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

#include <PackDaemon.hh>

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List of all members.

Public Types

typedef core::pose::Pose Pose
typedef core::pose::PoseOP PoseOP
typedef
core::scoring::ScoreFunction 
ScoreFunction
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
typedef
core::pack::task::PackerTask 
PackerTask
typedef
core::pack::task::PackerTaskOP 
PackerTaskOP
typedef
core::pack::task::ResfileContentsOP 
ResfileContentsOP
typedef
protocols::genetic_algorithm::Entity 
Entity
typedef
protocols::genetic_algorithm::EntityOP 
EntityOP
typedef utility::vector1
< core::Size
DaemonIndices
typedef utility::vector1
< std::pair< core::Size,
PackDaemonCOP > > 
ConstDaemonList
typedef
ConstDaemonList::const_iterator 
ConstDaemonListIter
typedef utility::vector1
< std::pair< core::Size,
PackDaemonOP > > 
DaemonList
typedef DaemonList::const_iterator DaemonListIter
typedef std::pair< core::Size,
core::Real
SizeRealPair
typedef std::list< SizeRealPairSizeRealPairs
typedef std::pair
< SizeRealPairs, SizeRealPairs
StateEsAndNPDs
typedef std::pair< core::Size,
NPDPropCalculatorOP
NPDIndAndCalc

Public Member Functions

 DaemonSet ()
 ~DaemonSet ()
void set_entity_resfile (std::string const &resfile)
void set_entity_resfile (std::istream &resfile, std::string const &resfile_name)
void set_score_function (ScoreFunction const &)
void set_task_factory (core::pack::task::TaskFactoryOP factory)
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 add_npdpro_calculator_creator (NPDPropCalculatorCreatorOP)
void add_pack_daemon (Size daemon_index, std::string const &pdb_name, std::string const &correspondence_file_name, std::string const &secondary_resfile)
 Each daemon is associated with an index representing its position in some master list somewhere. The DaemonSet is responsible for keeping this index.
void add_pack_daemon (Size daemon_index, std::string const &pose_file_name, Pose const &pose, std::string const &correspondence_file_filename, std::istream &correspondence_file, std::string const &secondary_refile_file_filename, std::istream &secondary_resfile)
void add_npd_property_calculator_for_state (Size daemon_index, std::string const &npd_property, Size npd_index)
void setup_daemons ()
 call daemon->setup() on all daemons, which will trigger the precomputation of all rotamer pair energies.
core::Size ndaemons () const
core::Size n_npd_properties () const
StateEsAndNPDs compute_energy_for_assignment (Entity const &entity)
 Compute the state energies and, for those states requiring non-pairwise-decomposable-properties, the non-pairwise decomposable properties as well. Return them as a pair of lists.
ConstDaemonList daemons () const
void mark_last_entity_as_important ()
void mark_entity_as_unimportant (Entity const &)
std::list< std::pair< Size,
PoseOP > > 
retrieve_relevant_poses_for_entity (Entity const &, DaemonIndices const &) const
core::pack::task::PackerTaskOP entity_task () const
core::pack::task::ResfileContentsCOP entity_resfile () const
void activate_daemon_mode ()
 MPI related methods.

Member Typedef Documentation

typedef ConstDaemonList::const_iterator protocols::pack_daemon::DaemonSet::ConstDaemonListIter
typedef DaemonList::const_iterator protocols::pack_daemon::DaemonSet::DaemonListIter

Constructor & Destructor Documentation

protocols::pack_daemon::DaemonSet::DaemonSet ( )
protocols::pack_daemon::DaemonSet::~DaemonSet ( )

Member Function Documentation

void protocols::pack_daemon::DaemonSet::activate_daemon_mode ( )
void protocols::pack_daemon::DaemonSet::add_npd_property_calculator_for_state ( Size  daemon_index,
std::string const &  npd_property,
Size  npd_index 
)
void protocols::pack_daemon::DaemonSet::add_npdpro_calculator_creator ( NPDPropCalculatorCreatorOP  creator)
void protocols::pack_daemon::DaemonSet::add_pack_daemon ( Size  daemon_index,
std::string const &  pose_file_name,
Pose const &  pose,
std::string const &  correspondence_file_filename,
std::istream &  correspondence_file,
std::string const &  secondary_refile_file_filename,
std::istream &  secondary_resfile 
)
void protocols::pack_daemon::DaemonSet::add_pack_daemon ( Size  daemon_index,
std::string const &  pdb_name,
std::string const &  correspondence_file_name,
std::string const &  secondary_resfile 
)

Each daemon is associated with an index representing its position in some master list somewhere. The DaemonSet is responsible for keeping this index.

References core::import_pose::pose_from_pdb().

DaemonSet::StateEsAndNPDs protocols::pack_daemon::DaemonSet::compute_energy_for_assignment ( Entity const &  entity)

Compute the state energies and, for those states requiring non-pairwise-decomposable-properties, the non-pairwise decomposable properties as well. Return them as a pair of lists.

References make_table_of_pilot_apps::begin, and core::sequence::end.

DaemonSet::ConstDaemonList protocols::pack_daemon::DaemonSet::daemons ( ) const
core::pack::task::ResfileContentsCOP protocols::pack_daemon::DaemonSet::entity_resfile ( ) const
core::pack::task::PackerTaskOP protocols::pack_daemon::DaemonSet::entity_task ( ) const
void protocols::pack_daemon::DaemonSet::mark_entity_as_unimportant ( Entity const &  ent)
void protocols::pack_daemon::DaemonSet::mark_last_entity_as_important ( )

Referenced by activate_daemon_mode().

core::Size protocols::pack_daemon::DaemonSet::n_npd_properties ( ) const
core::Size protocols::pack_daemon::DaemonSet::ndaemons ( ) const
std::list< std::pair< core::Size, core::pose::PoseOP > > protocols::pack_daemon::DaemonSet::retrieve_relevant_poses_for_entity ( Entity const &  ent,
DaemonIndices const &  daemon_indices 
) const
void protocols::pack_daemon::DaemonSet::set_dlig_nmeg_limit ( Size  setting)

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

void protocols::pack_daemon::DaemonSet::set_entity_resfile ( std::string const &  resfile)

The entity resfile is slightly different from a regular resfile. Its first line should consist of the number of residues that are entity; the rest of the resfile lists those residues numbering from 1.

void protocols::pack_daemon::DaemonSet::set_entity_resfile ( std::istream &  resfile,
std::string const &  resfile_name 
)
void protocols::pack_daemon::DaemonSet::set_include_background_energies ( bool  setting)
void protocols::pack_daemon::DaemonSet::set_score_function ( ScoreFunction const &  sfxn)
void protocols::pack_daemon::DaemonSet::set_task_factory ( core::pack::task::TaskFactoryOP  factory)
void protocols::pack_daemon::DaemonSet::setup_daemons ( )

call daemon->setup() on all daemons, which will trigger the precomputation of all rotamer pair energies.


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