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Public Types | Public Member Functions | Private Attributes | List of all members
protocols::wum::SilentStructStore Class Reference

#include <SilentStructStore.hh>

Inheritance diagram for protocols::wum::SilentStructStore:
Inheritance graph
[legend]

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::SilentStructOPget_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

Constructor & Destructor Documentation

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

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

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

Member Function Documentation

void protocols::wum::SilentStructStore::add ( const core::pose::Pose pose)
void protocols::wum::SilentStructStore::add ( core::io::silent::SilentStructOP  new_struct)
void protocols::wum::SilentStructStore::add ( const core::io::silent::SilentStruct new_struct)
void protocols::wum::SilentStructStore::add ( core::io::silent::SilentFileData const &  sfd)
void protocols::wum::SilentStructStore::add ( SilentStructStore mergestore)

Add the contents of another SilentStructStore.

References store_.

void protocols::wum::SilentStructStore::all_add_energy ( std::string const &  scorename,
core::Real  value,
core::Real  weight = 1.0 
)
void protocols::wum::SilentStructStore::all_sort_silent_scores ( )
iterator protocols::wum::SilentStructStore::begin ( )
inline
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 ( )
iterator protocols::wum::SilentStructStore::end ( )
inline
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
void protocols::wum::SilentStructStore::get_pose ( core::Size  index,
core::pose::Pose pose 
) const
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::mpi_refinement::MPI_Refinement::print_summary(), protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::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().

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

Get a structure with a certain index.

References store_.

SilentStructCOP protocols::wum::SilentStructStore::get_struct_random ( ) const
void protocols::wum::SilentStructStore::limit ( core::Size  limit_size)
inline
core::Size protocols::wum::SilentStructStore::mem_footprint ( ) const
virtual
void protocols::wum::SilentStructStore::print ( std::ostream &  out) const

Print silent file.

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::streams_from_cmd_line(), and core::kinematics::TR().

void protocols::wum::SilentStructStore::read_from_file ( const std::string &  filename)
void protocols::wum::SilentStructStore::read_from_stream ( std::istream &  input)
void protocols::wum::SilentStructStore::read_from_string ( const std::string &  input)
void protocols::wum::SilentStructStore::serialize ( std::ostream &  out) const
void protocols::wum::SilentStructStore::serialize ( std::string &  out) const

Print silent file.

void protocols::wum::SilentStructStore::serialize_to_file ( const std::string &  file) const
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::MPI_Refinement::load_structures_from_cmdline_into_library(), protocols::loophash::MPI_LoopHashRefine::load_structures_from_cmdline_into_library(), protocols::mpi_refinement::Serial_Refine::load_structures_from_cmdline_into_library(), protocols::wum::WorkUnitQueue::mem_stats(), protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus(), protocols::loophash::MPI_LoopHashRefine_Emperor::process_inbound_wus(), protocols::mpi_refinement::MPI_Refine_Emperor::process_inbound_wus(), protocols::mpi_refinement::MPI_Refine_Master::process_inbound_wus(), protocols::relax::WorkUnit_BatchRelax::run(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::mpi_refinement::WorkUnit_CombinePose::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::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().

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

return numner of structures

References store_.

void protocols::wum::SilentStructStore::sort_by ( std::string const &  field = "score")
std::vector< core::io::silent::SilentStructOP >& protocols::wum::SilentStructStore::store ( )
inline

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: