BFactor Class Reference

The class BFactor is used to initialize and store B-factors database, evaluate the probability densities of conformations according to B-factors. More...

#include <BFactor.h>

Public Member Functions
	BFactor (PProtein *protein)
	Construct a B-factors database for a specific chain. The chain must be the top level chain in the sampling problem.
double	evalAtomPositions (PProtein *chain, const int s, const int e)
	Evaluate a chain (or its subchain) according to B-factors. More...
void	output (char *filename)
	Output atom positions and their B-factors to a file. More...

Private Member Functions
double	getProbDensity_log (const Vector3 &mean, const double variance, const Vector3 &position) const
	Evaluate probability density of an atom position given desired atom position and B-factor. More...
double	getProbDensity_log (const double mean, const double variance, const double x)
	Get probability density of one value in a given normal distribution. More...

Private Attributes
vector< string >	residue_name
vector< vector< string > >	atom_name
vector< vector< Vector3 > >	atom_pos
vector< vector< double > >	atom_bfactors
vector< vector< double > >	atom_variance

Detailed Description

The class BFactor is used to initialize and store B-factors database, evaluate the probability densities of conformations according to B-factors.

Member Function Documentation

double BFactor::evalAtomPositions	(	PProtein *	chain,
		const int	s,
		const int	e
	)

Evaluate a chain (or its subchain) according to B-factors.

Parameters

chain	the chain to be evaluated
s	index of starting residue
e	index of ending residue

Returns

products of probability densities of all backbone atoms in logarithm

double BFactor::getProbDensity_log ( const Vector3 &  mean, const double  variance, const Vector3 &  position  ) const

private

Evaluate probability density of an atom position given desired atom position and B-factor.

Parameters

mean	desired atom position
variance	variance of each dimension
position	the atom position to be evaluated

Returns

probability density of the atom position in logarithm

double BFactor::getProbDensity_log ( const double  mean, const double  variance, const double  x  )

private

Get probability density of one value in a given normal distribution.

Parameters

mean	mean of the normal distribution
variance	variance of the normal distribution
x	value to be evaluated

Returns

probability density of x in logarithm

void BFactor::output

(

char *

filename

)

Output atom positions and their B-factors to a file.

Parameters

filename

output filename

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

• BFactor.h
• BFactor.cc