Bond Class Reference

Defines chemical and abstract bonds between objects which are compositions of atoms. More...

Inheritance diagram for Bond:

Collaboration diagram for Bond:

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)
void	copy (const Bond &orig)
virtual void	copy (const SimpleBond &orig)
virtual const SimpleBond &	getInBond (unsigned int n) const
virtual SimpleBond &	getInBond (unsigned int n)
virtual Atom &	getInBondRef (unsigned int n)
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)
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	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

Defines chemical and abstract bonds between objects which are compositions of atoms.

Eg. 'bond' between two amino acids.

Member Function Documentation

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

virtual

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  )

virtual

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.

void copy

(

const Bond &

orig

)

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

Parameters

bond

reference

Returns

void

void copy ( const SimpleBond &  orig )

virtualinherited

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

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 )

virtual

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

Parameters

unsigned

int

Returns

Atom reference

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 )

virtual

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 )

virtual

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 )

virtual

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

Parameters

unsigned

int

Returns

Atom reference

string getType ( ) const

virtualinherited

Is c bonded to this ?

Reimplemented in SideChain.

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 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

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

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 )

virtual

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 )

virtual

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/Bond.h
• Biopool/Sources/Bond.cc