Atom Class Reference

Implements a simple atom type. More...

Inheritance diagram for Atom:

Collaboration diagram for Atom:

Public Member Functions
	Atom (unsigned int mI=1, unsigned int mO=4)
	Atom (const Atom &orig)
virtual	~Atom ()
virtual void	bindIn (SimpleBond &c)
virtual void	bindOut (SimpleBond &c)
void	copy (const Atom &orig)
virtual void	copy (const SimpleBond &orig)
double	distance (Atom &other)
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	setCoords (double _x, double _y, double _z)
void	setCoords (vgVector3< double > c)
void	setMaxInBonds (unsigned int m)
void	setMaxOutBonds (unsigned int m)
void	setModified ()
void	setType (string _name)
void	setUnModified ()
unsigned int	sizeInBonds () const
unsigned int	sizeOutBonds () const
virtual void	sync ()
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

Implements a simple atom type.

Includes methods that allow you to get and set type, bind, unbind, coordinates , code, etc. NB: Angles are in degrees.

Constructor & Destructor Documentation

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

Initialize the Atom object with the following attributes: type, coords, Bfac, trans, rot, modified, superior

Parameters

Number

of in Bonds (unsigned int), number of out Bonds (unsigned Int)

Atom

(

const Atom &

orig

)

Constructor. Copy another Atom object.

Parameters

Atom

~Atom ( )

virtual

DESTRUCTOR

Parameters

none

Member Function Documentation

void bindIn ( SimpleBond &  c )

virtual

Sets and in-bond from this to c.

Reimplemented from SimpleBond.

void bindOut ( SimpleBond &  c )

virtual

Sets and out-bond from this to c

Reimplemented from SimpleBond.

void copy

(

const Atom &

orig

)

Copy an Atom object

Parameters

Atom

void copy ( const SimpleBond &  orig )

virtualinherited

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

double distance

(

Atom &

other

)

Calculate the Euclidean distance

Parameters

A	partner Atom

Returns

The Euclidean distance from the partner atom (double)

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.

unsigned int getMaxInBonds ( ) const

inherited

Get maximum of in-bonds.

unsigned int getMaxOutBonds ( ) const

inherited

Get maximum of out-bonds.

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.

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 setCoords	(	double	_x,
		double	_y,
		double	_z
	)

Set the 3D coordinates of the Atom

Parameters

X,Y	and Z (double)

void setCoords

(

vgVector3< double >

c

)

Set the 3D coordinates of the Atom

Parameters

Vector

with the X, Y, Z coordinates (vgVector3<double>)

void setMaxInBonds ( unsigned int  m )

inherited

Sets maximum of in-bonds.

void setMaxOutBonds ( unsigned int  m )

inherited

Sets maximum of out-bonds.

void setModified

(

)

Set the "Modified" flag. Sync() will syncronize only if "Modified" is true.

void setType ( string  _name )

virtual

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

Reimplemented from SimpleBond.

void setUnModified

(

)

Set the "Modified" flag to false. Sync() will syncronize only if "Modified" is true.

unsigned int sizeInBonds ( ) const

inherited

How many in-bonds are there ?

unsigned int sizeOutBonds ( ) const

inherited

How many out-bonds are there ?

void sync ( )

virtual

Synchronize coords with structure

void unbindIn ( SimpleBond &  c )

virtual

Removes an in-bond from this to c.

Reimplemented from SimpleBond.

void unbindOut ( SimpleBond &  c )

virtual

Removes an out-bond from this to c.

Reimplemented from SimpleBond.

---

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

• Biopool/Sources/Atom.h
• Biopool/Sources/Atom.cc