#include <SilentStructStore.hh>

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
virtual	~SilentStructStore ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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 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 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

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

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

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

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

inline

Member Function Documentation

void protocols::wum::SilentStructStore::add ( const core::pose::Pose & pose )

add a pose

References add(), lh::bss, core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), option, and ss.

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_direct(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), and protocols::wum::WorkUnit_MoverWrapper::run().

void protocols::wum::SilentStructStore::add ( core::io::silent::SilentStructOP new_struct )

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

void protocols::wum::SilentStructStore::add ( const core::io::silent::SilentStruct & new_struct )

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

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

void protocols::wum::SilentStructStore::add ( core::io::silent::SilentFileData const & sfd )

Add structures froma silent file data object.

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

void protocols::wum::SilentStructStore::add ( SilentStructStore & mergestore )

Add the contents of another SilentStructStore.

References runtime_assert, and store_.

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

Manipulators:

Referenced by protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus().

void protocols::wum::SilentStructStore::all_sort_silent_scores ( )

Manipulators:

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

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::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), protocols::loophash::MPI_LoopHashRefine_Emperor::add_structures_to_library(), protocols::loophash::MPI_LoopHashRefine::add_structures_to_library(), protocols::loophash::MPI_LoopHashRefine::dump_structures(), protocols::wum::WorkUnitQueue::mem_stats(), protocols::loophash::MPI_LoopHashRefine::print_library(), and protocols::wum::MPI_Relax::process_inbound_wus_master().

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

inline

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

References store_.

void protocols::wum::SilentStructStore::clear ( )

Remove all structures.

Referenced by protocols::wum::WorkUnit_SilentStructStore::deserialize(), protocols::loophash::MPI_LoopHashRefine::load_state(), protocols::loophash::WorkUnit_LoopHash::run(), and protocols::wum::WorkUnit_MoverWrapper::run().

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::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), protocols::loophash::MPI_LoopHashRefine_Emperor::add_structures_to_library(), protocols::loophash::MPI_LoopHashRefine::add_structures_to_library(), protocols::loophash::MPI_LoopHashRefine::dump_structures(), protocols::wum::WorkUnitQueue::mem_stats(), protocols::loophash::MPI_LoopHashRefine::print_library(), protocols::wum::MPI_Relax::process_inbound_wus_master(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), protocols::loophash::WorkUnit_LoopHash::run(), and protocols::wum::WorkUnit_MoverWrapper::run().

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

inline

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

References store_.

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

inline

return numner of structures

References store_.

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!

References runtime_assert.

Referenced by protocols::loophash::WorkUnit_LoopHash::run().

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

inline

Get a structure with a certain index.

References runtime_assert, and store_.

Referenced by protocols::loophash::MPI_LoopHashRefine_Master::add_relax_batch(), protocols::loophash::WorkUnit_LoopHash::run(), and protocols::relax::WorkUnit_BatchRelax::run().

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

inline

Get a structure with a certain index.

References runtime_assert, and store_.

SilentStructCOP protocols::wum::SilentStructStore::get_struct_random ( ) const

Get a random structure.

References numeric::random::RandomGenerator::random_range(), core::kinematics::RG, and runtime_assert.

Referenced by protocols::loophash::MPI_LoopHashRefine::send_random_library_struct().

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

inline

References size(), and store().

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

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

virtual

Return memory usage.

References protocols::analysis::total.

Referenced by protocols::loophash::MPI_LoopHashRefine::print_stats().

void protocols::wum::SilentStructStore::print ( std::ostream & out ) const

Print silent file.

References runtime_assert.

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 add(), in::file::fullatom, core::chemical::ChemicalManager::get_instance(), option, core::chemical::ChemicalManager::residue_type_set(), core::import_pose::pose_stream::streams_from_cmd_line(), and core::kinematics::TR.

void protocols::wum::SilentStructStore::read_from_file ( const std::string & filename )

read from string

References utility_exit_with_message.

Referenced by protocols::loophash::MPI_LoopHashRefine::load_state().

void protocols::wum::SilentStructStore::read_from_stream ( std::istream & input )

read from silent file

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

void protocols::wum::SilentStructStore::read_from_string ( const std::string & input )

read from string

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

void protocols::wum::SilentStructStore::serialize ( std::ostream & out ) const

Print silent file.

References runtime_assert, core::kinematics::TR, and core::io::silent::SilentFileData::write_silent_struct().

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

void protocols::wum::SilentStructStore::serialize ( std::string & out ) const

Print silent file.

References serialize(), and ss.

void protocols::wum::SilentStructStore::serialize_to_file ( const std::string & file ) const

Print silent file.

References out, serialize(), and utility_exit_with_message.

Referenced by protocols::loophash::MPI_LoopHashRefine::save_state().

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

inline

How many structures.

References store_.

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

inline

return numner of structures

References store_.

void protocols::wum::SilentStructStore::sort_by ( std::string field = "score" )

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_add_n_replace(), protocols::loophash::MPI_LoopHashRefine::limit_library(), and protocols::relax::WorkUnit_BatchRelax_and_PostRescore::trim().

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(), limit(), protocols::loophash::MPI_LoopHashRefine::limit_library(), and protocols::loophash::MPI_LoopHashRefine::print_library().

Member Data Documentation

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

Public Types

Public Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation