protocols::canonical_sampling Namespace Reference

Namespaces
	mc_convergence_checks

Classes
class	CanonicalSamplingMover
class	PatchOperation
class	HamiltonianExchange
class	HamiltonianExchangeCreator
class	MetricRecorder
class	MetricRecorderCreator
class	MetropolisHastingsMover
class	MetropolisHastingsMoverCreator
class	MultiTemperatureTrialCounter
class	ParallelTempering
class	ParallelTemperingCreator
class	PDBTrajectoryRecorder
class	PDBTrajectoryRecorderCreator
class	SidechainMetropolisHastingsMover
class	SidechainMetropolisHastingsMoverCreator
class	SilentTrajectoryRecorder
class	SilentTrajectoryRecorderCreator
class	SimulatedTempering
class	SimulatedTemperingCreator
class	TemperatureController
class	FixedTemperatureController
class	TemperingBase
class	ThermodynamicMover
class	ThermodynamicObserver
class	TrajectoryRecorder
class	TrialCounterObserver
class	TrialCounterObserverCreator

Typedefs
typedef utility::pointer::owning_ptr < CanonicalSamplingMover >	CanonicalSamplingMoverOP
typedef utility::pointer::owning_ptr < CanonicalSamplingMover const >	CanonicalSamplingMoverCOP
typedef utility::pointer::owning_ptr < HamiltonianExchange >	HamiltonianExchangeOP
typedef utility::pointer::owning_ptr < HamiltonianExchange const >	HamiltonianExchangeCOP
typedef utility::pointer::owning_ptr < MetropolisHastingsMover >	MetropolisHastingsMoverOP
typedef utility::pointer::owning_ptr < MetropolisHastingsMover const >	MetropolisHastingsMoverCOP
typedef utility::pointer::access_ptr < MetropolisHastingsMover >	MetropolisHastingsMoverAP
typedef utility::pointer::access_ptr < MetropolisHastingsMover const >	MetropolisHastingsMoverCAP
typedef utility::pointer::owning_ptr < ParallelTempering >	ParallelTemperingOP
typedef utility::pointer::owning_ptr < ParallelTempering const >	ParallelTemperingCOP
typedef utility::pointer::owning_ptr < SilentTrajectoryRecorder >	SilentTrajectoryRecorderOP
typedef utility::pointer::owning_ptr < SimulatedTempering >	SimulatedTemperingOP
typedef utility::pointer::owning_ptr < SimulatedTempering const >	SimulatedTemperingCOP
typedef utility::pointer::owning_ptr < SimulatedTemperingObserver >	SimulatedTemperingObserverOP
typedef utility::pointer::owning_ptr < SimulatedTemperingObserver const >	SimulatedTemperingObserverCOP
typedef utility::pointer::owning_ptr < TemperatureController >	TemperatureControllerOP
typedef utility::pointer::owning_ptr < TemperatureController const >	TemperatureControllerCOP
typedef utility::pointer::owning_ptr < TemperingBase >	TemperingBaseOP
typedef utility::pointer::owning_ptr < TemperingBase const >	TemperingBaseCOP
typedef utility::pointer::access_ptr < TemperingBase >	TemperingBaseAP
typedef utility::pointer::access_ptr < TemperingBase const >	TemperingBaseCAP
typedef utility::pointer::owning_ptr < ThermodynamicMover >	ThermodynamicMoverOP
typedef utility::pointer::owning_ptr < ThermodynamicMover const >	ThermodynamicMoverCOP
typedef utility::pointer::owning_ptr < ThermodynamicObserver >	ThermodynamicObserverOP
typedef utility::pointer::owning_ptr < ThermodynamicObserver const >	ThermodynamicObserverCOP
typedef utility::pointer::owning_ptr < TrajectoryRecorder >	TrajectoryRecorderOP

Enumerations
enum	InterpolationType { linear, exponential }

Functions
int	canonical_sampling_main ()
static basic::Tracer	tr ("protocols.canonical_sampling.CanonicalSamplingMover")
std::string	jobname_dirhash (std::string const &dir_prefix, core::Size nr_dirs)
std::ostream &	operator<< (std::ostream &os, HamiltonianExchange const &)
	Test IO operator for debug and Python bindings. More...
std::string	interpolation_type_enum_to_string (InterpolationType interp_enum)
InterpolationType	interpolation_type_string_to_enum (std::string const &interp_string)

Typedef Documentation

typedef utility::pointer::owning_ptr< CanonicalSamplingMover const > protocols::canonical_sampling::CanonicalSamplingMoverCOP

Definition at line 25 of file CanonicalSamplingMover.fwd.hh.

typedef utility::pointer::owning_ptr< CanonicalSamplingMover > protocols::canonical_sampling::CanonicalSamplingMoverOP

Definition at line 23 of file CanonicalSamplingMover.fwd.hh.

typedef utility::pointer::owning_ptr< HamiltonianExchange const > protocols::canonical_sampling::HamiltonianExchangeCOP

Definition at line 26 of file HamiltonianExchange.fwd.hh.

typedef utility::pointer::owning_ptr< HamiltonianExchange > protocols::canonical_sampling::HamiltonianExchangeOP

Definition at line 23 of file HamiltonianExchange.fwd.hh.

typedef utility::pointer::access_ptr< MetropolisHastingsMover > protocols::canonical_sampling::MetropolisHastingsMoverAP

Definition at line 28 of file MetropolisHastingsMover.fwd.hh.

typedef utility::pointer::access_ptr< MetropolisHastingsMover const > protocols::canonical_sampling::MetropolisHastingsMoverCAP

Definition at line 29 of file MetropolisHastingsMover.fwd.hh.

typedef utility::pointer::owning_ptr< MetropolisHastingsMover const > protocols::canonical_sampling::MetropolisHastingsMoverCOP

Definition at line 27 of file MetropolisHastingsMover.fwd.hh.

typedef utility::pointer::owning_ptr< MetropolisHastingsMover > protocols::canonical_sampling::MetropolisHastingsMoverOP

Definition at line 25 of file MetropolisHastingsMover.fwd.hh.

typedef utility::pointer::owning_ptr< ParallelTempering const > protocols::canonical_sampling::ParallelTemperingCOP

Definition at line 26 of file ParallelTempering.fwd.hh.

typedef utility::pointer::owning_ptr< ParallelTempering > protocols::canonical_sampling::ParallelTemperingOP

Definition at line 23 of file ParallelTempering.fwd.hh.

typedef utility::pointer::owning_ptr< SilentTrajectoryRecorder > protocols::canonical_sampling::SilentTrajectoryRecorderOP

Definition at line 39 of file SilentTrajectoryRecorder.fwd.hh.

typedef utility::pointer::owning_ptr< SimulatedTempering const > protocols::canonical_sampling::SimulatedTemperingCOP

Definition at line 26 of file SimulatedTempering.fwd.hh.

typedef utility::pointer::owning_ptr< SimulatedTemperingObserver const > protocols::canonical_sampling::SimulatedTemperingObserverCOP

Definition at line 26 of file SimulatedTemperingObserver.fwd.hh.

typedef utility::pointer::owning_ptr< SimulatedTemperingObserver > protocols::canonical_sampling::SimulatedTemperingObserverOP

Definition at line 23 of file SimulatedTemperingObserver.fwd.hh.

typedef utility::pointer::owning_ptr< SimulatedTempering > protocols::canonical_sampling::SimulatedTemperingOP

Definition at line 23 of file SimulatedTempering.fwd.hh.

typedef utility::pointer::owning_ptr< TemperatureController const > protocols::canonical_sampling::TemperatureControllerCOP

Definition at line 26 of file TemperatureController.fwd.hh.

typedef utility::pointer::owning_ptr< TemperatureController > protocols::canonical_sampling::TemperatureControllerOP

Definition at line 23 of file TemperatureController.fwd.hh.

typedef utility::pointer::access_ptr< TemperingBase > protocols::canonical_sampling::TemperingBaseAP

Definition at line 28 of file TemperingBase.fwd.hh.

typedef utility::pointer::access_ptr< TemperingBase const > protocols::canonical_sampling::TemperingBaseCAP

Definition at line 29 of file TemperingBase.fwd.hh.

typedef utility::pointer::owning_ptr< TemperingBase const > protocols::canonical_sampling::TemperingBaseCOP

Definition at line 27 of file TemperingBase.fwd.hh.

typedef utility::pointer::owning_ptr< TemperingBase > protocols::canonical_sampling::TemperingBaseOP

Definition at line 24 of file TemperingBase.fwd.hh.

typedef utility::pointer::owning_ptr< ThermodynamicMover const > protocols::canonical_sampling::ThermodynamicMoverCOP

Definition at line 26 of file ThermodynamicMover.fwd.hh.

typedef utility::pointer::owning_ptr< ThermodynamicMover > protocols::canonical_sampling::ThermodynamicMoverOP

Definition at line 24 of file ThermodynamicMover.fwd.hh.

typedef utility::pointer::owning_ptr< ThermodynamicObserver const > protocols::canonical_sampling::ThermodynamicObserverCOP

Definition at line 26 of file ThermodynamicObserver.fwd.hh.

typedef utility::pointer::owning_ptr< ThermodynamicObserver > protocols::canonical_sampling::ThermodynamicObserverOP

Definition at line 24 of file ThermodynamicObserver.fwd.hh.

typedef utility::pointer::owning_ptr< TrajectoryRecorder > protocols::canonical_sampling::TrajectoryRecorderOP

Definition at line 39 of file TrajectoryRecorder.fwd.hh.

Enumeration Type Documentation

enum protocols::canonical_sampling::InterpolationType

Enumerator
linear
exponential

Definition at line 44 of file TemperatureController.hh.

Function Documentation

int protocols::canonical_sampling::canonical_sampling_main

(

)

Definition at line 79 of file CanonicalSamplingApplication.cc.

References protocols::jd2::JobDistributor::get_instance(), core::scoring::getScoreFunction(), protocols::jd2::JobDistributor::go(), core::kinematics::MoveMap::init_from_file(), and core::chemical::tr().

std::string protocols::canonical_sampling::interpolation_type_enum_to_string

(

InterpolationType

interp_enum)

Definition at line 67 of file TemperatureController.cc.

References linear.

Referenced by protocols::canonical_sampling::TemperingBase::generate_temp_range().

InterpolationType protocols::canonical_sampling::interpolation_type_string_to_enum

(

std::string const &

interp_string)

Definition at line 73 of file TemperatureController.cc.

References exponential, and linear.

Referenced by protocols::canonical_sampling::TemperingBase::parse_my_tag().

std::string protocols::canonical_sampling::jobname_dirhash	(	std::string const &	dir_prefix,
		core::Size	nr_dirs
	)

Definition at line 341 of file CanonicalSamplingMover.cc.

References protocols::jd2::JobDistributor::current_job_id(), and protocols::jd2::JobDistributor::get_instance().

Referenced by protocols::canonical_sampling::CanonicalSamplingMover::apply(), and OPT_1GRP_KEY().

std::ostream & protocols::canonical_sampling::operator<<	(	std::ostream &	os,
		HamiltonianExchange const &	obj
	)

Test IO operator for debug and Python bindings.

Definition at line 696 of file HamiltonianExchange.cc.

References protocols::canonical_sampling::HamiltonianExchange::show().

static basic::Tracer protocols::canonical_sampling::tr ( "protocols.canonical_sampling.CanonicalSamplingMover"  )

static

Referenced by protocols::canonical_sampling::ParallelTempering::allocate_buffers(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::canonical_sampling::PatchOperation::apply(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::fill_pool(), protocols::canonical_sampling::TrialCounterObserver::finalize_simulation(), protocols::canonical_sampling::ParallelTempering::finalize_simulation(), protocols::canonical_sampling::TemperingBase::generate_temp_range(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::get(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::get_tag(), protocols::canonical_sampling::SimulatedTempering::init_from_options(), protocols::canonical_sampling::TemperingBase::init_from_options(), protocols::canonical_sampling::SimulatedTempering::initialize_from_file(), protocols::canonical_sampling::TemperingBase::initialize_from_file(), protocols::canonical_sampling::HamiltonianExchange::initialize_from_file(), protocols::canonical_sampling::TemperingBase::initialize_simulation(), protocols::canonical_sampling::SimulatedTempering::initialize_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::initialize_simulation(), protocols::canonical_sampling::ParallelTempering::initialize_simulation(), protocols::canonical_sampling::HamiltonianExchange::initialize_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(), protocols::canonical_sampling::TemperingBase::parse_my_tag(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::pop_back(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::canonical_sampling::ParallelTempering::setup_exchange_schedule(), protocols::canonical_sampling::MultiTemperatureTrialCounter::show(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), and protocols::canonical_sampling::SilentTrajectoryRecorder::write_model().