Rosetta 3.4
Public Member Functions | Static Public Member Functions | Protected Member Functions
protocols::jd2::archive::EvaluatedArchive Class Reference

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input. More...

#include <EvaluatedArchive.hh>

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List of all members.

Public Member Functions

 EvaluatedArchive (ArchiveManagerAP ptr)
 Constructor and Destructor.
 EvaluatedArchive ()
 ~EvaluatedArchive ()
virtual bool add_structure (core::io::silent::SilentStructOP from_batch)
 add decoy to Archive evaluate decoy and call add_evaluated_structure
core::Real select_score (core::io::silent::SilentStructOP evaluated_decoy)
 compute score according to select_weights --- this can contain any evaluator columns
void setup_default_evaluators ()
 set common evaluators: eg. ConstraintEvaluator if -cst_file is present
virtual bool restore_from_file ()
 overloaded that we can sort the pool after reading
virtual void read_structures (core::io::silent::SilentFileData &, Batch const &batch)
 only overloaded this to add some verbosity each time we read structures
virtual void init_from_decoy_set (core::io::silent::SilentFileData const &sfd)=0
 overloaded to make input decoys appear the same as decoys coming from batches

Static Public Member Functions

static void register_options ()
 Archive specific options.

Protected Member Functions

core::io::silent::SilentStructOP evaluate_silent_struct (core::io::silent::SilentStructOP from_batch) const
 yields an "evaluated" silent-struct which can be queried with select_score will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct
virtual bool add_evaluated_structure (core::io::silent::SilentStructOP evaluated_decoy)
 add an evaluated decoy to Archive (i.e, evaluated_decoy = evaluate( some_decoy ) );
bool evaluate_local () const
 specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)
void set_evaluate_local (bool setting)
void rescore ()
 recompute all score-values of all decoys and re-order the archive by (new) select_score
void add_evaluation (evaluation::PoseEvaluatorOP, core::Real weight=0.0)
 add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()
void remove_evaluation (std::string const &column)
 remove Evaluator
bool has_evaluator (std::string const &column)
 is a certain elvaluator present ?
void set_weight (std::string const &column, core::Real weight)
 set weight of an evaluator or a column otherwise present in silent-structs (i.e, score, chainbreak, external evaluation like score_final )
core::Real get_weight (std::string const &column)
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn_)
 set scorefxn used for evaluation
core::scoring::ScoreFunction
const & 
scorefxn () const
core::scoring::ScoreFunctionOP scorefxn_non_const ()

Detailed Description

Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.

This job distributor is meant for running jobs where the machine you are using has a large number of processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs could vary greatly. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all without MPI and the implementations of all but the interface functions have been put inside of ifdef directives. Generally each function has a master and slave version, and the interface functions call one or the other depending on processor rank.


Constructor & Destructor Documentation

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

Constructor and Destructor.

References setup_default_evaluators().

protocols::jd2::archive::EvaluatedArchive::EvaluatedArchive ( )
protocols::jd2::archive::EvaluatedArchive::~EvaluatedArchive ( )

Member Function Documentation

bool protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure ( core::io::silent::SilentStructOP  evaluated_decoy) [protected, virtual]
void protocols::jd2::archive::EvaluatedArchive::add_evaluation ( evaluation::PoseEvaluatorOP  eval,
core::Real  weight = 0.0 
) [protected]

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

Referenced by protocols::abinitio::IterativeBase::init_from_decoy_set(), setup_default_evaluators(), and protocols::abinitio::IterativeBase::setup_default_evaluators().

bool protocols::jd2::archive::EvaluatedArchive::add_structure ( core::io::silent::SilentStructOP  from_batch) [virtual]

add decoy to Archive evaluate decoy and call add_evaluated_structure

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

Reimplemented in protocols::abinitio::IterativeBase.

References add_evaluated_structure(), and evaluate_silent_struct().

bool protocols::jd2::archive::EvaluatedArchive::evaluate_local ( ) const [inline, protected]
core::io::silent::SilentStructOP protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct ( core::io::silent::SilentStructOP  iss) const [protected]

yields an "evaluated" silent-struct which can be queried with select_score will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

evaluate decoy... if non-local evaluation just copy silent-struct

References evaluate_local(), and protocols::jd2::tr().

Referenced by add_structure(), protocols::abinitio::IterativeBase::add_structure(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), and rescore().

core::Real protocols::jd2::archive::EvaluatedArchive::get_weight ( std::string const &  column) [protected]

References has_evaluator().

bool protocols::jd2::archive::EvaluatedArchive::has_evaluator ( std::string const &  column) [protected]

is a certain elvaluator present ?

Referenced by get_weight().

virtual void protocols::jd2::archive::EvaluatedArchive::init_from_decoy_set ( core::io::silent::SilentFileData const &  sfd) [pure virtual]

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

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

Implemented in protocols::abinitio::IterativeAbrelax, and protocols::abinitio::IterativeBase.

void protocols::jd2::archive::EvaluatedArchive::read_structures ( core::io::silent::SilentFileData sfd,
Batch const &  batch 
) [virtual]
void protocols::jd2::archive::EvaluatedArchive::register_options ( ) [static]
void protocols::jd2::archive::EvaluatedArchive::remove_evaluation ( std::string const &  column) [protected]
void protocols::jd2::archive::EvaluatedArchive::rescore ( ) [protected]
bool protocols::jd2::archive::EvaluatedArchive::restore_from_file ( ) [virtual]

overloaded that we can sort the pool after reading

restore archive and sort

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

Reimplemented in protocols::abinitio::IterativeAbrelax.

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

Referenced by protocols::abinitio::IterativeAbrelax::restore_from_file().

core::scoring::ScoreFunction const & protocols::jd2::archive::EvaluatedArchive::scorefxn ( ) const [protected]
core::scoring::ScoreFunctionOP protocols::jd2::archive::EvaluatedArchive::scorefxn_non_const ( ) [protected]
Real protocols::jd2::archive::EvaluatedArchive::select_score ( core::io::silent::SilentStructOP  evaluated_decoy)
void protocols::jd2::archive::EvaluatedArchive::set_evaluate_local ( bool  setting) [inline, protected]
void protocols::jd2::archive::EvaluatedArchive::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn_) [protected]
void protocols::jd2::archive::EvaluatedArchive::set_weight ( std::string const &  column,
core::Real  weight 
) [protected]

set weight of an evaluator or a column otherwise present in silent-structs (i.e, score, chainbreak, external evaluation like score_final )

Referenced by protocols::abinitio::IterativeBase::compute_cores(), protocols::abinitio::IterativeBase::init_from_decoy_set(), protocols::abinitio::IterativeBase::IterativeBase(), protocols::abinitio::IterativeFullatom::IterativeFullatom(), and setup_default_evaluators().

void protocols::jd2::archive::EvaluatedArchive::setup_default_evaluators ( )

set common evaluators: eg. ConstraintEvaluator if -cst_file is present

Reimplemented in protocols::abinitio::IterativeBase.

References add_evaluation(), protocols::evaluation::EvaluatorFactory::get_instance(), set_weight(), and SPECIAL_INITIAL_DECOY_PENALTY().

Referenced by EvaluatedArchive().


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