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SamplingManager Class Reference

Public Member Functions

 SamplingManager ()
 
void setup ()
 
void update ()
 
int get_iterations ()
 
 SamplingManager ()
 
void update ()
 
 SamplingManager ()
 
void setup ()
 
void update ()
 
int get_iterations ()
 

Public Attributes

Size first_residue
 
Size last_residue
 

Private Attributes

Pose pose
 
ClosureMoverOP closure_mover
 
BreadthMoverOP breadth_mover
 
SidechainMoverOP sidechain_mover
 
ScoreFunctionOP score_function
 
MonteCarloOP monte_carlo
 
string pdb_path
 
string closure_move
 
string sampling_move
 
string breadth_move
 
string score_name
 
Size first_index
 
Size cut_index
 
Size last_index
 
utility::vector1< Real > weights
 
Size iterations
 
Real temperature
 
pose::Pose pose
 
KinematicMoverOP closure_mover
 
MoverOP breadth_mover
 
string topology
 
Real closure_ratio
 

Friends

class OutputManager
 

Constructor & Destructor Documentation

◆ SamplingManager() [1/3]

SamplingManager::SamplingManager ( )
inline

References autocorrelation::iterations, ObjexxFCL::last_index(), basic::options::OptionKeys::magnesium::monte_carlo, basic::options::OptionKeys::MonteCarlo::MonteCarlo, option, kic_runner::pdb, test.G203_Module_SQLPDB::pdb_path, run_backbone::pivots, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::remodel::rama, basic::options::OptionKeys::dna::specificity::score_function, local::temperature, utility_exit_with_message, and weights().

◆ SamplingManager() [2/3]

SamplingManager::SamplingManager ( )
inline

References create_a3b_hbs::i, autocorrelation::iterations, basic::options::OptionKeys::magnesium::monte_carlo, basic::options::OptionKeys::MonteCarlo::MonteCarlo, option, kic_runner::pdb, test.G203_Module_SQLPDB::pdb_path, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::packing::prevent_repacking, execute::residues, and basic::options::OptionKeys::dna::specificity::score_function.

◆ SamplingManager() [3/3]

SamplingManager::SamplingManager ( )
inline

References autocorrelation::iterations, ObjexxFCL::last_index(), option, kic_runner::pdb, test.G203_Module_SQLPDB::pdb_path, run_backbone::pivots, local::temperature, and utility_exit_with_message.

Member Function Documentation

◆ get_iterations() [1/2]

int SamplingManager::get_iterations ( )
inline

References autocorrelation::iterations.

Referenced by main().

◆ get_iterations() [2/2]

int SamplingManager::get_iterations ( )
inline

References autocorrelation::iterations.

◆ setup() [1/2]

void SamplingManager::setup ( )
inline

References create_a3b_hbs::first, ObjexxFCL::last_index(), and beta_nonlocal::pose.

Referenced by main(), and pyrosetta.distributed.tasks.taskbase.TaskBase::maybe_setup().

◆ setup() [2/2]

void SamplingManager::setup ( )
inline

References SetupMover::apply(), basic::options::OptionKeys::cycles, create_a3b_hbs::first, ObjexxFCL::last_index(), test.G203_Module_SQLPDB::pdb_path, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file(), and utility_exit_with_message.

Referenced by pyrosetta.distributed.tasks.taskbase.TaskBase::maybe_setup().

◆ update() [1/3]

void SamplingManager::update ( )
inline

References utility::io::oc::cout, basic::options::OptionKeys::magnesium::monte_carlo, beta_nonlocal::pose, basic::options::OptionKeys::rdc::total_weight, numeric::random::uniform(), utility_exit_with_message, and weights().

Referenced by main().

◆ update() [2/3]

void SamplingManager::update ( )
inline

References basic::options::OptionKeys::magnesium::monte_carlo, and beta_nonlocal::pose.

◆ update() [3/3]

void SamplingManager::update ( )
inline

References beta_nonlocal::pose, numeric::random::uniform(), and utility_exit_with_message.

Friends And Related Function Documentation

◆ OutputManager

OutputManager
friend

Member Data Documentation

◆ breadth_move

string SamplingManager::breadth_move
private

◆ breadth_mover [1/2]

BreadthMoverOP SamplingManager::breadth_mover
private

◆ breadth_mover [2/2]

MoverOP SamplingManager::breadth_mover
private

◆ closure_move

string SamplingManager::closure_move
private

◆ closure_mover [1/2]

ClosureMoverOP SamplingManager::closure_mover
private

◆ closure_mover [2/2]

KinematicMoverOP SamplingManager::closure_mover
private

◆ closure_ratio

Real SamplingManager::closure_ratio
private

◆ cut_index

Size SamplingManager::cut_index
private

◆ first_index

Size SamplingManager::first_index
private

◆ first_residue

Size SamplingManager::first_residue

◆ iterations

Size SamplingManager::iterations
private

Referenced by pyrosetta.distributed.utility.log.ProgressLogger::increment(), and main().

◆ last_index

Size SamplingManager::last_index
private

◆ last_residue

Size SamplingManager::last_residue

◆ monte_carlo

MonteCarloOP SamplingManager::monte_carlo
private

◆ pdb_path

string SamplingManager::pdb_path
private

◆ pose [1/2]

Pose SamplingManager::pose
private

Referenced by pyrosetta.bindings.pose.PoseScoreAccessor::__delitem__(), pyrosetta.bindings.scores.core.PoseCacheAccessor::__delitem__(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase::__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricStringDataAccessor::__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricRealDataAccessor::__delitem__(), pyrosetta.bindings.pose.PoseResidueAccessor::__getitem__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__getitem__(), pyrosetta.bindings.pose.PoseResidueAccessor::__iadd__(), pyrosetta.bindings.pose.PoseResidueAccessor::__imul__(), pyrosetta.bindings.pose.PoseResidueAccessor::__iter__(), pyrosetta.bindings.pose.PoseResidueAccessor::__len__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__len__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__repr__(), pyrosetta.bindings.pose.PoseResidueAccessor::__reversed__(), pyrosetta.bindings.pose.PoseScoreAccessor::__setitem__(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_get_sm_data_dict(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_has_reserved_custom_metric_keys(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_reserved_keys_from_sm_data(), pyrosetta.bindings.pose.PoseScoreAccessor::all(), pyrosetta.bindings.scores.energies.EnergiesAccessor::all(), pyrosetta.bindings.scores.extra_scores.ExtraFloatScoresDataAccessor::all(), pyrosetta.bindings.scores.extra_scores.ExtraStringScoresDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricStringDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricRealDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeStringDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeRealDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueStringDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueRealDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueProbabilitiesDataAccessor::all(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::apply(), pyrosetta.bindings.pose.PoseScoreAccessor::clear(), pyrosetta.bindings.scores.core.PoseCacheAccessor::clear(), pyrosetta.bindings.scores.energies.EnergiesAccessor::clear(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase::clear(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor::clear(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::clear(), pyrosetta.distributed.packed_pose.core.PackedPose::clone(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::composite_real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::composite_string(), pyrosetta.distributed.packed_pose.core.PackedPose::empty(), pyrosetta.bindings.pose.PoseScoreAccessor::energies(), pyrosetta.bindings.scores.core.PoseCacheAccessor::energies(), pyrosetta.bindings.pose.PoseScoreAccessor::extra(), pyrosetta.bindings.scores.core.PoseCacheAccessor::extra(), pyrosetta.bindings.scores.core.PoseCacheAccessor::metrics(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::per_residue_probabilities(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::per_residue_real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::per_residue_string(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor::real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::real(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor::string(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::string(), test.T300_PyJobDistributor.TestPyJobDistributor::test_jd(), test.T300_PyJobDistributor.TestPyJobDistributor::test_jd_at(), test.T300_PyJobDistributor.TestPyJobDistributor::test_jd_serializable_scores(), test.T300_PyJobDistributor.TestPyJobDistributor::test_jd_unserializable_scores(), test.T010_LoadPDB.LoadPDBTest::test_pdbstring_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseCacheAccessor::test_pose_cache(), test.T010_LoadPDB.LoadPDBTest::test_roundtrip_file(), test.T010_LoadPDB.LoadPDBTest::test_roundtrip_pdb(), test.T010_LoadPDB.LoadPDBTest::test_roundtrip_scored_pdb(), and pyrosetta.distributed.packed_pose.core.PackedPose::update_scores().

◆ pose [2/2]

pose::Pose SamplingManager::pose
private

Referenced by pyrosetta.bindings.pose.PoseScoreAccessor::__delitem__(), pyrosetta.bindings.scores.core.PoseCacheAccessor::__delitem__(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase::__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricStringDataAccessor::__delitem__(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricRealDataAccessor::__delitem__(), pyrosetta.bindings.pose.PoseResidueAccessor::__getitem__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__getitem__(), pyrosetta.bindings.pose.PoseResidueAccessor::__iadd__(), pyrosetta.bindings.pose.PoseResidueAccessor::__imul__(), pyrosetta.bindings.pose.PoseResidueAccessor::__iter__(), pyrosetta.bindings.pose.PoseResidueAccessor::__len__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__len__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__repr__(), pyrosetta.bindings.pose.PoseResidueAccessor::__reversed__(), pyrosetta.bindings.pose.PoseScoreAccessor::__setitem__(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_get_sm_data_dict(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_has_reserved_custom_metric_keys(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_reserved_keys_from_sm_data(), pyrosetta.bindings.pose.PoseScoreAccessor::all(), pyrosetta.bindings.scores.energies.EnergiesAccessor::all(), pyrosetta.bindings.scores.extra_scores.ExtraFloatScoresDataAccessor::all(), pyrosetta.bindings.scores.extra_scores.ExtraStringScoresDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricStringDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricRealDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeStringDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeRealDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueStringDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueRealDataAccessor::all(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueProbabilitiesDataAccessor::all(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::apply(), pyrosetta.bindings.pose.PoseScoreAccessor::clear(), pyrosetta.bindings.scores.core.PoseCacheAccessor::clear(), pyrosetta.bindings.scores.energies.EnergiesAccessor::clear(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessorBase::clear(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor::clear(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::clear(), pyrosetta.distributed.packed_pose.core.PackedPose::clone(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::composite_real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::composite_string(), pyrosetta.distributed.packed_pose.core.PackedPose::empty(), pyrosetta.bindings.pose.PoseScoreAccessor::energies(), pyrosetta.bindings.scores.core.PoseCacheAccessor::energies(), pyrosetta.bindings.pose.PoseScoreAccessor::extra(), pyrosetta.bindings.scores.core.PoseCacheAccessor::extra(), pyrosetta.bindings.scores.core.PoseCacheAccessor::metrics(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::per_residue_probabilities(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::per_residue_real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::per_residue_string(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor::real(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::real(), pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor::string(), pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor::string(), test.T300_PyJobDistributor.TestPyJobDistributor::test_jd(), test.T300_PyJobDistributor.TestPyJobDistributor::test_jd_at(), test.T300_PyJobDistributor.TestPyJobDistributor::test_jd_serializable_scores(), test.T300_PyJobDistributor.TestPyJobDistributor::test_jd_unserializable_scores(), test.T010_LoadPDB.LoadPDBTest::test_pdbstring_io(), pyrosetta.tests.bindings.core.test_pose.TestPoseCacheAccessor::test_pose_cache(), test.T010_LoadPDB.LoadPDBTest::test_roundtrip_file(), test.T010_LoadPDB.LoadPDBTest::test_roundtrip_pdb(), test.T010_LoadPDB.LoadPDBTest::test_roundtrip_scored_pdb(), and pyrosetta.distributed.packed_pose.core.PackedPose::update_scores().

◆ sampling_move

string SamplingManager::sampling_move
private

◆ score_function

ScoreFunctionOP SamplingManager::score_function
private

Referenced by pyrosetta.distributed.tasks.score.ScorePoseTask::execute().

◆ score_name

string SamplingManager::score_name
private

◆ sidechain_mover

SidechainMoverOP SamplingManager::sidechain_mover
private

◆ temperature

Real SamplingManager::temperature
private

Referenced by schema.Temperature::__repr__(), and schema.Temperature::formatted().

◆ topology

string SamplingManager::topology
private

◆ weights

utility::vector1<Real> SamplingManager::weights
private

Referenced by pyrosetta.distributed.tasks.score.ScorePoseTask::score_function().

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