#include <PackDaemon.hh>

Inheritance diagram for protocols::pack_daemon::DaemonSet:

Collaboration diagram for protocols::pack_daemon::DaemonSet:

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< SizeRealPair >	SizeRealPairs

typedef std::pair < SizeRealPairs, SizeRealPairs >	StateEsAndNPDs

typedef std::pair< core::Size, NPDPropCalculatorOP >	NPDIndAndCalc

Public Member Functions
	DaemonSet ()

virtual	~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; More...

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. More...

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. More...

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. More...

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. More...

Private Member Functions
void	process_add_daemon_message ()
	Private MPI related methods. More...

void	process_state_energy_evaluations_for_entity ()
	When we receive a evaluate_entity signal, calculate the energies for that entity for each PackDaemon and send those energies back to the master node. More...

void	process_discard_entity_message ()
	When we receive a discard_entity signal, pass that message on to the Daemons. More...

void	process_pose_request_for_entity ()
	When we receive a pose_request signal, have the desired PackDaemons create the poses for that entity, and, ship them as PDB strings back to node 0. More...

EntityOP	recieve_entity () const
	Receive an entity string from node 0 and create an Entity object from that string. More...

DaemonIndices	recieve_daemon_inds_requiring_pose_creation () const
	Accept a list of daemon indices which should return a pose based on their state in the presence of a particular entity. More...

void	graceful_exit () const
	Call MPI_Finalize and exit. More...

Detailed Description

Definition at line 196 of file PackDaemon.hh.

Member Typedef Documentation

typedef utility::vector1< std::pair< core::Size, PackDaemonCOP > > protocols::pack_daemon::DaemonSet::ConstDaemonList

Definition at line 210 of file PackDaemon.hh.

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

Definition at line 211 of file PackDaemon.hh.

typedef utility::vector1< core::Size > protocols::pack_daemon::DaemonSet::DaemonIndices

Definition at line 209 of file PackDaemon.hh.

typedef utility::vector1< std::pair< core::Size, PackDaemonOP > > protocols::pack_daemon::DaemonSet::DaemonList

Definition at line 212 of file PackDaemon.hh.

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

Definition at line 213 of file PackDaemon.hh.

typedef protocols::genetic_algorithm::Entity protocols::pack_daemon::DaemonSet::Entity

Definition at line 206 of file PackDaemon.hh.

typedef protocols::genetic_algorithm::EntityOP protocols::pack_daemon::DaemonSet::EntityOP

Definition at line 207 of file PackDaemon.hh.

typedef std::pair< core::Size, NPDPropCalculatorOP > protocols::pack_daemon::DaemonSet::NPDIndAndCalc

Definition at line 219 of file PackDaemon.hh.

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

Definition at line 203 of file PackDaemon.hh.

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

Definition at line 204 of file PackDaemon.hh.

typedef core::pose::Pose protocols::pack_daemon::DaemonSet::Pose

Definition at line 199 of file PackDaemon.hh.

typedef core::pose::PoseOP protocols::pack_daemon::DaemonSet::PoseOP

Definition at line 200 of file PackDaemon.hh.

typedef core::pack::task::ResfileContentsOP protocols::pack_daemon::DaemonSet::ResfileContentsOP

Definition at line 205 of file PackDaemon.hh.

typedef core::scoring::ScoreFunction protocols::pack_daemon::DaemonSet::ScoreFunction

Definition at line 201 of file PackDaemon.hh.

typedef core::scoring::ScoreFunctionOP protocols::pack_daemon::DaemonSet::ScoreFunctionOP

Definition at line 202 of file PackDaemon.hh.

typedef std::pair< core::Size, core::Real > protocols::pack_daemon::DaemonSet::SizeRealPair

Definition at line 215 of file PackDaemon.hh.

typedef std::list< SizeRealPair > protocols::pack_daemon::DaemonSet::SizeRealPairs

Definition at line 216 of file PackDaemon.hh.

typedef std::pair< SizeRealPairs, SizeRealPairs > protocols::pack_daemon::DaemonSet::StateEsAndNPDs

Definition at line 217 of file PackDaemon.hh.

Constructor & Destructor Documentation

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

Definition at line 455 of file PackDaemon.cc.

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

virtual

Definition at line 465 of file PackDaemon.cc.

Member Function Documentation

void protocols::pack_daemon::DaemonSet::activate_daemon_mode ( )

MPI related methods.

receive and respond to remote repacking requests from node 0 until a spin-down signal is broadcast. This function does not return until all MPI requests have completed.

Definition at line 894 of file PackDaemon.cc.

void protocols::pack_daemon::DaemonSet::add_npd_property_calculator_for_state	(	Size	daemon_index,
		std::string const &	npd_property,
		Size	npd_index
	)

Definition at line 742 of file PackDaemon.cc.

References daemon_poses_, daemon_tasks_, daemons_, n_npd_properties_, npd_calcs_for_poses_, and npd_calculator_creators_.

Referenced by process_add_daemon_message().

void protocols::pack_daemon::DaemonSet::add_npdpro_calculator_creator ( NPDPropCalculatorCreatorOP creator)

Definition at line 548 of file PackDaemon.cc.

References npd_calculator_creators_.

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.

Definition at line 560 of file PackDaemon.cc.

References core::import_pose::pose_from_pdb().

Referenced by process_add_daemon_message().

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
	)

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.

Definition at line 799 of file PackDaemon.cc.

References daemon_poses_, daemons_, core::sequence::end, n_npd_properties_, and npd_calcs_for_poses_.

Referenced by process_state_energy_evaluations_for_entity().

DaemonSet::ConstDaemonList protocols::pack_daemon::DaemonSet::daemons ( ) const

Definition at line 840 of file PackDaemon.cc.

References daemons_.

core::pack::task::ResfileContentsCOP protocols::pack_daemon::DaemonSet::entity_resfile ( ) const

Definition at line 892 of file PackDaemon.cc.

References entity_resfile_.

core::pack::task::PackerTaskOP protocols::pack_daemon::DaemonSet::entity_task ( ) const

Definition at line 891 of file PackDaemon.cc.

References entity_task_.

void protocols::pack_daemon::DaemonSet::graceful_exit ( ) const

private

Call MPI_Finalize and exit.

Definition at line 1128 of file PackDaemon.cc.

Referenced by activate_daemon_mode(), and process_add_daemon_message().

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

Definition at line 860 of file PackDaemon.cc.

References daemons_.

Referenced by process_discard_entity_message().

void protocols::pack_daemon::DaemonSet::mark_last_entity_as_important ( )

Definition at line 853 of file PackDaemon.cc.

References daemons_.

Referenced by activate_daemon_mode().

core::Size protocols::pack_daemon::DaemonSet::n_npd_properties ( ) const

Definition at line 796 of file PackDaemon.cc.

References n_npd_properties_.

core::Size protocols::pack_daemon::DaemonSet::ndaemons ( ) const

Definition at line 794 of file PackDaemon.cc.

References ndaemons_.

Referenced by process_state_energy_evaluations_for_entity().

void protocols::pack_daemon::DaemonSet::process_add_daemon_message ( )

private

Private MPI related methods.

When we recieve an add_daemons message, recieve all the input files that go along with the set of daemons that should be added, and then proceed to read these files. Send back a shut-down signal and a message if any of the input files cannot be properly read. If all goes well, send back the ok signal.

Definition at line 948 of file PackDaemon.cc.

References add_npd_property_calculator_for_state(), add_pack_daemon(), core::sequence::end, protocols::pack_daemon::error_message, graceful_exit(), core::import_pose::pose_from_pdbstring(), setup_daemons(), and protocols::pack_daemon::success_message.

Referenced by activate_daemon_mode().

void protocols::pack_daemon::DaemonSet::process_discard_entity_message ( )

private

When we receive a discard_entity signal, pass that message on to the Daemons.

Definition at line 1076 of file PackDaemon.cc.

References mark_entity_as_unimportant(), and recieve_entity().

Referenced by activate_daemon_mode().

void protocols::pack_daemon::DaemonSet::process_pose_request_for_entity ( )

private

When we receive a pose_request signal, have the desired PackDaemons create the poses for that entity, and, ship them as PDB strings back to node 0.

Definition at line 1085 of file PackDaemon.cc.

References core::io::pdb::dump_pdb(), recieve_daemon_inds_requiring_pose_creation(), recieve_entity(), and retrieve_relevant_poses_for_entity().

Referenced by activate_daemon_mode().

void protocols::pack_daemon::DaemonSet::process_state_energy_evaluations_for_entity ( )

private

When we receive a evaluate_entity signal, calculate the energies for that entity for each PackDaemon and send those energies back to the master node.

Definition at line 1024 of file PackDaemon.cc.

References compute_energy_for_assignment(), n_npd_properties_, ndaemons(), and recieve_entity().

Referenced by activate_daemon_mode().

DaemonSet::DaemonIndices protocols::pack_daemon::DaemonSet::recieve_daemon_inds_requiring_pose_creation ( ) const

private

Accept a list of daemon indices which should return a pose based on their state in the presence of a particular entity.

Definition at line 1117 of file PackDaemon.cc.

Referenced by process_pose_request_for_entity().

DaemonSet::EntityOP protocols::pack_daemon::DaemonSet::recieve_entity ( ) const

private

Receive an entity string from node 0 and create an Entity object from that string.

Definition at line 1105 of file PackDaemon.cc.

Referenced by process_discard_entity_message(), process_pose_request_for_entity(), and process_state_energy_evaluations_for_entity().

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

Definition at line 869 of file PackDaemon.cc.

References daemons_.

Referenced by process_pose_request_for_entity().

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;

Definition at line 538 of file PackDaemon.cc.

References dlig_nmeg_limit_, and limit_dlig_mem_usage_.

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.

Definition at line 471 of file PackDaemon.cc.

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

Definition at line 483 of file PackDaemon.cc.

References daemons_, entity_resfile_, entity_task_, core::chemical::FA_STANDARD, core::pose::make_pose_from_sequence(), and num_entities_.

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

Definition at line 533 of file PackDaemon.cc.

References include_background_energies_.

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

Definition at line 523 of file PackDaemon.cc.

References core::scoring::ScoreFunction::clone(), and score_function_.

void protocols::pack_daemon::DaemonSet::set_task_factory ( core::pack::task::TaskFactoryOP factory)

Definition at line 528 of file PackDaemon.cc.

References task_factory_.

void protocols::pack_daemon::DaemonSet::setup_daemons ( )

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

Definition at line 786 of file PackDaemon.cc.

References daemons_.

Referenced by process_add_daemon_message().

Member Data Documentation

utility::vector1< PoseOP > protocols::pack_daemon::DaemonSet::daemon_poses_

private

Definition at line 355 of file PackDaemon.hh.

Referenced by add_npd_property_calculator_for_state(), add_pack_daemon(), and compute_energy_for_assignment().

utility::vector1< core::pack::task::PackerTaskOP > protocols::pack_daemon::DaemonSet::daemon_tasks_

private

Definition at line 356 of file PackDaemon.hh.

Referenced by add_npd_property_calculator_for_state(), and add_pack_daemon().

DaemonList protocols::pack_daemon::DaemonSet::daemons_

private

Definition at line 350 of file PackDaemon.hh.

Referenced by add_npd_property_calculator_for_state(), add_pack_daemon(), compute_energy_for_assignment(), daemons(), mark_entity_as_unimportant(), mark_last_entity_as_important(), retrieve_relevant_poses_for_entity(), set_entity_resfile(), and setup_daemons().

Size protocols::pack_daemon::DaemonSet::dlig_nmeg_limit_

private

Definition at line 345 of file PackDaemon.hh.

Referenced by add_pack_daemon(), and set_dlig_nmeg_limit().

core::pack::task::ResfileContentsCOP protocols::pack_daemon::DaemonSet::entity_resfile_

private

Definition at line 349 of file PackDaemon.hh.

Referenced by add_pack_daemon(), entity_resfile(), and set_entity_resfile().

core::pack::task::PackerTaskOP protocols::pack_daemon::DaemonSet::entity_task_

private

Definition at line 348 of file PackDaemon.hh.

Referenced by add_pack_daemon(), entity_task(), and set_entity_resfile().

bool protocols::pack_daemon::DaemonSet::include_background_energies_

private

Definition at line 342 of file PackDaemon.hh.

Referenced by add_pack_daemon(), and set_include_background_energies().

bool protocols::pack_daemon::DaemonSet::limit_dlig_mem_usage_

private

Definition at line 344 of file PackDaemon.hh.

Referenced by add_pack_daemon(), and set_dlig_nmeg_limit().

Size protocols::pack_daemon::DaemonSet::n_npd_properties_

private

Definition at line 358 of file PackDaemon.hh.

Referenced by add_npd_property_calculator_for_state(), compute_energy_for_assignment(), n_npd_properties(), and process_state_energy_evaluations_for_entity().

core::Size protocols::pack_daemon::DaemonSet::ndaemons_

private

Definition at line 351 of file PackDaemon.hh.

Referenced by add_pack_daemon(), and ndaemons().

utility::vector1< std::list< NPDIndAndCalc > > protocols::pack_daemon::DaemonSet::npd_calcs_for_poses_

private

Definition at line 357 of file PackDaemon.hh.

Referenced by add_npd_property_calculator_for_state(), add_pack_daemon(), and compute_energy_for_assignment().

std::map< std::string, NPDPropCalculatorCreatorOP > protocols::pack_daemon::DaemonSet::npd_calculator_creators_

private

Definition at line 353 of file PackDaemon.hh.

Referenced by add_npd_property_calculator_for_state(), and add_npdpro_calculator_creator().

core::Size protocols::pack_daemon::DaemonSet::num_entities_

private

Definition at line 339 of file PackDaemon.hh.

Referenced by add_pack_daemon(), and set_entity_resfile().

ScoreFunctionOP protocols::pack_daemon::DaemonSet::score_function_

private

Definition at line 338 of file PackDaemon.hh.

Referenced by add_pack_daemon(), and set_score_function().

core::pack::task::TaskFactoryOP protocols::pack_daemon::DaemonSet::task_factory_

private

Definition at line 340 of file PackDaemon.hh.

Referenced by add_pack_daemon(), and set_task_factory().

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

src/protocols/pack_daemon/PackDaemon.hh
src/protocols/pack_daemon/PackDaemon.cc

Private Attributes
ScoreFunctionOP	score_function_

core::Size	num_entities_

core::pack::task::TaskFactoryOP	task_factory_

bool	include_background_energies_

bool	limit_dlig_mem_usage_

Size	dlig_nmeg_limit_

core::pack::task::PackerTaskOP	entity_task_

core::pack::task::ResfileContentsCOP	entity_resfile_

DaemonList	daemons_

core::Size	ndaemons_

std::map< std::string, NPDPropCalculatorCreatorOP >	npd_calculator_creators_

utility::vector1< PoseOP >	daemon_poses_

utility::vector1 < core::pack::task::PackerTaskOP >	daemon_tasks_

utility::vector1< std::list < NPDIndAndCalc > >	npd_calcs_for_poses_

Size	n_npd_properties_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation