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protocols::monte_carlo Namespace Reference

Classes

class  AcceptedScores
 Represents a set of filter scores that have been accepted. More...
 
class  GenericMonteCarloMover
 
class  GenericMonteCarloMoverCreator
 
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::Reallinear_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

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

Trigger API definition.

typedef utility::pointer::shared_ptr< MonteCarloInterface const > protocols::monte_carlo::MonteCarloInterfaceCOP
typedef utility::pointer::shared_ptr< MonteCarloInterface > protocols::monte_carlo::MonteCarloInterfaceOP
typedef utility::pointer::shared_ptr< MonteCarloRecover const > protocols::monte_carlo::MonteCarloRecoverCOP
typedef utility::pointer::shared_ptr< MonteCarloRecover > protocols::monte_carlo::MonteCarloRecoverOP
typedef utility::pointer::shared_ptr< MonteCarloReset const > protocols::monte_carlo::MonteCarloResetCOP
typedef utility::pointer::shared_ptr< MonteCarloReset > protocols::monte_carlo::MonteCarloResetOP
typedef utility::pointer::shared_ptr< MonteCarloTest const > protocols::monte_carlo::MonteCarloTestCOP
typedef utility::pointer::shared_ptr< MonteCarloTest > protocols::monte_carlo::MonteCarloTestOP
typedef utility::pointer::shared_ptr< ResetBaselineMover const > protocols::monte_carlo::ResetBaselineMoverCOP
typedef utility::pointer::shared_ptr< ResetBaselineMover > protocols::monte_carlo::ResetBaselineMoverOP

Enumeration Type Documentation

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

core::Real protocols::monte_carlo::calc_mean ( utility::vector1< core::Real > const &  vec)

References calc_sum().

core::Real protocols::monte_carlo::calc_sum ( utility::vector1< core::Real > const &  vec)
core::Real protocols::monte_carlo::calc_sum_squares ( utility::vector1< core::Real > const &  vec)
core::Real protocols::monte_carlo::calc_sum_xy ( utility::vector1< core::Real > const &  x,
utility::vector1< core::Real > const &  y 
)
std::string protocols::monte_carlo::gen_mc_ct_namer ( std::string const &  element_name)
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().

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