The class MHSample is a sampler based on standard Metropolis-Hastings algorithm. This class can be used to generate free-end conformations. More...

Public Member Functions
	MHSampler (PProtein *chain)
	Construct a standard Metropolis-Hastings sampler for specific chain.

virtual	~MHSampler ()
	Destructor.

void	sample (const double time, const double radius)
	Sample conformations of protein. More...

void	enableBfactors (PProtein *chain=NULL)
	Enable using B-factors as priors. More...

void	disableBfactors ()
	Disable using B-factors as priors.

Private Member Functions
bool	MHStep (double P, double Q, double P_proposal, double Q_proposal)
	Metropolis-Hastings step to decide whether to accept a proposal conformation. More...

double	getP_log (PProtein *chain)
	Evaluate probability density given one conformation. More...

Detailed Description

The class MHSample is a sampler based on standard Metropolis-Hastings algorithm. This class can be used to generate free-end conformations.

Member Function Documentation

void MHSampler::enableBfactors ( PProtein * chain = NULL )

Enable using B-factors as priors.

Parameters

chain a chain conformation with desired atom positions and B-factors.

double MHSampler::getP_log ( PProtein * chain )

private

Evaluate probability density given one conformation.

Parameters

conformation to be evaluated

private

Metropolis-Hastings step to decide whether to accept a proposal conformation.

Parameters

P	Probability density of initial conformation
Q	Proposal density of initial conformation to proposal conformation
P_proposal	Probability density of proposal conformation
Q_proposal	Proposal density of proposal conformation to initial conformation

Sample conformations of protein.

Parameters

time	time duration for sampling
radius	perturbation radius in degrees

The documentation for this class was generated from the following files: