Rosetta 3.4
Public Types | Public Member Functions
protocols::pack_daemon::PackDaemon Class Reference

#include <PackDaemon.hh>

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List of all members.

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< intRotamerAssignment
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;
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.
utility::vector0< intselect_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

Member Typedef Documentation


Constructor & Destructor Documentation

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

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
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 protocols::genetic_algorithm::Entity::clone(), and select_rotamer_subset().

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

Referenced by setup().

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

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