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protocols::pack_daemon::PackDaemon Class Reference

#include <PackDaemon.hh>

Inheritance diagram for protocols::pack_daemon::PackDaemon:
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Collaboration diagram for protocols::pack_daemon::PackDaemon:
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Public Types

typedef core::Real Real
 
typedef core::Size Size
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseOP PoseOP
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
core::scoring::ScoreFunction 		ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 		ScoreFunctionOP
 
typedef
core::scoring::ScoreFunctionCOP 		ScoreFunctionCOP
 
typedef
core::pack::task::PackerTask 		PackerTask
 
typedef
core::pack::task::PackerTaskOP 		PackerTaskOP
 
typedef
core::pack::task::PackerTaskCOP 		PackerTaskCOP
 
typedef
core::pack::interaction_graph::InteractionGraphBaseOP 		InteractionGraphBaseOP
 
typedef
core::pack::interaction_graph::InteractionGraphBaseCOP 		InteractionGraphBaseCOP
 
typedef
core::pack::interaction_graph::FixedBBInteractionGraphOP 		FixedBBInteractionGraphOP
 
typedef
core::pack::interaction_graph::FixedBBInteractionGraphCOP 		FixedBBInteractionGraphCOP
 
typedef
core::pack::rotamer_set::RotamerSets 		RotamerSets
 
typedef
core::pack::rotamer_set::RotamerSetsOP 		RotamerSetsOP
 
typedef
core::pack::rotamer_set::RotamerSetsCOP 		RotamerSetsCOP
 
typedef
protocols::genetic_algorithm::Entity 		Entity
 
typedef
protocols::genetic_algorithm::EntityOP 		EntityOP
 
typedef
protocols::genetic_algorithm::EntityElement 		EntityElement
 
typedef
protocols::genetic_algorithm::EntityElements 		EntityElements
 
typedef
protocols::genetic_algorithm::EntityElementOP 		EntityElementOP
 
typedef
protocols::genetic_algorithm::Vec1Hash 		Vec1Hash
 
typedef utility::vector1< int > RotamerAssignment
 
typedef std::pair
< RotamerAssignment, Real > 		RotamerAssignmentAndEnergy
 
typedef
protocols::genetic_algorithm::EntityElementsEqual 		EntElemEq
 
typedef boost::unordered_map
< EntityElements,
RotamerAssignmentAndEnergy,
Vec1Hash, EntElemEq > 		EntityToRotamerHash
 

Public Member Functions

 PackDaemon ()
 
virtual ~PackDaemon ()
 
void set_pose_and_task (Pose const &, PackerTask const &)
 
void set_score_function (ScoreFunction const &)
 
void set_entity_correspondence (EntityCorrespondence const &)
 
void set_include_background_energies (bool setting)
 
void set_dlig_nmeg_limit (Size setting)
 restrict the amount of memory spent on storing Rotamer Pair Energies in the DoubleLazyInteractionGraph; More...
 
void setup ()
 
Real compute_energy_for_assignment (Entity const &)
 Repack the structure with the Entity This function proceeds in two steps: it creates a list of rotamer indices to be used during the repacking, and then it uses that list to repack the rotamers. The first step is taken care of by the select_rotamer_subset method. More...
 
utility::vector0< int > select_rotamer_subset (Entity const &) const
 
void mark_last_entity_as_important ()
 
void mark_entity_as_unimportant (Entity const &)
 
PoseCOP pose () const
 
ScoreFunctionCOP score_function () const
 
PackerTaskCOP task () const
 
EntityCorrespondenceCOP correspondence () const
 
FixedBBInteractionGraphCOP ig () const
 
RotamerSetsCOP rot_sets () const
 
RotamerAssignmentAndEnergy const & best_assignment () const
 
RotamerAssignmentAndEnergy const & last_assignment () const
 
PoseOP recreate_pose_for_entity (Entity const &) const
 
void assign_last_rotamers_to_pose (Pose &pose) const
 
void print_entity_history () const
 

Private Member Functions

void calculate_background_energies ()
 

Private Attributes

PoseOP pose_
 
ScoreFunctionOP score_function_
 
PackerTaskOP task_
 
EntityCorrespondenceOP correspondence_
 
bool include_background_energies_
 
Real background_energies_
 
bool setup_complete_
 
FixedBBInteractionGraphOP ig_
 
RotamerSetsOP rot_sets_
 
QuickRepackerOP repacker_
 
bool best_assignment_valid_
 
RotamerAssignmentAndEnergy best_assignment_
 
EntityOP best_entity_
 
RotamerAssignmentAndEnergy last_assignment_
 
EntityOP last_entity_
 
EntityToRotamerHash prev_state_hash_
 

Detailed Description

Definition at line 64 of file PackDaemon.hh.

Member Typedef Documentation

typedef protocols::genetic_algorithm::EntityElementsEqual protocols::pack_daemon::PackDaemon::EntElemEq

Definition at line 96 of file PackDaemon.hh.

typedef protocols::genetic_algorithm::Entity protocols::pack_daemon::PackDaemon::Entity

Definition at line 87 of file PackDaemon.hh.

typedef protocols::genetic_algorithm::EntityElement protocols::pack_daemon::PackDaemon::EntityElement

Definition at line 89 of file PackDaemon.hh.

typedef protocols::genetic_algorithm::EntityElementOP protocols::pack_daemon::PackDaemon::EntityElementOP

Definition at line 91 of file PackDaemon.hh.

typedef protocols::genetic_algorithm::EntityElements protocols::pack_daemon::PackDaemon::EntityElements

Definition at line 90 of file PackDaemon.hh.

typedef protocols::genetic_algorithm::EntityOP protocols::pack_daemon::PackDaemon::EntityOP

Definition at line 88 of file PackDaemon.hh.

typedef boost::unordered_map< EntityElements, RotamerAssignmentAndEnergy, Vec1Hash, EntElemEq > protocols::pack_daemon::PackDaemon::EntityToRotamerHash

Definition at line 97 of file PackDaemon.hh.

typedef core::pack::interaction_graph::FixedBBInteractionGraphCOP protocols::pack_daemon::PackDaemon::FixedBBInteractionGraphCOP

Definition at line 82 of file PackDaemon.hh.

typedef core::pack::interaction_graph::FixedBBInteractionGraphOP protocols::pack_daemon::PackDaemon::FixedBBInteractionGraphOP

Definition at line 81 of file PackDaemon.hh.

typedef core::pack::interaction_graph::InteractionGraphBaseCOP protocols::pack_daemon::PackDaemon::InteractionGraphBaseCOP

Definition at line 80 of file PackDaemon.hh.

typedef core::pack::interaction_graph::InteractionGraphBaseOP protocols::pack_daemon::PackDaemon::InteractionGraphBaseOP

Definition at line 79 of file PackDaemon.hh.

typedef core::pack::task::PackerTask protocols::pack_daemon::PackDaemon::PackerTask

Definition at line 75 of file PackDaemon.hh.

typedef core::pack::task::PackerTaskCOP protocols::pack_daemon::PackDaemon::PackerTaskCOP

Definition at line 77 of file PackDaemon.hh.

typedef core::pack::task::PackerTaskOP protocols::pack_daemon::PackDaemon::PackerTaskOP

Definition at line 76 of file PackDaemon.hh.

typedef core::pose::Pose protocols::pack_daemon::PackDaemon::Pose

Definition at line 69 of file PackDaemon.hh.

typedef core::pose::PoseCOP protocols::pack_daemon::PackDaemon::PoseCOP

Definition at line 71 of file PackDaemon.hh.

typedef core::pose::PoseOP protocols::pack_daemon::PackDaemon::PoseOP

Definition at line 70 of file PackDaemon.hh.

typedef core::Real protocols::pack_daemon::PackDaemon::Real

Definition at line 66 of file PackDaemon.hh.

typedef utility::vector1< int > protocols::pack_daemon::PackDaemon::RotamerAssignment

Definition at line 94 of file PackDaemon.hh.

typedef std::pair< RotamerAssignment, Real > protocols::pack_daemon::PackDaemon::RotamerAssignmentAndEnergy

Definition at line 95 of file PackDaemon.hh.

typedef core::pack::rotamer_set::RotamerSets protocols::pack_daemon::PackDaemon::RotamerSets

Definition at line 83 of file PackDaemon.hh.

typedef core::pack::rotamer_set::RotamerSetsCOP protocols::pack_daemon::PackDaemon::RotamerSetsCOP

Definition at line 85 of file PackDaemon.hh.

typedef core::pack::rotamer_set::RotamerSetsOP protocols::pack_daemon::PackDaemon::RotamerSetsOP

Definition at line 84 of file PackDaemon.hh.

typedef core::scoring::ScoreFunction protocols::pack_daemon::PackDaemon::ScoreFunction

Definition at line 72 of file PackDaemon.hh.

typedef core::scoring::ScoreFunctionCOP protocols::pack_daemon::PackDaemon::ScoreFunctionCOP

Definition at line 74 of file PackDaemon.hh.

typedef core::scoring::ScoreFunctionOP protocols::pack_daemon::PackDaemon::ScoreFunctionOP

Definition at line 73 of file PackDaemon.hh.

typedef core::Size protocols::pack_daemon::PackDaemon::Size

Definition at line 67 of file PackDaemon.hh.

typedef protocols::genetic_algorithm::Vec1Hash protocols::pack_daemon::PackDaemon::Vec1Hash

Definition at line 92 of file PackDaemon.hh.

Constructor & Destructor Documentation

protocols::pack_daemon::PackDaemon::PackDaemon ( )

Definition at line 76 of file PackDaemon.cc.

References best_assignment_, and last_assignment_.

protocols::pack_daemon::PackDaemon::~PackDaemon ( )
virtual

Definition at line 86 of file PackDaemon.cc.

Member Function Documentation

void protocols::pack_daemon::PackDaemon::assign_last_rotamers_to_pose ( Pose &  pose) const

Definition at line 395 of file PackDaemon.cc.

References last_assignment_, core::pose::Pose::replace_residue(), and rot_sets_.

PackDaemon::RotamerAssignmentAndEnergy const & protocols::pack_daemon::PackDaemon::best_assignment ( ) const

Definition at line 365 of file PackDaemon.cc.

References best_assignment_.

void protocols::pack_daemon::PackDaemon::calculate_background_energies ( )
private

Definition at line 429 of file PackDaemon.cc.

References background_energies_, core::graph::Node::const_upper_edge_list_end(), core::scoring::EnergyEdge::fill_energy_map(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), pose_, score_function_, and task_.

Referenced by setup().

PackDaemon::Real protocols::pack_daemon::PackDaemon::compute_energy_for_assignment ( Entity const &  entity)

Repack the structure with the Entity This function proceeds in two steps: it creates a list of rotamer indices to be used during the repacking, and then it uses that list to repack the rotamers. The first step is taken care of by the select_rotamer_subset method.

Definition at line 213 of file PackDaemon.cc.

References background_energies_, best_assignment_, best_assignment_valid_, best_entity_, protocols::genetic_algorithm::Entity::clone(), last_assignment_, last_entity_, repacker_, and select_rotamer_subset().

EntityCorrespondenceCOP protocols::pack_daemon::PackDaemon::correspondence ( ) const

Definition at line 360 of file PackDaemon.cc.

References correspondence_.

PackDaemon::FixedBBInteractionGraphCOP protocols::pack_daemon::PackDaemon::ig ( ) const

Definition at line 361 of file PackDaemon.cc.

References ig_.

Referenced by setup().

PackDaemon::RotamerAssignmentAndEnergy const & protocols::pack_daemon::PackDaemon::last_assignment ( ) const

Definition at line 368 of file PackDaemon.cc.

References last_assignment_.

void protocols::pack_daemon::PackDaemon::mark_entity_as_unimportant ( Entity const &  ent)

Definition at line 351 of file PackDaemon.cc.

References prev_state_hash_, and protocols::genetic_algorithm::Entity::traits().

void protocols::pack_daemon::PackDaemon::mark_last_entity_as_important ( )

Definition at line 339 of file PackDaemon.cc.

References last_assignment_, last_entity_, and prev_state_hash_.

PackDaemon::PoseCOP protocols::pack_daemon::PackDaemon::pose ( ) const

Definition at line 357 of file PackDaemon.cc.

References pose_.

void protocols::pack_daemon::PackDaemon::print_entity_history ( ) const

Definition at line 411 of file PackDaemon.cc.

References prev_state_hash_, and protocols::pack_daemon::TR().

Referenced by recreate_pose_for_entity().

PackDaemon::PoseOP protocols::pack_daemon::PackDaemon::recreate_pose_for_entity ( Entity const &  ent) const

Definition at line 370 of file PackDaemon.cc.

References pose_, prev_state_hash_, print_entity_history(), rot_sets_, protocols::pack_daemon::TR(), and protocols::genetic_algorithm::Entity::traits().

PackDaemon::RotamerSetsCOP protocols::pack_daemon::PackDaemon::rot_sets ( ) const

Definition at line 362 of file PackDaemon.cc.

References rot_sets_.

PackDaemon::ScoreFunctionCOP protocols::pack_daemon::PackDaemon::score_function ( ) const

Definition at line 358 of file PackDaemon.cc.

References score_function_.

utility::vector0< int > protocols::pack_daemon::PackDaemon::select_rotamer_subset ( Entity const &  entity) const

Definition at line 289 of file PackDaemon.cc.

References correspondence_, rot_sets_, and protocols::genetic_algorithm::Entity::traits().

Referenced by compute_energy_for_assignment().

void protocols::pack_daemon::PackDaemon::set_dlig_nmeg_limit ( Size  setting)

restrict the amount of memory spent on storing Rotamer Pair Energies in the DoubleLazyInteractionGraph;

Definition at line 123 of file PackDaemon.cc.

References setup_complete_, task_, and protocols::pack_daemon::TR().

void protocols::pack_daemon::PackDaemon::set_entity_correspondence ( EntityCorrespondence const &  ec)

Definition at line 108 of file PackDaemon.cc.

References correspondence_, protocols::pack_daemon::EntityCorrespondence::num_residues(), pose_, and setup_complete_.

void protocols::pack_daemon::PackDaemon::set_include_background_energies ( bool  setting)

Definition at line 130 of file PackDaemon.cc.

References include_background_energies_, and setup_complete_.

void protocols::pack_daemon::PackDaemon::set_pose_and_task ( Pose const &  pose,
PackerTask const &  task 
)

Definition at line 90 of file PackDaemon.cc.

References core::pack::task::PackerTask::clone(), pose_, setup_complete_, task_, and core::pack::task::PackerTask::total_residue().

Referenced by protocols::pack_daemon::DaemonSet::add_pack_daemon().

void protocols::pack_daemon::PackDaemon::set_score_function ( ScoreFunction const &  sfxn)

Definition at line 102 of file PackDaemon.cc.

References score_function_, and setup_complete_.

void protocols::pack_daemon::PackDaemon::setup ( )

Definition at line 136 of file PackDaemon.cc.

References best_assignment_, calculate_background_energies(), correspondence_, ig(), ig_, include_background_energies_, last_assignment_, core::pack::pack_rotamers_setup(), pose_, repacker_, rot_sets_, score_function_, setup_complete_, task_, and protocols::pack_daemon::TR().

PackDaemon::PackerTaskCOP protocols::pack_daemon::PackDaemon::task ( ) const

Definition at line 359 of file PackDaemon.cc.

References task_.

Member Data Documentation

Real protocols::pack_daemon::PackDaemon::background_energies_
private

Definition at line 158 of file PackDaemon.hh.

Referenced by calculate_background_energies(), and compute_energy_for_assignment().

RotamerAssignmentAndEnergy protocols::pack_daemon::PackDaemon::best_assignment_
private

Definition at line 175 of file PackDaemon.hh.

Referenced by best_assignment(), compute_energy_for_assignment(), PackDaemon(), and setup().

bool protocols::pack_daemon::PackDaemon::best_assignment_valid_
private

Definition at line 174 of file PackDaemon.hh.

Referenced by compute_energy_for_assignment().

EntityOP protocols::pack_daemon::PackDaemon::best_entity_
private

Definition at line 176 of file PackDaemon.hh.

Referenced by compute_energy_for_assignment().

EntityCorrespondenceOP protocols::pack_daemon::PackDaemon::correspondence_
private

Definition at line 151 of file PackDaemon.hh.

Referenced by correspondence(), select_rotamer_subset(), set_entity_correspondence(), and setup().

FixedBBInteractionGraphOP protocols::pack_daemon::PackDaemon::ig_
private

Definition at line 162 of file PackDaemon.hh.

Referenced by ig(), and setup().

bool protocols::pack_daemon::PackDaemon::include_background_energies_
private

Should one-body energies for background residues and two body energies for pairs of background residues be included in the total energy for the state after repacking, along with the energies of those residues which have been repacked?

Definition at line 157 of file PackDaemon.hh.

Referenced by set_include_background_energies(), and setup().

RotamerAssignmentAndEnergy protocols::pack_daemon::PackDaemon::last_assignment_
private

Definition at line 177 of file PackDaemon.hh.

Referenced by assign_last_rotamers_to_pose(), compute_energy_for_assignment(), last_assignment(), mark_last_entity_as_important(), PackDaemon(), and setup().

EntityOP protocols::pack_daemon::PackDaemon::last_entity_
private

Definition at line 178 of file PackDaemon.hh.

Referenced by compute_energy_for_assignment(), and mark_last_entity_as_important().

PoseOP protocols::pack_daemon::PackDaemon::pose_
private

Definition at line 148 of file PackDaemon.hh.

Referenced by calculate_background_energies(), pose(), recreate_pose_for_entity(), set_entity_correspondence(), set_pose_and_task(), and setup().

EntityToRotamerHash protocols::pack_daemon::PackDaemon::prev_state_hash_
private

Definition at line 180 of file PackDaemon.hh.

Referenced by mark_entity_as_unimportant(), mark_last_entity_as_important(), print_entity_history(), and recreate_pose_for_entity().

QuickRepackerOP protocols::pack_daemon::PackDaemon::repacker_
private

Definition at line 165 of file PackDaemon.hh.

Referenced by compute_energy_for_assignment(), and setup().

RotamerSetsOP protocols::pack_daemon::PackDaemon::rot_sets_
private

Definition at line 163 of file PackDaemon.hh.

Referenced by assign_last_rotamers_to_pose(), recreate_pose_for_entity(), rot_sets(), select_rotamer_subset(), and setup().

ScoreFunctionOP protocols::pack_daemon::PackDaemon::score_function_
private

Definition at line 149 of file PackDaemon.hh.

Referenced by calculate_background_energies(), score_function(), set_score_function(), and setup().

bool protocols::pack_daemon::PackDaemon::setup_complete_
private

Definition at line 161 of file PackDaemon.hh.

Referenced by set_dlig_nmeg_limit(), set_entity_correspondence(), set_include_background_energies(), set_pose_and_task(), set_score_function(), and setup().

PackerTaskOP protocols::pack_daemon::PackDaemon::task_
private

Definition at line 150 of file PackDaemon.hh.

Referenced by calculate_background_energies(), set_dlig_nmeg_limit(), set_pose_and_task(), setup(), and task().

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