Sub-Loop Inverse Kinematic Markov Chain (SLIKMC) sampler. Support chain/subchain close-loop sampling, free-end sampling. Side-chain sampling is also supported. More...

#include <SLIKMC.h>

Public Member Functions
	SLIKMCSampler (PProtein *chain)
	Construct a SLIKMC sampler for specific chain.

virtual	~SLIKMCSampler ()
	Destructor.

void	sample (const double time, const int s, const int e)
	Sample conformations of sub-loop from residue s to residue e. More...

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

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

void	enableSidechain ()
	Enable side-chain conformation sampling.

void	disableSidechain ()
	Disable side-chain in sampling.

void	enableFreeEnd ()
	Enable free-end sampling (terminal atoms will stay at fixed positions).

void	disableFreeEnd ()
	Disable free-end sampling.

void	enableLog (const int skip=0)
	Enable saving generated conformations. More...

void	disableLog ()
	Disable saving generated conformations.

void	enableCollisionChecking ()
	Enable steric clash checking for samples.

void	disableCollisionChecking ()
	Disable steric clash checking for samples.

void	enableRamachandran ()
	Enable using Ramachandran plot as prior.

void	disableRamachandran ()
	Disable using Ramachandran plot as prior.

void	dispSettings ()
	Print current settings for sampling.

void	enableCustomPriors ()
	Enable custom defined priors.

void	disableCustomPriors ()
	Disable custom defined priors.

void	addCustomPrior (Prior &prior)
	Add a custom defined prior.

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 block. More...

double	getP_log (PProtein *chain)
	Evaluate probability density of one block or sub-chain. More...

double	getQ_log (PProtein *chain, const int num_solutions, int &status)
	Evaluate proposal density given one block or sub-chain. Initial block and proposal block are assumed to be independent. More...

double	getMetricTensor_log (PProtein *protein, int &status)
	Calculate the metric tensor for one block. More...

Private Attributes
PProtein *	protein
	The protein chain to sample.

vector< PProtein * >	subchains
	Collection of 4-residue size blocks.

BFactor *	bfactor

RamachandranPlot *	rplot

SidechainRotater *	scRotater

bool	use_BFactor

bool	use_Rotamer

bool	freeEnd

bool	use_colChecking

bool	use_RPlot

bool	use_customPrior

bool	init_Rotamer

bool	logFile

int	skipLength

vector< Prior * >	priors

Static Private Attributes
static const int	MAX_IK_SAMPLE = 100
	Maximum number of dihedral angles we try for the first residue in the subchain in case that IK cannot find a solution.

static const int	MAX_METROPOLIS_REJECT = 1
	Maximum number of Metropolis Hasting rejects before we giving up.

static const int	MAX_COLLISION_DETECT = 1
	Maximum number of collision detected before we giving up.

Detailed Description

Sub-Loop Inverse Kinematic Markov Chain (SLIKMC) sampler. Support chain/subchain close-loop sampling, free-end sampling. Side-chain sampling is also supported.

Member Function Documentation

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

Enable using B-factors as priors.

Parameters

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

void SLIKMCSampler::enableLog ( const int skip = 0 )

Enable saving generated conformations.

Parameters

skip	number of conformations to skip after last saving conformation.

double SLIKMCSampler::getMetricTensor_log	(	PProtein *	protein,
		int &	status
	)

private

Calculate the metric tensor for one block.

Parameters

protein	a block to be evaluated
status	an indicator if matrix is not invertible in calculating metric tensor

Returns

double SLIKMCSampler::getP_log ( PProtein * chain )

private

Evaluate probability density of one block or sub-chain.

Returns: probability density in logarithm

double SLIKMCSampler::getQ_log	(	PProtein *	chain,
		const int	num_solutions,
		int &	status
	)

private

Evaluate proposal density given one block or sub-chain. Initial block and proposal block are assumed to be independent.

Parameters

num_solutions	number of IK solution for the block or sub-chain
status	an indicator if matrix is not invertible in calculating metric tensor

Returns: proposal density in logarithm

bool SLIKMCSampler::MHStep	(	double	P,
		double	Q,
		double	P_proposal,
		double	Q_proposal
	)

private

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

Parameters

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

Returns: true: accept; false: reject

void SLIKMCSampler::sample	(	const double	time,
		const int	s,
		const int	e
	)

Sample conformations of sub-loop from residue s to residue e.

Parameters

time	time duration for sampling
s	index of starting residue
e	index of ending residue

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

SLIKMC.h
SLIKMC.cc

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Function Documentation