protocols::wum::SilentStructStore Class Reference

#include <SilentStructStore.hh>

Inheritance diagram for protocols::wum::SilentStructStore:

Public Types
typedef std::vector< core::io::silent::SilentStructOP >::iterator	iterator
typedef std::vector< core::io::silent::SilentStructOP >::const_iterator	const_iterator

Public Member Functions
	~SilentStructStore () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
	SilentStructStore ()
iterator	begin ()
	Returns an iterator to the start of the members of this container. More...
const_iterator	begin () const
	Returns an iterator to the start of the members of this container. More...
iterator	end ()
	Returns an iterator to the end of the members of this container. More...
const_iterator	end () const
	Returns an iterator to the end of the members of this container. More...
void	sort_by (std::string const &field="score")
void	clear ()
	Remove all structures. More...
void	add (const core::pose::Pose &pose)
	add a pose More...
void	add (core::io::silent::SilentStructOP new_struct)
	Add a core::io::silent::SilentStruct. More...
void	add (const core::io::silent::SilentStruct &new_struct)
	Add a core::io::silent::SilentStruct. More...
void	add (core::io::silent::SilentFileData const &sfd)
	Add structures froma silent file data object. More...
void	add (SilentStructStore &mergestore)
	Add the contents of another SilentStructStore. More...
void	read_from_cmd_line ()
	THis uses the pose stream to read in everything from -l, -s and -in:file:silent into this store. More...
void	read_from_string (const std::string &input)
	read from string More...
void	read_from_stream (std::istream &input)
	read from silent file More...
void	read_from_file (const std::string &filename)
	read from string More...
void	get_pose (core::Size index, core::pose::Pose &pose) const
	Obtain a new pose from a given index. must provide a template pose though! More...
core::Size	size ()
	How many structures. More...
core::io::silent::SilentStructCOP	get_struct (core::Size index) const
	Get a structure with a certain index. More...
core::io::silent::SilentStructOP &	get_struct (core::Size index)
	Get a structure with a certain index. More...
core::io::silent::SilentStructCOP	get_struct_random () const
	Get a random structure. More...
void	serialize (std::ostream &out) const
	Print silent file. More...
void	serialize (std::string &out) const
	Print silent file. More...
void	serialize_to_file (const std::string &file) const
	Print silent file. More...
void	print (std::ostream &out) const
	Print silent file. More...
std::vector< core::io::silent::SilentStructOP > &	store ()
void	limit (core::Size limit_size)
virtual core::Size	mem_footprint () const
	Return memory usage. More...
core::Size	size () const
	return numner of structures More...
void	erase (iterator it)
	return numner of structures More...
void	all_add_energy (std::string const &scorename, core::Real value, core::Real weight=1.0)
	Manipulators: More...
void	all_sort_silent_scores ()
	Manipulators: More...

Private Attributes
std::vector< core::io::silent::SilentStructOP >	store_

Member Typedef Documentation

const_iterator

typedef std::vector< core::io::silent::SilentStructOP >::const_iterator protocols::wum::SilentStructStore::const_iterator

iterator

typedef std::vector< core::io::silent::SilentStructOP >::iterator protocols::wum::SilentStructStore::iterator

Constructor & Destructor Documentation

~SilentStructStore()

protocols::wum::SilentStructStore::~SilentStructStore ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

SilentStructStore()

protocols::wum::SilentStructStore::SilentStructStore ( )

inline

Member Function Documentation

add() [1/5]

void protocols::wum::SilentStructStore::add

(

const core::io::silent::SilentStruct &

new_struct

)

Add a core::io::silent::SilentStruct.

References core::io::silent::SilentStruct::clone().

add() [2/5]

void protocols::wum::SilentStructStore::add

(

const core::pose::Pose &

pose

)

add a pose

References protocols::mean_field::add().

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace(), protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_direct(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_direct(), protocols::mpi_refinement::MPI_Refine_Emperor::add_structures_to_library(), protocols::mpi_refinement::Serial_Refine::apply(), protocols::mpi_refinement::Clusterer::energy_sort_cluster(), protocols::mpi_refinement::MultiObjective::filter_similar(), protocols::mpi_refinement::Serial_Refine::get_average_structure(), protocols::mpi_refinement::MPI_Refine_Master::get_average_structure(), protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refine_Master::process_round(), protocols::wum::WorkUnit_MoverWrapper::run(), protocols::mpi_refinement::superimpose_all(), protocols::mpi_refinement::MultiObjective::update_library_NSGAII(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

add() [3/5]

void protocols::wum::SilentStructStore::add

(

core::io::silent::SilentFileData const &

sfd

)

Add structures froma silent file data object.

References protocols::mean_field::add(), core::io::silent::SilentFileData::begin(), and core::io::silent::SilentFileData::end().

add() [4/5]

void protocols::wum::SilentStructStore::add

(

core::io::silent::SilentStructOP

new_struct

)

Add a core::io::silent::SilentStruct.

add() [5/5]

void protocols::wum::SilentStructStore::add

(

SilentStructStore &

mergestore

)

Add the contents of another SilentStructStore.

References store_.

all_add_energy()

void protocols::wum::SilentStructStore::all_add_energy	(	std::string const &	scorename,
		core::Real	value,
		core::Real	weight = 1.0
	)

Manipulators:

Referenced by protocols::mpi_refinement::Serial_Refine::apply(), protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus(), protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus(), and protocols::mpi_refinement::MultiObjective::update_library_NSGAII().

all_sort_silent_scores()

void protocols::wum::SilentStructStore::all_sort_silent_scores

(

)

Manipulators:

Referenced by protocols::loophash::MPI_LoopHashRefine_Emperor::process_inbound_wus(), protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus(), and protocols::mpi_refinement::MPI_Refine_Emperor::process_inbound_wus().

begin() [1/2]

iterator protocols::wum::SilentStructStore::begin ( )

inline

Returns an iterator to the start of the members of this container.

References store_.

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace(), protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_single_replace(), protocols::loophash::MPI_LoopHashRefine::add_structures_to_library(), protocols::mpi_refinement::MPI_Refinement::add_structures_to_library(), protocols::loophash::MPI_LoopHashRefine_Emperor::add_structures_to_library(), protocols::mpi_refinement::MPI_Refine_Emperor::add_structures_to_library(), protocols::mpi_refinement::Serial_Refine::apply(), protocols::mpi_refinement::MultiObjective::filter_similar(), protocols::mpi_refinement::Serial_Refine::get_average_structure(), protocols::mpi_refinement::MPI_Refine_Master::get_average_structure(), protocols::mpi_refinement::Scheduler::pick_enrich_methods(), protocols::loophash::MPI_LoopHashRefine::print_library(), protocols::mpi_refinement::MPI_Refinement::print_library(), protocols::mpi_refinement::MPI_Refinement::retag_library(), protocols::mpi_refinement::MPI_Refinement::send_sortedpick_library_structs(), and protocols::mpi_refinement::StructAvrgMover::StructAvrgMover().

begin() [2/2]

const_iterator protocols::wum::SilentStructStore::begin ( ) const

inline

Returns an iterator to the start of the members of this container.

References store_.

clear()

void protocols::wum::SilentStructStore::clear

(

)

Remove all structures.

Referenced by protocols::wum::WorkUnit_SilentStructStore::deserialize(), protocols::loophash::MPI_LoopHashRefine::load_state(), protocols::mpi_refinement::MPI_Refinement::load_state(), protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_Relax::run(), protocols::wum::WorkUnit_MoverWrapper::run(), protocols::mpi_refinement::superimpose_all(), protocols::mpi_refinement::MultiObjective::update_library_NSGAII(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

end() [1/2]

iterator protocols::wum::SilentStructStore::end ( )

inline

Returns an iterator to the end of the members of this container.

References store_.

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace(), protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_single_replace(), protocols::loophash::MPI_LoopHashRefine::add_structures_to_library(), protocols::mpi_refinement::MPI_Refinement::add_structures_to_library(), protocols::loophash::MPI_LoopHashRefine_Emperor::add_structures_to_library(), protocols::mpi_refinement::MPI_Refine_Emperor::add_structures_to_library(), protocols::mpi_refinement::Serial_Refine::apply(), protocols::mpi_refinement::MultiObjective::filter_similar(), protocols::mpi_refinement::Serial_Refine::get_average_structure(), protocols::mpi_refinement::MPI_Refine_Master::get_average_structure(), protocols::mpi_refinement::Scheduler::pick_enrich_methods(), protocols::loophash::MPI_LoopHashRefine::print_library(), protocols::mpi_refinement::MPI_Refinement::print_library(), protocols::mpi_refinement::MPI_Refinement::retag_library(), protocols::wum::WorkUnit_MoverWrapper::run(), protocols::mpi_refinement::MPI_Refinement::send_sortedpick_library_structs(), and protocols::mpi_refinement::StructAvrgMover::StructAvrgMover().

end() [2/2]

const_iterator protocols::wum::SilentStructStore::end ( ) const

inline

Returns an iterator to the end of the members of this container.

References store_.

erase()

void protocols::wum::SilentStructStore::erase ( iterator  it )

inline

return numner of structures

References store_.

Referenced by protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace().

get_pose()

void protocols::wum::SilentStructStore::get_pose	(	core::Size	index,
		core::pose::Pose &	pose
	)		const

Obtain a new pose from a given index. must provide a template pose though!

Referenced by protocols::loophash::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_Relax::run(), and protocols::mpi_refinement::StructAvrgMover::StructAvrgMover().

get_struct() [1/2]

core::io::silent::SilentStructOP& protocols::wum::SilentStructStore::get_struct ( core::Size  index )

inline

Get a structure with a certain index.

References store_.

get_struct() [2/2]

core::io::silent::SilentStructCOP protocols::wum::SilentStructStore::get_struct ( core::Size  index ) const

inline

Get a structure with a certain index.

References store_.

Referenced by protocols::mpi_refinement::add_init_dev_penalty(), protocols::mpi_refinement::MultiObjective::add_objective_function_info(), protocols::loophash::MPI_LoopHashRefine_Master::add_relax_batch(), protocols::mpi_refinement::MPI_Refine_Master::add_relax_simple(), protocols::mpi_refinement::MultiObjective::calculate_pool_diversity(), protocols::mpi_refinement::MultiObjective::calculate_structure_diversity(), protocols::mpi_refinement::Clusterer::energy_sort_cluster(), protocols::mpi_refinement::MultiObjective::filter_similar(), protocols::mpi_refinement::Serial_Refine::get_average_structure(), protocols::mpi_refinement::MPI_Refine_Master::get_average_structure(), protocols::mpi_refinement::MPI_Refinement::limit_library(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refinement::print_summary(), protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_Relax::run(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::mpi_refinement::MPI_Refinement::send_random_library_structs(), protocols::mpi_refinement::MPI_Refinement::send_sortedpick_library_structs(), protocols::mpi_refinement::superimpose_all(), protocols::mpi_refinement::MultiObjective::update_library_NSGAII(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

get_struct_random()

SilentStructCOP protocols::wum::SilentStructStore::get_struct_random

(

)

const

Get a random structure.

References core::scoring::rg.

Referenced by protocols::loophash::MPI_LoopHashRefine::send_random_library_struct(), and protocols::mpi_refinement::MPI_Refinement::send_random_library_struct().

limit()

void protocols::wum::SilentStructStore::limit ( core::Size  limit_size )

inline

References size(), and store().

Referenced by protocols::relax::WorkUnit_BatchRelax_and_PostRescore::trim().

mem_footprint()

core::Size protocols::wum::SilentStructStore::mem_footprint ( ) const

virtual

Return memory usage.

References protocols::analysis::total.

Referenced by protocols::loophash::MPI_LoopHashRefine::print_stats(), and protocols::mpi_refinement::MPI_Refinement::print_stats().

print()

void protocols::wum::SilentStructStore::print

(

std::ostream &

out

)

const

Print silent file.

References core::conformation::membrane::out.

read_from_cmd_line()

void protocols::wum::SilentStructStore::read_from_cmd_line

(

)

THis uses the pose stream to read in everything from -l, -s and -in:file:silent into this store.

References protocols::mean_field::add(), core::import_pose::pose_stream::MetaPoseInputStream::fill_pose(), core::import_pose::pose_stream::MetaPoseInputStream::has_another_pose(), core::import_pose::pose_stream::streams_from_cmd_line(), and core::kinematics::TR().

read_from_file()

void protocols::wum::SilentStructStore::read_from_file

(

const std::string &

filename

)

read from string

References protocols::abinitio::filename().

Referenced by protocols::loophash::MPI_LoopHashRefine::load_state(), and protocols::mpi_refinement::MPI_Refinement::load_state().

read_from_stream()

void protocols::wum::SilentStructStore::read_from_stream

(

std::istream &

input

)

read from silent file

References protocols::mean_field::add(), core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::comment_lines(), core::io::silent::SilentFileData::end(), core::sequence::end, and core::io::silent::SilentFileData::read_stream().

read_from_string()

void protocols::wum::SilentStructStore::read_from_string

(

const std::string &

input

)

read from string

Referenced by protocols::wum::WorkUnit_SilentStructStore::deserialize().

serialize() [1/2]

void protocols::wum::SilentStructStore::serialize

(

std::ostream &

out

)

const

Print silent file.

References core::conformation::membrane::out, core::kinematics::TR(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::wum::WorkUnit_SilentStructStore::serialize().

serialize() [2/2]

void protocols::wum::SilentStructStore::serialize

(

std::string &

out

)

const

Print silent file.

References core::conformation::membrane::out.

serialize_to_file()

void protocols::wum::SilentStructStore::serialize_to_file

(

const std::string &

file

)

const

Print silent file.

References protocols::abinitio::filename(), and core::conformation::membrane::out.

Referenced by protocols::loophash::MPI_LoopHashRefine::save_state(), and protocols::mpi_refinement::MPI_Refinement::save_state().

size() [1/2]

core::Size protocols::wum::SilentStructStore::size ( )

inline

How many structures.

References store_.

Referenced by protocols::mpi_refinement::add_init_dev_penalty(), protocols::mpi_refinement::MultiObjective::add_objective_function_info(), protocols::loophash::MPI_LoopHashRefine_Master::add_relax_batch(), protocols::mpi_refinement::MPI_Refine_Master::add_relax_simple(), protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::Serial_Refine::apply(), protocols::mpi_refinement::MultiObjective::calculate_pool_diversity(), protocols::mpi_refinement::MultiObjective::calculate_structure_diversity(), protocols::mpi_refinement::Clusterer::energy_sort_cluster(), protocols::mpi_refinement::MultiObjective::filter_similar(), protocols::mpi_refinement::Serial_Refine::get_average_structure(), protocols::mpi_refinement::MPI_Refine_Master::get_average_structure(), limit(), protocols::loophash::MPI_LoopHashRefine::limit_library(), protocols::mpi_refinement::MPI_Refinement::limit_library(), protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::wum::WorkUnitQueue::mem_stats(), protocols::loophash::MPI_LoopHashRefine_Emperor::process_inbound_wus(), protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus(), protocols::mpi_refinement::MPI_Refine_Emperor::process_inbound_wus(), protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), protocols::mpi_refinement::WorkUnit_Relax::run(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::loophash::MPI_LoopHashRefine::save_state(), protocols::mpi_refinement::MPI_Refinement::save_state(), protocols::loophash::MPI_LoopHashRefine::send_random_library_struct(), protocols::mpi_refinement::MPI_Refinement::send_random_library_struct(), protocols::mpi_refinement::MPI_Refinement::send_random_library_structs(), protocols::mpi_refinement::MPI_Refinement::send_sortedpick_library_structs(), protocols::mpi_refinement::MPI_Refinement::shave_library(), protocols::mpi_refinement::StructAvrgMover::StructAvrgMover(), protocols::mpi_refinement::superimpose_all(), protocols::mpi_refinement::MultiObjective::update_library_NSGAII(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

size() [2/2]

core::Size protocols::wum::SilentStructStore::size ( ) const

inline

return numner of structures

References store_.

sort_by()

void protocols::wum::SilentStructStore::sort_by

(

std::string const &

field = "score"

)

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::Serial_Refine::apply(), protocols::mpi_refinement::Clusterer::energy_sort_cluster(), protocols::loophash::MPI_LoopHashRefine::limit_library(), protocols::mpi_refinement::MPI_Refinement::limit_library(), protocols::mpi_refinement::MPI_Refinement::print_summary(), protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus(), protocols::mpi_refinement::MPI_Refinement::send_sortedpick_library_structs(), protocols::mpi_refinement::MPI_Refinement::shave_library(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::trim(), protocols::mpi_refinement::MultiObjective::update_library_NSGAII(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

store()

std::vector< core::io::silent::SilentStructOP >& protocols::wum::SilentStructStore::store ( )

inline

References store_.

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_add_n_replace(), protocols::mpi_refinement::Serial_Refine::apply(), limit(), protocols::loophash::MPI_LoopHashRefine::limit_library(), protocols::mpi_refinement::MPI_Refinement::limit_library(), protocols::loophash::MPI_LoopHashRefine::print_library(), protocols::mpi_refinement::MPI_Refinement::print_library(), protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::MPI_Refinement::shave_library(), protocols::mpi_refinement::WorkUnit_Sampler::store_to_decoys(), and protocols::mpi_refinement::MultiObjective::update_library_seeds().

Member Data Documentation

store_

std::vector< core::io::silent::SilentStructOP > protocols::wum::SilentStructStore::store_

private

Referenced by add(), begin(), end(), erase(), get_struct(), size(), and store().

---

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

• src/protocols/wum/SilentStructStore.hh
• src/protocols/wum/SilentStructStore.cc