Residue-level task class. More...

#include <ResidueLevelTask_.hh>

Inheritance diagram for core::pack::task::ResidueLevelTask_:

Public Member Functions
	ResidueLevelTask_ (conformation::Residue const &original_residue, core::pose::Pose const &pose, core::pack::palette::PackerPaletteCOP packer_palette_in=utility::pointer::make_shared< core::pack::palette::DefaultPackerPalette >())
	constructor; requires a Residue object and a PackerPalette object. More...

	ResidueLevelTask_ ()

	~ResidueLevelTask_ () override
	dtor More...

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

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

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

void	initialize_from_options (utility::options::OptionCollection const &options) override

void	initialize_extra_rotamer_flags_from_options (utility::options::OptionCollection const &options) override

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

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

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

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

bool	has_behavior () const override

void	target_type (chemical::ResidueTypeCOP type) override

void	target_type (chemical::AA aa) override

void	target_type (std::string name) override

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

bool	adducts () const override

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	or_operate_on_ex1 (bool operate) override

void	or_operate_on_ex2 (bool operate) override

void	or_operate_on_ex3 (bool operate) override

void	or_operate_on_ex4 (bool operate) override

void	or_exdna_sample_level (ExtraRotSample exdna_sample_level) override

void	or_optimize_h (bool setting) override

bool	optimize_h () const override

void	or_preserve_c_beta (bool setting) override

bool	preserve_c_beta () const override

void	or_flip_HNQ (bool setting) override

bool	flip_HNQ () const override

void	or_fix_his_tautomer (bool setting) override

bool	fix_his_tautomer () const override

void	or_include_virtual_side_chain (bool setting) override

bool	include_virtual_side_chain () const override

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

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

bool	ex1 () const override

bool	ex2 () const override

bool	ex3 () const override

bool	ex4 () const override

ExtraRotSample	ex1_sample_level () const override

ExtraRotSample	ex2_sample_level () const override

ExtraRotSample	ex3_sample_level () const override

ExtraRotSample	ex4_sample_level () const override

bool	ex1aro () const override

bool	ex2aro () const override

bool	ex1aro_exposed () const override

bool	ex2aro_exposed () const override

ExtraRotSample	ex1aro_sample_level () const override

ExtraRotSample	ex2aro_sample_level () const override

ExtraRotSample	ex1aro_exposed_sample_level () const override

ExtraRotSample	ex2aro_exposed_sample_level () const override

ExtraRotSample	exdna_sample_level () const override

bool	operate_on_ex1 () const override

bool	operate_on_ex2 () const override

bool	operate_on_ex3 () const override

bool	operate_on_ex4 () const override

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

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

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

void	restrict_restypes (utility::vector1< std::string > const &basenames_to_keep) override
	Restrict residue types. More...

void	disable_restypes (utility::vector1< std::string > const &basenames_to_disable) override
	Disable residue types. More...

void	restrict_to_restypes_with_at_least_one_property (utility::vector1< core::chemical::ResidueProperty > const &properties) override
	Given a list of residue properties, eliminate any residue type that does not have at least one of the properties in the list. More...

void	restrict_to_restypes_with_all_properties (utility::vector1< core::chemical::ResidueProperty > const &properties) override
	Given a list of residue properties, eliminate any residue type that does not have ALL of the properties in the list. More...

void	disable_restypes_with_at_least_one_property (utility::vector1< core::chemical::ResidueProperty > const &properties) override
	Given a list of residue properties, eliminate any residue type that has any of the properties in the list. More...

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

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

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

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

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

bool	is_original_type (chemical::ResidueTypeCOP type) const override

chemical::ResidueTypeSetCOP	get_original_residue_set () const override

chemical::AA const &	get_original_residue () const override

ResidueTypeCOPList const &	allowed_residue_types () const override

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

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

chemical::ResidueTypeCOP	target_type () const override

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

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

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

rotamer_set::RotamerOperations const &	rotamer_operations () const override

void	append_rotamer_operation (rotamer_set::RotamerOperationOP rotop) override

rotamer_set::RotSetOperationListIterator	rotamer_set_operation_begin () const override

rotamer_set::RotSetOperationListIterator	rotamer_set_operation_end () const override

void	append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop) override

std::string	command_string () const override
	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 override

rna::RNA_ResidueLevelTask &	nonconst_rna_task () override

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

Private Attributes
bool	include_current_ = false

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

bool	adducts_ = true
	include adducts at this residue More...

chemical::ResidueTypeSetCOP	original_residue_type_set_
	What ResidueTypeSet does this set of allowed residues come from? More...

ResidueTypeCOPList	allowed_residue_types_

chemical::ResidueTypeCOP	original_residue_type_

chemical::ResidueTypeCOP	target_residue_type_ = nullptr

bool	designing_

bool	repacking_ = true

bool	optimize_H_mode_ = false

bool	preserve_c_beta_ = false

bool	flip_HNQ_ = false

bool	fix_his_tautomer_ = false

bool	include_virtual_side_chain_ = false

bool	disabled_ = false

bool	design_disabled_ = false

bool	sample_proton_chi_ = true

bool	ex1_ = false

bool	ex2_ = false

bool	ex3_ = false

bool	ex4_ = false

bool	ex1aro_ = false

bool	ex2aro_ = false

bool	ex1aro_exposed_ = false

bool	ex2aro_exposed_ = false

ExtraRotSample	ex1_sample_level_ = NO_EXTRA_CHI_SAMPLES

ExtraRotSample	ex2_sample_level_ = NO_EXTRA_CHI_SAMPLES

ExtraRotSample	ex3_sample_level_ = NO_EXTRA_CHI_SAMPLES

ExtraRotSample	ex4_sample_level_ = NO_EXTRA_CHI_SAMPLES

ExtraRotSample	ex1aro_sample_level_ = NO_EXTRA_CHI_SAMPLES

ExtraRotSample	ex2aro_sample_level_ = NO_EXTRA_CHI_SAMPLES

ExtraRotSample	ex1aro_exposed_sample_level_ = NO_EXTRA_CHI_SAMPLES

ExtraRotSample	ex2aro_exposed_sample_level_ = NO_EXTRA_CHI_SAMPLES

ExtraRotSample	exdna_sample_level_ = NO_EXTRA_CHI_SAMPLES

Size	extrachi_cutoff_ = EXTRACHI_CUTOFF_LIMIT

bool	operate_on_ex1_ = false

bool	operate_on_ex2_ = false

bool	operate_on_ex3_ = false

bool	operate_on_ex4_ = false

rotamer_set::RotamerOperations	rotamer_operations_

rotamer_set::RotSetOperationList	rotsetops_

std::vector< std::string >	mode_tokens_

rna::RNA_ResidueLevelTaskOP	rna_task_ = nullptr

core::pack::palette::PackerPaletteCOP	packer_palette_
	The PackerPalette, which is responsible for initializing the allowed_residue_types_ vector. More...

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

Static Public Member Functions inherited from core::pack::task::ResidueLevelTask
static void	list_options_read (utility::options::OptionKeyList &read_options)

Detailed Description

Residue-level task class.

Constructor & Destructor Documentation

core::pack::task::ResidueLevelTask_::ResidueLevelTask_	(	conformation::Residue const &	original_residue,
		core::pose::Pose const &	pose,
		core::pack::palette::PackerPaletteCOP	packer_palette_in = `utility::pointer::make_shared< core::pack::palette::DefaultPackerPalette >()`
	)

constructor; requires a Residue object and a PackerPalette 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. Constructs a DefaultPackerPalette if not provided with an alternative.

References allowed_residue_types_, being_packed(), determine_if_designing(), determine_if_repacking(), core::conformation::Residue::is_RNA(), original_residue_type_set_, packer_palette_, and rna_task_.

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

default

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

overridedefault

dtor

Member Function Documentation

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

overridevirtual

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

References behaviors_.

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

overridevirtual

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

References adducts_.

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

overridevirtual

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

References allowed_residue_types_.

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

overridevirtual

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

overridevirtual

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 )

overridevirtual

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_options().

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

overridevirtual

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

References rotamer_operations_.

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

overridevirtual

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

References rotsetops_.

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

overridevirtual

is this residue up for design (variable sequence)?

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

References designing_.

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

overridevirtual

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

overridevirtual

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

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

References 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_, and original_residue_type_.

Referenced by 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 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_::disable_restypes ( utility::vector1< std::string > const & basenames_to_disable )

overridevirtual

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).

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

References allowed_residue_types_.

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

overridevirtual

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).

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

References allowed_residue_types_.

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(), and core::chemical::num_canonical_aas.

Referenced by restrict_absent_canonical_aas().

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

overridevirtual

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

References ex1_.

Referenced by or_ex1().

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

overridevirtual

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

References ex1_sample_level_.

Referenced by or_ex1_sample_level().

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

overridevirtual

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

References ex1aro_.

Referenced by or_ex1aro().

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

overridevirtual

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

References ex1aro_exposed_.

Referenced by or_ex1aro_exposed().

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

overridevirtual

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

overridevirtual

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

References ex1aro_sample_level_.

Referenced by or_ex1aro_sample_level().

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

overridevirtual

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

References ex2_.

Referenced by or_ex2().

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

overridevirtual

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

References ex2_sample_level_.

Referenced by or_ex2_sample_level().

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

overridevirtual

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

References ex2aro_.

Referenced by or_ex2aro().

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

overridevirtual

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

References ex2aro_exposed_.

Referenced by or_ex2aro_exposed().

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

overridevirtual

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

overridevirtual

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

References ex2aro_sample_level_.

Referenced by or_ex2aro_sample_level().

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

overridevirtual

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

References ex3_.

Referenced by or_ex3().

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

overridevirtual

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

References ex3_sample_level_.

Referenced by or_ex3_sample_level().

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

overridevirtual

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

References ex4_.

Referenced by or_ex4().

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

overridevirtual

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

References ex4_sample_level_.

Referenced by or_ex4_sample_level().

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

overridevirtual

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

References exdna_sample_level_.

Referenced by or_exdna_sample_level().

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

overridevirtual

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::ResidueType const &	concrete_residue
	)		const

overridevirtual

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::chemical::ResidueType::is_aromatic(), core::chemical::ResidueTypeBase::is_DNA(), and core::pack::task::NO_EXTRA_CHI_SAMPLES.

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

overridevirtual

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

References fix_his_tautomer_.

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

overridevirtual

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

overridevirtual

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

References original_residue_type_.

chemical::ResidueTypeSetCOP core::pack::task::ResidueLevelTask_::get_original_residue_set ( ) const

overridevirtual

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

References original_residue_type_set_.

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

overridevirtual

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

References behaviors_.

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

overridevirtual

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

References behaviors_.

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

overridevirtual

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

overridevirtual

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

References include_virtual_side_chain_.

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

overridevirtual

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

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

References initialize_extra_rotamer_flags_from_options().

void core::pack::task::ResidueLevelTask_::initialize_extra_rotamer_flags_from_options ( utility::options::OptionCollection const & options )

overridevirtual

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

overridevirtual

initialize options from command line flags

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

References initialize_from_options().

void core::pack::task::ResidueLevelTask_::initialize_from_options ( utility::options::OptionCollection const & options )

overridevirtual

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

References initialize_extra_rotamer_flags_from_options(), or_include_current(), or_preserve_c_beta(), and prevent_repacking().

Referenced by initialize_from_command_line().

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

overridevirtual

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

References core::chemical::aa_his, 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 ( )

overrideprivatevirtual

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

References rna_task_.

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

overridevirtual

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

References operate_on_ex1_.

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

overridevirtual

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

References operate_on_ex2_.

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

overridevirtual

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

References operate_on_ex3_.

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

overridevirtual

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

References operate_on_ex4_.

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

overridevirtual

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

References optimize_H_mode_.

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

overridevirtual

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 )

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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_options().

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

overridevirtual

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

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

Referenced by initialize_extra_rotamer_flags_from_options().

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

overridevirtual

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 )

overridevirtual

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

References flip_HNQ_, and or_optimize_h().

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

overridevirtual

include the pre-existing rotamer while packing

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

References include_current(), and include_current_.

Referenced by initialize_from_options().

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

overridevirtual

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 )

overridevirtual

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

References operate_on_ex1_.

Referenced by initialize_extra_rotamer_flags_from_options().

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

overridevirtual

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

References operate_on_ex2_.

Referenced by initialize_extra_rotamer_flags_from_options().

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

overridevirtual

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

References operate_on_ex3_.

Referenced by initialize_extra_rotamer_flags_from_options().

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

overridevirtual

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

References operate_on_ex4_.

Referenced by initialize_extra_rotamer_flags_from_options().

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

overridevirtual

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 )

overridevirtual

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

References preserve_c_beta_.

Referenced by initialize_from_options().

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

overridevirtual

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

References preserve_c_beta_.

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

overridevirtual

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_options().

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

overridevirtual

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

References allowed_residue_types_begin(), and allowed_residue_types_end().

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 )

overridevirtual

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
	)

overridevirtual

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 )

overridevirtual

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 )

overridevirtual

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

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

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

overridevirtual

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).

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

References allowed_residue_types_.

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

overridevirtual

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 protocols::relax::LocalRelax::apply(), and or_optimize_h().

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

overridevirtual

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).

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

References allowed_residue_types_.

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

overridevirtual

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).

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

References allowed_residue_types_.

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

overrideprivatevirtual

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

References rna_task_.

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

overridevirtual

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

References rotamer_operations_.

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

overridevirtual

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

References rotsetops_.

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

overridevirtual

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

References rotsetops_.

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

overridevirtual

sample proton chi.

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

References sample_proton_chi_.

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

overridevirtual

sample proton chi.

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

References sample_proton_chi_.

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

overridevirtual

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

References allowed_residue_types_, core::pack::task::T(), and target_residue_type_.

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

overridevirtual

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

References original_residue_type_set_, and target_type().

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

overridevirtual

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

References original_residue_type_set_, and target_type().

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

overridevirtual

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

References adducts_, allowed_residue_types_, behaviors_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, ex1_, ex1_sample_level_, ex1aro_, ex1aro_exposed_, ex1aro_exposed_sample_level_, ex1aro_sample_level_, ex2_, ex2_sample_level_, ex2aro_, ex2aro_exposed_, ex2aro_exposed_sample_level_, ex2aro_sample_level_, ex3_, ex3_sample_level_, ex4_, ex4_sample_level_, exdna_sample_level_, extrachi_cutoff_, fix_his_tautomer_, flip_HNQ_, include_current_, include_virtual_side_chain_, protocols::mean_field::max(), protocols::mean_field::min(), mode_tokens_, myend(), operate_on_ex1_, operate_on_ex2_, operate_on_ex3_, operate_on_ex4_, optimize_H_mode_, preserve_c_beta_, rotamer_operations_, rotsetops_, sample_proton_chi_, and target_residue_type_.

Referenced by protocols::simple_ddg::ddG::setup_solvated_task().

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_ = true

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 allowed_residue_types(), allowed_residue_types_begin(), allowed_residue_types_end(), determine_if_designing(), determine_if_repacking(), disable_restypes(), disable_restypes_with_at_least_one_property(), do_restrict_absent_canonical_aas(), or_adducts(), or_fix_his_tautomer(), prevent_repacking(), ResidueLevelTask_(), restrict_absent_nas(), restrict_nonnative_canonical_aas(), restrict_restypes(), restrict_to_repacking(), restrict_to_restypes_with_all_properties(), restrict_to_restypes_with_at_least_one_property(), 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_ = false

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 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_ = false

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 determine_if_designing(), prevent_repacking(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex1_ = false

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_ = NO_EXTRA_CHI_SAMPLES

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_ = false

private

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

bool core::pack::task::ResidueLevelTask_::ex1aro_exposed_ = false

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_ = NO_EXTRA_CHI_SAMPLES

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_ = NO_EXTRA_CHI_SAMPLES

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_ = false

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_ = NO_EXTRA_CHI_SAMPLES

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_ = false

private

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

bool core::pack::task::ResidueLevelTask_::ex2aro_exposed_ = false

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_ = NO_EXTRA_CHI_SAMPLES

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_ = NO_EXTRA_CHI_SAMPLES

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_ = false

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_ = NO_EXTRA_CHI_SAMPLES

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_ = false

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_ = NO_EXTRA_CHI_SAMPLES

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_ = NO_EXTRA_CHI_SAMPLES

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_ = EXTRACHI_CUTOFF_LIMIT

private

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

bool core::pack::task::ResidueLevelTask_::fix_his_tautomer_ = false

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_ = false

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().