Is a container of Polymers (a component of components). Each chain in a PDB (a Protein object) corresponds to a Polymers. Each Polymer corresponds to a Spacer and a LigandSet (if present). More...

Inheritance diagram for Protein:

Collaboration diagram for Protein:

Public Member Functions
virtual void	bindIn (Atom &_this, Bond &c, Atom &_other)

virtual void	bindIn (SimpleBond &c)

virtual void	bindOut (Atom &_this, Bond &c, Atom &_other)

virtual void	bindOut (SimpleBond &c)

virtual Protein *	clone ()

bool	collides (Component &other, double dist=0.0)

void	copy (const Bond &orig)

void	copy (const Polymer &orig)

virtual void	copy (const SimpleBond &orig)

void	copy (const Component &orig)

void	deleteComponent (Component *c)

char	getChainLetter (unsigned int i)

unsigned int	getChainNum (char c)

virtual const SimpleBond &	getInBond (unsigned int n) const

virtual SimpleBond &	getInBond (unsigned int n)

virtual Atom &	getInBondRef (unsigned int n)

LigandSet *	getLigandSet (char c)

LigandSet *	getLigandSet (unsigned int n)

virtual vgVector3< double >	getLowerBound (double dist=0.0)

unsigned int	getMaxInBonds () const

unsigned int	getMaxOutBonds () const

virtual Atom &	getOpenInBondRef (unsigned int n=0)

virtual Atom &	getOpenOutBondRef (unsigned int n=0)

virtual const SimpleBond &	getOutBond (unsigned int n) const

virtual SimpleBond &	getOutBond (unsigned int n)

virtual Atom &	getOutBondRef (unsigned int n)

Polymer &	getPolymer (unsigned int n)

Spacer *	getSpacer (char c)

Spacer *	getSpacer (unsigned int n)

virtual string	getType () const

virtual vgVector3< double >	getUpperBound (double dist=0.0)

void	insertComponent (Component *c)

bool	inSync ()

bool	isBond (const SimpleBond &c) const

bool	isInBond (const SimpleBond &c) const

bool	isIndirectBond (const SimpleBond &c) const

bool	isIndirectInBond (const SimpleBond &c) const

bool	isIndirectOutBond (const SimpleBond &c) const

bool	isOutBond (const SimpleBond &c) const

bool	isTorsionBond (const SimpleBond &c) const

void	removeComponent (Component *c)

virtual void	removeComponentFromIndex (unsigned int i)

void	setMaxInBonds (unsigned int m)

void	setMaxOutBonds (unsigned int m)

virtual void	setType (string _name)

unsigned int	sizeInBonds () const

unsigned int	sizeOpenInBonds () const

unsigned int	sizeOpenOutBonds () const

unsigned int	sizeOutBonds () const

virtual void	unbindIn (Bond &c)

virtual void	unbindIn (SimpleBond &c)

virtual void	unbindOut (Bond &c)

virtual void	unbindOut (SimpleBond &c)

Protected Member Functions
virtual void	pUnbindIn (SimpleBond &c)

virtual void	pUnbindOut (SimpleBond &c)

Detailed Description

Is a container of Polymers (a component of components). Each chain in a PDB (a Protein object) corresponds to a Polymers. Each Polymer corresponds to a Spacer and a LigandSet (if present).

Member Function Documentation

void bindIn	(	Atom &	_this,
		Bond &	c,
		Atom &	_other
	)

virtualinherited

In-going bond from this to c, from this' atom _this to c's _other atom.

Parameters

atom	reference, bond reference, atom reference

Returns: void

void bindIn ( SimpleBond & c )

virtualinherited

Sets and in-bond from this to c.

Reimplemented in Atom.

void bindOut	(	Atom &	_this,
		Bond &	c,
		Atom &	_other
	)

virtualinherited

Out-going bond from this to c, from this' atom _this to c's _other atom.

Parameters

atom	reference, bond reference, atom reference

Returns: void

void bindOut ( SimpleBond & c )

virtualinherited

Sets and out-bond from this to c

Reimplemented in Atom.

Protein * clone ( )

virtual

Parameters

Reimplemented from Polymer.

bool collides	(	Component &	other,
		double	dist = `0.0`
	)

inherited

Is other within dist of this' bounding box?

Parameters

other	(Component)
dist	(double)

Returns: True, if the component collides with "OTHER"

void copy ( const Bond & orig )

inherited

Copy operator. Attention: copy() strips orig from its bonds and attaches them to the new bond.

Parameters

bond reference

Returns: void

void copy ( const Polymer & orig )

inherited

Parameters

void copy ( const SimpleBond & orig )

virtualinherited

Copy operator. Attention: copy() strips orig from its bonds and attaches them to the new bond.

void copy ( const Component & orig )

inherited

Copy the component. Attention: new elements have to be copied also in Monomer::copy() since it does NOT invoke this function (segmentation fault if it does).

Parameters

orig

void deleteComponent ( Component * c )

virtual

Parameters

Reimplemented from Polymer.

char getChainLetter ( unsigned int i )

Returns the chainID by index

Parameters

i	(unsigned int) index

Returns: The chainID (char)

unsigned int getChainNum ( char c )

Returns the chain index by chainID

Parameters

c	(char) chainID

Returns: The chainID index in the chains vector

const SimpleBond & getInBond ( unsigned int n ) const

virtualinherited

Returns i-th in-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

SimpleBond & getInBond ( unsigned int n )

virtualinherited

Returns i-th in-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

Atom & getInBondRef ( unsigned int n )

virtualinherited

Returns reference to the i-th in-bond atom.

Parameters

unsigned int

Returns: Atom reference

LigandSet * getLigandSet ( char c )

Return a pointer to the LigandSet with the requested chainID

Parameters

c	(char), the chainID

Returns: A pointer to the LiganSet

LigandSet * getLigandSet ( unsigned int n )

Return a pointer to the LiganSet by an index in the Components vector.

Parameters

n	(unsigned int), the index of the Polymer in the Components vector

Returns: A pointer to the LiganSet

vgVector3< double > getLowerBound ( double dist = 0.0 )

virtualinherited

Return the lower bound coordinates.

Parameters

dist

Returns: The lowerBound vector (vgVector2<double>)

unsigned int getMaxInBonds ( ) const

inherited

Get maximum of in-bonds.

unsigned int getMaxOutBonds ( ) const

inherited

Get maximum of out-bonds.

Atom & getOpenInBondRef ( unsigned int n = 0 )

virtualinherited

Returns reference to the i-th open in-bond atom. NB: This is undefined (ie. returns error) for Bond, but is needed for later structures (AminoAcid, etc.).

Parameters

unsigned int

Returns: Atom reference

Reimplemented in Spacer, and AminoAcid.

Atom & getOpenOutBondRef ( unsigned int n = 0 )

virtualinherited

Returns reference to the i-th open out-bond atom. NB: This is undefined (ie. returns error) for Bond, but is needed for later structures (AminoAcid, etc.).

Parameters

unsigned int

Returns: atom reference

Reimplemented in Spacer, and AminoAcid.

const SimpleBond & getOutBond ( unsigned int n ) const

virtualinherited

Returns i-th out-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

SimpleBond & getOutBond ( unsigned int n )

virtualinherited

Returns i-th out-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

Atom & getOutBondRef ( unsigned int n )

virtualinherited

Returns reference to the i-th in-bond atom.

Parameters

unsigned int

Returns: Atom reference

Polymer & getPolymer ( unsigned int n )

Get the Polymer (Spacer + LigandSet) by an index.

Parameters

n	(unsigned int), the index of the Polymer in the Components vector

Returns: The reference to the Polymer

Spacer * getSpacer ( char c )

Return a pointer to the Spacer with the requested chainID

Parameters

c	(char), the chainID

Returns: A pointer to the Spacer

Spacer * getSpacer ( unsigned int n )

Return a pointer to the Spacer by an index in the Components vector.

Parameters

n	(unsigned int), the index of the Polymer in the Components vector

Returns: A pointer to the Spacer

string getType ( ) const

virtualinherited

Is c bonded to this ?

Reimplemented in SideChain.

vgVector3< double > getUpperBound ( double dist = 0.0 )

virtualinherited

Return the upper bound coordinates.

Parameters

dist

Returns: The upperBound vector (vgVector2<double>)

void insertComponent ( Component * p )

virtual

Insert a Polymer in the Protein. It is related to a single chain, and must contain a Spacer and possibly a LigandSet

Parameters

p	(Component*)

Reimplemented from Polymer.

bool inSync ( )

inherited

Checks the "Modified" flag in the component.

Returns: True, if the component coordinates have been already syncronized. Checks also for the "superior" class status.

bool isBond ( const SimpleBond & c ) const

inherited

Is c bonded to this ?

bool isInBond ( const SimpleBond & c ) const

inherited

Is c in-bonded to this ?

bool isIndirectBond ( const SimpleBond & c ) const

inherited

Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)

bool isIndirectInBond ( const SimpleBond & c ) const

inherited

Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)

bool isIndirectOutBond ( const SimpleBond & c ) const

inherited

Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)

bool isOutBond ( const SimpleBond & c ) const

inherited

Is c out-bonded to this ?

bool isTorsionBond ( const SimpleBond & c ) const

inherited

Checks if this is torsion bond to c. (ie. A to D if A indirect bond C and C bond D)

void pUnbindIn ( SimpleBond & c )

protectedvirtualinherited

Private method to find the matching in-bond from c to this to remove.

void pUnbindOut ( SimpleBond & c )

protectedvirtualinherited

Private method to find the matching out-bond from c to this to remove.

void removeComponent ( Component * c )

virtual

Parameters

Reimplemented from Polymer.

void removeComponentFromIndex ( unsigned int i )

virtualinherited

Parameters

Reimplemented in Spacer.

void setMaxInBonds ( unsigned int m )

inherited

Sets maximum of in-bonds.

void setMaxOutBonds ( unsigned int m )

inherited

Sets maximum of out-bonds.

void setType ( string _name )

virtualinherited

Sets type (eg. C atom, GLY amino acid, etc.) of this.

Reimplemented in AminoAcid, Atom, and Nucleotide.

unsigned int sizeInBonds ( ) const

inherited

How many in-bonds are there ?

unsigned int sizeOpenInBonds ( ) const

inherited

Returns the number of open in-bonds, ie. how many in-bonds can still be added.

Parameters

void

Returns: unsigned int

unsigned int sizeOpenOutBonds ( ) const

inherited

Returns the number of open out-bonds, ie. how many out-bonds can still be added.

Parameters

void

Returns: unsigned int

unsigned int sizeOutBonds ( ) const

inherited

How many out-bonds are there ?

void unbindIn ( Bond & c )

virtualinherited

Remove in-going bond from this to c.

Parameters

bond reference

Returns: void

void unbindIn ( SimpleBond & c )

virtualinherited

Removes an in-bond from this to c.

Reimplemented in Atom.

void unbindOut ( Bond & c )

virtualinherited

Remove out-going bond from this to c.

Parameters

bond reference

Returns: void

void unbindOut ( SimpleBond & c )

virtualinherited

Removes an out-bond from this to c.

Reimplemented in Atom.

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

Biopool/Sources/Protein.h
Biopool/Sources/Protein.cc

Public Member Functions

Protected Member Functions

Detailed Description

Member Function Documentation