Avogadro::Bond Class Reference

Representation of a chemical bond. More...

#include <avogadro/bond.h>

Inheritance diagram for Avogadro::Bond:

List of all members.

Public Member Functions
	Bond (QObject *parent=0)
Set bonding information
These functions are used to set bonding information.
void	setBegin (Atom *atom)
void	setEnd (Atom *atom)
void	setAtoms (unsigned long atom1, unsigned long atom2, short order=1)
void	setOrder (short order)
void	setAromaticity (bool isAromatic) const
void	setCustomLabel (const QString &label)
Get bonding information
These functions are used to get bonding information.
unsigned long	beginAtomId () const
Atom *	beginAtom () const
unsigned long	endAtomId () const
Atom *	endAtom () const
const Eigen::Vector3d *	beginPos () const
const Eigen::Vector3d *	midPos () const
const Eigen::Vector3d *	endPos () const
unsigned long	otherAtom (unsigned long atomId) const
short	order () const
bool	isAromatic () const
double	length () const
QString	customLabel () const
OpenBabel conversion functions
These functions are used convert between Avogadro and OpenBabel bonds.
bool	setOBBond (OpenBabel::OBBond *obbond)
Operators
Overloaded operators.
Bond &	operator= (const Bond &other)

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Detailed Description

Representation of a chemical bond.

Author:

Marcus D. Hanwell

The Bond class is a Primitive subclass that provides a Bond object.

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Constructor & Destructor Documentation

Avogadro::Bond::Bond

(

QObject *

parent = 0

)

Constructor

Parameters:

parent

the object parent.

References QObject::parent().

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Member Function Documentation

Atom * Avogadro::Bond::beginAtom

(

)

const

Returns:

Pointer to the first atom in the bond.

References Avogadro::Molecule::atomById().

Referenced by Avogadro::Molecule::operator=().

unsigned long Avogadro::Bond::beginAtomId

(

)

const [inline]

Returns:

the unique ID of the first atom in the bond.

Referenced by Avogadro::Molecule::OBMol(), Avogadro::Molecule::operator+=(), and Avogadro::Molecule::removeBond().

const Eigen::Vector3d * Avogadro::Bond::beginPos

(

)

const

Returns:

The position of the start of the Bond.

References Avogadro::Molecule::atomPos().

QString Avogadro::Bond::customLabel

(

)

const [inline]

Returns:

the custom label of the bond

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

Atom * Avogadro::Bond::endAtom

(

)

const

Returns:

Pointer to the second atom in the bond.

References Avogadro::Molecule::atomById().

Referenced by Avogadro::Molecule::operator=().

unsigned long Avogadro::Bond::endAtomId

(

)

const [inline]

Returns:

the unique ID of the second atom in the bond.

Referenced by Avogadro::Molecule::OBMol(), Avogadro::Molecule::operator+=(), and Avogadro::Molecule::removeBond().

const Eigen::Vector3d * Avogadro::Bond::endPos

(

)

const

Returns:

The position of the end of the Bond.

References Avogadro::Molecule::atomPos().

bool Avogadro::Bond::isAromatic

(

)

const

Returns:

True if the bond is aromatic.

References Avogadro::Molecule::calculateAromaticity().

Referenced by setAromaticity().

double Avogadro::Bond::length

(

)

const

Returns:

the length of the bond.

References Avogadro::Molecule::atomById(), and Avogadro::Atom::pos().

const Eigen::Vector3d * Avogadro::Bond::midPos

(

)

const

Returns:

The position of the mid-point of the Bond.

References Avogadro::Molecule::atomPos().

short Avogadro::Bond::order

(

)

const [inline]

Returns:

the order of the bond - 1 = single, 2 = double etc.

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

unsigned long Avogadro::Bond::otherAtom

(

unsigned long

atomId

)

const

Get the unique id of the other atom in the bond.

Parameters:

atomId

The unique id of the Atom.

Returns:

The unique if of the other Atom in the bond.

Note:

This function does not perform checks to ensure the supplied Atom is actually in the bond.

Referenced by Avogadro::Molecule::bond(), and Avogadro::Atom::neighbors().

void Avogadro::Bond::setAromaticity

(

bool

isAromatic

)

const

Set the aromaticity of the bond.

References isAromatic().

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

void Avogadro::Bond::setAtoms	(	unsigned long	atom1,
		unsigned long	atom2,
		short	order = 1
	)

Set the unique ID of both atoms in the bond.

Parameters:

atom1	First atom in the bond.
atom2	Second atom in the bond.
order	Bond order (defaults to 1).

References Avogadro::Atom::addBond(), Avogadro::Molecule::atomById(), and order().

Referenced by Avogadro::Molecule::addBond(), Avogadro::ZMatrix::addRow(), Avogadro::ZMatrix::setBond(), and Avogadro::Molecule::setOBMol().

void Avogadro::Bond::setBegin

(

Atom *

atom

)

Set the unique ID of the first atom in the bond.

References Avogadro::Atom::addBond(), Avogadro::Molecule::atomById(), Avogadro::Primitive::id(), and Avogadro::Atom::removeBond().

Referenced by Avogadro::Molecule::addHydrogens(), Avogadro::Molecule::operator+=(), and Avogadro::Animation::setFrame().

void Avogadro::Bond::setCustomLabel

(

const QString &

label

)

[inline]

Set the custom label for the bond

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

void Avogadro::Bond::setEnd

(

Atom *

atom

)

Set the unique ID of the second atom in the bond.

References Avogadro::Atom::addBond(), Avogadro::Molecule::atomById(), Avogadro::Primitive::id(), and Avogadro::Atom::removeBond().

Referenced by Avogadro::Molecule::addHydrogens(), Avogadro::Molecule::operator+=(), and Avogadro::Animation::setFrame().

bool Avogadro::Bond::setOBBond

(

OpenBabel::OBBond *

obbond

)

Copy the data from an OpenBabel::OBBond to create a similar bond.

References OpenBabel::OBBond::GetBondOrder(), OpenBabel::OBBond::GetData(), OpenBabel::OBGenericData::GetValue(), and OpenBabel::OBBond::HasData().

void Avogadro::Bond::setOrder

(

short

order

)

[inline]

Set the order of the bond.

Referenced by Avogadro::Animation::setFrame().

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

• /home/kitware/dashboards/avogadro/libavogadro/src/bond.h
• /home/kitware/dashboards/avogadro/libavogadro/src/bond.cpp