union ( )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::enzdes::DetectProteinLigandInterface::apply().

virtual ResidueLevelTask const& core::pack::task::PackerTask::residue_task ( Size  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_db(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::task_operations::MutationSetDesignOperation::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::build_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::build_rna_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::create_rotamers_from_chisets(), protocols::calc_taskop_movers::ConsensusDesignMover::create_sequence_profile_constraints(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::disallow_aas(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::enumerate_chi_sets(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::pack::rotamers::SingleLigandRotamerLibrary::fill_rotamer_vector(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::backrub::positions_incompatible_with_task(), protocols::enzdes::enzutil::recreate_task(), core::pack::task::POLAR::residue_action(), core::pack::task::APOLAR::residue_action(), core::pack::task::CHARGED::residue_action(), core::pack::task::AROMATIC::residue_action(), core::pack::rotamer_set::RotamerSet_::set_extra_samples(), and core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain().

virtual PackerTask& core::pack::task::PackerTask::restrict_to_repacking ( )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::symmetric_docking::SymRestrictTaskForDocking::apply(), core::pack::task::operation::RestrictToRepacking::apply(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::setup_energycut_task(), and protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::setup_energycut_task().

virtual PackerTask& core::pack::task::PackerTask::restrict_to_residues ( utility::vector1< bool > const &  residues_allowed_to_be_packed )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::RestrictByCalculatorsOperation::apply(), protocols::task_operations::RestrictToInterfaceOperation::apply(), protocols::task_operations::RestrictToNeighborhoodOperation::apply(), protocols::task_operations::RestrictToInterfaceVectorOperation::apply(), and protocols::task_operations::RestrictInterGroupVectorOperation::apply().

virtual RotamerCouplingsCOP core::pack::task::PackerTask::rotamer_couplings ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::dna::WatsonCrickRotamerCouplings::apply(), core::pack::task::operation::SetRotamerCouplings::apply(), and core::pack::rotamer_set::build_dna_rotamers().

virtual void core::pack::task::PackerTask::rotamer_couplings ( RotamerCouplingsCOP  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::rotamer_couplings_exist ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::rotamer_set::build_dna_rotamers().

virtual RotamerLinksCOP core::pack::task::PackerTask::rotamer_links ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::forge::remodel::RemodelRotamerLinks::apply(), protocols::task_operations::LinkResidues::apply(), and core::pack::task::operation::SetRotamerLinks::apply().

virtual void core::pack::task::PackerTask::rotamer_links ( RotamerLinksCOP  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::rotamer_links_exist ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual rotamer_set::RotSetsOperationListIterator core::pack::task::PackerTask::rotamer_sets_operation_begin ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual rotamer_set::RotSetsOperationListIterator core::pack::task::PackerTask::rotamer_sets_operation_end ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::set_bump_check ( bool  setting )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual IGEdgeReweightContainerOP core::pack::task::PackerTask::set_IGEdgeReweights ( )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::pack_interface::ProteinProteinInterfaceUpweighter::apply(), and protocols::enzdes::ProteinLigandInterfaceUpweighter::apply().

virtual void core::pack::task::PackerTask::show ( std::ostream &  out ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::apply(), and core::pack::task::operator<<().

virtual void core::pack::task::PackerTask::show ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::show_all_residue_tasks ( std::ostream &  out ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::show_all_residue_tasks ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::show_residue_task ( std::ostream &  out, Size  resid  ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::show_residue_task ( Size  resid ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::symmetrize_by_intersection ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual bool core::pack::task::PackerTask::symmetrize_by_union ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual std::string core::pack::task::PackerTask::task_string ( pose::Pose const &  pose ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::temporarily_fix_everything ( )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual void core::pack::task::PackerTask::temporarily_set_pack_residue ( int  resid, bool  setting  )

pure virtual

Implemented in core::pack::task::PackerTask_.

virtual Size core::pack::task::PackerTask::total_residue ( ) const

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), core::pack::task::operation::FillAUTOTaskOperation::apply(), core::pack::task::operation::OperateOnCertainResidues::apply(), core::pack::task::operation::OperateOnResidueSubset::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), core::pack::task::operation::DisallowIfNonnative::apply(), core::pack::task::operation::ExtraRotamersGeneric::apply(), core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::disallow_aas(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), protocols::backrub::positions_incompatible_with_task(), protocols::enzdes::enzutil::recreate_task(), core::pack::repackable_residues(), core::pack::repackable_residues_dup(), core::pack::task::operation::ReadResfileAndObeyLengthEvents::resfile_commands(), protocols::pack_daemon::PackDaemon::set_pose_and_task(), and core::pack::symmetric_repackable_residues().

virtual void core::pack::task::PackerTask::update_commutative ( PackerTask const &  to_copy )

pure virtual

Implemented in core::pack::task::PackerTask_.

Referenced by protocols::task_operations::RetrieveStoredTaskOperation::apply().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os, PackerTask const &  t  )

friend

output operator

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

• src/core/pack/task/PackerTask.hh
• src/core/pack/task/PackerTask_.cc