org.openscience.cdk.interfaces
Interface IBond

All Superinterfaces:

Cloneable, ICDKObject, IChemObject, IElectronContainer

All Known Subinterfaces:

IQueryBond

All Known Implementing Classes:

AnyOrderQueryBond, AromaticOrSingleQueryBond, AromaticQueryBond, Bond, Bond, CTFileQueryBond, DebugBond, LogicalOperatorBond, OrderQueryBond, OrderQueryBond, OrderQueryBondOrderOnly, PharmacophoreAngleBond, PharmacophoreBond, PharmacophoreQueryAngleBond, PharmacophoreQueryBond, QueryBond, RingBond, SMARTSBond, StereoBond

public interface IBond
extends IElectronContainer

Implements the concept of a covalent bond between two or more atoms. A bond is considered to be a number of electrons connecting two ore more atoms. type filter text

Author:

egonw

Keywords:

bond, atom, electron

Created on:

2005-08-24

Belongs to CDK module:

interfaces

Source code:

cdk-1.4.x

Nested Class Summary

static class	IBond.Order A list of permissible bond orders.
static class	IBond.Stereo Enumeration of possible stereo types of two-atom bonds.

Method Summary

Iterable<IAtom>	atoms() Returns the Iterable to atoms making up this bond.
boolean	compare(Object object) Compares a bond with this bond.
boolean	contains(IAtom atom) Returns true if the given atom participates in this bond.
javax.vecmath.Point2d	get2DCenter() Returns the geometric 2D center of the bond.
javax.vecmath.Point3d	get3DCenter() Returns the geometric 3D center of the bond.
IAtom	getAtom(int position) Returns an Atom from this bond.
int	getAtomCount() Returns the number of Atoms in this Bond.
IAtom	getConnectedAtom(IAtom atom) Returns the atom connected to the given atom.
IAtom[]	getConnectedAtoms(IAtom atom) Returns all the atoms in the bond connected to the given atom.
IBond.Order	getOrder() Returns the bond order of this bond.
IBond.Stereo	getStereo() Returns the stereo descriptor for this bond.
boolean	isConnectedTo(IBond bond) Checks whether a bond is connected to another one.
void	setAtom(IAtom atom, int position) Sets an Atom in this bond.
void	setAtoms(IAtom[] atoms) Sets the array of atoms making up this bond.
void	setOrder(IBond.Order order) Sets the bond order of this bond.
void	setStereo(IBond.Stereo stereo) Sets the stereo descriptor for this bond.

Methods inherited from interface org.openscience.cdk.interfaces.IElectronContainer

getElectronCount, setElectronCount

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, clone, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Method Detail

atoms

Iterable<IAtom> atoms()

Returns the Iterable to atoms making up this bond.

Returns:

An Iterable to atoms participating in this bond

See Also:

setAtoms(org.openscience.cdk.interfaces.IAtom[])

setAtoms

void setAtoms(IAtom[] atoms)

Sets the array of atoms making up this bond.

Parameters:

atoms - An array of atoms that forms this bond

See Also:

atoms()

getAtomCount

int getAtomCount()

Returns the number of Atoms in this Bond.

Returns:

The number of Atoms in this Bond

getAtom

IAtom getAtom(int position)

Returns an Atom from this bond.

Parameters:

position - The position in this bond where the atom is

Returns:

The atom at the specified position

See Also:

setAtom(org.openscience.cdk.interfaces.IAtom, int)

getConnectedAtom

IAtom getConnectedAtom(IAtom atom)

Returns the atom connected to the given atom.

Parameters:

atom - The atom the bond partner is searched of

Returns:

the connected atom or null if the given atom is not part of the bond

getConnectedAtoms

IAtom[] getConnectedAtoms(IAtom atom)

Returns all the atoms in the bond connected to the given atom.

Parameters:

atom - The atoms the bond partner is searched of

Returns:

the connected atoms or null if the given atom is not part of the bond

contains

boolean contains(IAtom atom)

Returns true if the given atom participates in this bond.

Parameters:

atom - The atom to be tested if it participates in this bond

Returns:

true if the atom participates in this bond

setAtom

void setAtom(IAtom atom,
             int position)

Sets an Atom in this bond.

Parameters:

atom - The atom to be set

position - The position in this bond where the atom is to be inserted

See Also:

getAtom(int)

getOrder

IBond.Order getOrder()

Returns the bond order of this bond.

Returns:

The bond order of this bond

See Also:

org.openscience.cdk.CDKConstants for predefined values., setOrder(org.openscience.cdk.interfaces.IBond.Order)

setOrder

void setOrder(IBond.Order order)

Sets the bond order of this bond.

Parameters:

order - The bond order to be assigned to this bond

See Also:

for predefined values., getOrder()

getStereo

IBond.Stereo getStereo()

Returns the stereo descriptor for this bond.

Returns:

The stereo descriptor for this bond

See Also:

setStereo(org.openscience.cdk.interfaces.IBond.Stereo)

setStereo

void setStereo(IBond.Stereo stereo)

Sets the stereo descriptor for this bond.

Parameters:

stereo - The stereo descriptor to be assigned to this bond.

See Also:

getStereo()

get2DCenter

javax.vecmath.Point2d get2DCenter()

Returns the geometric 2D center of the bond.

Returns:

The geometric 2D center of the bond

get3DCenter

javax.vecmath.Point3d get3DCenter()

Returns the geometric 3D center of the bond.

Returns:

The geometric 3D center of the bond

compare

boolean compare(Object object)

Compares a bond with this bond.

Parameters:

object - Object of type Bond

Returns:

Return true, if the bond is equal to this bond

isConnectedTo

boolean isConnectedTo(IBond bond)

Checks whether a bond is connected to another one. This can only be true if the bonds have an Atom in common.

Parameters:

bond - The bond which is checked to be connect with this one

Returns:

True, if the bonds share an atom, otherwise false