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

Namespaces
	mc_convergence_checks

Classes
class	CanonicalSamplingMover

class	DbTrajectoryReader
	Read poses from a DbTrajectoryRecorder trajectory. More...

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	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	MpiHamiltonianExchange

class	MpiHamiltonianExchangeCreator
	RosettaScripts factory for MpiHamiltonianExchange. More...

class	MpiParallelTempering
	Manage several replicas with periodic temperature swapping. More...

class	MpiParallelTemperingCreator
	RosettaScripts factory for MpiParallelTempering. More...

class	MultiTempTrialCounter
	Keep track of move statistics at different temperature levels. 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	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...

Typedefs
typedef utility::pointer::owning_ptr < CanonicalSamplingMover >	CanonicalSamplingMoverOP

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

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

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

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

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

typedef utility::pointer::owning_ptr < FixedTemperatureController >	FixedTemperatureControllerOP

typedef utility::pointer::owning_ptr < FixedTemperatureController const >	FixedTemperatureControllerCOP

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 < MpiHamiltonianExchange >	MpiHamiltonianExchangeOP

typedef utility::pointer::owning_ptr < MpiHamiltonianExchange const >	MpiHamiltonianExchangeCOP

typedef utility::pointer::owning_ptr < MpiParallelTempering >	MpiParallelTemperingOP

typedef utility::pointer::owning_ptr < MpiParallelTempering const >	MpiParallelTemperingCOP

typedef utility::pointer::owning_ptr < MultiTempTrialCounter >	MultiTempTrialCounterOP

typedef utility::pointer::owning_ptr < MultiTempTrialCounter const >	MultiTempTrialCounterCOP

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

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

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::access_ptr < TemperatureController >	TemperatureControllerAP

typedef utility::pointer::access_ptr < TemperatureController const >	TemperatureControllerCAP

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 ()

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

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

string	interpolation_type_enum_to_string (InterpolationType interp_enum)

InterpolationType	interpolation_type_string_to_enum (string const &interp_string)

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

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

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

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

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:

I didn't necessarily understand how everything worked when I was writing this documentation. As I went along, I certainly became more and more comfortable with the code. I even successfully refactored parts of it. But some of the documentation is speculative, so take everything with a grain of salt. And please fix any errors you find! With that said, and without any further ado, here is the description of the protocols::canonical_sampling namespace:

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. Related to ThermodynamicMover is ThermodynamicObserver. Observer subclasses are meant to observe the progress of the simulation. The most important of these derive from TrajectoryRecorder and are used to keep track of the poses being sampled. You can add a mover to your simulation using MetropolisHastingsMover.add_mover() or any of the similarly named convenience methods, and you can add an observer using MetropolisHastingsMover.add_observer().

Subclasses of TemperatureController are responsible for setting the temperature during the simulation. The most basic controller is FixedTemperatureControler, which simply maintains a constant temperature and is used by default. More sophisticated temperature protocols allow for faster equilibration. These include SimulatedTempering, ParallelTempering, and HamiltonianExchange. The former two algorithms can both be used to sample a defined thermodynamic ensemble, which is a nice feature.

The actual simulation itself is delegated to the standard MonteCarlo class. The temperature and the score function used in the simulation are taken from a MonteCarlo object provided via MetropolisHastingsMover.set_monte_carlo(). To smartly keep track of acceptance rates during simulations where the temperature changes, setup your MonteCarlo object to use the MultiTempTrialCounter by calling MonteCarlo.set_counter(). This custom counter separately keeps track of moves for each temperature level, which is useful information.