Representation of an atom. More...

#include <avogadro/atom.h>

Inheritance diagram for Avogadro::Atom:

Public Member Functions
	Atom (QObject *parent=0)
	~Atom ()
Set atomic information
These functions are used to set atomic information.
void	setPos (const Eigen::Vector3d &vec)
void	setPos (const Eigen::Vector3d *vec)
void	setAtomicNumber (int num)
void	setPartialCharge (double charge) const
void	setFormalCharge (int charge)
void	setGroupIndex (unsigned int index)
void	setForceVector (const Eigen::Vector3d &force)
void	setCustomLabel (const QString &label)
void	setCustomColorName (const QString &name)
void	setCustomRadius (const double radius)
Get atomic information
These functions are used to get atomic information.
Molecule *	molecule () const
const Eigen::Vector3d *	pos () const
int	atomicNumber () const
QList< unsigned long >	bonds () const
QList< unsigned long >	neighbors () const
Bond *	bond (const Atom *other) const
double	valence () const
unsigned int	groupIndex () const
bool	isHydrogen () const
double	partialCharge () const
int	formalCharge () const
QString	customLabel () const
QString	customColorName () const
double	customRadius () const
const Eigen::Vector3d	forceVector () const
unsigned long	residueId () const
Residue *	residue () const
OpenBabel conversion functions
These functions are used convert between Avogadro and OpenBabel atoms.
OpenBabel::OBAtom	OBAtom ()
bool	setOBAtom (OpenBabel::OBAtom *obatom)
Operators
Overloaded operators.
Atom &	operator= (const Atom &other)
Protected Member Functions
void	addBond (unsigned long bond)
void	addBond (Bond *bond)
void	removeBond (Bond *bond)
void	removeBond (unsigned long bond)
void	setResidue (unsigned long id)
void	setResidue (const Residue *residue)
Protected Attributes
AtomPrivate *const	d_ptr
Molecule *	m_molecule
int	m_atomicNumber
QList< unsigned long >	m_bonds

Detailed Description

Representation of an atom.

Author:: Marcus D. Hanwell

The Atom class is a Primitive subclass that provides an Atom object. All atoms must be owned by a Molecule. It should also be removed by the Molecule that owns it.

Constructor & Destructor Documentation

Avogadro::Atom::Atom ( QObject * parent = 0 )

Constructor.

Parameters:

parent the parent object, which should be a molecule.

References QObject::parent().

Avogadro::Atom::~Atom ( )

Destructor.

Member Function Documentation

void Avogadro::Atom::addBond ( unsigned long bond ) [protected]

Adds a reference to a bond to the atom.

References bond(), QList::indexOf(), and QList::push_back().

Referenced by addBond(), Avogadro::Molecule::operator=(), Avogadro::Bond::setAtoms(), Avogadro::Bond::setBegin(), and Avogadro::Bond::setEnd().

void Avogadro::Atom::addBond ( Bond * bond ) [protected]

Adds a reference to a bond to the atom.

References addBond(), and Avogadro::Primitive::id().

int Avogadro::Atom::atomicNumber ( ) const [inline]

Returns:: Atomic number of the atom.

Note:: Replaces GetAtomicNum()

Referenced by formalCharge(), and Avogadro::Molecule::OBMol().

Bond * Avogadro::Atom::bond ( const Atom * other ) const

Use this function to get the bond between this Atom and another.

Parameters:

other The other Atom to test for bonding.

Returns:: Pointer to the bond between the two atoms, or 0.

References Avogadro::Molecule::bond().

Referenced by addBond(), formalCharge(), and neighbors().

QList<unsigned long> Avogadro::Atom::bonds ( ) const [inline]

Returns:: List of bond ids to the atom.

Referenced by Avogadro::Molecule::bond(), and Avogadro::Molecule::removeAtom().

const Eigen::Vector3d Avogadro::Atom::forceVector ( ) const

Returns:: The force vector on this atom (if any)

int Avogadro::Atom::formalCharge ( ) const

Returns:: Formal charge of the atom (default = 0)

References atomicNumber(), bond(), Avogadro::Molecule::bondById(), and Avogadro::Bond::order().

unsigned int Avogadro::Atom::groupIndex ( ) const

The index of the atom in group of atoms of the same element in Molecule

References Avogadro::Molecule::calculateGroupIndices().

bool Avogadro::Atom::isHydrogen ( ) const [inline]

Returns:: True if the atom is a hydrogen.

Referenced by Avogadro::Molecule::removeHydrogens().

Molecule* Avogadro::Atom::molecule ( ) const [inline]

Returns:: A pointer to the Molecule that the Atom belongs to.

QList< unsigned long > Avogadro::Atom::neighbors ( ) const

Returns:: List of neighbor ids to the atom (atoms bonded to that atom).

References bond(), Avogadro::Molecule::bondById(), Avogadro::Bond::otherAtom(), QList::push_back(), and QList::size().

Referenced by Avogadro::Molecule::removeHydrogens().

OpenBabel::OBAtom Avogadro::Atom::OBAtom ( )

Returns:: An OpenBabel::OBAtom copy of the atom.

References Avogadro::Molecule::atomPos(), QByteArray::data(), QObject::dynamicPropertyNames(), m_atomicNumber, QString::number(), QObject::property(), OpenBabel::OBAtom::SetAtomicNum(), OpenBabel::OBPairData::SetAttribute(), OpenBabel::OBAtom::SetData(), OpenBabel::OBAtom::SetFormalCharge(), OpenBabel::OBAtom::SetPartialCharge(), OpenBabel::OBPairData::SetValue(), OpenBabel::OBAtom::SetVector(), and QString::toAscii().

Referenced by Avogadro::Molecule::OBMol(), and Avogadro::Animation::setFrame().

double Avogadro::Atom::partialCharge ( ) const

Returns:: Partial charge of the atom.

References Avogadro::Molecule::calculatePartialCharges(), and m_atomicNumber.

Referenced by Avogadro::Molecule::dipoleMoment().

const Eigen::Vector3d * Avogadro::Atom::pos ( ) const

Returns:: The position of the atom.

References Avogadro::Molecule::atomPos().

Referenced by Avogadro::Molecule::computeGeomInfo(), Avogadro::Molecule::dipoleMoment(), Avogadro::Bond::length(), Avogadro::NeighborList::nbrs(), Avogadro::Cube::setLimits(), Avogadro::ZMatrix::update(), and Avogadro::GLWidget::updateGeometry().

void Avogadro::Atom::removeBond ( Bond * bond ) [protected]

Removes the reference of the bond to the atom.

References Avogadro::Primitive::id().

Referenced by Avogadro::Bond::setBegin(), and Avogadro::Bond::setEnd().

void Avogadro::Atom::removeBond ( unsigned long bond ) [protected]

Removes the reference of the bond to the atom.

References Avogadro::Primitive::index(), QList::indexOf(), and QList::removeAt().

Residue * Avogadro::Atom::residue ( ) const

Returns:: A pointer to the Residue that the Atom is a part of.

References Avogadro::Molecule::residueById().

unsigned long Avogadro::Atom::residueId ( ) const

Returns:: The Id of the Residue that the Atom is a part of.

void Avogadro::Atom::setAtomicNumber ( int num )

Set the atomic number of the atom.

Note:: This will emit an updated signal

References m_atomicNumber, and Avogadro::Primitive::update().

Referenced by Avogadro::ZMatrix::update().

void Avogadro::Atom::setCustomColorName ( const QString & name )

Set the custom color for the atom using color name

References QObject::name().

void Avogadro::Atom::setCustomLabel ( const QString & label )

Set the custom label for the atom

void Avogadro::Atom::setCustomRadius ( const double radius )

Set the custom radius for the atom

void Avogadro::Atom::setForceVector ( const Eigen::Vector3d & force )

Set the force vector on the atom (e.g., used to display vibrations)

Referenced by Avogadro::Molecule::setOBMol().

void Avogadro::Atom::setFormalCharge ( int charge )

Set the formal charge of the atom.

void Avogadro::Atom::setGroupIndex ( unsigned int index )

Set the number of the atom in group of atoms of the same element.

References Avogadro::Primitive::index().

Referenced by Avogadro::Molecule::calculateGroupIndices().

bool Avogadro::Atom::setOBAtom ( OpenBabel::OBAtom * obatom )

Copies the data from an OpenBabel::OBAtom to the atom.

References OpenBabel::OBAtom::GetAllData(), OpenBabel::OBAtom::GetAtomicNum(), OpenBabel::OBPairData::GetAttribute(), OpenBabel::OBAtom::GetFormalCharge(), OpenBabel::OBAtom::GetPartialCharge(), OpenBabel::OBPairData::GetValue(), m_atomicNumber, OpenBabel::OBGenericDataType::PairData, QObject::property(), Avogadro::Molecule::setAtomPos(), QObject::setProperty(), OpenBabel::OBAtom::x(), OpenBabel::OBAtom::y(), and OpenBabel::OBAtom::z().

Referenced by Avogadro::Molecule::addHydrogens(), and Avogadro::Molecule::setOBMol().

void Avogadro::Atom::setPartialCharge ( double charge ) const

Set the partial charge of the atom.

Note:: This is not calculated by the atom, instead call Molecule::calculatePartialCharges()

Referenced by Avogadro::Molecule::addHydrogens(), and Avogadro::Molecule::calculatePartialCharges().

void Avogadro::Atom::setPos ( const Eigen::Vector3d & vec )

Sets the position of the atom.

Parameters:

vec	Position of the atom.

References Avogadro::Molecule::setAtomPos().

Referenced by Avogadro::ZMatrix::update().

void Avogadro::Atom::setPos ( const Eigen::Vector3d * vec ) [inline]

Sets the position of the atom.

Parameters:

vec	Position of the atom.

References setPos().

Referenced by setPos().

void Avogadro::Atom::setResidue ( unsigned long id ) [protected]

Set the Residue that this Atom is a part of.

References Avogadro::Primitive::id().

Referenced by Avogadro::Residue::addAtom(), and Avogadro::Residue::removeAtom().

void Avogadro::Atom::setResidue ( const Residue * residue ) [protected]

Set the Residue that this Atom is a part of.

References Avogadro::Primitive::id().

double Avogadro::Atom::valence ( ) const [inline]

The valence of the atom. FIXME - don't think this will cut it...

Member Data Documentation

int Avogadro::Atom::m_atomicNumber [protected]

Parent molecule - should always be valid.

Referenced by Avogadro::Molecule::addAtom(), OBAtom(), partialCharge(), setAtomicNumber(), and setOBAtom().

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

/home/kitware/dashboards/avogadro/libavogadro/src/atom.h
/home/kitware/dashboards/avogadro/libavogadro/src/atom.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation