Rosetta 3.4
Public Member Functions
core::pack::task::PackerTask_ Class Reference

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

#include <PackerTask_.hh>

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List of all members.

Public Member Functions

 PackerTask_ (pose::Pose const &pose)
 constructor; the PackerTask will always need a pose!
virtual ~PackerTask_ ()
 dtor
PackerTaskOP clone () const
 copy method
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!!!!
virtual Size total_residue () const
 number of residues in the input pose, for convienience (PackerTask does not handle variable length)
virtual void temporarily_fix_everything ()
 turn off packing at all positions
virtual void temporarily_set_pack_residue (int resid, bool setting)
 reset packer mutability arbitrarily for a given residue
virtual bool pack_residue (int resid) const
 get function: can this position have a rotamer change?
virtual bool being_packed (Size resid) const
 alias for above
virtual Size num_to_be_packed () const
 get function: how many positions can have rotamer changes?
virtual bool design_residue (int resid) const
 get function: can this position have a sequence change?
virtual bool being_designed (Size resid) const
 alias for above
virtual bool design_any () const
 get function: can any positions have a sequence change?
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.
virtual bool bump_check () const
 get function: has bump_check been requested?
virtual void and_max_rotbump_energy (Real setting)
 Decrease the max_rotbump_energy threshold above which rotamers are rejected.
virtual Real max_rotbump_energy () const
 get function: what is the energy threshold above which rotamers should be rejected
virtual void or_include_current (bool setting)
 for all positions, turn on include_current if false, do nothing if already true
virtual void or_include_current (bool setting, Size resid)
 for one position, turn on include_current if false, do nothing if already true
virtual bool include_current (Size resid) const
 get function: what is include_current for this residue?
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::ResidueTypeCAP target_type (Size resid) const
 return the targeted type (may be null pointer)
virtual void or_adducts (bool setting)
 for all positions, disable adducts if false, do nothing if true
virtual void or_adducts (bool setting, Size resid)
 for one position, disable adducts if false, do nothing if true
virtual bool adducts (Size resid) const
 include adducts at this residue
virtual void or_optimize_h_mode (bool setting)
 if setting == true, turns on optimize_H_mode for all residues
virtual void or_preserve_c_beta (bool setting)
 if setting == true, preserves c-beta during rotamer building for all residues
virtual void or_flip_HNQ (bool setting)
 if setting == true, turns on optimize_H_mode and flip_HNQ for all residues
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
virtual void or_linmem_ig (bool setting)
 if setting == true, turns on linear-memory interaction graph usage
virtual bool linmem_ig () const
 returns the linear-memory interaction graph flag
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.
virtual bool lazy_ig () const
 returns the lazy interaction interaction graph flag
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.
virtual bool double_lazy_ig () const
 Returns the double-lazy interaction graph flag.
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.
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.
virtual void or_multi_cool_annealer (bool setting)
 if setting == true, turns on MultiCoolAnnealer -- so long as rotamer couplings are not also turned on.
virtual bool multi_cool_annealer () const
 use MultiCoolAnnealer?
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.
virtual Size multi_cool_annealer_history_size () const
 returns the requested size for the MultiCoolAnnealer
virtual PackerTaskinitialize_from_command_line ()
 read command line options (but not resfile) to set the state of the PackerTask, NOT IN CONSTRUCTOR
virtual PackerTaskinitialize_extra_rotamer_flags_from_command_line ()
 read only the command line options for extra rotamer building;
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
virtual PackerTaskrestrict_to_repacking ()
 turn off designing (sequence changing) all residues
virtual ResidueLevelTask const & residue_task (Size resid) const
 const accessor for underlying ResidueLevelTask object
virtual ResidueLevelTasknonconst_residue_task (Size resid)
 nonconst access to underlying ResidueLevelTask object
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)
virtual RotamerCouplingsCOP rotamer_couplings () const
 const accessor for the RotamerCouplings object
virtual void rotamer_couplings (RotamerCouplingsCOP setting)
 setter for the RotamerCouplings object
virtual bool rotamer_links_exist () const
 is there at RotamerLinks object to worry about? (for repeat linking
virtual RotamerLinksCOP rotamer_links () const
 const accessor for the RotamerLinks object
virtual void rotamer_links (RotamerLinksCOP setting)
 setter for the RotamerLinks object
virtual IGEdgeReweightContainerCOP IGEdgeReweights () const
 accesor for residue residue weight map
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 &pose)

Detailed Description

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


Constructor & Destructor Documentation

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

constructor; the PackerTask will always need a 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 core::pose::Pose::residue().

Referenced by clone().

core::pack::task::PackerTask_::~PackerTask_ ( ) [virtual]

dtor


Member Function Documentation

void core::pack::task::PackerTask_::add_behavior ( std::string const &  behavior) [virtual]
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.

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.

Referenced by initialize_from_command_line().

void core::pack::task::PackerTask_::append_rotamer_operation ( rotamer_set::RotamerOperationOP  rotop) [virtual]
void core::pack::task::PackerTask_::append_rotamerset_operation ( rotamer_set::RotamerSetOperationOP  rotsetop) [virtual]
virtual bool core::pack::task::PackerTask_::being_designed ( Size  resid) const [inline, virtual]

alias for above

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

References design_residue().

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

virtual bool core::pack::task::PackerTask_::being_packed ( Size  resid) const [inline, virtual]

alias for above

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

References pack_residue().

Referenced by repacking_residues().

bool core::pack::task::PackerTask_::bump_check ( ) const [virtual]

get function: has bump_check been requested?

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

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.

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.

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().

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().

Referenced by being_designed().

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.

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.

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.

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]
Real core::pack::task::PackerTask_::high_temp ( ) const [virtual]

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

Referenced by high_temp().

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

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

References high_temp().

IGEdgeReweightContainerCOP core::pack::task::PackerTask_::IGEdgeReweights ( ) const [virtual]

accesor for residue residue weight map

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

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.

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.

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.

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.

bool core::pack::task::PackerTask_::linmem_ig ( ) const [virtual]

returns the linear-memory interaction graph flag

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

Real core::pack::task::PackerTask_::low_temp ( ) const [virtual]

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

Referenced by low_temp().

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

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

References 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.

bool core::pack::task::PackerTask_::multi_cool_annealer ( ) const [virtual]

use MultiCoolAnnealer?

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

Size core::pack::task::PackerTask_::multi_cool_annealer_history_size ( ) const [virtual]

returns the requested size for the MultiCoolAnnealer

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

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

nonconst access to underlying ResidueLevelTask object

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Referenced by being_packed().

void core::pack::task::PackerTask_::remap_residue_level_tasks ( core::id::SequenceMappingCOP  seqmap,
core::pose::Pose pose 
) [virtual]
utility::vector1< bool > core::pack::task::PackerTask_::repacking_residues ( ) const [virtual]
ResidueLevelTask const & core::pack::task::PackerTask_::residue_task ( Size  resid) const [virtual]

const accessor for underlying ResidueLevelTask object

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

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 core::pack::task::PackerTask::restrict_to_repacking().

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.

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

setter for the RotamerCouplings object

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

PackerTask::RotamerCouplingsCOP core::pack::task::PackerTask_::rotamer_couplings ( ) const [virtual]

const accessor for the RotamerCouplings object

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

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.

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.

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.

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.

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.

IGEdgeReweightContainerOP core::pack::task::PackerTask_::set_IGEdgeReweights ( ) [virtual]
chemical::ResidueTypeCAP core::pack::task::PackerTask_::target_type ( Size  resid) const [virtual]

return the targeted type (may be null pointer)

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]

turn off packing at all positions

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.

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

reset packer mutability arbitrarily for a given residue

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

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

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.

Referenced by task_string().


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