VGPFunction2 Class Reference

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

Inheritance diagram for VGPFunction2:

Collaboration diagram for VGPFunction2:

Public Member Functions
	VGPFunction2 (string secFileName)
	Default constructor. More...
	VGPFunction2 (string secFileName, double o, double e, unsigned int extType, double wH, double wS)
	Constructor assigning o, e and weights. More...
	VGPFunction2 (const VGPFunction2 &orig)
	Copy constructor.
virtual	~VGPFunction2 ()
	Destructor.
virtual void	copy (const GapFunction &orig)
	Copy orig object to this object ("deep copy").
virtual void	copy (const VGPFunction2 &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 VGPFunction2 *	newCopy ()
	Construct a new "deep copy" of this object. More...
VGPFunction2 &	operator= (const VGPFunction2 &orig)
	Assignment operator. More...
void	pExtractSecInfo (string secFileName)
	Extract structural infos from template secondary structure. 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

VGPFunction2

(

string

secFileName

)

Default constructor.

Parameters

secFileName

VGPFunction2	(	string	secFileName,
		double	o,
		double	e,
		unsigned int	extType,
		double	wH,
		double	wS
	)

Constructor assigning o, e and weights.

Parameters

secFileName
o
e
extType
wH
wS

Member Function Documentation

void copy ( const VGPFunction2 &  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.

VGPFunction2 * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements GapFunction.

VGPFunction2 & operator=

(

const VGPFunction2 &

orig

)

Assignment operator.

Parameters

orig

Returns

void pExtractSecInfo

(

string

secFileName

)

Extract structural infos from template secondary structure.

Parameters

secFileName

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

• Align2/Sources/VGPFunction2.h
• Align2/Sources/VGPFunction2.cc