Rosetta 3.4
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core::pack::task::PackerTask Class Reference

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

#include <PackerTask.hh>

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List of all members.

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).
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.
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.
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 PackerTaskinitialize_from_command_line ()=0
virtual PackerTaskinitialize_extra_rotamer_flags_from_command_line ()=0
virtual PackerTaskrestrict_to_residues (utility::vector1< bool > const &residues_allowed_to_be_packed)=0
virtual PackerTaskrestrict_to_repacking ()=0
virtual ResidueLevelTask const & residue_task (Size resid) const =0
virtual ResidueLevelTasknonconst_residue_task (Size resid)=0
virtual utility::vector1< boolrepacking_residues () const =0
virtual utility::vector1< booldesigning_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 &pose)=0

Friends

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

Detailed Description

Task class that gives instructions to the packer.


Member Typedef Documentation


Constructor & Destructor Documentation

core::pack::task::PackerTask::~PackerTask ( ) [pure virtual]

Member Function Documentation

virtual void core::pack::task::PackerTask::add_behavior ( std::string const &  behavior) [pure virtual]
virtual void core::pack::task::PackerTask::add_behavior ( std::string const &  behavior,
Size  resid 
) [pure virtual]
virtual bool core::pack::task::PackerTask::adducts ( Size  resid) const [pure virtual]
virtual void core::pack::task::PackerTask::and_max_rotbump_energy ( Real  setting) [pure virtual]
virtual void core::pack::task::PackerTask::append_rotamer_operation ( rotamer_set::RotamerOperationOP  rotop) [pure virtual]
virtual void core::pack::task::PackerTask::append_rotamerset_operation ( rotamer_set::RotamerSetOperationOP  rotsetop) [pure virtual]
virtual bool core::pack::task::PackerTask::being_designed ( Size  resid) const [pure virtual]
virtual bool core::pack::task::PackerTask::being_packed ( Size  resid) const [pure virtual]
virtual bool core::pack::task::PackerTask::bump_check ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::clean_residue_task ( conformation::Residue const &  original_residue,
Size const  seqpos 
) [pure virtual]
virtual PackerTaskOP core::pack::task::PackerTask::clone ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::decrease_double_lazy_ig_memlimit ( Size  nbytes_for_rpes) [pure virtual]
virtual bool core::pack::task::PackerTask::design_any ( ) const [pure virtual]
virtual bool core::pack::task::PackerTask::design_residue ( int  resid) const [pure virtual]
virtual utility::vector1< bool > core::pack::task::PackerTask::designing_residues ( ) const [pure virtual]
virtual bool core::pack::task::PackerTask::disallow_quench ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::disallow_quench ( bool const &  disallow_quench) [pure virtual]
virtual bool core::pack::task::PackerTask::double_lazy_ig ( ) const [pure virtual]
virtual Size core::pack::task::PackerTask::double_lazy_ig_memlimit ( ) const [pure virtual]
virtual bool core::pack::task::PackerTask::has_behavior ( std::string const &  behavior,
Size  resid 
) const [pure virtual]
virtual bool core::pack::task::PackerTask::has_behavior ( Size  resid) const [pure virtual]
virtual Real core::pack::task::PackerTask::high_temp ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::high_temp ( Real const &  high_temp) [pure virtual]
virtual IGEdgeReweightContainerCOP core::pack::task::PackerTask::IGEdgeReweights ( ) const [pure virtual]
virtual bool core::pack::task::PackerTask::include_current ( Size  resid) const [pure virtual]
virtual void core::pack::task::PackerTask::increase_multi_cool_annealer_history_size ( Size  setting) [pure virtual]
virtual PackerTask& core::pack::task::PackerTask::initialize_extra_rotamer_flags_from_command_line ( ) [pure virtual]
virtual PackerTask& core::pack::task::PackerTask::initialize_from_command_line ( ) [pure virtual]
virtual bool core::pack::task::PackerTask::lazy_ig ( ) const [pure virtual]
virtual bool core::pack::task::PackerTask::linmem_ig ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::low_temp ( Real const &  low_temp) [pure virtual]
virtual Real core::pack::task::PackerTask::low_temp ( ) const [pure virtual]
virtual Real core::pack::task::PackerTask::max_rotbump_energy ( ) const [pure virtual]
virtual bool core::pack::task::PackerTask::multi_cool_annealer ( ) const [pure virtual]
virtual Size core::pack::task::PackerTask::multi_cool_annealer_history_size ( ) const [pure virtual]
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::RestrictConservedLowDdgOperation::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), core::pack::task::operation::ExtraChiCutoff::apply(), core::pack::task::operation::ExtraRotamers::apply(), core::pack::task::operation::RestrictYSDesign::apply(), core::pack::task::operation::PreventRepacking::apply(), core::pack::task::operation::AppendResidueRotamerSet::apply(), core::pack::task::operation::ExtraRotamersGeneric::apply(), core::pack::task::operation::RotamerExplosion::apply(), core::pack::task::operation::DisallowIfNonnative::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), core::pack::task::operation::RestrictResidueToRepacking::apply(), core::pack::task::operation::RestrictToInterface::apply(), core::pack::task::operation::DockingNoRepack2::apply(), core::pack::task::operation::DockingNoRepack1::apply(), core::pack::task::operation::ReplicateTask::apply(), core::pack::task::operation::OptH::apply(), core::pack::task::operation::OperateOnCertainResidues::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::FIX_HIS_TAUTOMER::residue_action(), core::pack::task::NO_ADDUCTS::residue_action(), core::pack::task::TARGET::residue_action(), core::pack::task::SCAN::residue_action(), core::pack::task::AUTO::residue_action(), core::pack::task::USE_INPUT_SC::residue_action(), core::pack::task::EX_CUTOFF::residue_action(), core::pack::task::NC::residue_action(), core::pack::task::EX::residue_action(), core::pack::task::APOLAR::residue_action(), core::pack::task::POLAR::residue_action(), core::pack::task::EMPTY::residue_action(), core::pack::task::NOTAA::residue_action(), core::pack::task::PIKRNA::residue_action(), core::pack::task::PIKNA::residue_action(), core::pack::task::PIKAA::residue_action(), core::pack::task::ALLAAxc::residue_action(), core::pack::task::NATAA::residue_action(), core::pack::task::NATRO::residue_action(), protocols::motifs::LigandMotifSearch::run(), protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::simple_moves::EnergyCutRotamerTrialsMover::setup_energycut_task(), and core::pack::task::operation::RestrictToInterface::symmetric_task().

virtual Size core::pack::task::PackerTask::num_to_be_packed ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::or_adducts ( bool  setting) [pure virtual]
virtual void core::pack::task::PackerTask::or_adducts ( bool  setting,
Size  resid 
) [pure virtual]
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_.

virtual void core::pack::task::PackerTask::or_fix_his_tautomer ( utility::vector1< int > const &  positions,
bool  setting 
) [pure virtual]
virtual void core::pack::task::PackerTask::or_flip_HNQ ( bool  setting) [pure virtual]
virtual void core::pack::task::PackerTask::or_include_current ( bool  setting) [pure virtual]
virtual void core::pack::task::PackerTask::or_include_current ( bool  setting,
Size  resid 
) [pure virtual]
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_.

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_.

virtual void core::pack::task::PackerTask::or_multi_cool_annealer ( bool  setting) [pure virtual]
virtual void core::pack::task::PackerTask::or_optimize_h_mode ( bool  setting) [pure virtual]
virtual void core::pack::task::PackerTask::or_preserve_c_beta ( bool  setting) [pure virtual]
virtual bool core::pack::task::PackerTask::pack_residue ( int  resid) const [pure virtual]
virtual void core::pack::task::PackerTask::remap_residue_level_tasks ( core::id::SequenceMappingCOP  seqmap,
core::pose::Pose pose 
) [pure virtual]
virtual utility::vector1< bool > core::pack::task::PackerTask::repacking_residues ( ) const [pure virtual]
virtual ResidueLevelTask const& core::pack::task::PackerTask::residue_task ( Size  resid) const [pure virtual]

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

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::alter_rotamer_set(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), protocols::flxbb::LayerDesignOperation::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::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::RotamerSet_::build_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::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(), core::pack::task::operator<<(), protocols::enzdes::enzutil::recreate_task(), core::pack::task::NC::residue_action(), core::pack::task::APOLAR::residue_action(), core::pack::task::POLAR::residue_action(), and core::pack::rotamer_set::RotamerSet_::set_extra_samples().

virtual PackerTask& core::pack::task::PackerTask::restrict_to_repacking ( ) [pure virtual]
virtual PackerTask& core::pack::task::PackerTask::restrict_to_residues ( utility::vector1< bool > const &  residues_allowed_to_be_packed) [pure virtual]
virtual RotamerCouplingsCOP core::pack::task::PackerTask::rotamer_couplings ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::rotamer_couplings ( RotamerCouplingsCOP  setting) [pure virtual]
virtual bool core::pack::task::PackerTask::rotamer_couplings_exist ( ) const [pure virtual]
virtual RotamerLinksCOP core::pack::task::PackerTask::rotamer_links ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::rotamer_links ( RotamerLinksCOP  setting) [pure virtual]
virtual bool core::pack::task::PackerTask::rotamer_links_exist ( ) const [pure virtual]
virtual void core::pack::task::PackerTask::set_bump_check ( bool  setting) [pure virtual]
virtual IGEdgeReweightContainerOP core::pack::task::PackerTask::set_IGEdgeReweights ( ) [pure virtual]
virtual std::string core::pack::task::PackerTask::task_string ( pose::Pose const &  pose) const [pure virtual]
virtual void core::pack::task::PackerTask::temporarily_fix_everything ( ) [pure virtual]
virtual void core::pack::task::PackerTask::temporarily_set_pack_residue ( int  resid,
bool  setting 
) [pure virtual]
virtual Size core::pack::task::PackerTask::total_residue ( ) const [pure virtual]

Friends And Related Function Documentation

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

output operator


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