gcu::Atom Class Reference

#include <gcu/atom.h>

Inheritance diagram for gcu::Atom:

gcu::Object gcu::CrystalAtom List of all members.

Public Member Functions

 Atom ()
 Atom (int Z, double x, double y, double z=0.)
 Atom (Atom &a)
Atomoperator= (Atom &a)
virtual ~Atom ()
double Distance (Atom *pAtom)
void zoom (double ZoomFactor)
virtual bool GetCoords (double *x, double *y, double *z=NULL)
void SetCoords (double x, double y, double z=0)
int GetZ ()
virtual void SetZ (int Z)
void SetCharge (char Charge)
char GetCharge ()
const gchar * GetSymbol ()
virtual void AddBond (Bond *pBond)
virtual void RemoveBond (Bond *pBond)
double x ()
double y ()
double z ()
BondGetFirstBond (map< Atom *, Bond * >::iterator &i)
BondGetNextBond (map< Atom *, Bond * >::iterator &i)
BondGetBond (Atom *pAtom)
int GetBondsNumber ()
virtual xmlNodePtr Save (xmlDocPtr xml)
virtual bool Load (xmlNodePtr node)
virtual bool LoadNode (xmlNodePtr node)
virtual bool SaveNode (xmlDocPtr xml, xmlNodePtr node)
virtual void Move (double x, double y, double z=0.)
virtual void Transform2D (Matrix2D &m, double x, double y)

Protected Attributes

int m_Z
double m_x
double m_y
double m_z
char m_Charge
map< Atom *, Bond * > m_Bonds

Detailed Description

This class is used to represent atoms.

Definition at line 42 of file atom.h.


Constructor & Destructor Documentation

gcu::Atom::Atom (  ) 

The default constructor. Creates an atom with atomic number set to 0.

gcu::Atom::Atom ( int  Z,
double  x,
double  y,
double  z = 0. 
)

Parameters:
Z,: the atomic number of the new atom.
x,: the x coordinate of the new atom.
y,: the y coordinate of the new atom.
z,: the z coordinate of the new atom.
Creates an atom.

gcu::Atom::Atom ( Atom a  ) 

Parameters:
a,: the Atom to duplicate.
Creates a new atom identical to a without any bond.

virtual gcu::Atom::~Atom (  )  [virtual]

The destructor of Atom. It removes bonds but do not delete the associated Bond instances.


Member Function Documentation

virtual void gcu::Atom::AddBond ( Bond pBond  )  [virtual]

Parameters:
pBond,: a pointer to the new Bond to this Atom.
Adds a Bond.

double gcu::Atom::Distance ( Atom pAtom  ) 

Parameters:
pAtom,: a pointer to an Atom.
Returns:
the distance between the Atom at pAtom and this Atom.

Bond* gcu::Atom::GetBond ( Atom pAtom  ) 

Parameters:
pAtom,: a pointer to an Atom instance.
Returns:
a pointer to the Bond shared by pAtom and this Atom if it exists or NULL.

int gcu::Atom::GetBondsNumber (  )  [inline]

Returns:
the number of Bond instances shared by this Atom. It does not take multiplicity of bonds into account.

Definition at line 175 of file atom.h.

References m_Bonds.

char gcu::Atom::GetCharge (  )  [inline]

Returns:
the formal charge of this Atom.

Definition at line 124 of file atom.h.

References m_Charge.

virtual bool gcu::Atom::GetCoords ( double *  x,
double *  y,
double *  z = NULL 
) [virtual]

Parameters:
x,: a pointer to the double value which will receive the x coordiante of the Atom.
y,: a pointer to the double value which will receive the y coordiante of the Atom.
z,: a pointer to the double value which will receive the z coordiante of the Atom or NULL for 2D representations.
Retrieves the coordinates of this Atom.
Returns:
true if successful and false if an error occurs (if x or y is NULL).

Bond* gcu::Atom::GetFirstBond ( map< Atom *, Bond * >::iterator &  i  ) 

Parameters:
i,: a C++ std::map iterator.
Use this function to retrieve the first Bond of this Atom and initialize the iterator.
Returns:
the first Bond of this Atom or NULL if the Atom has is not bonded.

Bond* gcu::Atom::GetNextBond ( map< Atom *, Bond * >::iterator &  i  ) 

Parameters:
i,: a C++ std::map iterator initialized by Atom::GetFirstBond.
Use this method to iterate through the list of Bond instances of this Atom.
Returns:
the next Bond of this Atom or NULL.

const gchar* gcu::Atom::GetSymbol (  ) 

Returns:
the atomic symbol of this Atom or NULL if the element is unknown.

int gcu::Atom::GetZ (  )  [inline]

Returns:
the atomic number of the atom.

Definition at line 107 of file atom.h.

References m_Z.

virtual bool gcu::Atom::Load ( xmlNodePtr  node  )  [virtual]

Parameters:
node,: a pointer to the xmlNode containing the serialized Atom.
Loads an atom from an xmlNode.

Reimplemented from gcu::Object.

virtual bool gcu::Atom::LoadNode ( xmlNodePtr  node  )  [virtual]

Parameters:
node,: a pointer to the xmlNode containing the serialized Atom.
This virtual method is called at the end of the Atom::Load method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the Atom::Load method.

Reimplemented in gcu::CrystalAtom.

virtual void gcu::Atom::Move ( double  x,
double  y,
double  z = 0. 
) [virtual]

Parameters:
x,: the x component of the transation vector.
y,: the y component of the transation vector.
z,: the z component of the transation vector.
Used to move an Atom.

Reimplemented from gcu::Object.

Atom& gcu::Atom::operator= ( Atom a  ) 

Parameters:
a,: the Atom to copy.
Returns:
an Atom identical to a without any bond.

virtual void gcu::Atom::RemoveBond ( Bond pBond  )  [virtual]

Parameters:
pBond,: a pointer to the Bond to remove from this Atom.
Removes a Bond.

virtual xmlNodePtr gcu::Atom::Save ( xmlDocPtr  xml  )  [virtual]

Parameters:
xml,: the xmlDoc used to save the document.
Returns:
a pointer to the xmlNode representing this Atom or NULL if an error occured.

Reimplemented from gcu::Object.

virtual bool gcu::Atom::SaveNode ( xmlDocPtr  xml,
xmlNodePtr  node 
) [virtual]

Parameters:
xml,: the xmlDoc used to save the document.
node,: a pointer to the xmlNode to which this Atom is serialized.
This virtual method is called at the end of the Atom::Save method. The default behavior is to do nothing. It might be overrided for derived class when it is not convenient to override the Atom::Save method.

Reimplemented in gcu::CrystalAtom.

void gcu::Atom::SetCharge ( char  Charge  )  [inline]

Parameters:
Charge,: the new formal charge of the Atom.
Changes the formal charge of this Atom.

Definition at line 120 of file atom.h.

References m_Charge.

void gcu::Atom::SetCoords ( double  x,
double  y,
double  z = 0 
) [inline]

Parameters:
x,: the new x coordinate of the Atom.
y,: the new y coordinate of the Atom.
z,: the new z coordinate of the Atom.
Changes the position of this Atom.

Definition at line 103 of file atom.h.

References m_x, m_y, m_z, and z().

virtual void gcu::Atom::SetZ ( int  Z  )  [virtual]

Parameters:
Z,: the new atomic number of the Atom.
This method might be overrided by derived class since changing the atomic number generally changes most properties. The default behavior is just to change the atomic number and nothing else.

virtual void gcu::Atom::Transform2D ( Matrix2D m,
double  x,
double  y 
) [virtual]

Parameters:
m,: the 2D Matrix of the transformation.
x,: the x component of the center of the transformation.
y,: the y component of the center of the transformation.
Used to move and/or transform an atom.

Reimplemented from gcu::Object.

double gcu::Atom::x (  )  [inline]

Returns:
the x coordinate of this Atom.

Definition at line 144 of file atom.h.

References m_x.

double gcu::Atom::y (  )  [inline]

Returns:
the y coordinate of this Atom.

Definition at line 148 of file atom.h.

References m_y.

double gcu::Atom::z (  )  [inline]

Returns:
the z coordinate of this Atom.

Definition at line 152 of file atom.h.

References m_z.

Referenced by SetCoords().

void gcu::Atom::zoom ( double  ZoomFactor  ) 

Parameters:
ZoomFactor,: the zoom factor.
Multiplies all three coordinates of this Atom by ZoomFactor.


Member Data Documentation

map<Atom*, Bond*> gcu::Atom::m_Bonds [protected]

The Bond instances of the Atom. The index of the map is a pointer to the other end of the Bond.

Definition at line 243 of file atom.h.

Referenced by GetBondsNumber().

char gcu::Atom::m_Charge [protected]

The charge of the Atom.

Definition at line 239 of file atom.h.

Referenced by GetCharge(), and SetCharge().

double gcu::Atom::m_x [protected]

The x coordinate of the Atom.

Definition at line 227 of file atom.h.

Referenced by SetCoords(), and x().

double gcu::Atom::m_y [protected]

The x coordinate of the Atom.

Definition at line 231 of file atom.h.

Referenced by SetCoords(), and y().

double gcu::Atom::m_z [protected]

The x coordinate of the Atom.

Definition at line 235 of file atom.h.

Referenced by SetCoords(), and z().

int gcu::Atom::m_Z [protected]

The atomic number of the Atom.

Definition at line 223 of file atom.h.

Referenced by GetZ().


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