core::pack::task::PackerTask_ Class Reference

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

#include <PackerTask_.hh>

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	decrease_linmem_ig_history_size (Size setting)
	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...
virtual Size	linmem_ig_history_size () const
	Return the linear memory interaction graph's recent history size. 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	linmem_ig_history_size_at_default_
Size	linmem_ig_history_size_
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

Constructor & Destructor Documentation

core::pack::task::PackerTask_::PackerTask_

(

)

constructor; the PackerTask will always need a pose!

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!

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

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

virtual

dtor

Member Function Documentation

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

virtual

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

References nres_, and residue_tasks_.

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

virtual

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

References residue_tasks_.

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

virtual

include adducts at this residue

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

References residue_tasks_.

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

virtual

Decrease the max_rotbump_energy threshold above which rotamers are rejected.

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

References max_rotbump_energy_.

Referenced by initialize_from_command_line().

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

virtual

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

References nres_, and residue_tasks_.

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

virtual

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

References nres_, and residue_tasks_.

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

inlinevirtual

alias for above

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

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

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

inlinevirtual

alias for above

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

Referenced by repacking_residues(), and update_n_to_be_packed().

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

virtual

get function: has bump_check been requested?

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

References bump_check_.

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

virtual

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_, and residue_tasks_.

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

virtual

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 )

virtual

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 )

virtual

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_command_line().

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

virtual

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

virtual

get function: can this position have a sequence change?

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

References being_designed(), pack_residue_, and residue_tasks_.

Referenced by show(), and show_residue_task().

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

virtual

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

References being_designed(), nres_, and residue_tasks_.

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

virtual

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

References disallow_quench(), and disallow_quench_.

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

virtual

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

References disallow_quench_.

Referenced by disallow_quench().

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

virtual

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

virtual

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

virtual

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

References residue_tasks_.

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

virtual

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

References residue_tasks_.

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

virtual

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

References high_temp(), and high_temp_.

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

virtual

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

References high_temp_.

Referenced by high_temp().

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

virtual

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

virtual

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 )

virtual

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_command_line().

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

virtual

read only the command line options for extra rotamer building;

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

References nres_, and residue_tasks_.

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

virtual

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

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

References and_max_rotbump_energy(), decrease_linmem_ig_history_size(), packing::double_lazy_ig, empty, packing::fix_his_tautomer, increase_multi_cool_annealer_history_size(), packing::lazy_ig, packing::linmem_ig, packing::max_rotbump_energy, packing::multi_cool_annealer, nres_, optimize_H_, option, or_double_lazy_ig(), or_fix_his_tautomer(), or_lazy_ig(), or_linmem_ig(), or_multi_cool_annealer(), packing::repack_only, residue_tasks_, restrict_to_repacking(), core::pack::task::T, update_n_to_be_packed(), and user.

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

virtual

returns the lazy interaction interaction graph flag

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

References lazy_ig_.

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

virtual

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

virtual

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 )

virtual

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

References low_temp(), and low_temp_.

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

virtual

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

References low_temp_.

Referenced by low_temp().

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

virtual

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

virtual

use MultiCoolAnnealer?

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

References multi_cool_annealer_.

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

virtual

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 )

virtual

nonconst access to underlying ResidueLevelTask object

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

References n_to_be_packed_up_to_date_, and residue_tasks_.

Referenced by core::pack::make_new_symmetric_PackerTask_by_intersection(), and core::pack::make_new_symmetric_PackerTask_by_union().

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

virtual

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

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

References utility_exit_with_message.

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

virtual

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  )

virtual

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 )

virtual

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_command_line().

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

virtual

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_command_line().

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

virtual

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 )

virtual

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  )

virtual

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 )

virtual

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_command_line().

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

virtual

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

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

References linmem_ig_.

Referenced by initialize_from_command_line().

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

virtual

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_command_line().

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

virtual

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_preserve_c_beta ( bool  setting )

virtual

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

virtual

get function: can this position have a rotamer change?

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

References pack_residue_, and residue_tasks_.

Referenced by show(), and show_residue_task().

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

virtual

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

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

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

virtual

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

References being_packed(), nres_, and residue_tasks_.

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

virtual

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

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

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

virtual

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

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

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

virtual

const accessor for underlying ResidueLevelTask object

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

References residue_tasks_.

Referenced by core::pack::make_new_symmetric_PackerTask_by_intersection(), core::pack::make_new_symmetric_PackerTask_by_union(), show(), and show_residue_task().

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

virtual

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_command_line().

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

virtual

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

virtual

const accessor for the RotamerCouplings object

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

References rotamer_couplings_.

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

virtual

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

virtual

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

virtual

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 )

virtual

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

virtual

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

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

References rotamer_links_.

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

virtual

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 ( )

virtual

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

References IG_edge_reweights_, and nres_.

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

virtual

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

References core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), design_residue(), basic::options::option, pack_residue(), basic::options::OptionKeys::packing::print_pymol_selection, residue_task(), and total_residue().

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

virtual

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

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

virtual

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

References show_residue_task(), and total_residue().

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

virtual

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

virtual

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

References core::pack::task::ResidueLevelTask::adducts(), design_residue(), core::pack::task::ResidueLevelTask::ex1(), core::pack::task::ResidueLevelTask::ex1aro(), core::pack::task::ResidueLevelTask::ex1aro_exposed(), core::pack::task::ResidueLevelTask::ex2(), core::pack::task::ResidueLevelTask::ex2aro(), core::pack::task::ResidueLevelTask::ex2aro_exposed(), core::pack::task::ResidueLevelTask::ex3(), core::pack::task::ResidueLevelTask::ex4(), core::pack::task::ResidueLevelTask::extrachi_cutoff(), core::pack::task::ResidueLevelTask::fix_his_tautomer(), core::pack::task::ResidueLevelTask::flip_HNQ(), core::pack::task::ResidueLevelTask::get_original_residue(), core::pack::task::ResidueLevelTask::has_behavior(), core::pack::task::ResidueLevelTask::include_current(), core::pack::task::ResidueLevelTask::optimize_h(), pack_residue(), core::pack::task::ResidueLevelTask::preserve_c_beta(), residue_task(), and core::pack::task::ResidueLevelTask::sample_proton_chi().

Referenced by show_all_residue_tasks(), and show_residue_task().

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

virtual

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

References show_residue_task().

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

virtual

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

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

Referenced by core::pack::make_new_symmetric_PackerTask_by_intersection(), and core::pack::make_new_symmetric_PackerTask_by_requested_method().

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

virtual

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

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

Referenced by core::pack::make_new_symmetric_PackerTask_by_requested_method(), and core::pack::make_new_symmetric_PackerTask_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

virtual

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

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

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

virtual

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  )

virtual

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

virtual

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 )

virtual

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

References bump_check_, disallow_quench_, dlig_mem_limit_, double_lazy_ig_, high_temp_, IG_edge_reweights_, lazy_ig_, linmem_ig_, linmem_ig_history_size_, linmem_ig_history_size_at_default_, low_temp_, max_rotbump_energy_, mca_history_size_, multi_cool_annealer_, n_to_be_packed_, nres_, o, optimize_H_, residue_tasks_, rotamer_couplings_, rotamer_links_, core::pack::task::ResidueLevelTask_::update_commutative(), and utility_exit_with_message.

Referenced by core::pack::make_new_symmetric_PackerTask_by_intersection(), and core::pack::make_new_symmetric_PackerTask_by_union().

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_command_line(), 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

References o.

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

virtual

References o.

Referenced by core::pack::make_new_symmetric_PackerTask_by_intersection().

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

virtual

References o.

Referenced by core::pack::make_new_symmetric_PackerTask_by_union().

Member Data Documentation

bool core::pack::task::PackerTask_::bump_check_

private

Referenced by bump_check(), set_bump_check(), and update_commutative().

bool core::pack::task::PackerTask_::disallow_quench_

private

Referenced by disallow_quench(), and update_commutative().

Size core::pack::task::PackerTask_::dlig_mem_limit_

private

Referenced by decrease_double_lazy_ig_memlimit(), double_lazy_ig_memlimit(), and update_commutative().

bool core::pack::task::PackerTask_::double_lazy_ig_

private

linmem_ig overrides DoubleLazyIG

Referenced by double_lazy_ig(), or_double_lazy_ig(), and update_commutative().

Real core::pack::task::PackerTask_::high_temp_

private

Referenced by high_temp(), and update_commutative().

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

private

holds specific residue residue weights to be used in packing

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

bool core::pack::task::PackerTask_::lazy_ig_

private

linmem_ig overrides LazyIG

Referenced by lazy_ig(), or_lazy_ig(), and update_commutative().

bool core::pack::task::PackerTask_::linmem_ig_

private

linmem_ig overrides PDInteractionGraph

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

Size core::pack::task::PackerTask_::linmem_ig_history_size_

private

Referenced by decrease_linmem_ig_history_size(), linmem_ig_history_size(), and update_commutative().

bool core::pack::task::PackerTask_::linmem_ig_history_size_at_default_

private

Referenced by decrease_linmem_ig_history_size(), and update_commutative().

Real core::pack::task::PackerTask_::low_temp_

private

Referenced by low_temp(), and update_commutative().

Real core::pack::task::PackerTask_::max_rotbump_energy_

private

Referenced by and_max_rotbump_energy(), max_rotbump_energy(), and update_commutative().

Size core::pack::task::PackerTask_::mca_history_size_

private

Referenced by increase_multi_cool_annealer_history_size(), multi_cool_annealer_history_size(), and update_commutative().

bool core::pack::task::PackerTask_::multi_cool_annealer_

private

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

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(), update_commutative(), and update_n_to_be_packed().

bool core::pack::task::PackerTask_::n_to_be_packed_up_to_date_

mutableprivate

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

Size core::pack::task::PackerTask_::nres_

private

Referenced by add_behavior(), append_rotamer_operation(), append_rotamerset_operation(), design_any(), designing_residues(), initialize_extra_rotamer_flags_from_command_line(), initialize_from_command_line(), or_adducts(), or_fix_his_tautomer(), or_flip_HNQ(), or_include_current(), or_optimize_h_mode(), or_preserve_c_beta(), PackerTask_(), remap_residue_level_tasks(), repacking_residues(), restrict_to_repacking(), restrict_to_residues(), set_IGEdgeReweights(), temporarily_fix_everything(), total_residue(), update_commutative(), and update_n_to_be_packed().

bool core::pack::task::PackerTask_::optimize_H_

private

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

Referenced by initialize_from_command_line(), or_optimize_h_mode(), and update_commutative().

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().

utility::vector1< ResidueLevelTask_ > core::pack::task::PackerTask_::residue_tasks_

private

vector of ResidueLevelTasks

Referenced by add_behavior(), adducts(), append_rotamer_operation(), append_rotamerset_operation(), clean_residue_task(), design_any(), design_residue(), designing_residues(), has_behavior(), include_current(), initialize_extra_rotamer_flags_from_command_line(), initialize_from_command_line(), nonconst_residue_task(), or_adducts(), or_fix_his_tautomer(), or_flip_HNQ(), or_include_current(), or_optimize_h_mode(), or_preserve_c_beta(), pack_residue(), PackerTask_(), remap_residue_level_tasks(), repacking_residues(), residue_task(), restrict_to_repacking(), restrict_to_residues(), target_type(), task_string(), update_commutative(), and update_n_to_be_packed().

RotamerCouplingsCOP core::pack::task::PackerTask_::rotamer_couplings_

private

Referenced by or_multi_cool_annealer(), rotamer_couplings(), rotamer_couplings_exist(), and update_commutative().

RotamerLinksCOP core::pack::task::PackerTask_::rotamer_links_

private

Referenced by or_multi_cool_annealer(), rotamer_links(), rotamer_links_exist(), and update_commutative().

PackerTaskSymmetryStatus core::pack::task::PackerTask_::symmetry_status_

private

---

The documentation for this class was generated from the following files:

• src/core/pack/task/PackerTask_.hh
• src/core/pack/task/PackerTask_.cc