Algorithms for rigorously sampling native state ensembles. See disclaimer in detailed description. More...

Namespaces
	mc_convergence_checks

Classes
class	AsyncMPITemperingBase

class	BiasedMonteCarlo

class	BiasEnergy

class	CanonicalSamplingMover

class	DbTrajectoryReader

class	DbTrajectoryRecorder
	Record a trajectory to an SQL database. More...

class	DbTrajectoryRecorderCreator
	RosettaScripts factory for DbTrajectoryRecorder. More...

class	FixedTemperatureController
	Maintain a constant temperature. More...

class	HamiltonianExchange

class	HamiltonianExchangeCreator
	RosettaScripts factory for HamiltonianExchange. More...

class	MetricRecorder
	Periodically output miscellaneous information. More...

class	MetricRecorderCreator
	RosettaScripts factory for MetricRecorder. More...

class	MetropolisHastingsMover
	Manage the main loop of a canonical Monte Carlo simulation. More...

class	MetropolisHastingsMoverCreator
	RosettaScripts factory for MetropolisHastingsMover. More...

class	MultiTemperatureTrialCounter
	Keep track of trial statistics for any number of replicas. More...

class	ParallelTempering

class	ParallelTemperingCreator
	RosettaScripts factory for ParallelTempering. More...

class	PatchOperation

class	PDBTrajectoryRecorder
	Record a trajectory to the PDB file format. More...

class	PDBTrajectoryRecorderCreator
	RosettaScripts factory for PDBTrajectoryRecorder. More...

class	ProgressBarObserver
	Print an progress bar that updated on each iteration. More...

class	ProgressBarObserverCreator
	RosettaScripts factory for ProgressBarObserver. More...

class	SidechainMetropolisHastingsMover
	Run a sidechain-only canonical Monte Carlo simulation. More...

class	SidechainMetropolisHastingsMoverCreator
	RosettaScripts factory for SidechainMetropolisHastingsMover. More...

class	SilentTrajectoryRecorder
	Record a trajectory to the rosetta-specific silent file format. More...

class	SilentTrajectoryRecorderCreator
	RosettaScripts factory for SilentTrajectoryRecorder. More...

class	SimulatedTempering

class	SimulatedTemperingCreator
	RosettaScripts factory for SimulatedTempering. More...

class	TemperatureController
	Base class for controlling the temperature of a simulation. More...

class	TemperingBase
	Base class for tempering Monte Carlo optimizations. More...

class	ThermodynamicMover
	Base class for moves that can obey detailed balance. More...

class	ThermodynamicObserver
	Base class for reporting and recording data from a simulation. More...

class	TrajectoryRecorder
	Base class for recording a simulation trajectory. More...

class	TrialCounterObserver
	Record the acceptance rate for every type of move attempted. More...

class	TrialCounterObserverCreator
	RosettaScripts factory for TrialCounterObserver. More...

class	WTEBiasEnergy

Typedefs
typedef utility::pointer::shared_ptr < BiasedMonteCarlo >	BiasedMonteCarloOP

typedef utility::pointer::shared_ptr < BiasedMonteCarlo const >	BiasedMonteCarloCOP

typedef utility::pointer::shared_ptr < BiasEnergy >	BiasEnergyOP

typedef utility::pointer::shared_ptr < BiasEnergy const >	BiasEnergyCOP

typedef utility::pointer::weak_ptr < BiasEnergy >	BiasEnergyAP

typedef utility::pointer::weak_ptr < BiasEnergy const >	BiasEnergyCAP

typedef utility::pointer::shared_ptr < CanonicalSamplingMover >	CanonicalSamplingMoverOP

typedef utility::pointer::shared_ptr < CanonicalSamplingMover const >	CanonicalSamplingMoverCOP

typedef utility::pointer::shared_ptr < DbTrajectoryReader >	DbTrajectoryReaderOP

typedef utility::pointer::shared_ptr < DbTrajectoryReader const >	DbTrajectoryReaderCOP

typedef utility::pointer::shared_ptr < DbTrajectoryRecorder >	DbTrajectoryRecorderOP

typedef utility::pointer::shared_ptr < DbTrajectoryRecorder const >	DbTrajectoryRecorderCOP

typedef utility::pointer::shared_ptr < HamiltonianExchange >	HamiltonianExchangeOP

typedef utility::pointer::shared_ptr < HamiltonianExchange const >	HamiltonianExchangeCOP

typedef utility::pointer::shared_ptr < MetropolisHastingsMover >	MetropolisHastingsMoverOP

typedef utility::pointer::shared_ptr < MetropolisHastingsMover const >	MetropolisHastingsMoverCOP

typedef utility::pointer::weak_ptr < MetropolisHastingsMover >	MetropolisHastingsMoverAP

typedef utility::pointer::weak_ptr < MetropolisHastingsMover const >	MetropolisHastingsMoverCAP

typedef utility::pointer::shared_ptr < ParallelTempering >	ParallelTemperingOP

typedef utility::pointer::shared_ptr < ParallelTempering const >	ParallelTemperingCOP

typedef utility::pointer::shared_ptr < ProgressBarObserver >	ProgressBarObserverOP

typedef utility::pointer::shared_ptr < ProgressBarObserver const >	ProgressBarObserverCOP

typedef utility::pointer::shared_ptr < SilentTrajectoryRecorder >	SilentTrajectoryRecorderOP

typedef utility::pointer::shared_ptr < SimulatedTempering >	SimulatedTemperingOP

typedef utility::pointer::shared_ptr < SimulatedTempering const >	SimulatedTemperingCOP

typedef utility::pointer::shared_ptr < TemperatureController >	TemperatureControllerOP

typedef utility::pointer::shared_ptr < TemperatureController const >	TemperatureControllerCOP

typedef utility::pointer::shared_ptr < TemperingBase >	TemperingBaseOP

typedef utility::pointer::shared_ptr < TemperingBase const >	TemperingBaseCOP

typedef utility::pointer::weak_ptr < TemperingBase >	TemperingBaseAP

typedef utility::pointer::weak_ptr < TemperingBase const >	TemperingBaseCAP

typedef utility::pointer::shared_ptr < ThermodynamicMover >	ThermodynamicMoverOP

typedef utility::pointer::shared_ptr < ThermodynamicMover const >	ThermodynamicMoverCOP

typedef utility::pointer::shared_ptr < ThermodynamicObserver >	ThermodynamicObserverOP

typedef utility::pointer::shared_ptr < ThermodynamicObserver const >	ThermodynamicObserverCOP

typedef utility::pointer::shared_ptr < TrajectoryRecorder >	TrajectoryRecorderOP

Enumerations
enum	InterpolationType { linear, exponential }

Functions
std::ostream &	operator<< (std::ostream &os, AsyncMPITemperingBase::ExchangeRequest const &er)

template<typename FLOAT >
void	_toggle (FLOAT &ptr1, FLOAT &ptr2)

int	canonical_sampling_main ()

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

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

static thread_local basic::Tracer	tr ("protocols.canonical_sampling.DbTrajectoryRecorder")

std::ostream &	operator<< (std::ostream &os, HamiltonianExchange const &)
	Test IO operator for debug and Python bindings. More...

static thread_local basic::Tracer	tr ("protocols.canonical_sampling.ProgressBar")

std::string	interpolation_type_enum_to_string (InterpolationType interp_enum)

InterpolationType	interpolation_type_string_to_enum (std::string const &interp_string)

Variables
int const	mpi_size_XCHANGE_READY = 2

int const	mpi_size_SWAP_INVITE = 1

int const	mpi_size_FINISHED = 1

Detailed Description

Algorithms for rigorously sampling native state ensembles. See disclaimer in detailed description.

When I started using the algorithms in this namespace, I had a difficult time orienting myself due to the complete lack of documentation. I decided that it would be helpful to write documentation as part of the process of figuring out how the code works. I mention all this to get to my point, which is a disclaimer:

All of the documentation in the module was written by someone who didn't really understand how the code works. I was more just taking notes on how I felt particular pieces of code should work. The idea was to draw attention to pieces of code that didn't work like I expected. Therefore, even though the documentation is phrased in an authoritative way, it is based primarily on my feelings and secondarily on the code.

The central class in this namespace is MetropolisHastingsMover. Its responsibility is to run a Monte Carlo loop. This class is a Mover, and like all movers it has an apply() method that does all the work. It also provides a number of getters and setters so you can control exactly what the algorithm does. In particular, there are three classes that most influence how the MetropolisHastingsMover behaves. These are ThermoynamicMover, TemperatureController, and MonteCarlo.

Subclasses of ThermodynamicMover are responsible for making moves which obey detailed balance. Some classes which fulfill this interface include BackrubMover, LoopClosureMover, ShearMover, SmallMover, SidechainMover, and SidechainMCMover. Note that both sidechain and backbone moves are available. To add a particular move to your simulation, use MetropolisHastingsMover.add_mover() or any of the similarly-named convenience methods.

Related to the ThermodynamicMover class is the ThermodynamicObserver class. Observer subclasses are meant to observe and change the parameters of this simulation itself. There are three major subclasses: TrialCounterObserver, TrajectoryRecorder, and TemperatureController. The trial counters keep track of move statistics and the trajectory recorders keep track of the poses being sampled. TemperatureController is an especially important class because it is setup to manage the temperature of the Metropolis Hastings simulation. Protocols like simulated annealing and parallel tempering are implemented by children of this class. You can add an observer to your simulation using MetropolisHastingsMover.add_observer().

The actual simulation itself is delegated to the standard MonteCarlo class. You can use a custom MonteCarlo object in a canonical simulation by calling MetropolisHastingsMover.set_monte_carlo().