Rosetta 3.4
Public Member Functions | Static Public Member Functions
protocols::abinitio::IterativeAbrelax Class Reference

#include <IterativeAbrelax.hh>

Inheritance diagram for protocols::abinitio::IterativeAbrelax:
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Collaboration diagram for protocols::abinitio::IterativeAbrelax:
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List of all members.

Public Member Functions

 IterativeAbrelax ()
virtual bool finished () const
 archive is finished when at last stage
virtual bool still_interested (jd2::archive::Batch const &batch) const
 we are not interested in batches that were generated in old stages
virtual void generate_batch ()
virtual void idle ()
 while waiting for jobs to finish
virtual void save_to_file (std::string suffix="")
 save and restore archive to file-system
virtual void save_status (std::ostream &) const
 save and restore status of archive to file-system
virtual bool restore_from_file ()
 overloaded that we can sort the pool after reading
virtual void init_from_decoy_set (core::io::silent::SilentFileData const &)
 overloaded to make input decoys appear the same as decoys coming from batches
virtual void read_structures (core::io::silent::SilentFileData &, jd2::archive::Batch const &batch)
 overloaded so we can test for end of IterationStage after reading
void set_manager (jd2::archive::ArchiveManagerAP manager)

Static Public Member Functions

static void register_options ()
 Archive specific options.

Constructor & Destructor Documentation

protocols::abinitio::IterativeAbrelax::IterativeAbrelax ( )

Member Function Documentation

bool protocols::abinitio::IterativeAbrelax::finished ( ) const [virtual]

archive is finished when at last stage

Reimplemented from protocols::abinitio::IterativeBase.

References protocols::abinitio::IterativeBase::finished().

void protocols::abinitio::IterativeAbrelax::generate_batch ( ) [virtual]

ready for new batch .... if queue is empty batch will be generated any way, but otherwise we only generate if this yields true. logic here: new batch at beginning, but only if we are in startup phase ( not a reload of a full archive ) otherwise make new batch if sufficiently many structures have been accepted since last batch

generate new batch... type of batch depends on stage_. we switch to next stage based on some convergence criteria: right now it is how many decoys were accepted from last batch.. if this number drops sufficiently ---> next stage... (maybe need to put a safeguard in here: ratio small but at least XXX decoys proposed since last batch... )

Reimplemented from protocols::abinitio::IterativeBase.

References protocols::abinitio::IterativeBase::generate_batch(), protocols::abinitio::IterativeFullatom::generate_batch(), and protocols::abinitio::IterativeFullatom::ready_for_batch().

void protocols::abinitio::IterativeAbrelax::idle ( ) [virtual]

while waiting for jobs to finish

Reimplemented from protocols::abinitio::IterativeBase.

References protocols::abinitio::IterativeBase::idle().

void protocols::abinitio::IterativeAbrelax::init_from_decoy_set ( core::io::silent::SilentFileData const &  sfd) [virtual]

overloaded to make input decoys appear the same as decoys coming from batches

load decoys into archive from -archive:input_pool or so

Reimplemented from protocols::abinitio::IterativeBase.

References protocols::abinitio::IterativeBase::init_from_decoy_set().

void protocols::abinitio::IterativeAbrelax::read_structures ( core::io::silent::SilentFileData returned_decoys,
jd2::archive::Batch const &  batch 
) [virtual]
void protocols::abinitio::IterativeAbrelax::register_options ( ) [static]
bool protocols::abinitio::IterativeAbrelax::restore_from_file ( ) [virtual]

overloaded that we can sort the pool after reading

restore archive and sort

Reimplemented from protocols::jd2::archive::EvaluatedArchive.

References protocols::jd2::archive::EvaluatedArchive::restore_from_file().

void protocols::abinitio::IterativeAbrelax::save_status ( std::ostream &  os) const [virtual]

save and restore status of archive to file-system

Reimplemented from protocols::abinitio::IterativeBase.

References protocols::abinitio::IterativeBase::save_status().

void protocols::abinitio::IterativeAbrelax::save_to_file ( std::string  suffix = "") [virtual]

save and restore archive to file-system

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

References protocols::jd2::archive::ArchiveBase::save_to_file().

void protocols::abinitio::IterativeAbrelax::set_manager ( jd2::archive::ArchiveManagerAP  manager) [virtual]
bool protocols::abinitio::IterativeAbrelax::still_interested ( jd2::archive::Batch const &  batch) const [virtual]

we are not interested in batches that were generated in old stages

batch is expired ?

ready for new batch .... if queue is empty batch will be generated any way, but otherwise we only generate if this yields true. logic here: new batch at beginning, but only if we are in startup phase ( not a reload of a full archive ) otherwise make new batch if sufficiently many structures have been accepted since last batch ----------------- stage control ----------------------

Reimplemented from protocols::abinitio::IterativeBase.

References protocols::abinitio::IterativeBase::still_interested().


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