#include <PackDaemon.hh>

Inheritance 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 ()

	~DaemonSet () override

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 (core::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 (core::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 (core::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 (core::Size daemon_index, std::string const &npd_property, core::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< core::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...

Private Attributes
ScoreFunctionOP	score_function_

core::Size	num_entities_

core::pack::task::TaskFactoryOP	task_factory_

bool	include_background_energies_

bool	limit_dlig_mem_usage_

core::Size	dlig_nmeg_limit_

core::pack::task::PackerTaskOP	entity_task_

core::pack::task::ResfileContentsOP	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_

core::Size	n_npd_properties_

Member Typedef Documentation

◆ ConstDaemonList

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

◆ ConstDaemonListIter

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

◆ DaemonIndices

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

◆ DaemonList

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

◆ DaemonListIter

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

◆ Entity

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

◆ EntityOP

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

◆ NPDIndAndCalc

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

◆ PackerTask

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

◆ PackerTaskOP

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

◆ Pose

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

◆ PoseOP

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

◆ ResfileContentsOP

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

◆ ScoreFunction

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

◆ ScoreFunctionOP

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

◆ SizeRealPair

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

◆ SizeRealPairs

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

◆ StateEsAndNPDs

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

Constructor & Destructor Documentation

◆ DaemonSet()

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

◆ ~DaemonSet()

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

overridedefault

Member Function Documentation

◆ activate_daemon_mode()

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.

◆ add_npd_property_calculator_for_state()

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

References daemon_poses_, daemon_tasks_, daemons_, n_npd_properties_, npd_calcs_for_poses_, npd_calculator_creators_, and core::id::to_string().

Referenced by process_add_daemon_message().

◆ add_npdpro_calculator_creator()

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

References npd_calculator_creators_.

◆ add_pack_daemon() [1/2]

void protocols::pack_daemon::DaemonSet::add_pack_daemon	(	core::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::PDB_file, and core::import_pose::pose_from_file().

Referenced by process_add_daemon_message().

◆ add_pack_daemon() [2/2]

void protocols::pack_daemon::DaemonSet::add_pack_daemon	(	core::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
	)

◆ compute_energy_for_assignment()

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 daemon_poses_, daemons_, core::sequence::end, protocols::buns::energy, n_npd_properties_, and npd_calcs_for_poses_.

Referenced by process_state_energy_evaluations_for_entity().

◆ daemons()

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

References daemons_.

◆ entity_resfile()

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

References entity_resfile_.

◆ entity_task()

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

References entity_task_.

◆ graceful_exit()

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

private

Call MPI_Finalize and exit.

Referenced by activate_daemon_mode(), and process_add_daemon_message().

◆ mark_entity_as_unimportant()

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

References daemons_.

Referenced by process_discard_entity_message().

◆ mark_last_entity_as_important()

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

References daemons_.

Referenced by activate_daemon_mode().

◆ n_npd_properties()

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

References n_npd_properties_.

◆ ndaemons()

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

References ndaemons_.

Referenced by process_state_energy_evaluations_for_entity().

◆ process_add_daemon_message()

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.

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().

◆ process_discard_entity_message()

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

private

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

References mark_entity_as_unimportant(), and recieve_entity().

Referenced by activate_daemon_mode().

◆ process_pose_request_for_entity()

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.

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().

◆ process_state_energy_evaluations_for_entity()

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.

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

Referenced by activate_daemon_mode().

◆ recieve_daemon_inds_requiring_pose_creation()

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.

Referenced by process_pose_request_for_entity().

◆ recieve_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.

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

◆ retrieve_relevant_poses_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

References daemons_.

Referenced by process_pose_request_for_entity().

◆ set_dlig_nmeg_limit()

void protocols::pack_daemon::DaemonSet::set_dlig_nmeg_limit ( core::Size setting )

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

References dlig_nmeg_limit_, and limit_dlig_mem_usage_.

◆ set_entity_resfile() [1/2]

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

References protocols::pack_daemon::create_entity_resfile_contents(), daemons_, entity_resfile_, entity_task_, and num_entities_.

◆ set_entity_resfile() [2/2]

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.

◆ set_include_background_energies()

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

References include_background_energies_.

◆ set_score_function()

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

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

◆ set_task_factory()

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

References task_factory_.

◆ setup_daemons()

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

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

References daemons_.

Referenced by process_add_daemon_message().

Member Data Documentation

◆ daemon_poses_

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

private

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

◆ daemon_tasks_

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

private

Referenced by add_npd_property_calculator_for_state(), and add_pack_daemon().

◆ daemons_

DaemonList protocols::pack_daemon::DaemonSet::daemons_

private

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().

◆ dlig_nmeg_limit_

core::Size protocols::pack_daemon::DaemonSet::dlig_nmeg_limit_

private

Referenced by add_pack_daemon(), and set_dlig_nmeg_limit().

◆ entity_resfile_

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

private

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

◆ entity_task_

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

private

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

◆ include_background_energies_

bool protocols::pack_daemon::DaemonSet::include_background_energies_

private

Referenced by add_pack_daemon(), and set_include_background_energies().

◆ limit_dlig_mem_usage_

bool protocols::pack_daemon::DaemonSet::limit_dlig_mem_usage_

private

Referenced by add_pack_daemon(), and set_dlig_nmeg_limit().

◆ n_npd_properties_

core::Size protocols::pack_daemon::DaemonSet::n_npd_properties_

private

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

◆ ndaemons_

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

private

Referenced by add_pack_daemon(), and ndaemons().

◆ npd_calcs_for_poses_

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

private

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

◆ npd_calculator_creators_

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

private

Referenced by add_npd_property_calculator_for_state(), and add_npdpro_calculator_creator().

◆ num_entities_

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

private

Referenced by add_pack_daemon(), and set_entity_resfile().

◆ score_function_

ScoreFunctionOP protocols::pack_daemon::DaemonSet::score_function_

private

Referenced by add_pack_daemon(), and set_score_function().

◆ task_factory_

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

private

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ ConstDaemonList

◆ ConstDaemonListIter

◆ DaemonIndices

◆ DaemonList

◆ DaemonListIter

◆ Entity

◆ EntityOP

◆ NPDIndAndCalc

◆ PackerTask

◆ PackerTaskOP

◆ Pose

◆ PoseOP

◆ ResfileContentsOP

◆ ScoreFunction

◆ ScoreFunctionOP

◆ SizeRealPair

◆ SizeRealPairs

◆ StateEsAndNPDs

Constructor & Destructor Documentation

◆ DaemonSet()

◆ ~DaemonSet()

Member Function Documentation

◆ activate_daemon_mode()

◆ add_npd_property_calculator_for_state()

◆ add_npdpro_calculator_creator()

◆ add_pack_daemon() [1/2]

◆ add_pack_daemon() [2/2]

◆ compute_energy_for_assignment()

◆ daemons()

◆ entity_resfile()

◆ entity_task()

◆ graceful_exit()

◆ mark_entity_as_unimportant()

◆ mark_last_entity_as_important()

◆ n_npd_properties()

◆ ndaemons()

◆ process_add_daemon_message()

◆ process_discard_entity_message()

◆ process_pose_request_for_entity()

◆ process_state_energy_evaluations_for_entity()

◆ recieve_daemon_inds_requiring_pose_creation()

◆ recieve_entity()

◆ retrieve_relevant_poses_for_entity()

◆ set_dlig_nmeg_limit()

◆ set_entity_resfile() [1/2]

◆ set_entity_resfile() [2/2]

◆ set_include_background_energies()

◆ set_score_function()

◆ set_task_factory()

◆ setup_daemons()

Member Data Documentation

◆ daemon_poses_

◆ daemon_tasks_

◆ daemons_

◆ dlig_nmeg_limit_

◆ entity_resfile_

◆ entity_task_

◆ include_background_energies_

◆ limit_dlig_mem_usage_

◆ n_npd_properties_

◆ ndaemons_

◆ npd_calcs_for_poses_

◆ npd_calculator_creators_

◆ num_entities_

◆ score_function_

◆ task_factory_