Rosetta Core  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
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 PackerTaskinitialize_from_command_line ()
 read command line options (but not resfile) to set the state of the PackerTask, NOT IN CONSTRUCTOR More...
 
virtual PackerTaskinitialize_extra_rotamer_flags_from_command_line ()
 read only the command line options for extra rotamer building; More...
 
virtual PackerTaskrestrict_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 PackerTaskrestrict_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 ResidueLevelTasknonconst_residue_task (Size resid)
 nonconst access to underlying ResidueLevelTask object More...
 
virtual utility::vector1< boolrepacking_residues () const
 
virtual utility::vector1< booldesigning_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 PackerTaskoperator= (PackerTask const &)
 

Private Attributes

Size nres_
 
utility::vector1< boolpack_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
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
void core::pack::task::PackerTask_::disallow_quench ( bool const &  disallow_quench)
virtual
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
bool core::pack::task::PackerTask_::has_behavior ( Size  resid) const
virtual
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
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
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
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
utility::vector1< bool > core::pack::task::PackerTask_::repacking_residues ( ) const
virtual
void core::pack::task::PackerTask_::request_symmetrize_by_intersection ( )
virtual
void core::pack::task::PackerTask_::request_symmetrize_by_union ( )
virtual
ResidueLevelTask const & core::pack::task::PackerTask_::residue_task ( Size  resid) const
virtual
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
void core::pack::task::PackerTask_::show ( std::ostream &  out) const
virtual
void core::pack::task::PackerTask_::show ( ) const
virtual
void core::pack::task::PackerTask_::show_all_residue_tasks ( std::ostream &  out) const
virtual
void core::pack::task::PackerTask_::show_all_residue_tasks ( ) const
virtual
void core::pack::task::PackerTask_::show_residue_task ( std::ostream &  out,
Size  resid 
) const
virtual
void core::pack::task::PackerTask_::show_residue_task ( Size  resid) const
virtual
bool core::pack::task::PackerTask_::symmetrize_by_intersection ( ) const
virtual
bool core::pack::task::PackerTask_::symmetrize_by_union ( ) const
virtual
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
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
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

References o.

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_
private
bool core::pack::task::PackerTask_::disallow_quench_
private
Size core::pack::task::PackerTask_::dlig_mem_limit_
private
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
bool core::pack::task::PackerTask_::linmem_ig_history_size_at_default_
private
Real core::pack::task::PackerTask_::low_temp_
private

Referenced by low_temp(), and update_commutative().

Real core::pack::task::PackerTask_::max_rotbump_energy_
private
Size core::pack::task::PackerTask_::mca_history_size_
private
bool core::pack::task::PackerTask_::multi_cool_annealer_
private
Size core::pack::task::PackerTask_::n_to_be_packed_
mutableprivate
bool core::pack::task::PackerTask_::n_to_be_packed_up_to_date_
mutableprivate
Size core::pack::task::PackerTask_::nres_
private
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
RotamerCouplingsCOP core::pack::task::PackerTask_::rotamer_couplings_
private
RotamerLinksCOP core::pack::task::PackerTask_::rotamer_links_
private
PackerTaskSymmetryStatus core::pack::task::PackerTask_::symmetry_status_
private

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