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

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_:
Inheritance graph
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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...
 
PackerTaskinitialize_from_command_line () override
 read command line options (but not resfile) to set the state of the PackerTask, NOT IN CONSTRUCTOR More...
 
PackerTaskinitialize_extra_rotamer_flags_from_command_line () override
 read only the command line options for extra rotamer building; More...
 
PackerTaskinitialize_from_options (utility::options::OptionCollection const &options) override
 
PackerTaskinitialize_extra_rotamer_flags_from_options (utility::options::OptionCollection const &options) override
 read only the command line options for extra rotamer building; More...
 
PackerTaskrestrict_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...
 
PackerTaskrestrict_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...
 
ResidueLevelTasknonconst_residue_task (Size resid) override
 nonconst access to underlying ResidueLevelTask object More...
 
utility::vector1< boolrepacking_residues () const override
 
utility::vector1< booldesigning_residues () const override
 
bool keep_sequence_symmetry () const override
 
void keep_sequence_symmetry (bool const setting) override
 
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 PackerTaskoperator= (PackerTask const &)
 

Private Attributes

bool is_initialized_ = false
 Has this PackerTask been initialized with a PackerPalette? More...
 
Size nres_
 
utility::vector1< boolpack_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
 
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
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
void core::pack::task::PackerTask_::disallow_quench ( bool const &  disallow_quench)
overridevirtual
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
bool core::pack::task::PackerTask_::has_behavior ( Size  resid) const
overridevirtual
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?

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
void core::pack::task::PackerTask_::keep_sequence_symmetry ( bool const  setting)
inlineoverridevirtual
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
void core::pack::task::PackerTask_::remap_residue_level_tasks ( core::id::SequenceMappingCOP  seqmap,
core::pose::Pose const &  pose 
)
overridevirtual
utility::vector1< bool > core::pack::task::PackerTask_::repacking_residues ( ) const
overridevirtual
void core::pack::task::PackerTask_::request_symmetrize_by_intersection ( )
overridevirtual
void core::pack::task::PackerTask_::request_symmetrize_by_union ( )
overridevirtual
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_.

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
void core::pack::task::PackerTask_::set_smart_annealer ( bool  setting)
inlineoverridevirtual
void core::pack::task::PackerTask_::set_smart_annealer_cutoff ( core::Real  setting)
inlineoverridevirtual
void core::pack::task::PackerTask_::set_smart_annealer_disable_during_quench ( bool  setting)
inlineoverridevirtual
void core::pack::task::PackerTask_::set_smart_annealer_model ( std::string const &  setting)
inlineoverridevirtual
void core::pack::task::PackerTask_::set_smart_annealer_pick_again ( bool  setting)
inlineoverridevirtual
void core::pack::task::PackerTask_::show ( std::ostream &  out) const
overridevirtual
void core::pack::task::PackerTask_::show ( ) const
overridevirtual
void core::pack::task::PackerTask_::show_all_residue_tasks ( std::ostream &  out) const
overridevirtual
void core::pack::task::PackerTask_::show_all_residue_tasks ( ) const
overridevirtual
void core::pack::task::PackerTask_::show_residue_task ( std::ostream &  out,
Size  resid 
) const
overridevirtual
void core::pack::task::PackerTask_::show_residue_task ( Size  resid) const
overridevirtual
bool core::pack::task::PackerTask_::smart_annealer ( ) const
inlineoverridevirtual
core::Real core::pack::task::PackerTask_::smart_annealer_cutoff ( ) const
inlineoverridevirtual
bool core::pack::task::PackerTask_::smart_annealer_disable_during_quench ( ) const
inlineoverridevirtual
std::string core::pack::task::PackerTask_::smart_annealer_model ( ) const
inlineoverridevirtual
bool core::pack::task::PackerTask_::smart_annealer_pick_again ( ) const
inlineoverridevirtual
bool core::pack::task::PackerTask_::symmetrize_by_intersection ( ) const
overridevirtual
bool core::pack::task::PackerTask_::symmetrize_by_union ( ) const
overridevirtual
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
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
void core::pack::task::PackerTask_::update_n_to_be_packed ( ) const
private
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
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
bool core::pack::task::PackerTask_::linmem_ig_history_size_at_default_ = true
private
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
Size core::pack::task::PackerTask_::mca_history_size_ = 1
private
bool core::pack::task::PackerTask_::multi_cool_annealer_ = false
private
Size core::pack::task::PackerTask_::n_to_be_packed_
mutableprivate
bool core::pack::task::PackerTask_::n_to_be_packed_up_to_date_ = true
mutableprivate
Size core::pack::task::PackerTask_::nres_
private
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().

core::pack::palette::PackerPaletteCOP core::pack::task::PackerTask_::packer_palette_
private

The PackerPalette, which tells the PackerTask what the default set of residue types is in the absence of TaskOperations.

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

Referenced by clean_residue_task(), PackerTask_(), and remap_residue_level_tasks().

bool core::pack::task::PackerTask_::precompute_ig_ = false
private

Referenced by or_precompute_ig(), and precompute_ig().

utility::vector1< ResidueLevelTask_ > core::pack::task::PackerTask_::residue_tasks_
private
RotamerCouplingsCOP core::pack::task::PackerTask_::rotamer_couplings_
private
RotamerLinksCOP core::pack::task::PackerTask_::rotamer_links_
private
rotamer_set::RotSetsOperationList core::pack::task::PackerTask_::rotsetsops_
private
bool core::pack::task::PackerTask_::smart_annealer_ = false
private
core::Real core::pack::task::PackerTask_::smart_annealer_cutoff_ = 0.25
private
bool core::pack::task::PackerTask_::smart_annealer_disable_during_quench_ = true
private
std::string core::pack::task::PackerTask_::smart_annealer_model_ = "generation2"
private
bool core::pack::task::PackerTask_::smart_annealer_pick_again_ = true
private
PackerTaskSymmetryStatus core::pack::task::PackerTask_::symmetry_status_ = NO_SYMMETRIZATION_REQUEST
private

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