#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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

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

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

overridedefault

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.

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().

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

References npd_calculator_creators_.

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().

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
	)

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().

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

References daemons_.

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

References entity_resfile_.

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

References entity_task_.

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

private

Call MPI_Finalize and exit.

Referenced by activate_daemon_mode(), and process_add_daemon_message().

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

References daemons_.

Referenced by process_discard_entity_message().

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

References daemons_.

Referenced by activate_daemon_mode().

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

References n_npd_properties_.

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

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.

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.

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.

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.

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.

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.

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

References daemons_.

Referenced by process_pose_request_for_entity().

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_.

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.