Class PharmacophoreBond

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ElectronContainer

org.openscience.cdk.Bond

org.openscience.cdk.pharmacophore.PharmacophoreBond

All Implemented Interfaces:

Serializable, Cloneable, IBond, ICDKObject, IChemObject, IElectronContainer

public class PharmacophoreBond
extends Bond

Represents a distance relationship between two pharmacophore groups.

Author:

Rajarshi Guha

See Also:

• PharmacophoreAtom
• Serialized Form

Keywords:

pharmacophore, 3D isomorphism

Nested Class Summary

Nested classes/interfaces inherited from interface IBond

IBond.Display, IBond.Order, IBond.Stereo

Field Summary

Fields inherited from class Bond

atomCount, atoms, display, order

Fields inherited from class ElectronContainer

electronCount

Fields inherited from interface IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	Description
PharmacophoreBond(PharmacophoreAtom patom1, PharmacophoreAtom patom2)	Create a pharmacophore distance constraint.

Method Summary

Modifier and Type	Method	Description
static PharmacophoreBond	get(IBond bond)
double	getBondLength()	Get the distance between the two pharmacophore groups that make up the constraint.

Methods inherited from class Bond

atoms, clone, compare, contains, equals, get2DCenter, get3DCenter, getAtom, getAtomCount, getBegin, getConnectedAtom, getConnectedAtoms, getContainer, getDisplay, getEnd, getIndex, getOrder, getOther, getStereo, hashCode, isAromatic, isConnectedTo, isInRing, setAtom, setAtoms, setDisplay, setIsAromatic, setIsInRing, setOrder, setStereo, toString

Methods inherited from class ElectronContainer

getElectronCount, setElectronCount

Methods inherited from class ChemObject

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

Methods inherited from class Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface IBond

getConnectedAtom

Methods inherited from interface ICDKObject

getBuilder

Methods inherited from interface IChemObject

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

Methods inherited from interface IElectronContainer

getElectronCount, setElectronCount

Constructor Details

PharmacophoreBond

public PharmacophoreBond(PharmacophoreAtom patom1,
 PharmacophoreAtom patom2)

Create a pharmacophore distance constraint.

Parameters:

patom1 - The first pharmacophore group

patom2 - The second pharmacophore group

Method Details

get

public static PharmacophoreBond get(IBond bond)

getBondLength

public double getBondLength()

Get the distance between the two pharmacophore groups that make up the constraint.

Returns:

The distance between the two groups