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protocols::pack_daemon::PackDaemon Class Reference

#include <PackDaemon.hh>

Inheritance 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_
 

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

References best_assignment_, and last_assignment_.

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

Member Function Documentation

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

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

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

References best_assignment_.

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

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.

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

References correspondence_.

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

References ig_.

Referenced by setup().

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

References last_assignment_.

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

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

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

References last_assignment_, last_entity_, and prev_state_hash_.

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

References pose_.

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

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

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

References rot_sets_.

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

References score_function_.

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

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;

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

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

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

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

References include_background_energies_, and setup_complete_.

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

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)

References score_function_, and setup_complete_.

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

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

References task_.

Member Data Documentation

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

Referenced by calculate_background_energies(), and compute_energy_for_assignment().

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

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

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

Referenced by compute_energy_for_assignment().

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

Referenced by compute_energy_for_assignment().

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

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

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

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?

Referenced by set_include_background_energies(), and setup().

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

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

Referenced by compute_energy_for_assignment(), and mark_last_entity_as_important().

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

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

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

Referenced by compute_energy_for_assignment(), and setup().

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

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

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

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

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

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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