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:

Collaboration 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	~PackerTask ()=0
virtual PackerTaskOP	clone () const =0
virtual void	clean_residue_task (conformation::Residue const &original_residue, Size const seqpos)=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 bool	linmem_ig () 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 PackerTask &	initialize_from_command_line ()=0
virtual PackerTask &	initialize_extra_rotamer_flags_from_command_line ()=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	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 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

Private Member Functions
virtual PackerTask &	operator= (PackerTask const &)=0

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

Detailed Description

Task class that gives instructions to the packer.

Definition at line 249 of file PackerTask.hh.

Member Typedef Documentation

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

Definition at line 252 of file PackerTask.hh.

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

Definition at line 253 of file PackerTask.hh.

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

Definition at line 254 of file PackerTask.hh.

Constructor & Destructor Documentation

core::pack::task::PackerTask::~PackerTask ( )

pure virtual

Definition at line 26 of file PackerTask.cc.

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_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::toolbox::task_operations::JointSequenceOperation::apply(), protocols::toolbox::task_operations::LimitAromaChi2Operation::apply(), and core::pack::task::operation::AppendRotamerSet::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(), and protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache().

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::rotamer_set::RotamerSet_::build_rotamers_for_concrete().

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

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::simple_moves::RotamerTrialsMinMover::RotamerTrialsMinMover(), protocols::simple_moves::RotamerTrialsMover::RotamerTrialsMover(), 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::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 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_.

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

pure virtual

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

Referenced by protocols::toolbox::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().

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

pure virtual

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

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), and protocols::enzdes::enzutil::recreate_task().

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::build_rna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), 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_.

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

pure virtual

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

Referenced by protocols::toolbox::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::RotamerSet_::build_rotamers_for_concrete().

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::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), core::pack::task::operation::ReplicateTask::apply(), protocols::toolbox::task_operations::RestrictToTerminiOperation::apply(), core::pack::task::operation::OperateOnCertainResidues::apply(), protocols::toolbox::task_operations::RestrictNativeResiduesOperation::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), core::pack::task::operation::DockingNoRepack1::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), protocols::hotspot_hashing::AddSearchPatternRotSetOp::apply(), core::pack::task::operation::RestrictResidueToRepacking::apply(), core::pack::task::operation::OptH::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), core::pack::task::operation::DockingNoRepack2::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::apply(), core::pack::task::operation::DisallowIfNonnative::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::pack::task::operation::RestrictToInterface::apply(), core::pack::task::operation::RotamerExplosion::apply(), protocols::enzdes::AddRigidBodyLigandConfs::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(), 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::PIKRNA::residue_action(), core::pack::task::NOTAA::residue_action(), core::pack::task::EMPTY::residue_action(), core::pack::task::POLAR::residue_action(), core::pack::task::APOLAR::residue_action(), core::pack::task::EX::residue_action(), core::pack::task::NC::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::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::simple_moves::EnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::simple_moves::EnergyCutRotamerTrialsMinMover::setup_energycut_task(), and core::pack::task::operation::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 PackerTask& core::pack::task::PackerTask::operator= ( PackerTask const &  )

privatepure virtual

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

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::toolbox::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::toolbox::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::toolbox::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::OptH::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::RotamerSet_::bump_check(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), 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::RRProtocolReferenceStructure::run(), protocols::rotamer_recovery::RRProtocolRTMin::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_.

Referenced by protocols::toolbox::task_operations::SeqprofConsensusOperation::apply().

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::dna::RestrictDesignToProteinDNAInterface::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 >::create_rotamers_from_chisets(), protocols::simple_moves::ConsensusDesignMover::create_sequence_profile_constraints(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::enumerate_chi_sets(), core::pack::dunbrack::SingleLigandRotamerLibrary::fill_rotamer_vector(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), protocols::enzdes::enzutil::recreate_task(), core::pack::task::POLAR::residue_action(), core::pack::task::APOLAR::residue_action(), core::pack::task::NC::residue_action(), and core::pack::rotamer_set::RotamerSet_::set_extra_samples().

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::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::simple_moves::EnergyCutRotamerTrialsMover::setup_energycut_task(), and protocols::simple_moves::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::toolbox::task_operations::RestrictToInterfaceOperation::apply(), protocols::toolbox::task_operations::RestrictByCalculatorsOperation::apply(), protocols::toolbox::task_operations::RestrictToNeighborhoodOperation::apply(), protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation::apply(), and protocols::toolbox::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(), 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 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::enzdes::ProteinLigandInterfaceUpweighter::apply().

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

pure virtual

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

Referenced by 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::OperateOnCertainResidues::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::forge::methods::parse_resfile_string_with_no_lockdown(), 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_.

Friends And Related Function Documentation

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

friend

output operator

Definition at line 2196 of file PackerTask_.cc.

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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