ObjCryst::MolAtom Class Reference

MolAtom : atom inside a Molecule. More...

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	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
void	SetX (const REAL) const
	Set the X,Y,Z coordinate - this is const because sometimes their coordinate must be changed even though the atom does not move, if the atom is part of a rigid group (its position is then described by a combination of atomic cooordinates, plus a global translation and rotation...
void	SetY (const REAL) const
void	SetZ (const REAL) const

Private Attributes
string	mName
	Name for this atom.
REAL	mX
	Cartesian oordinates in the Molecule reference frame.
REAL	mY
REAL	mZ
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

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.

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::SetX

(

const REAL

)

const

Set the X,Y,Z coordinate - this is const because sometimes their coordinate must be changed even though the atom does not move, if the atom is part of a rigid group (its position is then described by a combination of atomic cooordinates, plus a global translation and rotation...

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Member Data Documentation

REAL ObjCryst::MolAtom::mX

mutableprivate

Cartesian oordinates in the Molecule reference frame.

mutable because they may need to be changed when in a rigid group, even though the end position of the atom remains the same.

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

• Molecule.h