protocols::monte_carlo Namespace Reference

Classes
class	GenericMonteCarloMover
class	GenericMonteCarloMoverCreator
class	AcceptedScores
	Represents a set of filter scores that have been accepted. More...
class	GenericSimulatedAnnealer
	GenericSimulatedAnnealer mover for performing simulated annealing trajectories. More...
class	GenericSimulatedAnnealerCreator
class	MonteCarloInterface
	A MonteCarlo object for optimizing the interface dG as defined using InterfaceAnalyzer. The dG and Total energy can be weighted. This is so that the interface energy itself can be optimized through a protocol. More...
class	MonteCarloRecover
class	MonteCarloRecoverCreator
class	MonteCarloReset
class	MonteCarloResetCreator
class	MonteCarloTest
class	MonteCarloTestCreator
class	ResetBaselineMover
class	ResetBaselineMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< GenericMonteCarloMover >	GenericMonteCarloMoverOP
typedef utility::pointer::shared_ptr< GenericMonteCarloMover const >	GenericMonteCarloMoverCOP
typedef std::function< bool(core::Size, core::Size, const core::pose::Pose &, core::scoring::ScoreFunctionOP)>	GenericMonteCarloMoverTrigger
	Trigger API definition. More...
typedef utility::pointer::shared_ptr< GenericSimulatedAnnealer >	GenericSimulatedAnnealerOP
typedef utility::pointer::shared_ptr< GenericSimulatedAnnealer const >	GenericSimulatedAnnealerCOP
typedef utility::pointer::shared_ptr< MonteCarloInterface >	MonteCarloInterfaceOP
typedef utility::pointer::shared_ptr< MonteCarloInterface const >	MonteCarloInterfaceCOP
typedef utility::pointer::shared_ptr< MonteCarloRecover >	MonteCarloRecoverOP
typedef utility::pointer::shared_ptr< MonteCarloRecover const >	MonteCarloRecoverCOP
typedef utility::pointer::shared_ptr< MonteCarloReset >	MonteCarloResetOP
typedef utility::pointer::shared_ptr< MonteCarloReset const >	MonteCarloResetCOP
typedef utility::pointer::shared_ptr< MonteCarloTest >	MonteCarloTestOP
typedef utility::pointer::shared_ptr< MonteCarloTest const >	MonteCarloTestCOP
typedef utility::pointer::shared_ptr< ResetBaselineMover >	ResetBaselineMoverOP
typedef utility::pointer::shared_ptr< ResetBaselineMover const >	ResetBaselineMoverCOP

Enumerations
enum	TrialResult { REJECTED , ACCEPTED , FAILED , FINISHED }
	Describes result of a trial. More...

Functions
std::string	gen_mc_ct_namer (std::string const &element_name)
core::Real	calc_sum (utility::vector1< core::Real > const &vec)
core::Real	calc_mean (utility::vector1< core::Real > const &vec)
core::Real	calc_sum_squares (utility::vector1< core::Real > const &vec)
core::Real	calc_sum_xy (utility::vector1< core::Real > const &x, utility::vector1< core::Real > const &y)
utility::vector1< core::Real >	linear_regression (utility::vector1< core::Real > const &x, utility::vector1< core::Real > const &y)
	Given a set of x and y points, returns the linear regression. More...
std::ostream &	operator<< (std::ostream &os, AcceptedScores const &scores)
void	replace_file (std::string const &origfile, std::string const &newfile)
	safely replaces a file with another More...

Typedef Documentation

GenericMonteCarloMoverCOP

typedef utility::pointer::shared_ptr< GenericMonteCarloMover const > protocols::monte_carlo::GenericMonteCarloMoverCOP

GenericMonteCarloMoverOP

typedef utility::pointer::shared_ptr< GenericMonteCarloMover > protocols::monte_carlo::GenericMonteCarloMoverOP

GenericMonteCarloMoverTrigger

typedef std::function<bool(core::Size, core::Size, const core::pose::Pose&, core::scoring::ScoreFunctionOP)> protocols::monte_carlo::GenericMonteCarloMoverTrigger

Trigger API definition.

GenericSimulatedAnnealerCOP

typedef utility::pointer::shared_ptr< GenericSimulatedAnnealer const > protocols::monte_carlo::GenericSimulatedAnnealerCOP

GenericSimulatedAnnealerOP

typedef utility::pointer::shared_ptr< GenericSimulatedAnnealer > protocols::monte_carlo::GenericSimulatedAnnealerOP

MonteCarloInterfaceCOP

typedef utility::pointer::shared_ptr< MonteCarloInterface const > protocols::monte_carlo::MonteCarloInterfaceCOP

MonteCarloInterfaceOP

typedef utility::pointer::shared_ptr< MonteCarloInterface > protocols::monte_carlo::MonteCarloInterfaceOP

MonteCarloRecoverCOP

typedef utility::pointer::shared_ptr< MonteCarloRecover const > protocols::monte_carlo::MonteCarloRecoverCOP

MonteCarloRecoverOP

typedef utility::pointer::shared_ptr< MonteCarloRecover > protocols::monte_carlo::MonteCarloRecoverOP

MonteCarloResetCOP

typedef utility::pointer::shared_ptr< MonteCarloReset const > protocols::monte_carlo::MonteCarloResetCOP

MonteCarloResetOP

typedef utility::pointer::shared_ptr< MonteCarloReset > protocols::monte_carlo::MonteCarloResetOP

MonteCarloTestCOP

typedef utility::pointer::shared_ptr< MonteCarloTest const > protocols::monte_carlo::MonteCarloTestCOP

MonteCarloTestOP

typedef utility::pointer::shared_ptr< MonteCarloTest > protocols::monte_carlo::MonteCarloTestOP

ResetBaselineMoverCOP

typedef utility::pointer::shared_ptr< ResetBaselineMover const > protocols::monte_carlo::ResetBaselineMoverCOP

ResetBaselineMoverOP

typedef utility::pointer::shared_ptr< ResetBaselineMover > protocols::monte_carlo::ResetBaselineMoverOP

Enumeration Type Documentation

TrialResult

enum protocols::monte_carlo::TrialResult

Describes result of a trial.

REJECTED : Move was rejected ACCEPTED : Move was accepted FAILED : Some failure occurred during the move FINISHED : The stopping condition was met

Enumerator
REJECTED
ACCEPTED
FAILED
FINISHED

Function Documentation

calc_mean()

core::Real protocols::monte_carlo::calc_mean

(

utility::vector1< core::Real > const &

vec

)

References calc_sum().

calc_sum()

core::Real protocols::monte_carlo::calc_sum

(

utility::vector1< core::Real > const &

vec

)

References core::simple_metrics::metrics::sum.

Referenced by calc_mean(), and linear_regression().

calc_sum_squares()

core::Real protocols::monte_carlo::calc_sum_squares

(

utility::vector1< core::Real > const &

vec

)

References core::simple_metrics::metrics::sum.

Referenced by linear_regression().

calc_sum_xy()

core::Real protocols::monte_carlo::calc_sum_xy	(	utility::vector1< core::Real > const &	x,
		utility::vector1< core::Real > const &	y
	)

References core::simple_metrics::metrics::sum.

Referenced by linear_regression().

gen_mc_ct_namer()

std::string protocols::monte_carlo::gen_mc_ct_namer

(

std::string const &

element_name

)

Referenced by protocols::monte_carlo::GenericMonteCarloMover::define_composition_schema().

linear_regression()

utility::vector1< core::Real > protocols::monte_carlo::linear_regression	(	utility::vector1< core::Real > const &	x,
		utility::vector1< core::Real > const &	y
	)

Given a set of x and y points, returns the linear regression.

the first element of the vector is slope

the second is intercept

the third is the sum of squares error

References calc_sum(), calc_sum_squares(), calc_sum_xy(), and protocols::TR().

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::calculate_temps().

operator<<()

std::ostream& protocols::monte_carlo::operator<<	(	std::ostream &	os,
		AcceptedScores const &	scores
	)

replace_file()

void protocols::monte_carlo::replace_file	(	std::string const &	origfile,
		std::string const &	newfile
	)

safely replaces a file with another

helper function that safely replaces a file with another

References protocols::TR().

Referenced by protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file().