ObjCryst::MolAtom Class Reference

MolAtom : atom inside a Molecule. More...

Collaboration diagram for ObjCryst::MolAtom:

[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 Molecule &	GetMolecule () const
Molecule &	GetMolecule ()
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 ScatteringPower &	GetScatteringPower () 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 ScatteringPower *	mpScattPow
	ScatteringPower.
Molecule *	mpMol
	Parent Molecule.
bool	mIsInRing
	Is the atom in a ring ?

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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

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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.

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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

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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.

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

• Molecule.h

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