Residue-level task class; contained within PackerTask. More...

#include <PackerTask_.hh>

Public Member Functions
	ResidueLevelTask_ (conformation::Residue const &original_residue)
	constructor; requires a Residue object More...

	ResidueLevelTask_ ()

virtual	~ResidueLevelTask_ ()
	dtor More...

virtual ExtraRotSample	extrachi_sample_level (bool buried, int chi, chemical::ResidueTypeCOP concrete_residue) const
	returns the extra chi sampling level More...

virtual void	initialize_from_command_line ()
	initialize options from command line flags More...

virtual void	initialize_extra_rotamer_flags_from_command_line ()
	Initialize only the extra rotamer building flags from the command line; invoked by intialize_from_command_line();. More...

virtual void	or_include_current (bool include_current)
	include the pre-existing rotamer while packing More...

virtual bool	include_current () const
	is the pre-existing rotamer specifically allowed while packing? More...

virtual void	add_behavior (std::string const &behavior)

virtual bool	has_behavior (std::string const &behavior) const

virtual bool	has_behavior () const

virtual void	target_type (chemical::ResidueTypeCOP type)

virtual void	target_type (chemical::AA aa)

virtual void	target_type (std::string name)

virtual void	or_adducts (bool setting)
	include adducts at this residue More...

virtual bool	adducts () const

virtual void	or_ex1 (bool ex1)
	activate ex1 when passed true; do nothing otherwise More...

virtual void	or_ex2 (bool ex2)
	activate ex2 when passed true; do nothing otherwise More...

virtual void	or_ex3 (bool ex3)
	activate ex3 when passed true; do nothing otherwise More...

virtual void	or_ex4 (bool ex4)
	activate ex4 when passed true; do nothing otherwise More...

virtual void	or_ex1_sample_level (ExtraRotSample ex1_sample_level)
	increase ex1 sample level; do nothing if not an increase More...

virtual void	or_ex2_sample_level (ExtraRotSample ex2_sample_level)
	increase ex2 sample level; do nothing if not an increase More...

virtual void	or_ex3_sample_level (ExtraRotSample ex3_sample_level)
	increase ex3 sample level; do nothing if not an increase More...

virtual void	or_ex4_sample_level (ExtraRotSample ex4_sample_level)
	increase ex4 sample level; do nothing if not an increase More...

virtual void	or_ex1aro (bool ex1aro)
	activate ex1 for aromatics when passed true; do nothing otherwise More...

virtual void	or_ex2aro (bool ex2aro_only)
	activate ex2 for aromatics when passed true; do nothing otherwise More...

virtual void	or_ex1aro_exposed (bool ex1aro_exposed)
	activate ex1 for exposed aromatics when passed true; do nothing otherwise More...

virtual void	or_ex2aro_exposed (bool ex2aro_exposed)
	activate ex2 for exposed aromatics when passed true; do nothing otherwise More...

virtual void	or_ex1aro_sample_level (ExtraRotSample ex1aro_sample_level)
	increase ex1aro sample level; do nothing if not an increase More...

virtual void	or_ex2aro_sample_level (ExtraRotSample ex2aro_only_sample_level)
	increase ex2aro sample level; do nothing if not an increase More...

virtual void	or_ex1aro_exposed_sample_level (ExtraRotSample ex1aro_exposed_sample_level)
	increase ex1aro_exposed sample level; do nothing if not an increase More...

virtual void	or_ex2aro_exposed_sample_level (ExtraRotSample ex2aro_exposed_sample_level)
	increase ex2aro_exposed sample level; do nothing if not an increase More...

virtual void	or_operate_on_ex1 (bool operate)

virtual void	or_operate_on_ex2 (bool operate)

virtual void	or_operate_on_ex3 (bool operate)

virtual void	or_operate_on_ex4 (bool operate)

virtual void	or_exdna_sample_level (ExtraRotSample exdna_sample_level)

virtual void	or_optimize_h (bool setting)

virtual bool	optimize_h () const

virtual void	or_preserve_c_beta (bool setting)

virtual bool	preserve_c_beta () const

virtual void	or_flip_HNQ (bool setting)

virtual bool	flip_HNQ () const

virtual void	or_fix_his_tautomer (bool setting)

virtual bool	fix_his_tautomer () const

virtual void	or_include_virtual_side_chain (bool setting)

virtual bool	include_virtual_side_chain () const

virtual void	sample_proton_chi (bool setting)
	sample proton chi. More...

virtual bool	sample_proton_chi () const
	sample proton chi. More...

virtual bool	ex1 () const

virtual bool	ex2 () const

virtual bool	ex3 () const

virtual bool	ex4 () const

virtual ExtraRotSample	ex1_sample_level () const

virtual ExtraRotSample	ex2_sample_level () const

virtual ExtraRotSample	ex3_sample_level () const

virtual ExtraRotSample	ex4_sample_level () const

virtual bool	ex1aro () const

virtual bool	ex2aro () const

virtual bool	ex1aro_exposed () const

virtual bool	ex2aro_exposed () const

virtual ExtraRotSample	ex1aro_sample_level () const

virtual ExtraRotSample	ex2aro_sample_level () const

virtual ExtraRotSample	ex1aro_exposed_sample_level () const

virtual ExtraRotSample	ex2aro_exposed_sample_level () const

virtual ExtraRotSample	exdna_sample_level () const

virtual bool	operate_on_ex1 () const

virtual bool	operate_on_ex2 () const

virtual bool	operate_on_ex3 () const

virtual bool	operate_on_ex4 () const

virtual void	and_extrachi_cutoff (Size num_neighbors_to_be_called_buried)
	lower extrachi_cutoff to given value; do nothing if not a decrease More...

virtual Size	extrachi_cutoff () const
	get function for extrachi_cutoff More...

virtual void	prevent_repacking ()
	remove all ResidueTypes from the list of allowed residue types, preventing repacking More...

virtual void	restrict_absent_canonical_aas (utility::vector1< bool > const &)
	disables designing to residues not in the passed list More...

virtual void	restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas, std::string const &mode)
	disables designing to residues not in the passed list–and specifies the resfile command that made this list More...

virtual void	restrict_nonnative_canonical_aas (utility::vector1< bool > const &allowed_aas)

virtual void	restrict_absent_nas (utility::vector1< chemical::AA > const &keep_nas)
	disables designing to nucleic acid residues not in the passed list More...

virtual void	restrict_to_repacking ()
	only let this residue repack – prevent redesign More...

virtual bool	is_original_type (chemical::ResidueTypeCOP type) const

virtual chemical::ResidueTypeSet const &	get_original_residue_set () const

virtual chemical::AA const &	get_original_residue () const

virtual void	allow_noncanonical_aa (std::string const &interchangeability_group, chemical::ResidueTypeSet const &residue_set)
	explicitly allow a NCAA More...

virtual void	allow_noncanonical_aa (std::string const &aaname)
	explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_ More...

virtual void	allow_noncanonical_aa (chemical::AA aa)
	explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_ More...

virtual void	disallow_noncanonical_aas ()
	expliciitly disallow all NCAAs More...

virtual void	allow_aa (chemical::AA const &aa)
	explicitly allow a canonical AA More...

virtual ResidueTypeCOPList const &	allowed_residue_types () const

virtual ResidueTypeCOPListConstIter	allowed_residue_types_begin () const
	returns iterator to beginning of allowed residue types list (traversal only) More...

virtual ResidueTypeCOPListConstIter	allowed_residue_types_end () const
	returns iterator to end of allowed residue types list (traversal only) More...

virtual chemical::ResidueTypeCOP	target_type () const

virtual void	print_allowed_types (std::ostream &os) const

virtual bool	being_designed () const
	is this residue up for design (variable sequence)? More...

virtual bool	being_packed () const
	is this residue modififable at all by the packer? More...

virtual rotamer_set::RotamerOperations const &	rotamer_operations () const

virtual void	append_rotamer_operation (rotamer_set::RotamerOperationOP rotop)

virtual rotamer_set::RotSetOperationListIterator	rotamer_set_operation_begin () const

virtual rotamer_set::RotSetOperationListIterator	rotamer_set_operation_end () const

virtual void	append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop)

virtual std::string	command_string () const
	create a string the resfile format of all the commands applied to this residue level task More...

virtual void	update_union (ResidueLevelTask const &res_task_in)

virtual void	update_intersection (ResidueLevelTask const &res_task_in)

virtual void	update_commutative (ResidueLevelTask const &res_task_in)

Public Member Functions inherited from core::pack::task::ResidueLevelTask
virtual	~ResidueLevelTask ()

Private Member Functions
void	refresh_ex1_sample_levels ()
	private: bookkeeping for ex1 More...

void	refresh_ex2_sample_levels ()
	private: bookkeeping for ex2 More...

void	refresh_ex3_sample_levels ()
	private: bookkeeping for ex3 More...

void	refresh_ex4_sample_levels ()
	private: bookkeeping for ex4 More...

void	determine_if_designing ()
	private: bookkeeping for whether sequence can change More...

void	determine_if_repacking ()
	private: bookkeeping for whether rotamer can change More...

std::string	get_ex_flags (Size chiid, Size const exaro_sample_level, Size const ex_sample_level) const
	private: return the EX command for the packer task More...

std::string	task_mode () const
	private: return the task mode that can be used to recreate the task. If the residue level task was made with POLAR it should return the string "POLAR". More...

rna::RNA_ResidueLevelTask const &	rna_task () const

rna::RNA_ResidueLevelTask &	nonconst_rna_task ()

void	do_restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas)

Private Attributes
bool	include_current_

utility::vector1< std::string >	behaviors_
	here we store any flagged protocol-level behaviors for this residue More...

bool	adducts_
	include adducts at this residue More...

ResidueTypeCOPList	allowed_residue_types_

chemical::ResidueTypeCOP	original_residue_type_

chemical::ResidueTypeCOP	target_residue_type_

bool	designing_

bool	repacking_

bool	optimize_H_mode_

bool	preserve_c_beta_

bool	flip_HNQ_

bool	fix_his_tautomer_

bool	include_virtual_side_chain_

bool	disabled_

bool	design_disabled_

bool	sample_proton_chi_

bool	ex1_

bool	ex2_

bool	ex3_

bool	ex4_

bool	ex1aro_

bool	ex2aro_

bool	ex1aro_exposed_

bool	ex2aro_exposed_

ExtraRotSample	ex1_sample_level_

ExtraRotSample	ex2_sample_level_

ExtraRotSample	ex3_sample_level_

ExtraRotSample	ex4_sample_level_

ExtraRotSample	ex1aro_sample_level_

ExtraRotSample	ex2aro_sample_level_

ExtraRotSample	ex1aro_exposed_sample_level_

ExtraRotSample	ex2aro_exposed_sample_level_

ExtraRotSample	exdna_sample_level_

Size	extrachi_cutoff_

bool	operate_on_ex1_

bool	operate_on_ex2_

bool	operate_on_ex3_

bool	operate_on_ex4_

rotamer_set::RotamerOperations	rotamer_operations_

rotamer_set::RotSetOperationList	rotsetops_

std::vector< std::string >	mode_tokens_

rna::RNA_ResidueLevelTaskOP	rna_task_

Additional Inherited Members
Public Types inherited from core::pack::task::ResidueLevelTask
typedef std::list < chemical::ResidueTypeCOP >	ResidueTypeCOPList

typedef std::list < chemical::ResidueTypeCOP > ::iterator	ResidueTypeCOPListIter

typedef std::list < chemical::ResidueTypeCOP > ::const_iterator	ResidueTypeCOPListConstIter

Detailed Description

Residue-level task class; contained within PackerTask.

Constructor & Destructor Documentation

core::pack::task::ResidueLevelTask_::ResidueLevelTask_ ( conformation::Residue const & original_residue )

constructor; requires a Residue object

ResidueLevelTask constructor has following defaults: all ex set to false with zero sample level position is packable and designable to any of the canonical aa's, with variant matching (for termini, etc) current rotamer is not included for packer. bump check is deactivated by default.

References core::conformation::Residue::aa(), core::chemical::aa_unk, allowed_residue_types_, being_packed(), chemical, determine_if_designing(), determine_if_repacking(), core::sequence::end, core::chemical::is_canonical_D_aa(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::chemical::ResidueType::nonadduct_variants_match(), core::chemical::num_canonical_aas, core::conformation::Residue::residue_type_set(), rna_task_, runtime_assert, type, and core::conformation::Residue::type().

core::pack::task::ResidueLevelTask_::ResidueLevelTask_ ( )

core::pack::task::ResidueLevelTask_::~ResidueLevelTask_ ( )

virtual

dtor

Member Function Documentation

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

virtual

Implements core::pack::task::ResidueLevelTask.

References behaviors_.

bool core::pack::task::ResidueLevelTask_::adducts ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References adducts_.

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

virtual

explicitly allow a canonical AA

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, and original_residue_type_.

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

virtual

explicitly allow a NCAA

expand (or) the list of available aa's for non-cannonicals looking for ResidueTypes that share the input "interchangeability_group" id

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, core::chemical::ResidueTypeSet::interchangeability_group_map(), mode_tokens_, core::chemical::num_canonical_aas, and original_residue_type_.

Referenced by allow_noncanonical_aa().

void core::pack::task::ResidueLevelTask_::allow_noncanonical_aa ( std::string const & interchangeability_group )

virtual

explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_

Calls the overloaded allow_noncanonical_aas method using the same ResidueTypeSet as original_residue_type_

Implements core::pack::task::ResidueLevelTask.

References allow_noncanonical_aa(), and original_residue_type_.

void core::pack::task::ResidueLevelTask_::allow_noncanonical_aa ( chemical::AA aa )

virtual

explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_

Calls the overloaded allow_noncanonical_aas method using the same ResidueTypeSet as original_residue_type_ taking as the interchangeability group what is returned by the "name_from_aa" function.

Implements core::pack::task::ResidueLevelTask.

References allow_noncanonical_aa(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, and core::pack::task::T.

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

virtual

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_.

ResidueLevelTask::ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask_::allowed_residue_types_begin ( ) const

virtual

returns iterator to beginning of allowed residue types list (traversal only)

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_.

Referenced by print_allowed_types().

ResidueLevelTask::ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask_::allowed_residue_types_end ( ) const

virtual

returns iterator to end of allowed residue types list (traversal only)

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_.

Referenced by print_allowed_types().

void core::pack::task::ResidueLevelTask_::and_extrachi_cutoff ( Size num_neighbors_to_be_called_buried )

virtual

lower extrachi_cutoff to given value; do nothing if not a decrease

and operation – min – move only toward a lower cutoff for neighbors w/i 10A that qualify a residue to be considered buried.

Implements core::pack::task::ResidueLevelTask.

References extrachi_cutoff_.

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::append_rotamer_operation ( rotamer_set::RotamerOperationOP rotop )

virtual

Implements core::pack::task::ResidueLevelTask.

References rotamer_operations_.

void core::pack::task::ResidueLevelTask_::append_rotamerset_operation ( rotamer_set::RotamerSetOperationOP rotsetop )

virtual

Implements core::pack::task::ResidueLevelTask.

References rotsetops_.

bool core::pack::task::ResidueLevelTask_::being_designed ( ) const

virtual

is this residue up for design (variable sequence)?

Implements core::pack::task::ResidueLevelTask.

References designing_.

bool core::pack::task::ResidueLevelTask_::being_packed ( ) const

virtual

is this residue modififable at all by the packer?

Implements core::pack::task::ResidueLevelTask.

References repacking_.

Referenced by ResidueLevelTask_().

std::string core::pack::task::ResidueLevelTask_::command_string ( ) const

virtual

create a string the resfile format of all the commands applied to this residue level task

Implements core::pack::task::ResidueLevelTask.

References ex1, ex2, ex3, ex4, core::pack::task::PackerTask_::include_current(), and core::pack::task::PackerTask_::target_type().

void core::pack::task::ResidueLevelTask_::determine_if_designing ( )

private

private: bookkeeping for whether sequence can change

References allowed_residue_types_, design_disabled_, designing_, disabled_, original_residue_type_, and runtime_assert.

Referenced by allow_aa(), allow_noncanonical_aa(), disallow_noncanonical_aas(), do_restrict_absent_canonical_aas(), or_adducts(), prevent_repacking(), ResidueLevelTask_(), restrict_absent_nas(), restrict_nonnative_canonical_aas(), restrict_to_repacking(), update_commutative(), update_intersection(), and update_union().

void core::pack::task::ResidueLevelTask_::determine_if_repacking ( )

private

private: bookkeeping for whether rotamer can change

References allowed_residue_types_, and repacking_.

Referenced by allow_aa(), allow_noncanonical_aa(), disallow_noncanonical_aas(), do_restrict_absent_canonical_aas(), or_adducts(), prevent_repacking(), ResidueLevelTask_(), restrict_absent_nas(), restrict_nonnative_canonical_aas(), restrict_to_repacking(), update_commutative(), update_intersection(), and update_union().

void core::pack::task::ResidueLevelTask_::disallow_noncanonical_aas ( )

virtual

expliciitly disallow all NCAAs

expand (or) the list of available aa's for non-cannonicals looking for ResidueTypes that share the input "interchangeability_group" id

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), mode_tokens_, and core::chemical::num_canonical_aas.

void core::pack::task::ResidueLevelTask_::do_restrict_absent_canonical_aas ( utility::vector1< bool > const & allowed_aas )

private

References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), core::chemical::num_canonical_aas, and runtime_assert.

Referenced by restrict_absent_canonical_aas().

bool core::pack::task::ResidueLevelTask_::ex1 ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex1_.

Referenced by or_ex1().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex1_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex1_sample_level_.

Referenced by or_ex1_sample_level().

bool core::pack::task::ResidueLevelTask_::ex1aro ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex1aro_.

Referenced by or_ex1aro().

bool core::pack::task::ResidueLevelTask_::ex1aro_exposed ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex1aro_exposed_.

Referenced by or_ex1aro_exposed().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_exposed_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex1aro_exposed_sample_level_.

Referenced by or_ex1aro_exposed_sample_level().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex1aro_sample_level_.

Referenced by or_ex1aro_sample_level().

bool core::pack::task::ResidueLevelTask_::ex2 ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex2_.

Referenced by or_ex2().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex2_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex2_sample_level_.

Referenced by or_ex2_sample_level().

bool core::pack::task::ResidueLevelTask_::ex2aro ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex2aro_.

Referenced by or_ex2aro().

bool core::pack::task::ResidueLevelTask_::ex2aro_exposed ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex2aro_exposed_.

Referenced by or_ex2aro_exposed().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_exposed_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex2aro_exposed_sample_level_.

Referenced by or_ex2aro_exposed_sample_level().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex2aro_sample_level_.

Referenced by or_ex2aro_sample_level().

bool core::pack::task::ResidueLevelTask_::ex3 ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex3_.

Referenced by or_ex3().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex3_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex3_sample_level_.

Referenced by or_ex3_sample_level().

bool core::pack::task::ResidueLevelTask_::ex4 ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex4_.

Referenced by or_ex4().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex4_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References ex4_sample_level_.

Referenced by or_ex4_sample_level().

ExtraRotSample core::pack::task::ResidueLevelTask_::exdna_sample_level ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References exdna_sample_level_.

Referenced by or_exdna_sample_level().

Size core::pack::task::ResidueLevelTask_::extrachi_cutoff ( ) const

virtual

get function for extrachi_cutoff

Implements core::pack::task::ResidueLevelTask.

References extrachi_cutoff_.

ExtraRotSample core::pack::task::ResidueLevelTask_::extrachi_sample_level	(	bool	buried,
		int	chi,
		chemical::ResidueTypeCOP	concrete_residue
	)		const

virtual

returns the extra chi sampling level

Implements core::pack::task::ResidueLevelTask.

References ex1_sample_level_, ex1aro_exposed_sample_level_, ex1aro_sample_level_, ex2_sample_level_, ex2aro_exposed_sample_level_, ex2aro_sample_level_, ex3_sample_level_, ex4_sample_level_, exdna_sample_level_, core::pack::task::NO_EXTRA_CHI_SAMPLES, and runtime_assert.

bool core::pack::task::ResidueLevelTask_::fix_his_tautomer ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References fix_his_tautomer_.

bool core::pack::task::ResidueLevelTask_::flip_HNQ ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References flip_HNQ_.

std::string core::pack::task::ResidueLevelTask_::get_ex_flags	(	Size	chiid,
		Size const	exaro_sample_level,
		Size const	ex_sample_level
	)		const

private

private: return the EX command for the packer task

chemical::AA const & core::pack::task::ResidueLevelTask_::get_original_residue ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References original_residue_type_.

chemical::ResidueTypeSet const & core::pack::task::ResidueLevelTask_::get_original_residue_set ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References original_residue_type_.

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

virtual

Implements core::pack::task::ResidueLevelTask.

References behaviors_.

bool core::pack::task::ResidueLevelTask_::has_behavior ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References behaviors_.

bool core::pack::task::ResidueLevelTask_::include_current ( ) const

virtual

is the pre-existing rotamer specifically allowed while packing?

Implements core::pack::task::ResidueLevelTask.

References include_current_.

Referenced by or_include_current().

bool core::pack::task::ResidueLevelTask_::include_virtual_side_chain ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References include_virtual_side_chain_.

void core::pack::task::ResidueLevelTask_::initialize_extra_rotamer_flags_from_command_line ( )

virtual

Initialize only the extra rotamer building flags from the command line; invoked by intialize_from_command_line();.

Implements core::pack::task::ResidueLevelTask.

Referenced by initialize_from_command_line().

void core::pack::task::ResidueLevelTask_::initialize_from_command_line ( )

virtual

initialize options from command line flags

Implements core::pack::task::ResidueLevelTask.

References initialize_extra_rotamer_flags_from_command_line(), option, or_include_current(), or_preserve_c_beta(), prevent_repacking(), use_input_sc, and user.

bool core::pack::task::ResidueLevelTask_::is_original_type ( chemical::ResidueTypeCOP type ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References core::chemical::aa_his, core::chemical::aa_unk, fix_his_tautomer_, and original_residue_type_.

Referenced by restrict_nonnative_canonical_aas(), and restrict_to_repacking().

rna::RNA_ResidueLevelTask & core::pack::task::ResidueLevelTask_::nonconst_rna_task ( )

privatevirtual

Implements core::pack::task::ResidueLevelTask.

References rna_task_.

bool core::pack::task::ResidueLevelTask_::operate_on_ex1 ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References operate_on_ex1_.

bool core::pack::task::ResidueLevelTask_::operate_on_ex2 ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References operate_on_ex2_.

bool core::pack::task::ResidueLevelTask_::operate_on_ex3 ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References operate_on_ex3_.

bool core::pack::task::ResidueLevelTask_::operate_on_ex4 ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References operate_on_ex4_.

bool core::pack::task::ResidueLevelTask_::optimize_h ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References optimize_H_mode_.

void core::pack::task::ResidueLevelTask_::or_adducts ( bool setting )

virtual

include adducts at this residue

Implements core::pack::task::ResidueLevelTask.

References core::chemical::ADDUCT_VARIANT, adducts_, allowed_residue_types_, determine_if_designing(), and determine_if_repacking().

void core::pack::task::ResidueLevelTask_::or_ex1 ( bool ex1 )

virtual

activate ex1 when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex1(), ex1_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1_sample_level ( ExtraRotSample ex1_sample_level )

virtual

increase ex1 sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex1_sample_level(), ex1_sample_level_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1aro ( bool ex1aro )

virtual

activate ex1 for aromatics when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex1aro(), ex1aro_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1aro_exposed ( bool ex1aro_exposed )

virtual

activate ex1 for exposed aromatics when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex1aro_exposed(), ex1aro_exposed_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1aro_exposed_sample_level ( ExtraRotSample ex1aro_exposed_sample_level )

virtual

increase ex1aro_exposed sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex1aro_exposed_sample_level(), ex1aro_exposed_sample_level_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1aro_sample_level ( ExtraRotSample ex1aro_sample_level )

virtual

increase ex1aro sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex1aro_sample_level(), ex1aro_sample_level_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2 ( bool ex2 )

virtual

activate ex2 when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex2(), ex2_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2_sample_level ( ExtraRotSample ex2_sample_level )

virtual

increase ex2 sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex2_sample_level(), ex2_sample_level_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2aro ( bool ex2aro_only )

virtual

activate ex2 for aromatics when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex2aro(), ex2aro_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2aro_exposed ( bool ex2aro_exposed )

virtual

activate ex2 for exposed aromatics when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex2aro_exposed(), ex2aro_exposed_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2aro_exposed_sample_level ( ExtraRotSample ex2aro_exposed_sample_level )

virtual

increase ex2aro_exposed sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex2aro_exposed_sample_level(), ex2aro_exposed_sample_level_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2aro_sample_level ( ExtraRotSample ex2aro_only_sample_level )

virtual

increase ex2aro sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex2aro_sample_level(), ex2aro_sample_level_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex3 ( bool ex3 )

virtual

activate ex3 when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex3(), ex3_, and refresh_ex3_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex3_sample_level ( ExtraRotSample ex3_sample_level )

virtual

increase ex3 sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex3_sample_level(), ex3_sample_level_, and refresh_ex3_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex4 ( bool ex4 )

virtual

activate ex4 when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex4(), ex4_, and refresh_ex4_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex4_sample_level ( ExtraRotSample ex4_sample_level )

virtual

increase ex4 sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex4_sample_level(), ex4_sample_level_, and refresh_ex4_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_exdna_sample_level ( ExtraRotSample exdna_sample_level )

virtual

Implements core::pack::task::ResidueLevelTask.

References exdna_sample_level(), exdna_sample_level_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_fix_his_tautomer ( bool setting )

virtual

this function forces a fixed histidine tautomer by removing the alternate tautomer from the ResidueTypesCAPList. The fix_his_tautomer_ boolean is maintained for reference that this has been done, but the boolean is not the source of the effect.

Implements core::pack::task::ResidueLevelTask.

References core::chemical::aa_his, allowed_residue_types_, fix_his_tautomer_, and original_residue_type_.

void core::pack::task::ResidueLevelTask_::or_flip_HNQ ( bool setting )

virtual

Implements core::pack::task::ResidueLevelTask.

References flip_HNQ_, and or_optimize_h().

void core::pack::task::ResidueLevelTask_::or_include_current ( bool include_current )

virtual

include the pre-existing rotamer while packing

Implements core::pack::task::ResidueLevelTask.

References include_current(), and include_current_.

Referenced by initialize_from_command_line().

void core::pack::task::ResidueLevelTask_::or_include_virtual_side_chain ( bool setting )

virtual

this function samples a protein conformation with a virtualized side chain.

Implements core::pack::task::ResidueLevelTask.

References include_virtual_side_chain_.

void core::pack::task::ResidueLevelTask_::or_operate_on_ex1 ( bool operate )

virtual

Implements core::pack::task::ResidueLevelTask.

References operate_on_ex1_.

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_operate_on_ex2 ( bool operate )

virtual

Implements core::pack::task::ResidueLevelTask.

References operate_on_ex2_.

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_operate_on_ex3 ( bool operate )

virtual

Implements core::pack::task::ResidueLevelTask.

References operate_on_ex3_.

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_operate_on_ex4 ( bool operate )

virtual

Implements core::pack::task::ResidueLevelTask.

References operate_on_ex4_.

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_optimize_h ( bool setting )

virtual

Implements core::pack::task::ResidueLevelTask.

References optimize_H_mode_, and restrict_to_repacking().

Referenced by or_flip_HNQ().

void core::pack::task::ResidueLevelTask_::or_preserve_c_beta ( bool setting )

virtual

Implements core::pack::task::ResidueLevelTask.

References preserve_c_beta_.

Referenced by initialize_from_command_line().

bool core::pack::task::ResidueLevelTask_::preserve_c_beta ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References preserve_c_beta_.

void core::pack::task::ResidueLevelTask_::prevent_repacking ( )

virtual

remove all ResidueTypes from the list of allowed residue types, preventing repacking

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, and mode_tokens_.

Referenced by initialize_from_command_line().

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

virtual

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_begin(), allowed_residue_types_end(), and type.

void core::pack::task::ResidueLevelTask_::refresh_ex1_sample_levels ( )

private

private: bookkeeping for ex1

bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero (AS IT SHOULD!)

References ex1_, ex1_sample_level_, ex1aro_, ex1aro_exposed_, ex1aro_exposed_sample_level_, ex1aro_sample_level_, and core::pack::task::EX_ONE_STDDEV.

Referenced by or_ex1(), or_ex1_sample_level(), or_ex1aro(), or_ex1aro_exposed(), or_ex1aro_exposed_sample_level(), or_ex1aro_sample_level(), and or_exdna_sample_level().

void core::pack::task::ResidueLevelTask_::refresh_ex2_sample_levels ( )

private

private: bookkeeping for ex2

bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero

References ex2_, ex2_sample_level_, ex2aro_, ex2aro_exposed_, ex2aro_exposed_sample_level_, ex2aro_sample_level_, and core::pack::task::EX_ONE_STDDEV.

Referenced by or_ex2(), or_ex2_sample_level(), or_ex2aro(), or_ex2aro_exposed(), or_ex2aro_exposed_sample_level(), and or_ex2aro_sample_level().

void core::pack::task::ResidueLevelTask_::refresh_ex3_sample_levels ( )

private

private: bookkeeping for ex3

bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero

References ex3_, ex3_sample_level_, and core::pack::task::EX_ONE_STDDEV.

Referenced by or_ex3(), and or_ex3_sample_level().

void core::pack::task::ResidueLevelTask_::refresh_ex4_sample_levels ( )

private

private: bookkeeping for ex4

bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero

References ex4_, ex4_sample_level_, and core::pack::task::EX_ONE_STDDEV.

Referenced by or_ex4(), and or_ex4_sample_level().

void core::pack::task::ResidueLevelTask_::restrict_absent_canonical_aas ( utility::vector1< bool > const & allowed_aas )

virtual

disables designing to residues not in the passed list

contract (and) the list of available aas for canonical aa's if an amino acid is not present (false) in the boolean vector, then do not allow it at this position boolean vector is based on the aa enum; see another example with PIKAA. The boolean vector is a 20-length vector in alphabetical order by one-letter code.

Implements core::pack::task::ResidueLevelTask.

References do_restrict_absent_canonical_aas(), mode_tokens_, and core::chemical::num_canonical_aas.

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

virtual

disables designing to residues not in the passed list–and specifies the resfile command that made this list

Implements core::pack::task::ResidueLevelTask.

References do_restrict_absent_canonical_aas(), and mode_tokens_.

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

virtual

disables designing to nucleic acid residues not in the passed list

contract (and) the list of available nas for canonical na's if a nucleic acid is not present in the vector, then do not allow it at this position

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), mode_tokens_, and core::chemical::name_from_aa().

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

virtual

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), is_original_type(), core::chemical::num_canonical_aas, and runtime_assert.

void core::pack::task::ResidueLevelTask_::restrict_to_repacking ( )

virtual

only let this residue repack – prevent redesign

removes all residues from the allowed residue types list, except the one that matches the original residue; this means only rotameric and not sequence changes are allowed if the original residue type has been disabled elsewhere, this function will prevent repacking at that residue.

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), is_original_type(), and mode_tokens_.

Referenced by or_optimize_h().

rna::RNA_ResidueLevelTask const & core::pack::task::ResidueLevelTask_::rna_task ( ) const

privatevirtual

Implements core::pack::task::ResidueLevelTask.

References rna_task_.

rotamer_set::RotamerOperations const & core::pack::task::ResidueLevelTask_::rotamer_operations ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References rotamer_operations_.

rotamer_set::RotSetOperationListIterator core::pack::task::ResidueLevelTask_::rotamer_set_operation_begin ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References rotsetops_.

rotamer_set::RotSetOperationListIterator core::pack::task::ResidueLevelTask_::rotamer_set_operation_end ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References rotsetops_.

void core::pack::task::ResidueLevelTask_::sample_proton_chi ( bool setting )

virtual

sample proton chi.

Implements core::pack::task::ResidueLevelTask.

References sample_proton_chi_.

bool core::pack::task::ResidueLevelTask_::sample_proton_chi ( ) const

virtual

sample proton chi.

Implements core::pack::task::ResidueLevelTask.

References sample_proton_chi_.

void core::pack::task::ResidueLevelTask_::target_type ( chemical::ResidueTypeCOP type )

virtual

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, core::pack::task::T, target_residue_type_, and utility_exit.

void core::pack::task::ResidueLevelTask_::target_type ( chemical::AA aa )

virtual

Implements core::pack::task::ResidueLevelTask.

References original_residue_type_, and target_type().

void core::pack::task::ResidueLevelTask_::target_type ( std::string name )

virtual

Implements core::pack::task::ResidueLevelTask.

References original_residue_type_, and target_type().

chemical::ResidueTypeCOP core::pack::task::ResidueLevelTask_::target_type ( ) const

virtual

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, and target_residue_type_.

Referenced by target_type().

std::string core::pack::task::ResidueLevelTask_::task_mode ( ) const

private

private: return the task mode that can be used to recreate the task. If the residue level task was made with POLAR it should return the string "POLAR".

void core::pack::task::ResidueLevelTask_::update_commutative ( ResidueLevelTask const & res_task_in )

virtual

void core::pack::task::ResidueLevelTask_::update_intersection ( ResidueLevelTask const & res_task_in )

virtual

void core::pack::task::ResidueLevelTask_::update_union ( ResidueLevelTask const & res_task_in )

virtual

Member Data Documentation

bool core::pack::task::ResidueLevelTask_::adducts_

private

include adducts at this residue

Referenced by adducts(), or_adducts(), update_commutative(), update_intersection(), and update_union().

ResidueTypeCOPList core::pack::task::ResidueLevelTask_::allowed_residue_types_

private

std::list of ResidueTypeCOP objects - these are only residue types allowed at position

Referenced by allow_aa(), allow_noncanonical_aa(), allowed_residue_types(), allowed_residue_types_begin(), allowed_residue_types_end(), determine_if_designing(), determine_if_repacking(), disallow_noncanonical_aas(), do_restrict_absent_canonical_aas(), or_adducts(), or_fix_his_tautomer(), prevent_repacking(), ResidueLevelTask_(), restrict_absent_nas(), restrict_nonnative_canonical_aas(), restrict_to_repacking(), target_type(), update_commutative(), update_intersection(), and update_union().

utility::vector1< std::string > core::pack::task::ResidueLevelTask_::behaviors_

private

here we store any flagged protocol-level behaviors for this residue

Referenced by add_behavior(), has_behavior(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::design_disabled_

private

if this is true, this residue will only be allowed to repack; ResidueTypes that do not match the original_residue_type cannot be added. Design disabling takes precedence over SOMETHING, ANDREW TELL ME WHAT IT IS

Referenced by allow_aa(), allow_noncanonical_aa(), determine_if_designing(), prevent_repacking(), restrict_to_repacking(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::designing_

private

can the sequence change? true implies repacking_ is true as well

Referenced by being_designed(), determine_if_designing(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::disabled_

private

if this is true, this residue will be treated as part of the background. a disabling takes precedence over any ResidueType additions.

Referenced by allow_aa(), allow_noncanonical_aa(), determine_if_designing(), prevent_repacking(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex1_

private

Referenced by ex1(), or_ex1(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex1_sample_level_

private

Referenced by ex1_sample_level(), extrachi_sample_level(), or_ex1_sample_level(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex1aro_

private

Referenced by ex1aro(), or_ex1aro(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex1aro_exposed_

private

Referenced by ex1aro_exposed(), or_ex1aro_exposed(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_exposed_sample_level_

private

Referenced by ex1aro_exposed_sample_level(), extrachi_sample_level(), or_ex1aro_exposed_sample_level(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_sample_level_

private

Referenced by ex1aro_sample_level(), extrachi_sample_level(), or_ex1aro_sample_level(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex2_

private

Referenced by ex2(), or_ex2(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex2_sample_level_

private

Referenced by ex2_sample_level(), extrachi_sample_level(), or_ex2_sample_level(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex2aro_

private

Referenced by ex2aro(), or_ex2aro(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex2aro_exposed_

private

Referenced by ex2aro_exposed(), or_ex2aro_exposed(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_exposed_sample_level_

private

Referenced by ex2aro_exposed_sample_level(), extrachi_sample_level(), or_ex2aro_exposed_sample_level(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_sample_level_

private

Referenced by ex2aro_sample_level(), extrachi_sample_level(), or_ex2aro_sample_level(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex3_

private

Referenced by ex3(), or_ex3(), refresh_ex3_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex3_sample_level_

private

Referenced by ex3_sample_level(), extrachi_sample_level(), or_ex3_sample_level(), refresh_ex3_sample_levels(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex4_

private

Referenced by ex4(), or_ex4(), refresh_ex4_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex4_sample_level_

private

Referenced by ex4_sample_level(), extrachi_sample_level(), or_ex4_sample_level(), refresh_ex4_sample_levels(), update_commutative(), update_intersection(), and update_union().

ExtraRotSample core::pack::task::ResidueLevelTask_::exdna_sample_level_

private

Referenced by exdna_sample_level(), extrachi_sample_level(), or_exdna_sample_level(), update_commutative(), update_intersection(), and update_union().

Size core::pack::task::ResidueLevelTask_::extrachi_cutoff_

private

Referenced by and_extrachi_cutoff(), extrachi_cutoff(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::fix_his_tautomer_

private

has this histidine tautomer been fixed? This value is kept for bookkeeping; the tautomer's fixation is effected by removing the other tautomer from the ResidueTypeCOPList.

Referenced by fix_his_tautomer(), is_original_type(), or_fix_his_tautomer(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::flip_HNQ_

private

are we also considering heavy atom rearrangement for the crystallographically symmetric seeming residues: histadine, asparagine and glutamine? Implies optimize_H_mode_

Referenced by flip_HNQ(), or_flip_HNQ(), update_commutative(), update_intersection(), and update_union().