VGPFunction Class Reference

Implement VGP (Variable Gap Penalty) function. More...

Inheritance diagram for VGPFunction:

Collaboration diagram for VGPFunction:

Public Member Functions
	VGPFunction (string pdbFileName, string chainID)
	Default constructor. More...
	VGPFunction (string pdbFileName, string chainID, double o, double e, unsigned int extType, double wH, double wS, double wB, double wC, double wD)
	Constructor assigning o, e and weights. More...
	VGPFunction (const VGPFunction &orig)
	Copy constructor.
virtual	~VGPFunction ()
	Destructor.
virtual void	copy (const GapFunction &orig)
	Copy orig object to this object ("deep copy").
virtual void	copy (const VGPFunction &orig)
	Copy orig object to this object ("deep copy"). More...
virtual double	getExtensionPenalty (int p)
	Return extension gap penalty for template position p. More...
virtual double	getOpenPenalty (int p)
	Return open gap penalty for template position p. More...
virtual VGPFunction *	newCopy ()
	Construct a new "deep copy" of this object.
VGPFunction &	operator= (const VGPFunction &orig)
	Assignment operator. More...
void	pExtractPdbInfo (string pdbFileName, string chainID)
	Extract structural infos from PDB template file. More...
virtual void	setExtensionPenalty (double pen)
	Set extension gap penalty.
virtual void	setOpenPenalty (double pen)
	Set open gap penalty.

Detailed Description

Implement VGP (Variable Gap Penalty) function.

Some explanations can be found in: Madhusudhan MS., Marti-Renom MA., Sanchez R., Sali A. Variable gap penalty for protein sequence-structure alignment. Department of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California at San Francisco, 94143, USA. PMID: 16423846 [PubMed - indexed for MEDLINE]

Constructor & Destructor Documentation

VGPFunction	(	string	pdbFileName,
		string	chainID
	)

Default constructor.

Parameters

pdbFileName
chainID

VGPFunction	(	string	pdbFileName,
		string	chainID,
		double	o,
		double	e,
		unsigned int	extType,
		double	wH,
		double	wS,
		double	wB,
		double	wC,
		double	wD
	)

Constructor assigning o, e and weights.

Parameters

pdbFileName
chainID
o
e
extType
wH
wS
wB
wC
wD

Member Function Documentation

void copy ( const VGPFunction &  orig )

virtual

Copy orig object to this object ("deep copy").

Parameters

orig

double getExtensionPenalty ( int  p )

virtual

Return extension gap penalty for template position p.

Parameters

p

Returns

Implements GapFunction.

double getOpenPenalty ( int  p )

virtual

Return open gap penalty for template position p.

Parameters

p

Returns

Implements GapFunction.

VGPFunction & operator=

(

const VGPFunction &

orig

)

Assignment operator.

Parameters

orig

Returns

void pExtractPdbInfo	(	string	pdbFileName,
		string	chainID
	)

Extract structural infos from PDB template file.

Parameters

pdbFileName
chainID

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

• Align2/Sources/VGPFunction.h
• Align2/Sources/VGPFunction.cc