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Rosetta 3.4
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Rosetta 3.4
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the PackerTask controls what rotameric (including sequence) changes the packer is allowed to make More...
#include <PackerTask_.hh>
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 PackerTask & | initialize_from_command_line () |
| read command line options (but not resfile) to set the state of the PackerTask, NOT IN CONSTRUCTOR | |
| virtual PackerTask & | initialize_extra_rotamer_flags_from_command_line () |
| read only the command line options for extra rotamer building; | |
| virtual PackerTask & | restrict_to_residues (utility::vector1< bool > const &residues_allowed_to_be_packed) |
| turn off packing for residues passed false; can't turn on packing | |
| virtual PackerTask & | restrict_to_repacking () |
| turn off designing (sequence changing) all residues | |
| virtual ResidueLevelTask const & | residue_task (Size resid) const |
| const accessor for underlying ResidueLevelTask object | |
| virtual ResidueLevelTask & | nonconst_residue_task (Size resid) |
| nonconst access to underlying ResidueLevelTask object | |
| virtual utility::vector1< bool > | repacking_residues () const |
| virtual utility::vector1< bool > | designing_residues () const |
| virtual bool | rotamer_couplings_exist () const |
| is there at RotamerCouplings object to worry about? (for DNA GC AT pairing, etc) | |
| 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) |
the PackerTask controls what rotameric (including sequence) changes the packer is allowed to make
| 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
| void core::pack::task::PackerTask_::add_behavior | ( | std::string const & | behavior | ) | [virtual] |
Implements core::pack::task::PackerTask.
| void core::pack::task::PackerTask_::add_behavior | ( | std::string const & | behavior, |
| Size | resid | ||
| ) | [virtual] |
Implements core::pack::task::PackerTask.
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] |
Implements core::pack::task::PackerTask.
| void core::pack::task::PackerTask_::append_rotamerset_operation | ( | rotamer_set::RotamerSetOperationOP | rotsetop | ) | [virtual] |
Implements core::pack::task::PackerTask.
alias for above
Implements core::pack::task::PackerTask.
References design_residue().
Referenced by design_any(), design_residue(), and designing_residues().
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().
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] |
Implements core::pack::task::PackerTask.
References being_designed().
| void core::pack::task::PackerTask_::disallow_quench | ( | bool const & | disallow_quench | ) | [virtual] |
Implements core::pack::task::PackerTask.
References disallow_quench().
| 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] |
Implements core::pack::task::PackerTask.
Implements core::pack::task::PackerTask.
| 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.
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] |
read command line options (but not resfile) to set the state of the PackerTask, NOT IN CONSTRUCTOR
Implements core::pack::task::PackerTask.
References and_max_rotbump_energy(), increase_multi_cool_annealer_history_size(), or_double_lazy_ig(), or_fix_his_tautomer(), or_lazy_ig(), or_linmem_ig(), or_multi_cool_annealer(), restrict_to_repacking(), and core::pack::task::T().
| 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.
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.
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.
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] |
Implements core::pack::task::PackerTask.
References core::pose::Pose::residue(), core::id::SequenceMapping::reverse(), and core::pose::Pose::total_residue().
| utility::vector1< bool > core::pack::task::PackerTask_::repacking_residues | ( | ) | const [virtual] |
Implements core::pack::task::PackerTask.
References being_packed().
| 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] |
Implements core::pack::task::PackerTask.
| 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] |
Implements core::pack::task::PackerTask.
References core::pose::Pose::pdb_info(), and total_residue().
| 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().
1.7.4
