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core::pack::task::ResidueLevelTask Class Referenceabstract

#include <ResidueLevelTask.hh>

Inheritance diagram for core::pack::task::ResidueLevelTask:
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Public Types

typedef std::list
< chemical::ResidueTypeCOP > 		ResidueTypeCOPList
 
typedef std::list
< chemical::ResidueTypeCOP >
::iterator 		ResidueTypeCOPListIter
 
typedef std::list
< chemical::ResidueTypeCOP >
::const_iterator 		ResidueTypeCOPListConstIter
 

Public Member Functions

virtual ~ResidueLevelTask ()
 
virtual ExtraRotSample extrachi_sample_level (bool buried, int chi, chemical::ResidueType const &concrete_residue) const =0
 
virtual void initialize_from_command_line ()=0
 
virtual void initialize_extra_rotamer_flags_from_command_line ()=0
 
virtual void initialize_from_options (utility::options::OptionCollection const &options)=0
 
virtual void initialize_extra_rotamer_flags_from_options (utility::options::OptionCollection const &options)=0
 
virtual void or_include_current (bool include_current)=0
 
virtual bool include_current () const =0
 
virtual void add_behavior (std::string const &behavior)=0
 
virtual bool has_behavior (std::string const &behavior) const =0
 
virtual bool has_behavior () const =0
 
virtual void target_type (chemical::ResidueTypeCOP type)=0
 
virtual void target_type (chemical::AA aa)=0
 
virtual void target_type (std::string name)=0
 
virtual void or_adducts (bool setting)=0
 
virtual bool adducts () const =0
 
virtual void or_ex1 (bool ex1)=0
 
virtual void or_ex2 (bool ex2)=0
 
virtual void or_ex3 (bool ex3)=0
 
virtual void or_ex4 (bool ex4)=0
 
virtual void or_ex1_sample_level (ExtraRotSample ex1_sample_level)=0
 
virtual void or_ex2_sample_level (ExtraRotSample ex2_sample_level)=0
 
virtual void or_ex3_sample_level (ExtraRotSample ex3_sample_level)=0
 
virtual void or_ex4_sample_level (ExtraRotSample ex4_sample_level)=0
 
virtual void or_ex1aro (bool ex1aro)=0
 
virtual void or_ex2aro (bool ex2aro)=0
 
virtual void or_ex1aro_exposed (bool ex1aro_exposed)=0
 
virtual void or_ex2aro_exposed (bool ex2aro_exposed)=0
 
virtual void or_ex1aro_sample_level (ExtraRotSample ex1aro_sample_level)=0
 
virtual void or_ex2aro_sample_level (ExtraRotSample ex2aro_only_sample_level)=0
 
virtual void or_ex1aro_exposed_sample_level (ExtraRotSample ex1aro_exposed_sample_level)=0
 
virtual void or_ex2aro_exposed_sample_level (ExtraRotSample ex2aro_exposed_sample_level)=0
 
virtual void or_exdna_sample_level (ExtraRotSample exdna_sample_level)=0
 
virtual void or_operate_on_ex1 (bool operate)=0
 
virtual void or_operate_on_ex2 (bool operate)=0
 
virtual void or_operate_on_ex3 (bool operate)=0
 
virtual void or_operate_on_ex4 (bool operate)=0
 
virtual bool ex1 () const =0
 
virtual bool ex2 () const =0
 
virtual bool ex3 () const =0
 
virtual bool ex4 () const =0
 
virtual ExtraRotSample ex1_sample_level () const =0
 
virtual ExtraRotSample ex2_sample_level () const =0
 
virtual ExtraRotSample ex3_sample_level () const =0
 
virtual ExtraRotSample ex4_sample_level () const =0
 
virtual bool ex1aro () const =0
 
virtual bool ex2aro () const =0
 
virtual bool ex1aro_exposed () const =0
 
virtual bool ex2aro_exposed () const =0
 
virtual ExtraRotSample ex1aro_sample_level () const =0
 
virtual ExtraRotSample ex2aro_sample_level () const =0
 
virtual ExtraRotSample ex1aro_exposed_sample_level () const =0
 
virtual ExtraRotSample ex2aro_exposed_sample_level () const =0
 
virtual ExtraRotSample exdna_sample_level () const =0
 
virtual bool operate_on_ex1 () const =0
 
virtual bool operate_on_ex2 () const =0
 
virtual bool operate_on_ex3 () const =0
 
virtual bool operate_on_ex4 () const =0
 
virtual void sample_proton_chi (bool setting)=0
 
virtual bool sample_proton_chi () const =0
 
virtual void or_optimize_h (bool setting)=0
 
virtual bool optimize_h () const =0
 
virtual void or_preserve_c_beta (bool setting)=0
 
virtual bool preserve_c_beta () const =0
 
virtual void or_flip_HNQ (bool setting)=0
 
virtual bool flip_HNQ () const =0
 
virtual void or_fix_his_tautomer (bool setting)=0
 
virtual bool fix_his_tautomer () const =0
 
virtual void or_include_virtual_side_chain (bool include_virtual_side_chain)=0
 
virtual bool include_virtual_side_chain () const =0
 
virtual void and_extrachi_cutoff (Size num_neighbors_to_be_called_buried)=0
 
virtual Size extrachi_cutoff () const =0
 
virtual void prevent_repacking ()=0
 
virtual void restrict_restypes (utility::vector1< std::string > const &basenames_to_keep)=0
 Restrict residue types. More...
 
virtual void disable_restypes (utility::vector1< std::string > const &basenames_to_disable)=0
 Disable residue types. More...
 
virtual void restrict_to_restypes_with_at_least_one_property (utility::vector1< core::chemical::ResidueProperty > const &properties)=0
 Given a list of residue properties, eliminate any residue type that does not have at least one of the properties in the list. More...
 
virtual void restrict_to_restypes_with_all_properties (utility::vector1< core::chemical::ResidueProperty > const &properties)=0
 Given a list of residue properties, eliminate any residue type that does not have ALL of the properties in the list. More...
 
virtual void disable_restypes_with_at_least_one_property (utility::vector1< core::chemical::ResidueProperty > const &properties)=0
 Given a list of residue properties, eliminate any residue type that has any of the properties in the list. More...
 
virtual void restrict_absent_canonical_aas (utility::vector1< bool > const &)=0
 
virtual void restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas, std::string const &mode)=0
 
virtual void restrict_nonnative_canonical_aas (utility::vector1< bool > const &allowed_aas)=0
 
virtual void restrict_absent_nas (utility::vector1< chemical::AA > const &keep_nas)=0
 disables designing to nucleic acid residues not in the passed list More...
 
virtual void restrict_to_repacking ()=0
 
virtual bool is_original_type (chemical::ResidueTypeCOP type) const =0
 
virtual chemical::ResidueTypeSetCOP get_original_residue_set () const =0
 
virtual chemical::AA const & get_original_residue () const =0
 
virtual ResidueTypeCOPList const & allowed_residue_types () const =0
 
virtual ResidueTypeCOPListConstIter allowed_residue_types_begin () const =0
 
virtual ResidueTypeCOPListConstIter allowed_residue_types_end () const =0
 
virtual chemical::ResidueTypeCOP target_type () const =0
 
virtual void print_allowed_types (std::ostream &os) const =0
 
virtual bool being_designed () const =0
 
virtual bool being_packed () const =0
 
virtual
rotamer_set::RotamerOperations
const & 		rotamer_operations () const =0
 
virtual void append_rotamer_operation (rotamer_set::RotamerOperationOP rotop)=0
 
virtual
rotamer_set::RotSetOperationListIterator 		rotamer_set_operation_begin () const =0
 
virtual
rotamer_set::RotSetOperationListIterator 		rotamer_set_operation_end () const =0
 
virtual void append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop)=0
 
virtual std::string command_string () const =0
 
virtual
rna::RNA_ResidueLevelTask
const & 		rna_task () const =0
 
virtual rna::RNA_ResidueLevelTask & nonconst_rna_task ()=0
 

Static Public Member Functions

static void list_options_read (utility::options::OptionKeyList &read_options)
 

Member Typedef Documentation

typedef std::list< chemical::ResidueTypeCOP > core::pack::task::ResidueLevelTask::ResidueTypeCOPList
typedef std::list< chemical::ResidueTypeCOP >::const_iterator core::pack::task::ResidueLevelTask::ResidueTypeCOPListConstIter
typedef std::list< chemical::ResidueTypeCOP >::iterator core::pack::task::ResidueLevelTask::ResidueTypeCOPListIter

Constructor & Destructor Documentation

core::pack::task::ResidueLevelTask::~ResidueLevelTask ( )
virtualdefault

Member Function Documentation

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

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::FillAUTOTaskOperation::apply(), core::pack::task::operation::AddBehaviorRLT::apply(), core::pack::task::AUTO::residue_action(), core::pack::task::SCAN::residue_action(), and core::pack::task::TARGET::residue_action().

virtual bool core::pack::task::ResidueLevelTask::adducts ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual ResidueTypeCOPList const& core::pack::task::ResidueLevelTask::allowed_residue_types ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::multistate_design::list_amino_acid_options(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), and protocols::dna::DnaInterfacePacker::protein_scan().

virtual ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask::allowed_residue_types_begin ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_aas_after_disallowing(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_best_allowed_aas(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::is_residue_allowed(), protocols::dna::DnaInterfacePacker::measure_bp_specificities(), 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::CHARGED::residue_action(), core::pack::task::AROMATIC::residue_action(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), and core::pack::task::PackerTask_::show().

virtual ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask::allowed_residue_types_end ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_aas_after_disallowing(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::compute_best_allowed_aas(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::is_residue_allowed(), protocols::dna::DnaInterfacePacker::measure_bp_specificities(), 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::CHARGED::residue_action(), core::pack::task::AROMATIC::residue_action(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), and core::pack::task::PackerTask_::show().

virtual void core::pack::task::ResidueLevelTask::and_extrachi_cutoff ( Size  num_neighbors_to_be_called_buried)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::ExtraChiCutoffRLT::apply(), core::pack::task::operation::ExtraChiCutoff::apply(), core::pack::task::EX_CUTOFF::residue_action(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

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

Implemented in core::pack::task::ResidueLevelTask_.

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

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::hotspot_hashing::AddSearchPatternRotSetOp::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), core::pack::task::operation::AppendResidueRotamerSet::apply(), and protocols::motifs::LigandMotifSearch::run().

virtual bool core::pack::task::ResidueLevelTask::being_designed ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::calc_taskop_movers::ConsensusDesignMover::create_sequence_profile_constraints(), and protocols::enzdes::enzutil::recreate_task().

virtual bool core::pack::task::ResidueLevelTask::being_packed ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::dna::DnaInterfacePacker::protein_scan(), and protocols::enzdes::enzutil::recreate_task().

virtual std::string core::pack::task::ResidueLevelTask::command_string ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::flxbb::LayerDesignOperation::apply().

virtual void core::pack::task::ResidueLevelTask::disable_restypes ( utility::vector1< std::string > const &  basenames_to_disable)
pure virtual

Disable residue types.

This function takes a vector of base names to prohibit. Anything in this list is turned off.

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::ResidueLevelTask_.

Referenced by core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::apply(), and core::pack::task::NOTAA::residue_action().

virtual void core::pack::task::ResidueLevelTask::disable_restypes_with_at_least_one_property ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
pure virtual

Given a list of residue properties, eliminate any residue type that has any of the properties in the list.

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::ResidueLevelTask_.

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

virtual bool core::pack::task::ResidueLevelTask::ex1 ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex1_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::ex1aro ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual bool core::pack::task::ResidueLevelTask::ex1aro_exposed ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex1aro_exposed_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex1aro_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::ex2 ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex2_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::ex2aro ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual bool core::pack::task::ResidueLevelTask::ex2aro_exposed ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex2aro_exposed_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex2aro_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::ex3 ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex3_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::ex4 ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex4_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual ExtraRotSample core::pack::task::ResidueLevelTask::exdna_sample_level ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual Size core::pack::task::ResidueLevelTask::extrachi_cutoff ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::alter_rotamer_set(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::rotamer_set::RotamerSet_::set_extra_samples(), and core::pack::task::PackerTask_::show_residue_task().

virtual ExtraRotSample core::pack::task::ResidueLevelTask::extrachi_sample_level ( bool  buried,
int  chi,
chemical::ResidueType const &  concrete_residue 
) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::bbdep_chisamples_for_rotamer_chi(), core::pack::rotamer_set::build_dna_rotamers(), core::pack::rotamer_set::build_rna_rotamers(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::chisamples_for_rotamer_and_chi(), core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(), and core::pack::rotamer_set::RotamerSet_::set_extra_samples().

virtual bool core::pack::task::ResidueLevelTask::fix_his_tautomer ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PackerTask_::show_residue_task().

virtual bool core::pack::task::ResidueLevelTask::flip_HNQ ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), and core::pack::task::PackerTask_::show_residue_task().

virtual chemical::AA const& core::pack::task::ResidueLevelTask::get_original_residue ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::task_operations::MutationSetDesignOperation::apply(), protocols::task_operations::ResidueProbDesignOperation::apply(), and core::pack::task::PackerTask_::show_residue_task().

virtual chemical::ResidueTypeSetCOP core::pack::task::ResidueLevelTask::get_original_residue_set ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::has_behavior ( std::string const &  behavior) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::dna::DnaInterfacePacker::current_working_sequence(), and core::pack::task::PackerTask_::show_residue_task().

virtual bool core::pack::task::ResidueLevelTask::has_behavior ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::include_current ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), and core::pack::task::PackerTask_::show_residue_task().

virtual bool core::pack::task::ResidueLevelTask::include_virtual_side_chain ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::build_proton_chi_rotamers(), and core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain().

virtual void core::pack::task::ResidueLevelTask::initialize_extra_rotamer_flags_from_command_line ( )
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::initialize_extra_rotamer_flags_from_options ( utility::options::OptionCollection const &  options)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::initialize_from_command_line ( )
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::initialize_from_options ( utility::options::OptionCollection const &  options)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::is_original_type ( chemical::ResidueTypeCOP  type) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

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

Referenced by core::pack::task::PackerTask::list_options_read().

virtual rna::RNA_ResidueLevelTask& core::pack::task::ResidueLevelTask::nonconst_rna_task ( )
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual bool core::pack::task::ResidueLevelTask::operate_on_ex1 ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::dna::RotamerDNAHBondFilter::operator()().

virtual bool core::pack::task::ResidueLevelTask::operate_on_ex2 ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::dna::RotamerDNAHBondFilter::operator()().

virtual bool core::pack::task::ResidueLevelTask::operate_on_ex3 ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::dna::RotamerDNAHBondFilter::operator()().

virtual bool core::pack::task::ResidueLevelTask::operate_on_ex4 ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::dna::RotamerDNAHBondFilter::operator()().

virtual bool core::pack::task::ResidueLevelTask::optimize_h ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), and core::pack::task::PackerTask_::show_residue_task().

virtual void core::pack::task::ResidueLevelTask::or_adducts ( bool  setting)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::NO_ADDUCTS::residue_action().

virtual void core::pack::task::ResidueLevelTask::or_ex1 ( bool  ex1)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), core::pack::task::operation::ExtraRotamers::apply(), protocols::dna::argrot_dna_dis2(), protocols::ddg::ddGMover::initialize_rotamer_behavior_for_residue_level_task(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex1_sample_level ( ExtraRotSample  ex1_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), core::pack::task::operation::RotamerExplosion::apply(), core::pack::task::EX::residue_action(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex1aro ( bool  ex1aro)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex1aro_exposed ( bool  ex1aro_exposed)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex1aro_exposed_sample_level ( ExtraRotSample  ex1aro_exposed_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex1aro_sample_level ( ExtraRotSample  ex1aro_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::EX::residue_action(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex2 ( bool  ex2)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::ddg::ddGMover::initialize_rotamer_behavior_for_residue_level_task(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex2_sample_level ( ExtraRotSample  ex2_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), core::pack::task::EX::residue_action(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex2aro ( bool  ex2aro)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex2aro_exposed ( bool  ex2aro_exposed)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex2aro_exposed_sample_level ( ExtraRotSample  ex2aro_exposed_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex2aro_sample_level ( ExtraRotSample  ex2aro_only_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::EX::residue_action(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex3 ( bool  ex3)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex3_sample_level ( ExtraRotSample  ex3_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), core::pack::task::EX::residue_action(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex4 ( bool  ex4)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_ex4_sample_level ( ExtraRotSample  ex4_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), core::pack::task::EX::residue_action(), and core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_exdna_sample_level ( ExtraRotSample  exdna_sample_level)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::set_rotamer_sampling_data_for_RLT().

virtual void core::pack::task::ResidueLevelTask::or_fix_his_tautomer ( bool  setting)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::FIX_HIS_TAUTOMER::residue_action().

virtual void core::pack::task::ResidueLevelTask::or_flip_HNQ ( bool  setting)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::or_include_current ( bool  include_current)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::IncludeCurrentRLT::apply(), protocols::ddg::ddGMover::initialize_rotamer_behavior_for_residue_level_task(), and core::pack::task::USE_INPUT_SC::residue_action().

virtual void core::pack::task::ResidueLevelTask::or_include_virtual_side_chain ( bool  include_virtual_side_chain)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::or_operate_on_ex1 ( bool  operate)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::or_operate_on_ex2 ( bool  operate)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::or_operate_on_ex3 ( bool  operate)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::or_operate_on_ex4 ( bool  operate)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::or_optimize_h ( bool  setting)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::or_preserve_c_beta ( bool  setting)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

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

virtual bool core::pack::task::ResidueLevelTask::preserve_c_beta ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::create_rotamers_from_chisets(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection(), and core::pack::task::PackerTask_::show_residue_task().

virtual void core::pack::task::ResidueLevelTask::prevent_repacking ( )
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::task_operations::RestrictIdentitiesOperation::apply(), core::pack::task::operation::ReplicateTask::apply(), protocols::task_operations::RestrictToTerminiOperation::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::ClashBasedRepackShell::apply(), core::pack::task::operation::OptH::apply(), protocols::simple_task_operations::DockingNoRepack1::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::simple_task_operations::DockingNoRepack2::apply(), core::pack::task::operation::PreventRepackingRLT::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::pack::task::operation::PreventRepacking::apply(), protocols::loop_grower::LoopGrower::refine_cycle(), core::pack::task::NATRO::residue_action(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::setup_energycut_task(), and protocols::simple_task_operations::RestrictToInterface::symmetric_task().

virtual void core::pack::task::ResidueLevelTask::print_allowed_types ( std::ostream &  os) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply().

virtual void core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas ( utility::vector1< bool > const &  )
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::task_operations::ConservativeDesignOperation::apply(), core::pack::task::operation::RestrictAbsentCanonicalAASRLT::apply(), protocols::task_operations::MutationSetDesignOperation::apply(), protocols::task_operations::ResidueProbDesignOperation::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::task_operations::DsspDesignOperation::apply(), protocols::task_operations::RestrictConservedLowDdgOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), core::pack::task::operation::RestrictYSDesign::apply(), protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::disallow_aas(), core::pack::task::ALLAAxc::residue_action(), core::pack::task::POLAR::residue_action(), core::pack::task::APOLAR::residue_action(), core::pack::task::CHARGED::residue_action(), and core::pack::task::AROMATIC::residue_action().

virtual void core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas ( utility::vector1< bool > const &  allowed_aas,
std::string const &  mode 
)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::restrict_absent_nas ( utility::vector1< chemical::AA > const &  keep_nas)
pure virtual

disables designing to nucleic acid residues not in the passed list

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PIKNA::residue_action().

virtual void core::pack::task::ResidueLevelTask::restrict_nonnative_canonical_aas ( utility::vector1< bool > const &  allowed_aas)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT::apply(), core::pack::task::operation::DisallowIfNonnativeRLT::apply(), and core::pack::task::operation::DisallowIfNonnative::apply().

virtual void core::pack::task::ResidueLevelTask::restrict_restypes ( utility::vector1< std::string > const &  basenames_to_keep)
pure virtual

Restrict residue types.

This function takes a vector of base names to allow. Anything not in this list is turned off.

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::ResidueLevelTask_.

Referenced by protocols::task_operations::pHVariantTaskOperation::apply(), core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes::apply(), and core::pack::task::PIKAA::residue_action().

virtual void core::pack::task::ResidueLevelTask::restrict_to_repacking ( )
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::RestrictToRepackingRLT::apply(), protocols::task_operations::RestrictNonSurfaceToRepackingOperation::apply(), protocols::task_operations::pHVariantTaskOperation::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::task_operations::RestrictIdentitiesOperation::apply(), core::pack::task::operation::ReplicateTask::apply(), protocols::task_operations::RestrictToTerminiOperation::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::task_operations::RestrictConservedLowDdgOperation::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::pack::task::operation::RestrictResidueToRepacking::apply(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::pose_metric_calculators::RotamerBoltzCalculator::init_task(), and core::pack::task::NATAA::residue_action().

virtual void core::pack::task::ResidueLevelTask::restrict_to_restypes_with_all_properties ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
pure virtual

Given a list of residue properties, eliminate any residue type that does not have ALL of the properties in the list.

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::ResidueLevelTask_.

Referenced by core::pack::task::operation::RestrictToResidueProperties::apply(), and core::pack::task::PROPERTY::residue_action().

virtual void core::pack::task::ResidueLevelTask::restrict_to_restypes_with_at_least_one_property ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
pure virtual

Given a list of residue properties, eliminate any residue type that does not have at least one of the properties in the list.

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::ResidueLevelTask_.

virtual rna::RNA_ResidueLevelTask const& core::pack::task::ResidueLevelTask::rna_task ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

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

virtual rotamer_set::RotamerOperations const& core::pack::task::ResidueLevelTask::rotamer_operations ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::create_rotamers_from_chisets(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), and protocols::enzdes::enzutil::recreate_task().

virtual rotamer_set::RotSetOperationListIterator core::pack::task::ResidueLevelTask::rotamer_set_operation_begin ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::RotamerSet_::build_rotamers(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), and protocols::enzdes::enzutil::recreate_task().

virtual rotamer_set::RotSetOperationListIterator core::pack::task::ResidueLevelTask::rotamer_set_operation_end ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::RotamerSet_::build_rotamers(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), and protocols::enzdes::enzutil::recreate_task().

virtual void core::pack::task::ResidueLevelTask::sample_proton_chi ( bool  setting)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::rotamer_set::build_rna_rotamers(), and core::pack::task::PackerTask_::show_residue_task().

virtual bool core::pack::task::ResidueLevelTask::sample_proton_chi ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::target_type ( chemical::ResidueTypeCOP  type)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::dna::RestrictDesignToProteinDNAInterface::apply().

virtual void core::pack::task::ResidueLevelTask::target_type ( chemical::AA  aa)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual void core::pack::task::ResidueLevelTask::target_type ( std::string  name)
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

virtual chemical::ResidueTypeCOP core::pack::task::ResidueLevelTask::target_type ( ) const
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

The documentation for this class was generated from the following files:
Generated on Fri Apr 23 2021 03:44:38 for Rosetta by   doxygen 1.8.7