Rotamer Class Reference

The class Rotamer is used to initialize side-chain database by parsing Dunbrack's Backbone Dependent Rotamer Library, sample one side-chain conformation for a given residue, evaluate the probability given one side-chain conformation. More...

#include <Rotamer.h>

Public Member Functions
	Rotamer (PProtein *protein)
void	sample (const string &residue_name, const double &phi, const double &psi, int &rotamer_grid, vector< double > &dAngles)
	Randomly sample side-chain chi angles given residue name and backbone dihedral angle pair. More...
void	sample_common (const string &residue_name, const int &phi, const int &psi, int &rotamer_grid, vector< double > &dAngles)
	Randomly sample side-chain chi angles given rotameric residue name and backbone dihedral angle pair. More...
void	sample_Special (const string &residue_name, const int &phi, const int &psi, int &rotamer_grid, vector< double > &dAngles)
	Randomly sample side-chain chi angles given non-rotameric residue name and backbone dihedral angle pair. More...
void	output (char *filename)
	Output the database to a file. More...
double	evalSidechain_log (PChain *chain, const int s, const int e)
	Evaluate side-chain structures given one protein chain. More...
void	initSidechainDatabase (PProtein *protein)
	Initialize sidechain database according to residues the protein contains. More...

Private Member Functions
void	init ()
void	read (const string &res_name)
	Read sidechain library given residue name and construct corresponding database. More...
void	read_common (const string &res_name)
	Read sidechain library given the name of a rotameric residue and construct corresponding database. More...
void	read_special (const string &res_name)
	Read sidechain library given the name of a non-rotameric residue and construct corresponding database. More...
int	type (const string &res_name)
	Return the type of residue given residue name. More...
bool	isSpecial (const string &res_name)
	Check if the residue is rotameric or not. More...

Private Attributes
GridMap	gridMap
GridMapSpecial	gridMapSpecial
vector< int >	degree_start
vector< int >	degree_end
vector< int >	stepLength
map< string, int >	typeMap

Static Private Attributes
static const int	ASN = 0
static const int	ASP = 1
static const int	PHE = 2
static const int	TRP = 3
static const int	HIS = 4
static const int	TYR = 5
static const int	GLN = 6
static const int	GLU = 7

Detailed Description

The class Rotamer is used to initialize side-chain database by parsing Dunbrack's Backbone Dependent Rotamer Library, sample one side-chain conformation for a given residue, evaluate the probability given one side-chain conformation.

Constructor & Destructor Documentation

Rotamer::Rotamer

(

PProtein *

protein

)

Parameters

protein

protein chain to be sampled

Member Function Documentation

double Rotamer::evalSidechain_log	(	PChain *	chain,
		const int	s,
		const int	e
	)

Evaluate side-chain structures given one protein chain.

Parameters

chain	protein chain to be evaluated
s	index of starting residue in protein chain
e	index of ending residue in protein chain

Returns

probability density in logarithm

void Rotamer::initSidechainDatabase

(

PProtein *

protein

)

Initialize sidechain database according to residues the protein contains.

Parameters

protein

protein chain to be sampled

bool Rotamer::isSpecial ( const string &  res_name )

private

Check if the residue is rotameric or not.

Parameters

res_name

residue name

Returns

true, rotemeric; false, non-rotameric

void Rotamer::output

(

char *

filename

)

Output the database to a file.

Parameters

filename

output filename

void Rotamer::read ( const string &  res_name )

private

Read sidechain library given residue name and construct corresponding database.

Parameters

res_name

residue name

void Rotamer::read_common ( const string &  res_name )

private

Read sidechain library given the name of a rotameric residue and construct corresponding database.

Parameters

res_name

residue name

void Rotamer::read_special ( const string &  res_name )

private

Read sidechain library given the name of a non-rotameric residue and construct corresponding database.

Parameters

res_name

residue name

void Rotamer::sample	(	const string &	residue_name,
		const double &	phi,
		const double &	psi,
		int &	rotamer_grid,
		vector< double > &	dAngles
	)

Randomly sample side-chain chi angles given residue name and backbone dihedral angle pair.

Parameters

residue_name	name of the residue
phi	backbone phi angle
psi	backbone psi angle
rotamer_grid	stores the grid index of rotamer in the rotamer database (for evaluation purpose)
dAngles	stores the side-chain chi angles

void Rotamer::sample_common	(	const string &	residue_name,
		const int &	phi,
		const int &	psi,
		int &	rotamer_grid,
		vector< double > &	dAngles
	)

Randomly sample side-chain chi angles given rotameric residue name and backbone dihedral angle pair.

Parameters

residue_name	name of the residue
phi	backbone phi angle
psi	backbone psi angle
rotamer_grid	stores the grid index of rotamer in the rotamer database (for evaluation purpose)
dAngles	stores the side-chain chi angles

void Rotamer::sample_Special	(	const string &	residue_name,
		const int &	phi,
		const int &	psi,
		int &	rotamer_grid,
		vector< double > &	dAngles
	)

Randomly sample side-chain chi angles given non-rotameric residue name and backbone dihedral angle pair.

Parameters

residue_name	name of the residue
phi	backbone phi angle
psi	backbone psi angle
rotamer_grid	stores the grid index of rotamer in the rotamer database (for evaluation purpose)
dAngles	stores the side-chain chi angles

int Rotamer::type ( const string &  res_name )

private

Return the type of residue given residue name.

Returns

-1: rotameric residue; 0-7: ASN-GLU

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

• Rotamer.h
• Rotamer.cc