the PackerTask controls what rotameric (including sequence) changes the packer is allowed to make More...

#include <PackerTask_.hh>

Inheritance diagram for core::pack::task::PackerTask_:

Public Member Functions
	PackerTask_ (core::Size const ig_threads_to_request=0)
	constructor; the PackerTask will always need a pose! More...

	PackerTask_ (pose::Pose const &pose, core::Size const ig_threads_to_request=0)
	Initialization constructor that needs a pose. A DefaultPackerPalette is automatically created using the ResidueTypeSet of the pose. More...

	PackerTask_ (pose::Pose const &pose, core::pack::palette::PackerPaletteCOP const &packer_palette, core::Size const ig_threads_to_request=0)
	Initialization constructor that needs a pose and a PackerPalette. More...

	~PackerTask_ () override
	dtor More...

PackerTaskOP	clone () const override
	copy method More...

void	check_threads () const
	Check that the number of threads to request is reasonable. More...

void	clean_residue_task (conformation::Residue const &original_residue, Size const seqpos, core::pose::Pose const &pose) override
	replace a given residue task with a brand new one NOTE: This should be the only way to break commutativity!!!! More...

Size	total_residue () const override
	number of residues in the input pose, for convienience (PackerTask does not handle variable length) More...

bool	pack_residue (int resid) const override
	get function: can this position have a rotamer change? More...

bool	being_packed (Size resid) const override
	alias for above More...

Size	num_to_be_packed () const override
	get function: how many positions can have rotamer changes? More...

bool	design_residue (int resid) const override
	get function: can this position have a sequence change? More...

bool	being_designed (Size resid) const override
	alias for above More...

bool	design_any () const override
	get function: can any positions have a sequence change? More...

void	set_bump_check (bool setting) override
	set function: bump_check is activated for pack-rotamers' screening of rotamers that collide with the background. Bump-check is not used during rotamer trials, since it is nearly as expensive as rotamer trials itself. Energy methods may opt in to the bump check process. The "standard" behavior is for bump-check to include only the fa_atr and fa_rep terms. More...

bool	bump_check () const override
	get function: has bump_check been requested? More...

void	and_max_rotbump_energy (Real setting) override
	Decrease the max_rotbump_energy threshold above which rotamers are rejected. More...

Real	max_rotbump_energy () const override
	get function: what is the energy threshold above which rotamers should be rejected More...

void	or_include_current (bool setting) override
	for all positions, turn on include_current if false, do nothing if already true More...

void	or_include_current (bool setting, Size resid) override
	for one position, turn on include_current if false, do nothing if already true More...

bool	include_current (Size resid) const override
	get function: what is include_current for this residue? More...

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

void	add_behavior (std::string const &behavior, Size resid) override

bool	has_behavior (std::string const &behavior, Size resid) const override

bool	has_behavior (Size resid) const override

virtual chemical::ResidueTypeCOP	target_type (Size resid) const
	return the targeted type (may be null pointer) More...

void	or_adducts (bool setting) override
	for all positions, disable adducts if false, do nothing if true More...

void	or_adducts (bool setting, Size resid) override
	for one position, disable adducts if false, do nothing if true More...

bool	adducts (Size resid) const override
	include adducts at this residue More...

void	or_optimize_h_mode (bool setting) override
	if setting == true, turns on optimize_H_mode for all residues More...

void	or_preserve_c_beta (bool setting) override
	if setting == true, preserves c-beta during rotamer building for all residues More...

void	or_flip_HNQ (bool setting) override
	if setting == true, turns on optimize_H_mode and flip_HNQ for all residues More...

void	or_fix_his_tautomer (utility::vector1< int > const &positions, bool setting) override
	if setting == true, fix his tautomer state for defined residues during repacking or optimizeH mode More...

void	or_linmem_ig (bool setting) override
	if setting == true, turns on linear-memory interaction graph usage More...

void	and_linmem_ig (bool setting) override
	if setting == false, turns off linear-memory interaction graph usage More...

bool	linmem_ig () const override
	returns the linear-memory interaction graph flag More...

void	decrease_linmem_ig_history_size (Size setting) override
	Set the linear memory interaction graph's recent history size. Default is 10. It can be set once to any value larger than 10, but any subsequent setting will only alter the size if it decreases it. More...

Size	linmem_ig_history_size () const override
	Return the linear memory interaction graph's recent history size. More...

void	or_precompute_ig (bool setting) override
	Explicitly request the O( N^2 ) precomputed graph. More...

bool	precompute_ig () const override

void	or_lazy_ig (bool setting) override
	if setting == true, turns on lazy interaction graph usage NOTE: the linear memory interaction graph takes precedence over the LazyIG when the InteractionGraphFactory examines the PackerTask. More...

bool	lazy_ig () const override
	returns the lazy interaction interaction graph flag More...

void	or_double_lazy_ig (bool setting) override
	Activate the DoubleLazyInteractionGraph, which is particularly useful for multistate design, when memory and time are both limiting. Overriden by LinMemIG. More...

bool	double_lazy_ig () const override
	Returns the double-lazy interaction graph flag. More...

void	decrease_double_lazy_ig_memlimit (Size nbytes_for_rpes) override
	Set the memory limit, in bytes, for the storage that the DLIG should be allowed to spend on representing rotamer pair energies. The DLIG will start deallocating rotamer pair energy blocks if it exceeds this limit. This limit is occasionally breached by as much memory as is required to store a single amino-acid-pair submatrix block; the limit does not apply to the entirety of the packer or even the entirety of this interaction graph, merely to the amount of space for rotamer pair energies. Remember, rotamers are expensive, too! The default value of "0" signifies an unrestricted memory limit – 0 may not be set through this function. The value may increase once from 0 and then may only decrease from there. More...

Size	double_lazy_ig_memlimit () const override
	the memory limit, in bytes, for the double-lazy interaction graph. A value of 0 signifies an unrestricted limit. More...

void	or_multi_cool_annealer (bool setting) override
	if setting == true, turns on MultiCoolAnnealer – so long as rotamer couplings are not also turned on. More...

bool	multi_cool_annealer () const override
	use MultiCoolAnnealer? More...

void	increase_multi_cool_annealer_history_size (Size setting) override
	Increases the history size for the MultiCoolAnnealer if setting is larger than the existing setting. More...

Size	multi_cool_annealer_history_size () const override
	returns the requested size for the MultiCoolAnnealer More...

bool	smart_annealer () const override

std::string	smart_annealer_model () const override

core::Real	smart_annealer_cutoff () const override

bool	smart_annealer_pick_again () const override

bool	smart_annealer_disable_during_quench () const override

void	set_smart_annealer (bool setting) override

void	set_smart_annealer_model (std::string const &setting) override

void	set_smart_annealer_cutoff (core::Real setting) override

void	set_smart_annealer_pick_again (bool setting) override

void	set_smart_annealer_disable_during_quench (bool setting) override

void	show (std::ostream &out) const override

void	show () const override

void	show_residue_task (std::ostream &out, Size resid) const override

void	show_residue_task (Size resid) const override

void	show_all_residue_tasks (std::ostream &out) const override

void	show_all_residue_tasks () const override

bool	is_initialized () const override
	Has this PackerTask been initialized with a PackerPalette? More...

PackerTask &	initialize_from_command_line () override
	read command line options (but not resfile) to set the state of the PackerTask, NOT IN CONSTRUCTOR More...

PackerTask &	initialize_extra_rotamer_flags_from_command_line () override
	read only the command line options for extra rotamer building; More...

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

PackerTask &	initialize_extra_rotamer_flags_from_options (utility::options::OptionCollection const &options) override
	read only the command line options for extra rotamer building; More...

PackerTask &	restrict_to_residues (utility::vector1< bool > const &residues_allowed_to_be_packed) override
	turn off packing for residues passed false; can't turn on packing More...

PackerTask &	restrict_to_repacking () override
	turn off designing (sequence changing) all residues More...

ResidueLevelTask const &	residue_task (Size resid) const override
	const accessor for underlying ResidueLevelTask object More...

ResidueLevelTask &	nonconst_residue_task (Size resid) override
	nonconst access to underlying ResidueLevelTask object More...

utility::vector1< bool >	repacking_residues () const override

utility::vector1< bool >	designing_residues () const override

bool	keep_sequence_symmetry () const override

void	keep_sequence_symmetry (bool const setting) override
	Enables SequenceSymmetricAnnealer. More...

std::string	sequence_symmetric_uid_prefix () const override

void	sequence_symmetric_uid_prefix (std::string const &prefix) override
	Sets the prefix used when searching for symmetry defining residue selectors in the datacache. More...

bool	rotamer_couplings_exist () const override
	is there at RotamerCouplings object to worry about? (for DNA GC AT pairing, etc) More...

RotamerCouplingsCOP	rotamer_couplings () const override
	const accessor for the RotamerCouplings object More...

void	rotamer_couplings (RotamerCouplingsCOP setting) override
	setter for the RotamerCouplings object More...

bool	rotamer_links_exist () const override
	is there at RotamerLinks object to worry about? (for repeat linking More...

RotamerLinksCOP	rotamer_links () const override
	const accessor for the RotamerLinks object More...

void	rotamer_links (RotamerLinksCOP setting) override
	setter for the RotamerLinks object More...

IGEdgeReweightContainerCOP	IGEdgeReweights () const override
	accesor for residue residue weight map More...

IGEdgeReweightContainerOP	set_IGEdgeReweights () override

void	append_rotamer_operation (rotamer_set::RotamerOperationOP rotop) override

void	append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop) override

rotamer_set::RotSetsOperationListIterator	rotamer_sets_operation_begin () const override

rotamer_set::RotSetsOperationListIterator	rotamer_sets_operation_end () const override

void	append_rotamersets_operation (rotamer_set::RotamerSetsOperationOP rotsetsop) override

std::string	task_string (pose::Pose const &pose) const override

void	low_temp (Real const &low_temp) override

void	high_temp (Real const &high_temp) override

void	disallow_quench (bool const &disallow_quench) override

Real	low_temp () const override

Real	high_temp () const override

bool	disallow_quench () const override

void	remap_residue_level_tasks (core::id::SequenceMappingCOP seqmap, core::pose::Pose const &pose) override

virtual void	update_residue_union (Size resid, ResidueLevelTask const &res_task_in)

virtual void	update_residue_intersection (Size resid, ResidueLevelTask const &res_task_in)

virtual void	update_residue_commutative (Size resid, ResidueLevelTask const &res_task_in)

void	update_commutative (PackerTask const &tark_in) override

void	request_symmetrize_by_intersection () override

void	request_symmetrize_by_union () override

bool	symmetrize_by_union () const override

bool	symmetrize_by_intersection () const override

core::Size	ig_threads_to_request () const override
	For multithreading ///. More...

void	limit_ig_setup_threads (core::Size const setting) override
	Limit the interaction graph setup threads. More...

void	temporarily_fix_everything () override
	For use only inside the packer //. More...

void	temporarily_set_pack_residue (int resid, bool setting) override
	reset packer mutability arbitrarily for a given residue This is only to be used to control packing from within the packing functions rotamer_trials and rtmin. Otherwise, this function should not be used. This function is not commutative and therefor using it outside of rotamer_trials and rtmin would lead to disasterous behaviors More...

Public Member Functions inherited from core::pack::task::PackerTask
PackerTaskCOP	get_self_ptr () const
	self pointers More...

PackerTaskOP	get_self_ptr ()

Private Member Functions
void	update_n_to_be_packed () const

virtual PackerTask &	operator= (PackerTask const &)

Private Attributes
bool	is_initialized_ = false
	Has this PackerTask been initialized with a PackerPalette? More...

Size	nres_

utility::vector1< bool >	pack_residue_

utility::vector1 < ResidueLevelTask_ >	residue_tasks_

Size	n_to_be_packed_

bool	n_to_be_packed_up_to_date_ = true

bool	precompute_ig_ = false

bool	linmem_ig_ = false

bool	linmem_ig_history_size_at_default_ = true

Size	linmem_ig_history_size_ = 10

bool	lazy_ig_ = false

bool	double_lazy_ig_ = false

Size	dlig_mem_limit_ = 0

bool	multi_cool_annealer_ = false

Size	mca_history_size_ = 1

bool	smart_annealer_ = false

std::string	smart_annealer_model_ = "generation2"

core::Real	smart_annealer_cutoff_ = 0.25

bool	smart_annealer_pick_again_ = true

bool	smart_annealer_disable_during_quench_ = true

bool	keep_sequence_symmetry_ = false

std::string	seq_sym_uid_prefix_

bool	optimize_H_ = false
	keep track: are we optimizing H at all positions? don't use linmem_ig_ if so. More...

bool	bump_check_ = true

Real	max_rotbump_energy_ = 5.0

RotamerCouplingsCOP	rotamer_couplings_

RotamerLinksCOP	rotamer_links_

Real	low_temp_ = -1.0

Real	high_temp_ = -1.0

bool	disallow_quench_ = false

IGEdgeReweightContainerOP	IG_edge_reweights_

rotamer_set::RotSetsOperationList	rotsetsops_

PackerTaskSymmetryStatus	symmetry_status_ = NO_SYMMETRIZATION_REQUEST

core::pack::palette::PackerPaletteCOP	packer_palette_
	The PackerPalette, which tells the PackerTask what the default set of residue types is in the absence of TaskOperations. More...

core::Size	ig_threads_to_request_ = 0
	The number of threads to request for interaction graph precomputation. More...

Additional Inherited Members
Public Types inherited from core::pack::task::PackerTask
typedef chemical::AA	AA

typedef rotamer_set::RotamerCouplingsCOP	RotamerCouplingsCOP

typedef rotamer_set::RotamerLinksCOP	RotamerLinksCOP

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

Detailed Description

the PackerTask controls what rotameric (including sequence) changes the packer is allowed to make

Constructor & Destructor Documentation

core::pack::task::PackerTask_::PackerTask_ ( core::Size const ig_threads_to_request = 0 )

constructor; the PackerTask will always need a pose!

Note: Can optionally specify the number of interaction graph threads to request. The default (0) means to use all available threads. In the single-threaded build, must always be 0 or 1.

References check_threads(), and IG_edge_reweights_.

Referenced by clone().

core::pack::task::PackerTask_::PackerTask_	(	pose::Pose const &	pose,
		core::Size const	ig_threads_to_request = `0`
	)

Initialization constructor that needs a pose. A DefaultPackerPalette is automatically created using the ResidueTypeSet of the pose.

Note: Can optionally specify the number of interaction graph threads to request. The default (0) means to use all available threads. In the single-threaded build, must always be 0 or 1.

constructor requires a pose. most settings are in ResidueLevelTask nres_ is copied from the pose, all residues are set to be packable by default, and bump_check is true the constructor reads NEITHER the command line flags NOR a resfile; this must be done after creation!

References check_threads(), IG_edge_reweights_, is_initialized_, nres_, packer_palette_, core::pose::Pose::residue(), and residue_tasks_.

core::pack::task::PackerTask_::PackerTask_	(	pose::Pose const &	pose,
		core::pack::palette::PackerPaletteCOP const &	packer_palette,
		core::Size const	ig_threads_to_request = `0`
	)

Initialization constructor that needs a pose and a PackerPalette.

The input PackerPalette is cloned.

Note: Can optionally specify the number of interaction graph threads to request. The default (0) means to use all available threads. In the single-threaded build, must always be 0 or 1.

constructor requires a pose. most settings are in ResidueLevelTask nres_ is copied from the pose, all residues are set to be packable by default, and bump_check is true the constructor reads NEITHER the command line flags NOR a resfile; this must be done after creation!

References check_threads(), IG_edge_reweights_, is_initialized_, nres_, packer_palette_, core::pose::Pose::residue(), and residue_tasks_.

core::pack::task::PackerTask_::~PackerTask_ ( )

overridedefault

dtor

Member Function Documentation

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

overridevirtual

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

void core::pack::task::PackerTask_::add_behavior	(	std::string const &	behavior,
		Size	resid
	)

overridevirtual

Implements core::pack::task::PackerTask.

References residue_tasks_.

bool core::pack::task::PackerTask_::adducts ( Size resid ) const

overridevirtual

include adducts at this residue

Implements core::pack::task::PackerTask.

References residue_tasks_.

void core::pack::task::PackerTask_::and_linmem_ig ( bool setting )

overridevirtual

if setting == false, turns off linear-memory interaction graph usage

Implements core::pack::task::PackerTask.

References linmem_ig_.

void core::pack::task::PackerTask_::and_max_rotbump_energy ( Real setting )

overridevirtual

Decrease the max_rotbump_energy threshold above which rotamers are rejected.

Implements core::pack::task::PackerTask.

References max_rotbump_energy_.

Referenced by initialize_from_options().

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

overridevirtual

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

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

overridevirtual

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

void core::pack::task::PackerTask_::append_rotamersets_operation ( rotamer_set::RotamerSetsOperationOP rotsetsop )

overridevirtual

Implements core::pack::task::PackerTask.

References rotsetsops_.

bool core::pack::task::PackerTask_::being_designed ( Size resid ) const

inlineoverridevirtual

alias for above

Implements core::pack::task::PackerTask.

References design_residue().

Referenced by design_any(), design_residue(), and designing_residues().

bool core::pack::task::PackerTask_::being_packed ( Size resid ) const

inlineoverridevirtual

alias for above

Implements core::pack::task::PackerTask.

References pack_residue().

Referenced by repacking_residues(), and update_n_to_be_packed().

bool core::pack::task::PackerTask_::bump_check ( ) const

overridevirtual

get function: has bump_check been requested?

Implements core::pack::task::PackerTask.

References bump_check_.

void core::pack::task::PackerTask_::check_threads ( ) const

Check that the number of threads to request is reasonable.

Does nothing in multithreaded build. In single-threaded build, checks that number of threads to request is 0 (use all available, which is 1) or 1.

References ig_threads_to_request_.

Referenced by PackerTask_().

void core::pack::task::PackerTask_::clean_residue_task	(	conformation::Residue const &	original_residue,
		Size const	seqpos,
		core::pose::Pose const &	pose
	)

overridevirtual

replace a given residue task with a brand new one NOTE: This should be the only way to break commutativity!!!!

Implements core::pack::task::PackerTask.

References n_to_be_packed_, pack_residue_, packer_palette_, and residue_tasks_.

PackerTaskOP core::pack::task::PackerTask_::clone ( ) const

overridevirtual

copy method

uses compiler-generated copy ctor

Implements core::pack::task::PackerTask.

References PackerTask_().

void core::pack::task::PackerTask_::decrease_double_lazy_ig_memlimit ( Size nbytes_for_rpes )

overridevirtual

Set the memory limit, in bytes, for the storage that the DLIG should be allowed to spend on representing rotamer pair energies. The DLIG will start deallocating rotamer pair energy blocks if it exceeds this limit. This limit is occasionally breached by as much memory as is required to store a single amino-acid-pair submatrix block; the limit does not apply to the entirety of the packer or even the entirety of this interaction graph, merely to the amount of space for rotamer pair energies. Remember, rotamers are expensive, too! The default value of "0" signifies an unrestricted memory limit – 0 may not be set through this function. The value may increase once from 0 and then may only decrease from there.

Implements core::pack::task::PackerTask.

References dlig_mem_limit_.

void core::pack::task::PackerTask_::decrease_linmem_ig_history_size ( Size setting )

overridevirtual

Set the linear memory interaction graph's recent history size. Default is 10. It can be set once to any value larger than 10, but any subsequent setting will only alter the size if it decreases it.

Implements core::pack::task::PackerTask.

References linmem_ig_history_size_, and linmem_ig_history_size_at_default_.

Referenced by initialize_from_options().

bool core::pack::task::PackerTask_::design_any ( ) const

overridevirtual

get function: can any positions have a sequence change?

Implements core::pack::task::PackerTask.

References being_designed(), nres_, pack_residue_, and residue_tasks_.

bool core::pack::task::PackerTask_::design_residue ( int resid ) const

overridevirtual

get function: can this position have a sequence change?

Implements core::pack::task::PackerTask.

References being_designed(), pack_residue_, and residue_tasks_.

Referenced by being_designed(), show(), and show_residue_task().

utility::vector1< bool > core::pack::task::PackerTask_::designing_residues ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References being_designed(), nres_, and residue_tasks_.

void core::pack::task::PackerTask_::disallow_quench ( bool const & disallow_quench )

overridevirtual

Implements core::pack::task::PackerTask.

References disallow_quench(), and disallow_quench_.

bool core::pack::task::PackerTask_::disallow_quench ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References disallow_quench_.

Referenced by disallow_quench().

bool core::pack::task::PackerTask_::double_lazy_ig ( ) const

overridevirtual

Returns the double-lazy interaction graph flag.

Implements core::pack::task::PackerTask.

References double_lazy_ig_.

Size core::pack::task::PackerTask_::double_lazy_ig_memlimit ( ) const

overridevirtual

the memory limit, in bytes, for the double-lazy interaction graph. A value of 0 signifies an unrestricted limit.

Implements core::pack::task::PackerTask.

References dlig_mem_limit_.

bool core::pack::task::PackerTask_::has_behavior	(	std::string const &	behavior,
		Size	resid
	)		const

overridevirtual

Implements core::pack::task::PackerTask.

References residue_tasks_.

bool core::pack::task::PackerTask_::has_behavior ( Size resid ) const

overridevirtual

Implements core::pack::task::PackerTask.

References residue_tasks_.

void core::pack::task::PackerTask_::high_temp ( Real const & high_temp )

overridevirtual

Implements core::pack::task::PackerTask.

References high_temp(), and high_temp_.

Real core::pack::task::PackerTask_::high_temp ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References high_temp_.

Referenced by high_temp().

core::Size core::pack::task::PackerTask_::ig_threads_to_request ( ) const

overridevirtual

For multithreading ///.

How many threads should the packer request for interaction graph precomputation?

Must be implemented by derived class.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Must be implemented by derived class.

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::PackerTask.

IGEdgeReweightContainerCOP core::pack::task::PackerTask_::IGEdgeReweights ( ) const

overridevirtual

accesor for residue residue weight map

Implements core::pack::task::PackerTask.

References IG_edge_reweights_.

bool core::pack::task::PackerTask_::include_current ( Size resid ) const

overridevirtual

get function: what is include_current for this residue?

Implements core::pack::task::PackerTask.

References residue_tasks_.

Referenced by core::pack::task::ResidueLevelTask_::command_string().

void core::pack::task::PackerTask_::increase_multi_cool_annealer_history_size ( Size setting )

overridevirtual

Increases the history size for the MultiCoolAnnealer if setting is larger than the existing setting.

Implements core::pack::task::PackerTask.

References mca_history_size_.

Referenced by initialize_from_options().

PackerTask & core::pack::task::PackerTask_::initialize_extra_rotamer_flags_from_command_line ( )

overridevirtual

read only the command line options for extra rotamer building;

Implements core::pack::task::PackerTask.

References initialize_extra_rotamer_flags_from_options().

PackerTask & core::pack::task::PackerTask_::initialize_extra_rotamer_flags_from_options ( utility::options::OptionCollection const & options )

overridevirtual

read only the command line options for extra rotamer building;

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

Referenced by initialize_extra_rotamer_flags_from_command_line().

PackerTask & core::pack::task::PackerTask_::initialize_from_command_line ( )

overridevirtual

read command line options (but not resfile) to set the state of the PackerTask, NOT IN CONSTRUCTOR

Implements core::pack::task::PackerTask.

References initialize_from_options().

PackerTask & core::pack::task::PackerTask_::initialize_from_options ( utility::options::OptionCollection const & options )

overridevirtual

bool core::pack::task::PackerTask_::is_initialized ( ) const

overridevirtual

Has this PackerTask been initialized with a PackerPalette?

PackerTasks must be initialized with PackerPalettes before being modified with TaskOperations. The TaskFactory will initialize the PackerTask with a DefaultPackerPalette if no custom PackerPalette is provided.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Implements core::pack::task::PackerTask.

References is_initialized_.

bool core::pack::task::PackerTask_::keep_sequence_symmetry ( ) const

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References keep_sequence_symmetry_.

Referenced by initialize_from_options().

void core::pack::task::PackerTask_::keep_sequence_symmetry ( bool const setting )

inlineoverridevirtual

Enables SequenceSymmetricAnnealer.

Implements core::pack::task::PackerTask.

References keep_sequence_symmetry_.

bool core::pack::task::PackerTask_::lazy_ig ( ) const

overridevirtual

returns the lazy interaction interaction graph flag

Implements core::pack::task::PackerTask.

References lazy_ig_.

void core::pack::task::PackerTask_::limit_ig_setup_threads ( core::Size const setting )

overridevirtual

Limit the interaction graph setup threads.

If the current ig_threads_to_request_ is zero, setting replaces it. If setting is zero, this does nothing. Otherwise, setting replaces ig_threads_to_request_ if and only if it is less than ig_threads_to_request_. This preserves commutativity.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tue..nosp@m.org)

Implements core::pack::task::PackerTask.

bool core::pack::task::PackerTask_::linmem_ig ( ) const

overridevirtual

returns the linear-memory interaction graph flag

Implements core::pack::task::PackerTask.

References linmem_ig_.

Size core::pack::task::PackerTask_::linmem_ig_history_size ( ) const

overridevirtual

Return the linear memory interaction graph's recent history size.

Implements core::pack::task::PackerTask.

References linmem_ig_history_size_.

void core::pack::task::PackerTask_::low_temp ( Real const & low_temp )

overridevirtual

Implements core::pack::task::PackerTask.

References low_temp(), and low_temp_.

Real core::pack::task::PackerTask_::low_temp ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References low_temp_.

Referenced by low_temp().

Real core::pack::task::PackerTask_::max_rotbump_energy ( ) const

overridevirtual

get function: what is the energy threshold above which rotamers should be rejected

Implements core::pack::task::PackerTask.

References max_rotbump_energy_.

bool core::pack::task::PackerTask_::multi_cool_annealer ( ) const

overridevirtual

use MultiCoolAnnealer?

Implements core::pack::task::PackerTask.

References multi_cool_annealer_.

Size core::pack::task::PackerTask_::multi_cool_annealer_history_size ( ) const

overridevirtual

returns the requested size for the MultiCoolAnnealer

Implements core::pack::task::PackerTask.

References mca_history_size_.

ResidueLevelTask & core::pack::task::PackerTask_::nonconst_residue_task ( Size resid )

overridevirtual

nonconst access to underlying ResidueLevelTask object

Implements core::pack::task::PackerTask.

References n_to_be_packed_up_to_date_, and residue_tasks_.

Size core::pack::task::PackerTask_::num_to_be_packed ( ) const

overridevirtual

get function: how many positions can have rotamer changes?

Implements core::pack::task::PackerTask.

References n_to_be_packed_, n_to_be_packed_up_to_date_, and update_n_to_be_packed().

PackerTask & core::pack::task::PackerTask_::operator= ( PackerTask const & )

privatevirtual

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

overridevirtual

for all positions, disable adducts if false, do nothing if true

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

void core::pack::task::PackerTask_::or_adducts	(	bool	setting,
		Size	resid
	)

overridevirtual

for one position, disable adducts if false, do nothing if true

Implements core::pack::task::PackerTask.

References residue_tasks_.

void core::pack::task::PackerTask_::or_double_lazy_ig ( bool setting )

overridevirtual

Activate the DoubleLazyInteractionGraph, which is particularly useful for multistate design, when memory and time are both limiting. Overriden by LinMemIG.

Implements core::pack::task::PackerTask.

References double_lazy_ig_.

Referenced by initialize_from_options().

void core::pack::task::PackerTask_::or_fix_his_tautomer	(	utility::vector1< int > const &	positions,
		bool	setting
	)

overridevirtual

if setting == true, fix his tautomer state for defined residues during repacking or optimizeH mode

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

Referenced by initialize_from_options().

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

overridevirtual

if setting == true, turns on optimize_H_mode and flip_HNQ for all residues

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

void core::pack::task::PackerTask_::or_include_current ( bool setting )

overridevirtual

for all positions, turn on include_current if false, do nothing if already true

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

void core::pack::task::PackerTask_::or_include_current	(	bool	setting,
		Size	resid
	)

overridevirtual

for one position, turn on include_current if false, do nothing if already true

Implements core::pack::task::PackerTask.

References residue_tasks_.

void core::pack::task::PackerTask_::or_lazy_ig ( bool setting )

overridevirtual

if setting == true, turns on lazy interaction graph usage NOTE: the linear memory interaction graph takes precedence over the LazyIG when the InteractionGraphFactory examines the PackerTask.

Implements core::pack::task::PackerTask.

References lazy_ig_.

Referenced by initialize_from_options().

void core::pack::task::PackerTask_::or_linmem_ig ( bool setting )

overridevirtual

if setting == true, turns on linear-memory interaction graph usage

Implements core::pack::task::PackerTask.

References linmem_ig_.

Referenced by initialize_from_options().

void core::pack::task::PackerTask_::or_multi_cool_annealer ( bool setting )

overridevirtual

if setting == true, turns on MultiCoolAnnealer – so long as rotamer couplings are not also turned on.

Implements core::pack::task::PackerTask.

References multi_cool_annealer_, rotamer_couplings_, and rotamer_links_.

Referenced by initialize_from_options().

void core::pack::task::PackerTask_::or_optimize_h_mode ( bool setting )

overridevirtual

if setting == true, turns on optimize_H_mode for all residues

Implements core::pack::task::PackerTask.

References linmem_ig_, nres_, optimize_H_, and residue_tasks_.

void core::pack::task::PackerTask_::or_precompute_ig ( bool setting )

overridevirtual

Explicitly request the O( N^2 ) precomputed graph.

linmem_ig() is checked first and will override this setting

Implements core::pack::task::PackerTask.

References precompute_ig_.

Referenced by initialize_from_options().

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

overridevirtual

if setting == true, preserves c-beta during rotamer building for all residues

Implements core::pack::task::PackerTask.

References nres_, and residue_tasks_.

bool core::pack::task::PackerTask_::pack_residue ( int resid ) const

overridevirtual

get function: can this position have a rotamer change?

Implements core::pack::task::PackerTask.

References pack_residue_, and residue_tasks_.

Referenced by being_packed(), show(), and show_residue_task().

bool core::pack::task::PackerTask_::precompute_ig ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References precompute_ig_.

void core::pack::task::PackerTask_::remap_residue_level_tasks	(	core::id::SequenceMappingCOP	seqmap,
		core::pose::Pose const &	pose
	)

overridevirtual

Implements core::pack::task::PackerTask.

References nres_, pack_residue_, packer_palette_, core::id::SequenceMapping::push_back(), core::pose::Pose::residue(), residue_tasks_, core::id::SequenceMapping::reverse(), core::pose::Pose::size(), and update_n_to_be_packed().

utility::vector1< bool > core::pack::task::PackerTask_::repacking_residues ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References being_packed(), nres_, and residue_tasks_.

void core::pack::task::PackerTask_::request_symmetrize_by_intersection ( )

overridevirtual

Implements core::pack::task::PackerTask.

References core::pack::task::NO_SYMMETRIZATION_REQUEST, and core::pack::task::REQUEST_SYMMETRIZE_BY_INTERSECTION.

void core::pack::task::PackerTask_::request_symmetrize_by_union ( )

overridevirtual

Implements core::pack::task::PackerTask.

References core::pack::task::NO_SYMMETRIZATION_REQUEST, and core::pack::task::REQUEST_SYMMETRIZE_BY_UNION.

ResidueLevelTask const & core::pack::task::PackerTask_::residue_task ( Size resid ) const

overridevirtual

const accessor for underlying ResidueLevelTask object

Implements core::pack::task::PackerTask.

References residue_tasks_.

Referenced by show(), and show_residue_task().

PackerTask & core::pack::task::PackerTask_::restrict_to_repacking ( )

overridevirtual

turn off designing (sequence changing) all residues

vector boolean is based on residue position, disables packing at false positions does nothing to true positions. Cannot turn on packing. Will prevent packing at false positions if the original residue type has been otherwise disallowed.

Implements core::pack::task::PackerTask.

References nres_, residue_tasks_, and update_n_to_be_packed().

Referenced by initialize_from_options().

PackerTask & core::pack::task::PackerTask_::restrict_to_residues ( utility::vector1< bool > const & residues_allowed_to_be_packed )

overridevirtual

turn off packing for residues passed false; can't turn on packing

vector boolean is based on residue position, disables packing at false positions does nothing to true positions. Cannot turn on packing.

Implements core::pack::task::PackerTask.

References nres_, residue_tasks_, and update_n_to_be_packed().

PackerTask::RotamerCouplingsCOP core::pack::task::PackerTask_::rotamer_couplings ( ) const

overridevirtual

const accessor for the RotamerCouplings object

Implements core::pack::task::PackerTask.

References rotamer_couplings_.

void core::pack::task::PackerTask_::rotamer_couplings ( PackerTask::RotamerCouplingsCOP setting )

overridevirtual

setter for the RotamerCouplings object

Implements core::pack::task::PackerTask.

References multi_cool_annealer_, and rotamer_couplings_.

bool core::pack::task::PackerTask_::rotamer_couplings_exist ( ) const

overridevirtual

is there at RotamerCouplings object to worry about? (for DNA GC AT pairing, etc)

Implements core::pack::task::PackerTask.

References rotamer_couplings_.

PackerTask::RotamerLinksCOP core::pack::task::PackerTask_::rotamer_links ( ) const

overridevirtual

const accessor for the RotamerLinks object

const accessor for the RotamerCouplings object

Implements core::pack::task::PackerTask.

References rotamer_links_.

void core::pack::task::PackerTask_::rotamer_links ( PackerTask::RotamerLinksCOP setting )

overridevirtual

setter for the RotamerLinks object

setter for the RotamerCouplings object

Implements core::pack::task::PackerTask.

References multi_cool_annealer_, and rotamer_links_.

bool core::pack::task::PackerTask_::rotamer_links_exist ( ) const

overridevirtual

is there at RotamerLinks object to worry about? (for repeat linking

Implements core::pack::task::PackerTask.

References rotamer_links_.

rotamer_set::RotSetsOperationListIterator core::pack::task::PackerTask_::rotamer_sets_operation_begin ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References rotsetsops_.

rotamer_set::RotSetsOperationListIterator core::pack::task::PackerTask_::rotamer_sets_operation_end ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References rotsetsops_.

std::string core::pack::task::PackerTask_::sequence_symmetric_uid_prefix ( ) const

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References seq_sym_uid_prefix_.

void core::pack::task::PackerTask_::sequence_symmetric_uid_prefix ( std::string const & prefix )

inlineoverridevirtual

Sets the prefix used when searching for symmetry defining residue selectors in the datacache.

Implements core::pack::task::PackerTask.

References seq_sym_uid_prefix_.

void core::pack::task::PackerTask_::set_bump_check ( bool setting )

overridevirtual

set function: bump_check is activated for pack-rotamers' screening of rotamers that collide with the background. Bump-check is not used during rotamer trials, since it is nearly as expensive as rotamer trials itself. Energy methods may opt in to the bump check process. The "standard" behavior is for bump-check to include only the fa_atr and fa_rep terms.

Implements core::pack::task::PackerTask.

References bump_check_.

IGEdgeReweightContainerOP core::pack::task::PackerTask_::set_IGEdgeReweights ( )

overridevirtual

Implements core::pack::task::PackerTask.

References IG_edge_reweights_, and nres_.

void core::pack::task::PackerTask_::set_smart_annealer ( bool setting )

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_.

void core::pack::task::PackerTask_::set_smart_annealer_cutoff ( core::Real setting )

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_cutoff_.

void core::pack::task::PackerTask_::set_smart_annealer_disable_during_quench ( bool setting )

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_disable_during_quench_.

void core::pack::task::PackerTask_::set_smart_annealer_model ( std::string const & setting )

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_model_.

void core::pack::task::PackerTask_::set_smart_annealer_pick_again ( bool setting )

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_pick_again_.

void core::pack::task::PackerTask_::show ( std::ostream & out ) const

overridevirtual

Implements core::pack::task::PackerTask.

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), design_residue(), ig_threads_to_request_, pack_residue(), residue_task(), and total_residue().

void core::pack::task::PackerTask_::show ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

void core::pack::task::PackerTask_::show_all_residue_tasks ( std::ostream & out ) const

overridevirtual

Implements core::pack::task::PackerTask.

References show_residue_task(), and total_residue().

void core::pack::task::PackerTask_::show_all_residue_tasks ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References show_residue_task(), and total_residue().

void core::pack::task::PackerTask_::show_residue_task	(	std::ostream &	out,
		Size	resid
	)		const

overridevirtual

Implements core::pack::task::PackerTask.

Referenced by show_all_residue_tasks(), and show_residue_task().

void core::pack::task::PackerTask_::show_residue_task ( Size resid ) const

overridevirtual

Implements core::pack::task::PackerTask.

References show_residue_task().

bool core::pack::task::PackerTask_::smart_annealer ( ) const

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_.

core::Real core::pack::task::PackerTask_::smart_annealer_cutoff ( ) const

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_cutoff_.

bool core::pack::task::PackerTask_::smart_annealer_disable_during_quench ( ) const

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_disable_during_quench_.

std::string core::pack::task::PackerTask_::smart_annealer_model ( ) const

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_model_.

bool core::pack::task::PackerTask_::smart_annealer_pick_again ( ) const

inlineoverridevirtual

Implements core::pack::task::PackerTask.

References smart_annealer_pick_again_.

bool core::pack::task::PackerTask_::symmetrize_by_intersection ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References core::pack::task::REQUEST_SYMMETRIZE_BY_INTERSECTION.

bool core::pack::task::PackerTask_::symmetrize_by_union ( ) const

overridevirtual

Implements core::pack::task::PackerTask.

References core::pack::task::REQUEST_SYMMETRIZE_BY_UNION.

chemical::ResidueTypeCOP core::pack::task::PackerTask_::target_type ( Size resid ) const

virtual

return the targeted type (may be null pointer)

References residue_tasks_.

Referenced by core::pack::task::ResidueLevelTask_::command_string().

std::string core::pack::task::PackerTask_::task_string ( pose::Pose const & pose ) const

overridevirtual

Implements core::pack::task::PackerTask.

References core::pose::Pose::pdb_info(), residue_tasks_, and total_residue().

void core::pack::task::PackerTask_::temporarily_fix_everything ( )

overridevirtual

For use only inside the packer //.

turn off packing at all positions This is only to be used to control packing from within the packing functions rotamer_trials and rtmin. Otherwise, this function should not be used. This function is not commutative and therefor using it outside of rotamer_trials and rtmin would lead to disasterous behaviors

turn off packing at all positions. This does not affect underlying ResidueLevelTasks, but at the moment there is no method for reversing

Implements core::pack::task::PackerTask.

References n_to_be_packed_, n_to_be_packed_up_to_date_, nres_, and pack_residue_.

void core::pack::task::PackerTask_::temporarily_set_pack_residue	(	int	resid,
		bool	setting
	)

overridevirtual

reset packer mutability arbitrarily for a given residue This is only to be used to control packing from within the packing functions rotamer_trials and rtmin. Otherwise, this function should not be used. This function is not commutative and therefor using it outside of rotamer_trials and rtmin would lead to disasterous behaviors

arbitrarily set the packer mutability for a position reverse with same function, opposite bool input

Implements core::pack::task::PackerTask.

References n_to_be_packed_, n_to_be_packed_up_to_date_, pack_residue_, and update_n_to_be_packed().

Size core::pack::task::PackerTask_::total_residue ( ) const

overridevirtual

number of residues in the input pose, for convienience (PackerTask does not handle variable length)

Implements core::pack::task::PackerTask.

References nres_.

Referenced by show(), show_all_residue_tasks(), and task_string().

void core::pack::task::PackerTask_::update_commutative ( PackerTask const & tark_in )

overridevirtual

Implements core::pack::task::PackerTask.

References protocols::mean_field::max(), and protocols::mean_field::min().

void core::pack::task::PackerTask_::update_n_to_be_packed ( ) const

private

References being_packed(), n_to_be_packed_, n_to_be_packed_up_to_date_, nres_, pack_residue_, and residue_tasks_.

Referenced by initialize_from_options(), num_to_be_packed(), remap_residue_level_tasks(), restrict_to_repacking(), restrict_to_residues(), and temporarily_set_pack_residue().

void core::pack::task::PackerTask_::update_residue_commutative	(	Size	resid,
		ResidueLevelTask const &	res_task_in
	)

virtual

void core::pack::task::PackerTask_::update_residue_intersection	(	Size	resid,
		ResidueLevelTask const &	res_task_in
	)

virtual

void core::pack::task::PackerTask_::update_residue_union	(	Size	resid,
		ResidueLevelTask const &	res_task_in
	)

virtual

Member Data Documentation

bool core::pack::task::PackerTask_::bump_check_ = true

private

Referenced by bump_check(), and set_bump_check().

bool core::pack::task::PackerTask_::disallow_quench_ = false

private

Referenced by disallow_quench().

Size core::pack::task::PackerTask_::dlig_mem_limit_ = 0

private

Referenced by decrease_double_lazy_ig_memlimit(), and double_lazy_ig_memlimit().

bool core::pack::task::PackerTask_::double_lazy_ig_ = false

private

linmem_ig overrides DoubleLazyIG

Referenced by double_lazy_ig(), and or_double_lazy_ig().

Real core::pack::task::PackerTask_::high_temp_ = -1.0

private

Referenced by high_temp().

IGEdgeReweightContainerOP core::pack::task::PackerTask_::IG_edge_reweights_

private

holds specific residue residue weights to be used in packing

Referenced by IGEdgeReweights(), PackerTask_(), and set_IGEdgeReweights().

core::Size core::pack::task::PackerTask_::ig_threads_to_request_ = 0

private

The number of threads to request for interaction graph precomputation.

The default, 0, means to request all available threads (multithreaded build) or 1 thread (non-threaded build). In the non-threaded build, only 1 thread can be requested.

Referenced by check_threads(), and show().

bool core::pack::task::PackerTask_::is_initialized_ = false

private

Has this PackerTask been initialized with a PackerPalette?

PackerTasks must be initialized with PackerPalettes before being modified with TaskOperations. The TaskFactory will initialize the PackerTask with a DefaultPackerPalette if no custom PackerPalette is provided.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by is_initialized(), and PackerTask_().

bool core::pack::task::PackerTask_::keep_sequence_symmetry_ = false

private

Referenced by keep_sequence_symmetry().

bool core::pack::task::PackerTask_::lazy_ig_ = false

private

linmem_ig overrides LazyIG

Referenced by lazy_ig(), and or_lazy_ig().

bool core::pack::task::PackerTask_::linmem_ig_ = false

private

linmem_ig overrides PDInteractionGraph

Referenced by and_linmem_ig(), linmem_ig(), or_linmem_ig(), and or_optimize_h_mode().

Size core::pack::task::PackerTask_::linmem_ig_history_size_ = 10

private

Referenced by decrease_linmem_ig_history_size(), and linmem_ig_history_size().

bool core::pack::task::PackerTask_::linmem_ig_history_size_at_default_ = true

private

Referenced by decrease_linmem_ig_history_size().

Real core::pack::task::PackerTask_::low_temp_ = -1.0

private

Referenced by low_temp().

Real core::pack::task::PackerTask_::max_rotbump_energy_ = 5.0

private

Referenced by and_max_rotbump_energy(), and max_rotbump_energy().

Size core::pack::task::PackerTask_::mca_history_size_ = 1

private

Referenced by increase_multi_cool_annealer_history_size(), and multi_cool_annealer_history_size().

bool core::pack::task::PackerTask_::multi_cool_annealer_ = false

private

Referenced by multi_cool_annealer(), or_multi_cool_annealer(), rotamer_couplings(), and rotamer_links().

Size core::pack::task::PackerTask_::n_to_be_packed_

mutableprivate

Referenced by clean_residue_task(), num_to_be_packed(), temporarily_fix_everything(), temporarily_set_pack_residue(), and update_n_to_be_packed().

bool core::pack::task::PackerTask_::n_to_be_packed_up_to_date_ = true

mutableprivate

Referenced by nonconst_residue_task(), num_to_be_packed(), temporarily_fix_everything(), temporarily_set_pack_residue(), and update_n_to_be_packed().

bool core::pack::task::PackerTask_::optimize_H_ = false

private

keep track: are we optimizing H at all positions? don't use linmem_ig_ if so.

Referenced by initialize_from_options(), and or_optimize_h_mode().

utility::vector1< bool > core::pack::task::PackerTask_::pack_residue_

private

superficial on/off switch for repacking residues produces no impact on contents of residue_tasks_ vector. This is only to be used to control packing from within the packing functions rotamer_trials and rtmin. Otherwise, this vector should not be used.

Referenced by clean_residue_task(), design_any(), design_residue(), pack_residue(), remap_residue_level_tasks(), temporarily_fix_everything(), temporarily_set_pack_residue(), and update_n_to_be_packed().