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

Source code:

master

Belongs to CDK module:

interfaces

Keywords:

bond, atom, electron

Created on:

2005-08-24

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
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

Methods

Modifier and Type	Method and Description
Iterable<IAtom>	atoms() Returns the Iterable to atoms making up this bond.
IBond	clone() Returns a deep clone of this IChemObject.
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) Deprecated. use the method getOther(IAtom)
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 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.

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, 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()

getBegin

IAtom getBegin()

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

Returns:

the begin atom

getEnd

IAtom getEnd()

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

Returns:

the end atom

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

@Deprecated
IAtom getConnectedAtom(IAtom atom)

Deprecated. use the method getOther(IAtom)

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 getConnectedAtoms(IAtom) should be used.

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

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

getOther

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 getConnectedAtoms(IAtom) should be used.

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

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

isAromatic

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.

Returns:

aromatic status

See Also:

IChemObject.getFlag(int), Aromaticity

setIsAromatic

void setIsAromatic(boolean arom)

Mark this bond as being aromatic.

Parameters:

arom - aromatic status

See Also:

IChemObject.setFlag(int, boolean)

isInRing

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.

Returns:

ring status

See Also:

IChemObject.getFlag(int), RingSearch

setIsInRing

void setIsInRing(boolean ring)

Mark this bond as being in a ring.

Parameters:

ring - ring status

See Also:

IChemObject.setFlag(int, boolean)

clone

IBond clone()
            throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IChemObject

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned