core::pack::task::ResidueLevelTask Class Reference

#include <PackerTask.hh>

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::ResidueTypeCOP concrete_residue) const =0
virtual void	initialize_from_command_line ()=0
virtual void	initialize_extra_rotamer_flags_from_command_line ()=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_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::ResidueTypeSet const &	get_original_residue_set () const =0
virtual chemical::AA const &	get_original_residue () const =0
virtual void	allow_noncanonical_aa (std::string const &interchangeability_group, chemical::ResidueTypeSet const &residue_set)=0
	expand (or) the list of available residue types for non-cannonicals More...
virtual void	allow_noncanonical_aa (std::string const &aaname)=0
	expand (or) the list of available residue types for non-cannonicals. Assumes same restypeset as original residue More...
virtual void	allow_noncanonical_aa (chemical::AA aa)=0
	explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_ More...
virtual void	disallow_noncanonical_aas ()=0
	explicitly disallow all NCAAs More...
virtual void	allow_aa (chemical::AA const &aa)=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

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 ( )

virtual

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::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 void core::pack::task::ResidueLevelTask::allow_aa ( chemical::AA const &  aa )

pure virtual

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

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

virtual void core::pack::task::ResidueLevelTask::allow_noncanonical_aa ( std::string const &  interchangeability_group, chemical::ResidueTypeSet const &  residue_set  )

pure virtual

expand (or) the list of available residue types for non-cannonicals

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

Referenced by core::pack::task::PIKAA::residue_action(), and core::pack::task::NC::residue_action().

virtual void core::pack::task::ResidueLevelTask::allow_noncanonical_aa ( std::string const &  aaname )

pure virtual

expand (or) the list of available residue types for non-cannonicals. Assumes same restypeset as original residue

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

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

pure virtual

explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_

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

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

pure virtual

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

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(), core::pack::task::POLAR::residue_action(), core::pack::task::APOLAR::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(), core::pack::task::POLAR::residue_action(), core::pack::task::APOLAR::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::ExtraChiCutoff::apply(), and core::pack::task::EX_CUTOFF::residue_action().

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 core::pack::task::operation::AppendResidueRotamerSet::apply().

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

pure virtual

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

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

pure virtual

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

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

pure virtual

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

virtual void core::pack::task::ResidueLevelTask::disallow_noncanonical_aas ( )

pure virtual

explicitly disallow all NCAAs

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

Referenced by core::pack::task::EMPTY::residue_action(), and core::pack::task::RESET::residue_action().

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 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::ResidueTypeCOP  concrete_residue  ) const

pure virtual

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

Referenced by core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_chisamples_for_rotamer_chi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_chisamples_for_rotamer_chi(), core::pack::rotamer_set::build_dna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_optimize_H_rotamers(), core::pack::rotamer_set::build_proton_chi_rotamers(), core::pack::rotamer_set::build_rna_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), 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 core::pack::task::PackerTask_::show_residue_task().

virtual chemical::ResidueTypeSet const& core::pack::task::ResidueLevelTask::get_original_residue_set ( ) const

pure virtual

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

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

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

pure virtual

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

Referenced by 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::rotamer_set::RotamerSet_::build_rotamers_for_concrete().

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_from_command_line ( )

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_.

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_.

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

pure virtual

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

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

pure virtual

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

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

pure virtual

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

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 core::pack::task::operation::ExtraRotamersGeneric::apply(), and core::pack::task::operation::ExtraRotamers::apply().

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

pure virtual

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

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

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

pure virtual

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

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

pure virtual

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

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

pure virtual

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

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().

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

pure virtual

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

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

pure virtual

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

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

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

pure virtual

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

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

pure virtual

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

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

pure virtual

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

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().

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

pure virtual

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

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

pure virtual

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

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

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

pure virtual

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

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

pure virtual

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

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

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

pure virtual

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

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::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_.

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

pure virtual

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

Referenced by core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >::create_rotamers_from_chisets(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::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 core::pack::task::operation::ReplicateTask::apply(), core::pack::task::operation::DockingNoRepack1::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::OptH::apply(), core::pack::task::operation::PreventRepackingRLT::apply(), core::pack::task::operation::DockingNoRepack2::apply(), core::pack::task::operation::RestrictToInterface::apply(), core::pack::task::operation::PreventRepacking::apply(), core::pack::make_new_symmetric_PackerTask_by_intersection(), core::pack::make_new_symmetric_PackerTask_by_union(), core::pack::task::NATRO::residue_action(), and core::pack::task::operation::RestrictToInterface::symmetric_task().

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

pure virtual

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

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

pure virtual

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

Referenced by core::pack::task::operation::RestrictAbsentCanonicalAASRLT::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), core::pack::task::operation::RestrictYSDesign::apply(), core::pack::task::ALLAAxc::residue_action(), core::pack::task::PIKAA::residue_action(), core::pack::task::NOTAA::residue_action(), core::pack::task::EMPTY::residue_action(), core::pack::task::RESET::residue_action(), core::pack::task::POLAR::residue_action(), and core::pack::task::APOLAR::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::DisallowIfNonnativeRLT::apply(), and core::pack::task::operation::DisallowIfNonnative::apply().

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(), core::pack::task::operation::ReplicateTask::apply(), core::pack::task::operation::RestrictResidueToRepacking::apply(), and core::pack::task::NATAA::residue_action().

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::RotamericSingleResiduePeptoidLibrary< T >::create_rotamers_from_chisets(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::create_rotamers_from_chisets().

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().

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().

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_.

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_.

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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