SimpleBond Class Reference

Defines chemical and abstract bonds between objects. eg.: covalent bonds. Attention: copy() strips orig from its SimpleBonds and attaches them to the new SimpleBond. More...

Inheritance diagram for SimpleBond:

Collaboration diagram for SimpleBond:

Public Member Functions
	SimpleBond (unsigned int mI=1, unsigned int mO=4)
virtual void	bindIn (SimpleBond &c)
virtual void	bindOut (SimpleBond &c)
virtual void	copy (const SimpleBond &orig)
virtual const SimpleBond &	getInBond (unsigned int n) const
virtual SimpleBond &	getInBond (unsigned int n)
unsigned int	getMaxInBonds () const
unsigned int	getMaxOutBonds () const
virtual const SimpleBond &	getOutBond (unsigned int n) const
virtual SimpleBond &	getOutBond (unsigned int n)
virtual string	getType () const
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	setMaxInBonds (unsigned int m)
void	setMaxOutBonds (unsigned int m)
virtual void	setType (string _name)
unsigned int	sizeInBonds () const
unsigned int	sizeOutBonds () const
virtual void	unbindIn (SimpleBond &c)
virtual void	unbindOut (SimpleBond &c)

Protected Member Functions
virtual void	pUnbindIn (SimpleBond &c)
virtual void	pUnbindOut (SimpleBond &c)

Detailed Description

Defines chemical and abstract bonds between objects. eg.: covalent bonds. Attention: copy() strips orig from its SimpleBonds and attaches them to the new SimpleBond.

Constructor & Destructor Documentation

SimpleBond	(	unsigned int	mI = 1,
		unsigned int	mO = 4
	)

Basic constructor

Parameters

mI,maximum	in bonds
mO,maximum	out bonds

Member Function Documentation

void bindIn ( SimpleBond &  c )

virtual

Sets and in-bond from this to c.

Reimplemented in Atom.

void bindOut ( SimpleBond &  c )

virtual

Sets and out-bond from this to c

Reimplemented in Atom.

void copy ( const SimpleBond &  orig )

virtual

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

const SimpleBond & getInBond ( unsigned int  n ) const

virtual

Returns i-th in-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

SimpleBond & getInBond ( unsigned int  n )

virtual

Returns i-th in-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

unsigned int getMaxInBonds

(

)

const

Get maximum of in-bonds.

unsigned int getMaxOutBonds

(

)

const

Get maximum of out-bonds.

const SimpleBond & getOutBond ( unsigned int  n ) const

virtual

Returns i-th out-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

SimpleBond & getOutBond ( unsigned int  n )

virtual

Returns i-th out-bond.

Reimplemented in Spacer, AminoAcid, Group, and SideChain.

string getType ( ) const

virtual

Is c bonded to this ?

Reimplemented in SideChain.

bool isBond

(

const SimpleBond &

c

)

const

Is c bonded to this ?

bool isInBond

(

const SimpleBond &

c

)

const

Is c in-bonded to this ?

bool isIndirectBond

(

const SimpleBond &

c

)

const

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

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

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

Is c out-bonded to this ?

bool isTorsionBond

(

const SimpleBond &

c

)

const

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 )

protectedvirtual

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

void pUnbindOut ( SimpleBond &  c )

protectedvirtual

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

void setMaxInBonds

(

unsigned int

m

)

Sets maximum of in-bonds.

void setMaxOutBonds

(

unsigned int

m

)

Sets maximum of out-bonds.

void setType ( string  _name )

virtual

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

Reimplemented in AminoAcid, Atom, and Nucleotide.

unsigned int sizeInBonds

(

)

const

How many in-bonds are there ?

unsigned int sizeOutBonds

(

)

const

How many out-bonds are there ?

void unbindIn ( SimpleBond &  c )

virtual

Removes an in-bond from this to c.

Reimplemented in Atom.

void unbindOut ( SimpleBond &  c )

virtual

Removes an out-bond from this to c.

Reimplemented in Atom.

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

• Biopool/Sources/SimpleBond.h
• Biopool/Sources/SimpleBond.cc