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_:

Collaboration diagram for core::pack::task::PackerTask_:

Public Member Functions
	PackerTask_ ()
	constructor; the PackerTask will always need a pose! More...

	PackerTask_ (pose::Pose const &pose)

virtual	~PackerTask_ ()
	dtor More...

PackerTaskOP	clone () const
	copy method More...

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

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

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

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

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

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

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

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

virtual void	set_bump_check (bool setting)
	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...

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

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

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

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

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

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

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

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

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

virtual bool	has_behavior (Size resid) const

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

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

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

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

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

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

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

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

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

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

virtual void	or_lazy_ig (bool setting)
	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...

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

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

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

virtual void	decrease_double_lazy_ig_memlimit (Size nbytes_for_rpes)
	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...

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

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

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

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

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

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

virtual void	show () const

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

virtual void	show_residue_task (Size resid) const

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

virtual void	show_all_residue_tasks () const

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual IGEdgeReweightContainerOP	set_IGEdgeReweights ()

virtual void	append_rotamer_operation (rotamer_set::RotamerOperationOP rotop)

virtual void	append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop)

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

void	low_temp (Real const &low_temp)

void	high_temp (Real const &high_temp)

void	disallow_quench (bool const &disallow_quench)

Real	low_temp () const

Real	high_temp () const

bool	disallow_quench () const

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

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)

virtual void	update_commutative (PackerTask const &tark_in)

virtual void	request_symmetrize_by_intersection ()

virtual void	request_symmetrize_by_union ()

virtual bool	symmetrize_by_union () const

virtual bool	symmetrize_by_intersection () const

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

virtual void	temporarily_set_pack_residue (int resid, bool setting)
	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
virtual	~PackerTask ()=0

Private Member Functions
void	update_n_to_be_packed () const

virtual PackerTask &	operator= (PackerTask const &)

Private Attributes
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_

bool	linmem_ig_

bool	lazy_ig_

bool	double_lazy_ig_

Size	dlig_mem_limit_

bool	multi_cool_annealer_

Size	mca_history_size_

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

bool	bump_check_

Real	max_rotbump_energy_

RotamerCouplingsCOP	rotamer_couplings_

RotamerLinksCOP	rotamer_links_

Real	low_temp_

Real	high_temp_

bool	disallow_quench_

IGEdgeReweightContainerOP	IG_edge_reweights_

PackerTaskSymmetryStatus	symmetry_status_

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

Detailed Description

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

Definition at line 564 of file PackerTask_.hh.

Constructor & Destructor Documentation

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

constructor; the PackerTask will always need a pose!

Definition at line 1464 of file PackerTask_.cc.

References IG_edge_reweights_.

Referenced by clone().

core::pack::task::PackerTask_::PackerTask_ ( pose::Pose const & pose)

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!

Definition at line 1491 of file PackerTask_.cc.

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

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

virtual

dtor

Definition at line 1522 of file PackerTask_.cc.

Member Function Documentation

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

virtual

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation