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protocols::pack_daemon::PackDaemon Class Reference

#include <PackDaemon.hh>

Inheritance diagram for protocols::pack_daemon::PackDaemon:
Inheritance graph
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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 ()
 
 ~PackDaemon () override
 
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 (core::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

Constructor & Destructor Documentation

protocols::pack_daemon::PackDaemon::PackDaemon ( )
protocols::pack_daemon::PackDaemon::~PackDaemon ( )
overridedefault

Member Function Documentation

void protocols::pack_daemon::PackDaemon::assign_last_rotamers_to_pose ( Pose pose) const
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_, 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)
void protocols::pack_daemon::PackDaemon::mark_last_entity_as_important ( )
PackDaemon::PoseCOP protocols::pack_daemon::PackDaemon::pose ( ) const

References pose_.

Referenced by set_pose_and_task().

void protocols::pack_daemon::PackDaemon::print_entity_history ( ) const
PackDaemon::PoseOP protocols::pack_daemon::PackDaemon::recreate_pose_for_entity ( Entity const &  ent) const
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
void protocols::pack_daemon::PackDaemon::set_dlig_nmeg_limit ( core::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)
void protocols::pack_daemon::PackDaemon::set_include_background_energies ( bool  setting)
void protocols::pack_daemon::PackDaemon::set_pose_and_task ( Pose const &  pose,
PackerTask const &  task 
)
void protocols::pack_daemon::PackDaemon::set_score_function ( ScoreFunction const &  sfxn)
void protocols::pack_daemon::PackDaemon::setup ( )
PackDaemon::PackerTaskCOP protocols::pack_daemon::PackDaemon::task ( ) const

References task_.

Member Data Documentation

Real protocols::pack_daemon::PackDaemon::background_energies_
private
RotamerAssignmentAndEnergy protocols::pack_daemon::PackDaemon::best_assignment_
private
bool protocols::pack_daemon::PackDaemon::best_assignment_valid_
private
EntityOP protocols::pack_daemon::PackDaemon::best_entity_
private
EntityCorrespondenceOP protocols::pack_daemon::PackDaemon::correspondence_
private
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
EntityOP protocols::pack_daemon::PackDaemon::last_entity_
private
PoseOP protocols::pack_daemon::PackDaemon::pose_
private
EntityToRotamerHash protocols::pack_daemon::PackDaemon::prev_state_hash_
private
QuickRepackerOP protocols::pack_daemon::PackDaemon::repacker_
private
RotamerSetsOP protocols::pack_daemon::PackDaemon::rot_sets_
private
ScoreFunctionOP protocols::pack_daemon::PackDaemon::score_function_
private
bool protocols::pack_daemon::PackDaemon::setup_complete_
private
PackerTaskOP protocols::pack_daemon::PackDaemon::task_
private

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