#include <SilentStructStore.hh>

Inheritance diagram for protocols::wum::SilentStructStore:

Collaboration 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
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_

Detailed Description

Definition at line 51 of file SilentStructStore.hh.

Member Typedef Documentation

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

Definition at line 64 of file SilentStructStore.hh.

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

Definition at line 63 of file SilentStructStore.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 101 of file SilentStructStore.cc.

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

inline

Definition at line 55 of file SilentStructStore.hh.

Member Function Documentation

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

add a pose

Definition at line 140 of file SilentStructStore.cc.

References core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), and core::io::silent::SilentStructFactory::get_silent_struct_out().

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.

Definition at line 152 of file SilentStructStore.cc.

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

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

Definition at line 157 of file SilentStructStore.cc.

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

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

Add structures froma silent file data object.

Definition at line 163 of file SilentStructStore.cc.

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

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

Add the contents of another SilentStructStore.

Definition at line 172 of file SilentStructStore.cc.

References store_.

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

Manipulators:

Definition at line 329 of file SilentStructStore.cc.

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

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

Manipulators:

Definition at line 339 of file SilentStructStore.cc.

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.

Definition at line 67 of file SilentStructStore.hh.

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.

Definition at line 70 of file SilentStructStore.hh.

References store_.

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

Remove all structures.

Definition at line 134 of file SilentStructStore.cc.

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.

Definition at line 73 of file SilentStructStore.hh.

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.

Definition at line 76 of file SilentStructStore.hh.

References store_.

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

inline

return numner of structures

Definition at line 158 of file SilentStructStore.hh.

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!

Definition at line 242 of file SilentStructStore.cc.

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.

Definition at line 119 of file SilentStructStore.hh.

References 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.

Definition at line 125 of file SilentStructStore.hh.

References store_.

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

Get a random structure.

Definition at line 249 of file SilentStructStore.cc.

References core::kinematics::RG().

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

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

inline

Definition at line 147 of file SilentStructStore.hh.

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.

Definition at line 308 of file SilentStructStore.cc.

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

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

Print silent file.

Definition at line 291 of file SilentStructStore.cc.

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.

Definition at line 184 of file SilentStructStore.cc.

References core::chemical::ChemicalManager::get_instance(), 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

Definition at line 229 of file SilentStructStore.cc.

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

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

read from silent file

Definition at line 216 of file SilentStructStore.cc.

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::comment_lines(), core::sequence::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

Definition at line 209 of file SilentStructStore.cc.

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

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

Print silent file.

Definition at line 256 of file SilentStructStore.cc.

References 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.

Definition at line 271 of file SilentStructStore.cc.

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

Print silent file.

Definition at line 278 of file SilentStructStore.cc.

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

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

inline

How many structures.

Definition at line 116 of file SilentStructStore.hh.

References store_.

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

inline

return numner of structures

Definition at line 155 of file SilentStructStore.hh.

References store_.

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

Definition at line 320 of file SilentStructStore.cc.

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

Definition at line 145 of file SilentStructStore.hh.

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

Definition at line 169 of file SilentStructStore.hh.

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

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation