Rosetta 3.4
Public Member Functions | Static Public Member Functions | Protected Types | Protected Member Functions | Static Protected Attributes
protocols::jd2::archive::ArchiveBase Class Reference

#include <ArchiveBase.hh>

Inheritance diagram for protocols::jd2::archive::ArchiveBase:
Inheritance graph
[legend]
Collaboration diagram for protocols::jd2::archive::ArchiveBase:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 ArchiveBase (ArchiveManagerAP ptr=NULL)
 ~ArchiveBase ()
virtual bool finished () const
 is archive converged ?
virtual void generate_batch ()=0
 create a new batch with manager().start_new_batch() and manager().finalize_batch();
virtual bool add_structure (core::io::silent::SilentStructOP orig_from_batch)
 add structure to Archive.. return false if structure is rejected.
core::Size nstruct () const
 how many structures should be in archive .. varies from decoys().size() in startup phase.
void set_nstruct (core::Size set)
 set target size of pool
virtual void save_to_file (std::string suffix="")
 save and restore archive to file-system
virtual bool restore_from_file ()
 restore archive
virtual void save_status (std::ostream &) const
 save and restore status of archive to file-system
virtual void restore_status (std::istream &)
virtual void idle ()
 called when nothing is happening
virtual void init_from_decoy_set (core::io::silent::SilentFileData const &sfd)
 read externally provided structures from decoy_file into archive
virtual void read_structures (core::io::silent::SilentFileData &, Batch const &batch)
 SilentFileData contains the new structures belonging to this batch.
core::Sizeaccepts_since_last_batch ()
core::Size accepts_since_last_batch () const
core::Size proposed_since_last_batch () const
core::Real current_acceptance_ratio () const
void reset_accept_counter ()
core::Size total_proposed ()
core::Size total_accepts ()
bool statistics_valid ()

Static Public Member Functions

static void register_options ()

Protected Types

typedef std::list
< core::io::silent::SilentStructOP
SilentStructs
typedef
SilentStructs::const_iterator 
const_decoy_iterator
typedef
SilentStructs::const_iterator 
decoy_iterator

Protected Member Functions

virtual void count_structure (Batch const &batch, bool accepted)
 count the structure for the acceptance statistics only count if not from expired batch
void count_removed_structures (core::Size n_removed)
 count the structure for the acceptance statistics only count if not from expired batch
SilentStructsdecoys ()
SilentStructs const & decoys () const
void add_structure_at_position (SilentStructs::iterator iss, core::io::silent::SilentStructOP new_decoy)
 call to insert structure at position given by iterator

Static Protected Attributes

static std::string const TAG_IN_FILE
static std::string const SOURCE_FILE

Member Typedef Documentation

typedef SilentStructs::const_iterator protocols::jd2::archive::ArchiveBase::const_decoy_iterator [protected]
typedef SilentStructs::const_iterator protocols::jd2::archive::ArchiveBase::decoy_iterator [protected]

Constructor & Destructor Documentation

protocols::jd2::archive::ArchiveBase::ArchiveBase ( ArchiveManagerAP  ptr = NULL)
protocols::jd2::archive::ArchiveBase::~ArchiveBase ( )

Member Function Documentation

core::Size& protocols::jd2::archive::ArchiveBase::accepts_since_last_batch ( ) [inline]

---- methods to keep statistics of acceptance

Referenced by count_removed_structures(), protocols::abinitio::IterativeBase::idle(), and total_accepts().

core::Size protocols::jd2::archive::ArchiveBase::accepts_since_last_batch ( ) const [inline]
bool protocols::jd2::archive::ArchiveBase::add_structure ( core::io::silent::SilentStructOP  orig_from_batch) [virtual]

add structure to Archive.. return false if structure is rejected.

Reimplemented in protocols::abinitio::IterativeBase, protocols::jd2::archive::DebugArchive, and protocols::jd2::archive::EvaluatedArchive.

References add_structure_at_position().

Referenced by read_structures().

void protocols::jd2::archive::ArchiveBase::add_structure_at_position ( SilentStructs::iterator  iss,
core::io::silent::SilentStructOP  new_decoy 
) [protected]

call to insert structure at position given by iterator

Referenced by protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), and add_structure().

void protocols::jd2::archive::ArchiveBase::count_removed_structures ( core::Size  n_removed) [protected]

count the structure for the acceptance statistics only count if not from expired batch

References accepts_since_last_batch(), and decoys().

Referenced by protocols::abinitio::IterativeBase::cluster().

void protocols::jd2::archive::ArchiveBase::count_structure ( Batch const &  batch,
bool  accepted 
) [protected, virtual]

count the structure for the acceptance statistics only count if not from expired batch

References protocols::jd2::archive::AbstractArchiveBase::still_interested().

Referenced by read_structures().

core::Real protocols::jd2::archive::ArchiveBase::current_acceptance_ratio ( ) const [inline]
SilentStructs const& protocols::jd2::archive::ArchiveBase::decoys ( ) const [inline, protected]
SilentStructs& protocols::jd2::archive::ArchiveBase::decoys ( ) [inline, protected]
virtual bool protocols::jd2::archive::ArchiveBase::finished ( ) const [inline, virtual]
virtual void protocols::jd2::archive::ArchiveBase::generate_batch ( ) [pure virtual]
virtual void protocols::jd2::archive::ArchiveBase::idle ( ) [inline, virtual]
void protocols::jd2::archive::ArchiveBase::init_from_decoy_set ( core::io::silent::SilentFileData const &  sfd) [virtual]
core::Size protocols::jd2::archive::ArchiveBase::nstruct ( ) const [inline]
core::Size protocols::jd2::archive::ArchiveBase::proposed_since_last_batch ( ) const [inline]
void protocols::jd2::archive::ArchiveBase::read_structures ( core::io::silent::SilentFileData sfd,
Batch const &  batch 
) [virtual]
void protocols::jd2::archive::ArchiveBase::register_options ( ) [static]
void protocols::jd2::archive::ArchiveBase::reset_accept_counter ( ) [inline]
bool protocols::jd2::archive::ArchiveBase::restore_from_file ( ) [virtual]
void protocols::jd2::archive::ArchiveBase::restore_status ( std::istream &  is) [virtual]
void protocols::jd2::archive::ArchiveBase::save_status ( std::ostream &  os) const [virtual]
void protocols::jd2::archive::ArchiveBase::save_to_file ( std::string  suffix = "") [virtual]
void protocols::jd2::archive::ArchiveBase::set_nstruct ( core::Size  set) [inline]

set target size of pool

bool protocols::jd2::archive::ArchiveBase::statistics_valid ( ) [inline]
core::Size protocols::jd2::archive::ArchiveBase::total_accepts ( ) [inline]
core::Size protocols::jd2::archive::ArchiveBase::total_proposed ( ) [inline]

Member Data Documentation

std::string const protocols::jd2::archive::ArchiveBase::SOURCE_FILE [static, protected]

Referenced by read_structures().

std::string const protocols::jd2::archive::ArchiveBase::TAG_IN_FILE [static, protected]

Referenced by read_structures().


The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines