#include <WorkUnit_Sampler.hh>

Inheritance diagram for protocols::mpi_refinement::WorkUnit_Sampler:

Public Member Functions
	WorkUnit_Sampler ()

virtual void	run ()=0
	This Work unit doesnt do anything - its just keeps the structures. More...

virtual void	init_from_cmd (const core::Size mpi_rank)

Public Member Functions inherited from protocols::wum::WorkUnit_SilentStructStore
	WorkUnit_SilentStructStore ()

virtual	~WorkUnit_SilentStructStore ()

virtual protocols::wum::WorkUnitBaseOP	clone () const

virtual void	serialize ()
	write decoys into serial data store overwritinge whatever was there before. It basically syncs the silent struct store with the derial data More...

virtual void	deserialize ()
	Make ready for working. More...

const protocols::wum::SilentStructStore &	decoys () const
	Accessor for decoy store. More...

protocols::wum::SilentStructStore &	decoys ()
	Accessor for decoy store. More...

Public Member Functions inherited from protocols::wum::WorkUnitBase
	WorkUnitBase ()

virtual	~WorkUnitBase ()

virtual void	clear_serial_data ()
	Remove all data, make sure that the memory is also cleared, hence the cals to reserve. More...

void	print (std::ostream &out, bool verbose=false) const
	Print header information to the stream, single line by default or verbose if verbose is set to true. More...

core::Size	id ()
	Accessor to the ID of the WorkUnit. More...

core::Size	extra_data_1 ()
	Accessor to the extra_data_1 and 3 field of the header. More...

core::Size	extra_data_2 ()

core::Size	extra_data_3 ()

void	set_extra_data_1 (core::Size const value)

void	set_extra_data_2 (core::Size const value)

void	set_extra_data_3 (core::Size const value)

void	add_blacklist (int mpi_rank)
	Adds to the blacklist. More...

void	clear_blacklist ()
	Erases the blacklist. More...

bool	in_blacklist (int mpi_rank)
	Finds in blacklist, true if is, false if it isn't. More...

void	set_options (const std::string &text)
	Accesor to the "options" text field. More...

core::Size	get_run_time ()
	Returns the differrence between unix start and stop times. More...

std::string	get_wu_type () const
	Accessor to header structure, return the WorkUnit Type. More...

void	set_wu_type (const std::string &text)
	Accessor to header structure, sets the WorkUnit Type. More...

std::string	get_options () const
	Optain the options string from the header. More...

virtual core::Size	mem_footprint () const
	Return the memory usage of this WorkUnit. More...

core::Size	last_received_from ()

Protected Member Functions
core::kinematics::MoveMapOP	get_movemap (core::pose::Pose const &pose, std::string const mode, bool const nonideal) const

void	store_to_decoys (core::io::silent::SilentStructCOP start_struct, core::pose::Pose const pose, std::string const additional_tag="")

void	store_to_decoys (core::io::silent::SilentStructCOP start_struct, core::io::silent::SilentStructOP ss, std::string const additional_tag="")

void	repack (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn)

void	ramp_minpack_loop2 (core::pose::Pose &pose, utility::vector1< core::Size > const loopres, core::scoring::ScoreFunctionCOP sfxn, bool const nonideal=true, bool const ramp=true, bool const efficient=false, core::Real dist_cut=0.0)

void	superimpose_to_ref (core::pose::Pose const &pose_ref, core::pose::Pose &pose_work, utility::vector1< core::Size > exclude_res=utility::vector1< core::Size >(0)) const

core::scoring::ScoreFunctionOP	get_energy (std::string const sfxn_name, bool const softpack=false, core::Real const weight_coord_cst=0.0) const

void	revert_facts_params () const

Protected Member Functions inherited from protocols::wum::WorkUnitBase
virtual void	create_unique_id ()
	Make a unique number out of Processor Number and unix timestamp ? More...

std::string &	serial_data ()
	Accessor to the serial data field. More...

const std::string &	serial_data () const
	Accessor to the serial data field. More...

void	set_run_start ()
	Set the unixtime of the start of the execution of this WorkUnit. More...

void	set_run_stop ()
	Set the unixtime of the stop of the execution of this WorkUnit. More...

Additional Inherited Members
Protected Attributes inherited from protocols::wum::WorkUnitBase
WU_Header	header
	The header data. More...

core::Size	last_received_from_
	Contains the serial number of whatever Rank/Node this WU was last receeived from. More...

std::vector< int >	blacklist_
	Contains blacklist of nodes. This data is NOT sent, and is only used on the sending side to determine where not to send a workunit. More...

Constructor & Destructor Documentation

protocols::mpi_refinement::WorkUnit_Sampler::WorkUnit_Sampler ( )

inline

Member Function Documentation

core::scoring::ScoreFunctionOP protocols::mpi_refinement::WorkUnit_Sampler::get_energy	(	std::string const	sfxn_name,
		bool const	softpack = `false`,
		core::Real const	weight_coord_cst = `0.0`
	)		const

protected

References core::scoring::cart_bonded, core::scoring::cbeta_smooth, core::scoring::cen_env_smooth, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::fa_atr, core::scoring::fa_rep, and core::scoring::pro_close.

Referenced by protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_Relax::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), and protocols::mpi_refinement::WorkUnit_PartialAbinitio::run().

core::kinematics::MoveMapOP protocols::mpi_refinement::WorkUnit_Sampler::get_movemap	(	core::pose::Pose const &	pose,
		std::string const	mode,
		bool const	nonideal
	)		const

protected

References protocols::mpi_refinement::add_movemap_from_loopres(), core::id::D, protocols::mpi_refinement::loopstring_to_loopvector(), core::id::PHI, core::id::THETA, and protocols::mpi_refinement::TR().

Referenced by repack(), protocols::mpi_refinement::WorkUnit_MD::run(), and protocols::mpi_refinement::WorkUnit_NormalMode::run().

void protocols::mpi_refinement::WorkUnit_Sampler::init_from_cmd ( const core::Size mpi_rank )

virtual

Reimplemented in protocols::mpi_refinement::WorkUnit_RamaPerturber, protocols::mpi_refinement::WorkUnit_NormalMode, protocols::mpi_refinement::WorkUnit_CombinePose, and protocols::mpi_refinement::WorkUnit_LoopHash.

void protocols::mpi_refinement::WorkUnit_Sampler::ramp_minpack_loop2	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const	loopres,
		core::scoring::ScoreFunctionCOP	sfxn,
		bool const	nonideal = `true`,
		bool const	ramp = `true`,
		bool const	efficient = `false`,
		core::Real	dist_cut = `0.0`
	)

protected

References core::scoring::cart_bonded, core::id::D, core::scoring::fa_rep, protocols::mpi_refinement::get_touched_res(), core::optimization::MinimizerOptions::max_iter(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), protocols::mpi_refinement::setup_packer(), core::id::THETA, and protocols::mpi_refinement::TR().

Referenced by protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), and protocols::mpi_refinement::WorkUnit_PartialAbinitio::run().

void protocols::mpi_refinement::WorkUnit_Sampler::repack	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn
	)

protected

References get_movemap(), and protocols::mpi_refinement::setup_packer().

Referenced by protocols::mpi_refinement::WorkUnit_MD::run(), and protocols::mpi_refinement::WorkUnit_NormalMode::run().

void protocols::mpi_refinement::WorkUnit_Sampler::revert_facts_params ( ) const

protected

Referenced by protocols::mpi_refinement::WorkUnit_MD::run(), and protocols::mpi_refinement::WorkUnit_Relax::run().

virtual void protocols::mpi_refinement::WorkUnit_Sampler::run ( )

pure virtual

This Work unit doesnt do anything - its just keeps the structures.

Reimplemented from protocols::wum::WorkUnit_SilentStructStore.

Implemented in protocols::mpi_refinement::WorkUnit_PartialAbinitio, protocols::mpi_refinement::WorkUnit_RamaPerturber, protocols::mpi_refinement::WorkUnit_KicCloser, protocols::mpi_refinement::WorkUnit_Relax, protocols::mpi_refinement::WorkUnit_FragInsert, protocols::mpi_refinement::WorkUnit_NormalMode, protocols::mpi_refinement::WorkUnit_MD, protocols::mpi_refinement::WorkUnit_CombinePose, protocols::mpi_refinement::WorkUnit_LoopHash, and protocols::mpi_refinement::WorkUnit_bbGauss.

void protocols::mpi_refinement::WorkUnit_Sampler::store_to_decoys	(	core::io::silent::SilentStructCOP	start_struct,
		core::pose::Pose const	pose,
		std::string const	additional_tag = `""`
	)

protected

References protocols::wum::WorkUnit_SilentStructStore::decoys(), and protocols::wum::SilentStructStore::store().

void protocols::mpi_refinement::WorkUnit_Sampler::store_to_decoys	(	core::io::silent::SilentStructCOP	start_struct,
		core::io::silent::SilentStructOP	ss,
		std::string const	additional_tag = `""`
	)

protected

References protocols::wum::WorkUnit_SilentStructStore::decoys(), and protocols::wum::SilentStructStore::store().

void protocols::mpi_refinement::WorkUnit_Sampler::superimpose_to_ref	(	core::pose::Pose const &	pose_ref,
		core::pose::Pose &	pose_work,
		utility::vector1< core::Size >	exclude_res = `utility::vector1< core::Size >(0)`
	)		const

protected

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::pose::Pose::residue(), core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

Referenced by protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), and protocols::mpi_refinement::WorkUnit_PartialAbinitio::run().

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

src/protocols/mpi_refinement/WorkUnit_Sampler.hh
src/protocols/mpi_refinement/WorkUnit_Sampler.cc

Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation