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ObjCryst::MolAtom Class Reference

MolAtom : atom inside a Molecule. More...

Collaboration diagram for ObjCryst::MolAtom:

Collaboration graph
[legend]
List of all members.

Public Member Functions

 MolAtom (const REAL x, const REAL y, const REAL z, const ScatteringPower *pPow, const string &name, Molecule &parent)
 Constructor for a MolAtom.

virtual ~MolAtom ()
 Destructor.

void SetName (const string &name)
const string & GetName () const
string & GetName ()
const MoleculeGetMolecule () const
MoleculeGetMolecule ()
const REAL & X () const
const REAL & Y () const
const REAL & Z () const
REAL & X ()
REAL & Y ()
REAL & Z ()
REAL GetX () const
REAL GetY () const
REAL GetZ () const
REAL GetOccupancy () const
void SetX (const REAL)
void SetY (const REAL)
void SetZ (const REAL)
void SetOccupancy (const REAL)
bool IsDummy () const
 Returns true if this is a dummy atom, i.e.

const ScatteringPowerGetScatteringPower () const
void SetScatteringPower (const ScatteringPower &)
virtual void XMLOutput (ostream &os, int indent=0) const
virtual void XMLInput (istream &is, const XMLCrystTag &tag)
void SetIsInRing (const bool r) const
 Flag this atom as being in a ring (or not).

bool IsInRing () const

Private Attributes

string mName
 Name for this atom.

REAL mX
 Cartesian oordinates in the Molecule reference frame.

REAL mY
 Cartesian oordinates in the Molecule reference frame.

REAL mZ
 Cartesian oordinates in the Molecule reference frame.

REAL mOccupancy
 Occupancy.

const ScatteringPowermpScattPow
 ScatteringPower.

MoleculempMol
 Parent Molecule.

bool mIsInRing
 Is the atom in a ring ?


Detailed Description

MolAtom : atom inside a Molecule.

This keeps coordinates, recorded in a cartesian frame (in Angstroem), the associated scattering power and it also keeps in a list of all bonds in which this atom is involved.

Note:
maybe it's not a great idea to keep a reference of bonds for this atom in here


Constructor & Destructor Documentation

ObjCryst::MolAtom::MolAtom const REAL  x,
const REAL  y,
const REAL  z,
const ScatteringPower pPow,
const string &  name,
Molecule parent
 

Constructor for a MolAtom.

virtual ObjCryst::MolAtom::~MolAtom  )  [virtual]
 

Destructor.

Tells the parent Molecule and all Bond that it is being destroyed.


Member Function Documentation

Molecule& ObjCryst::MolAtom::GetMolecule  ) 
 

const Molecule& ObjCryst::MolAtom::GetMolecule  )  const
 

string& ObjCryst::MolAtom::GetName  ) 
 

const string& ObjCryst::MolAtom::GetName  )  const
 

REAL ObjCryst::MolAtom::GetOccupancy  )  const
 

const ScatteringPower& ObjCryst::MolAtom::GetScatteringPower  )  const
 

REAL ObjCryst::MolAtom::GetX  )  const
 

REAL ObjCryst::MolAtom::GetY  )  const
 

REAL ObjCryst::MolAtom::GetZ  )  const
 

bool ObjCryst::MolAtom::IsDummy  )  const
 

Returns true if this is a dummy atom, i.e.

without an associated scattering power.

Dummy atoms can be used to mark positions, or for restraints.

bool ObjCryst::MolAtom::IsInRing  )  const
 

void ObjCryst::MolAtom::SetIsInRing const bool  r  )  const
 

Flag this atom as being in a ring (or not).

This is a const method because the existence of a ring is only a consequence of the connectivity of the Molecule.

void ObjCryst::MolAtom::SetName const string &  name  ) 
 

void ObjCryst::MolAtom::SetOccupancy const  REAL  ) 
 

void ObjCryst::MolAtom::SetScatteringPower const ScatteringPower  ) 
 

void ObjCryst::MolAtom::SetX const  REAL  ) 
 

void ObjCryst::MolAtom::SetY const  REAL  ) 
 

void ObjCryst::MolAtom::SetZ const  REAL  ) 
 

REAL& ObjCryst::MolAtom::X  ) 
 

const REAL& ObjCryst::MolAtom::X  )  const
 

virtual void ObjCryst::MolAtom::XMLInput istream &  is,
const XMLCrystTag tag
[virtual]
 

virtual void ObjCryst::MolAtom::XMLOutput ostream &  os,
int  indent = 0
const [virtual]
 

REAL& ObjCryst::MolAtom::Y  ) 
 

const REAL& ObjCryst::MolAtom::Y  )  const
 

REAL& ObjCryst::MolAtom::Z  ) 
 

const REAL& ObjCryst::MolAtom::Z  )  const
 


Member Data Documentation

bool ObjCryst::MolAtom::mIsInRing [mutable, private]
 

Is the atom in a ring ?

string ObjCryst::MolAtom::mName [private]
 

Name for this atom.

REAL ObjCryst::MolAtom::mOccupancy [private]
 

Occupancy.

Molecule* ObjCryst::MolAtom::mpMol [private]
 

Parent Molecule.

const ScatteringPower* ObjCryst::MolAtom::mpScattPow [private]
 

ScatteringPower.

REAL ObjCryst::MolAtom::mX [private]
 

Cartesian oordinates in the Molecule reference frame.

REAL ObjCryst::MolAtom::mY [private]
 

Cartesian oordinates in the Molecule reference frame.

REAL ObjCryst::MolAtom::mZ [private]
 

Cartesian oordinates in the Molecule reference frame.


The documentation for this class was generated from the following file:
Generated on Tue Nov 14 15:03:52 2006 for ObjCryst++ by doxygen 1.3.6