org.openscience.cdk

Class Bond

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ElectronContainer

org.openscience.cdk.Bond

All Implemented Interfaces:

Serializable, Cloneable, IBond, ICDKObject, IChemObject, IElectronContainer

Direct Known Subclasses:

DebugBond, PharmacophoreAngleBond, PharmacophoreBond, PharmacophoreQueryAngleBond, PharmacophoreQueryBond

public class Bond
extends ElectronContainer
implements IBond, Serializable, Cloneable

Implements the concept of a covalent bond between two or more atoms. A bond is considered to be a number of electrons connecting two or more of atoms. It should be noted that the majority of applications will consider 2-center bonds, especially since the bond orders currently supported are really only valid for 2-center bonds. However the code does support multi-center bonds, though the orders may not make sense at this point. In general code that assumes bonds are 2-centered can use this class seamlessly, as the semantics are identical to the older versions. Care shoud be exercised when using multi-center bonds using this class as the orders may not make sense.

Author:

steinbeck

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

data

Keywords:

bond, atom, electron

Created on:

2003-10-02

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IBond

IBond.Order, IBond.Stereo

Field Summary

Fields

Modifier and Type	Field and Description
protected int	atomCount Number of atoms contained by this object.
protected IAtom[]	atoms A list of atoms participating in this bond.
protected IBond.Order	order The bond order of this bond.
protected IBond.Stereo	stereo A descriptor the stereochemical orientation of this bond.

Fields inherited from class org.openscience.cdk.ElectronContainer

electronCount

Constructor Summary

Constructors

Constructor and Description
Bond() Constructs an empty bond.
Bond(IAtom[] atoms) Constructs a multi-center bond, with undefined order and no stereo information.
Bond(IAtom[] atoms, IBond.Order order) Constructs a multi-center bond, with a specified order and no stereo information.
Bond(IAtom atom1, IAtom atom2) Constructs a bond with a single bond order..
Bond(IAtom atom1, IAtom atom2, IBond.Order order) Constructs a bond with a given order.
Bond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo) Constructs a bond with a given order and stereo orientation from an array of atoms.

Method Summary

Methods

Modifier and Type	Method and Description
Iterable<IAtom>	atoms() Returns the Iterator to atoms making up this bond.
IBond	clone() Clones this bond object, including clones of the atoms between which the bond is defined.
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	getBegin() Access the begin (or first) atom of the bond.
IAtom	getConnectedAtom(IAtom atom) Returns the other atom in the bond, the atom is connected to the given atom.
IAtom[]	getConnectedAtoms(IAtom atom) Returns all the atoms in the bond connected to the given atom.
IAtom	getEnd() Access the end (or second) atom of the bond.
IBond.Order	getOrder() Returns the bond order of this bond.
IAtom	getOther(IAtom atom) Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.
IBond.Stereo	getStereo() Returns the stereo descriptor for this bond.
boolean	isAromatic() Access whether this bond has been marked as aromatic.
boolean	isConnectedTo(IBond bond) Checks whether a bond is connected to another one.
boolean	isInRing() Access whether this bond has been flagged as in a ring.
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	setIsAromatic(boolean arom) Mark this bond as being aromatic.
void	setIsInRing(boolean ring) Mark this bond as being in a ring.
void	setOrder(IBond.Order order) Sets the bond order of this bond.
void	setStereo(IBond.Stereo stereo) Sets the stereo descriptor for this bond.
String	toString() Returns a one line string representation of this Container.

Methods inherited from class org.openscience.cdk.ElectronContainer

getElectronCount, setElectronCount

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

getElectronCount, setElectronCount

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

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

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

getBuilder

Field Detail

order

protected IBond.Order order

The bond order of this bond.

atomCount

protected int atomCount

Number of atoms contained by this object.

atoms

protected IAtom[] atoms

A list of atoms participating in this bond.

stereo

protected IBond.Stereo stereo

A descriptor the stereochemical orientation of this bond.

Constructor Detail

Bond

public Bond()

Constructs an empty bond.

Bond

public Bond(IAtom atom1,
    IAtom atom2)

Constructs a bond with a single bond order..

Parameters:

atom1 - the first Atom in the bond

atom2 - the second Atom in the bond

Bond

public Bond(IAtom atom1,
    IAtom atom2,
    IBond.Order order)

Constructs a bond with a given order.

Parameters:

atom1 - the first Atom in the bond

atom2 - the second Atom in the bond

order - the bond order

Bond

public Bond(IAtom[] atoms)

Constructs a multi-center bond, with undefined order and no stereo information.

Parameters:

atoms - An array of IAtom containing the atoms constituting the bond

Bond

public Bond(IAtom[] atoms,
    IBond.Order order)

Constructs a multi-center bond, with a specified order and no stereo information.

Parameters:

atoms - An array of IAtom containing the atoms constituting the bond

order - The order of the bond

Bond

public Bond(IAtom atom1,
    IAtom atom2,
    IBond.Order order,
    IBond.Stereo stereo)

Constructs a bond with a given order and stereo orientation from an array of atoms.

Parameters:

atom1 - the first Atom in the bond

atom2 - the second Atom in the bond

order - the bond order

stereo - a descriptor the stereochemical orientation of this bond

Method Detail

atoms

public Iterable<IAtom> atoms()

Returns the Iterator to atoms making up this bond. Iterator.remove() is not implemented.

Specified by:

atoms in interface IBond

Returns:

An Iterator to atoms participating in this bond

See Also:

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

setAtoms

public void setAtoms(IAtom[] atoms)

Sets the array of atoms making up this bond.

Specified by:

setAtoms in interface IBond

Parameters:

atoms - An array of atoms that forms this bond

See Also:

atoms

getAtomCount

public int getAtomCount()

Returns the number of Atoms in this Bond.

Specified by:

getAtomCount in interface IBond

Returns:

The number of Atoms in this Bond

getAtom

public IAtom getAtom(int position)

Returns an Atom from this bond.

Specified by:

getAtom in interface IBond

Parameters:

position - The position in this bond where the atom is

Returns:

The atom at the specified position, null if there are no atoms in the bond

See Also:

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

getBegin

public IAtom getBegin()

Access the begin (or first) atom of the bond.

Specified by:

getBegin in interface IBond

Returns:

the begin atom

getEnd

public IAtom getEnd()

Access the end (or second) atom of the bond.

Specified by:

getEnd in interface IBond

Returns:

the end atom

getOther

public IAtom getOther(IAtom atom)

Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

IAtom beg = bond.getBegin();
 IAtom end = bond.getEnd();
 // bond.getOther(beg) == end
 // bond.getOther(end) == beg
 

Specified by:

getOther in interface IBond

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

getConnectedAtom

public IAtom getConnectedAtom(IAtom atom)

Returns the other atom in the bond, the atom is connected to the given atom. This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

IAtom beg = bond.getBegin();
 IAtom end = bond.getEnd();
 // bond.getConnectedAtom(beg) == end
 // bond.getConnectedAtom(end) == beg
 

Specified by:

getConnectedAtom in interface IBond

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

public IAtom[] getConnectedAtoms(IAtom atom)

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

Specified by:

getConnectedAtoms in interface IBond

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

public boolean contains(IAtom atom)

Returns true if the given atom participates in this bond.

Specified by:

contains in interface IBond

Parameters:

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

Returns:

true if the atom participates in this bond

setAtom

public void setAtom(IAtom atom,
           int position)

Sets an Atom in this bond.

Specified by:

setAtom in interface IBond

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

public IBond.Order getOrder()

Returns the bond order of this bond.

Specified by:

getOrder in interface IBond

Returns:

The bond order of this bond

See Also:

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

setOrder

public void setOrder(IBond.Order order)

Sets the bond order of this bond.

Specified by:

setOrder in interface IBond

Parameters:

order - The bond order to be assigned to this bond

See Also:

org.openscience.cdk.CDKConstants for predefined values., getOrder()

getStereo

public IBond.Stereo getStereo()

Returns the stereo descriptor for this bond.

Specified by:

getStereo in interface IBond

Returns:

The stereo descriptor for this bond

See Also:

setStereo(org.openscience.cdk.interfaces.IBond.Stereo), for predefined values.

setStereo

public void setStereo(IBond.Stereo stereo)

Sets the stereo descriptor for this bond.

Specified by:

setStereo in interface IBond

Parameters:

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

See Also:

getStereo(), for predefined values.

get2DCenter

public javax.vecmath.Point2d get2DCenter()

Returns the geometric 2D center of the bond.

Specified by:

get2DCenter in interface IBond

Returns:

The geometric 2D center of the bond

get3DCenter

public javax.vecmath.Point3d get3DCenter()

Returns the geometric 3D center of the bond.

Specified by:

get3DCenter in interface IBond

Returns:

The geometric 3D center of the bond

compare

public boolean compare(Object object)

Compares a bond with this bond.

Specified by:

compare in interface IBond

Overrides:

compare in class ChemObject

Parameters:

object - Object of type Bond

Returns:

true if the bond is equal to this bond

isConnectedTo

public 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.

Specified by:

isConnectedTo in interface IBond

Parameters:

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

Returns:

true if the bonds share an atom, otherwise false

isAromatic

public boolean isAromatic()

Access whether this bond has been marked as aromatic. The default value is false and you must explicitly perceive aromaticity with one of the available models.

Specified by:

isAromatic in interface IBond

Returns:

aromatic status

See Also:

IChemObject.getFlag(int), Aromaticity

setIsAromatic

public void setIsAromatic(boolean arom)

Mark this bond as being aromatic.

Specified by:

setIsAromatic in interface IBond

Parameters:

arom - aromatic status

See Also:

IChemObject.setFlag(int, boolean)

isInRing

public boolean isInRing()

Access whether this bond has been flagged as in a ring. The default value is false and you must explicitly find rings first.

Specified by:

isInRing in interface IBond

Returns:

ring status

See Also:

IChemObject.getFlag(int), RingSearch

setIsInRing

public void setIsInRing(boolean ring)

Mark this bond as being in a ring.

Specified by:

setIsInRing in interface IBond

Parameters:

ring - ring status

See Also:

IChemObject.setFlag(int, boolean)

clone

public IBond clone()
            throws CloneNotSupportedException

Clones this bond object, including clones of the atoms between which the bond is defined.

Specified by:

clone in interface IBond

Specified by:

clone in interface IChemObject

Overrides:

clone in class ElectronContainer

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

toString

public String toString()

Returns a one line string representation of this Container. This method is conform RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class ElectronContainer

Returns:

The string representation of this Container