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Public Member Functions | Private Attributes | List of all members
protocols::jd2::archive::DebugArchive Class Reference

#include <ArchiveBase.hh>

Inheritance diagram for protocols::jd2::archive::DebugArchive:
Inheritance graph
Collaboration diagram for protocols::jd2::archive::DebugArchive:
Collaboration graph

Public Member Functions

 DebugArchive (ArchiveManagerAP ptr)
virtual bool add_structure (core::io::silent::SilentStructOP, Batch const &)
 add structure to Archive.. return false if structure is rejected. More...
virtual bool finished () const
 is archive converged ? More...
virtual void generate_batch ()
 create a new batch with manager().start_new_batch() and manager().finalize_batch(); More...
virtual void score (core::pose::Pose &pose) const
virtual void save_status (std::ostream &) const
 save and restore status of archive to file-system More...
virtual void restore_status (std::istream &)
- Public Member Functions inherited from protocols::jd2::archive::ArchiveBase
 ArchiveBase (ArchiveManagerAP ptr=NULL)
 ~ArchiveBase ()
virtual void initialize ()
core::Size nstruct () const
 how many structures should be in archive .. varies from decoys().size() in startup phase. More...
void set_nstruct (core::Size set)
 set target size of pool More...
virtual void save_to_file (std::string suffix="")
 save and restore archive to file-system More...
virtual bool restore_from_file ()
 restore archive More...
virtual void idle ()
 called when nothing is happening More...
virtual void init_from_decoy_set (core::io::silent::SilentFileData const &sfd)
 read externally provided structures from decoy_file into archive More...
virtual void read_structures (core::io::silent::SilentFileData &, Batch const &batch)
 SilentFileData contains the new structures belonging to this batch. More...
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 ()
SilentStructs const & decoys () const
SilentStructsdecoys ()
- Public Member Functions inherited from protocols::jd2::archive::AbstractArchiveBase
virtual ~AbstractArchiveBase ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
 AbstractArchiveBase (ArchiveManagerAP ptr)
 AbstractArchiveBase ()
virtual bool still_interested (jd2::archive::Batch const &) const
 old-batches might be outdated and should not be computed anymore return true for this query if this is the case for old_batch More...
void set_name (std::string const &set)
 set name of archive ( used also for save_to_file and restore_from_file ) More...
std::string const & name () const
ArchiveManagermanager ()
 access to the ArchiveManager (control of batches) More...
virtual void set_manager (ArchiveManagerAP manager)

Private Attributes

core::Size ct_batches_
core::scoring::ScoreFunctionOP cen_score_
bool make_mistake_

Additional Inherited Members

- Static Public Member Functions inherited from protocols::jd2::archive::ArchiveBase
static void register_options ()
- Protected Types inherited from protocols::jd2::archive::ArchiveBase
typedef std::list
< core::io::silent::SilentStructOP
- Protected Member Functions inherited from protocols::jd2::archive::ArchiveBase
virtual void count_structure (Batch const &batch, bool accepted)
 count the structure for the acceptance statistics only count if not from expired batch More...
void count_removed_structures (core::Size n_removed)
 count the structure for the acceptance statistics only count if not from expired batch More...
void set_max_nstruct (core::Size setting)
void add_structure_at_position (SilentStructs::iterator iss, core::io::silent::SilentStructOP new_decoy)
 call to insert structure at position given by iterator More...
- Static Protected Attributes inherited from protocols::jd2::archive::ArchiveBase
static std::string const TAG_IN_FILE
static std::string const SOURCE_FILE

Constructor & Destructor Documentation

protocols::jd2::archive::DebugArchive::DebugArchive ( ArchiveManagerAP  ptr)

Member Function Documentation

bool protocols::jd2::archive::DebugArchive::add_structure ( core::io::silent::SilentStructOP  orig_from_batch,
Batch const &   

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

Reimplemented from protocols::jd2::archive::ArchiveBase.

References protocols::jd2::archive::ArchiveBase::decoys(), and core::io::serialization::size().

virtual bool protocols::jd2::archive::DebugArchive::finished ( ) const

is archive converged ?

Reimplemented from protocols::jd2::archive::ArchiveBase.

References ct_batches_.

void protocols::jd2::archive::DebugArchive::generate_batch ( )
void protocols::jd2::archive::DebugArchive::restore_status ( std::istream &  in)
void protocols::jd2::archive::DebugArchive::save_status ( std::ostream &  os) const

save and restore status of archive to file-system

Reimplemented from protocols::jd2::archive::ArchiveBase.

References ct_batches_, and protocols::jd2::archive::ArchiveBase::save_status().

void protocols::jd2::archive::DebugArchive::score ( core::pose::Pose pose) const

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::jd2::archive::DebugArchive::cen_score_

Referenced by DebugArchive().

core::Size protocols::jd2::archive::DebugArchive::ct_batches_
bool protocols::jd2::archive::DebugArchive::make_mistake_

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