Package org.openscience.cdk.pharmacophore

Class PharmacophoreQueryBond

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ElectronContainer

org.openscience.cdk.Bond

org.openscience.cdk.pharmacophore.PharmacophoreQueryBond

All Implemented Interfaces:

Serializable, Cloneable, IBond, ICDKObject, IChemObject, IElectronContainer, IQueryBond

public class PharmacophoreQueryBond
extends Bond
implements IQueryBond

Represents a pharmacophore query distance constraint.

Author:

Rajarshi Guha

See Also:

• PharmacophoreQueryAtom
• PharmacophoreMatcher
• QueryAtomContainer
• Serialized Form

Source code:

main

Belongs to CDK module:

pcore

Keywords:

pharmacophore, 3D isomorphism

Nested Class Summary

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

IBond.Display, IBond.Order, IBond.Stereo

Field Summary

Fields inherited from class org.openscience.cdk.Bond

atomCount, atoms, display, order, stereo

Fields inherited from class org.openscience.cdk.ElectronContainer

electronCount

Constructor Summary

Constructors

Constructor	Description
PharmacophoreQueryBond()
PharmacophoreQueryBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, double distance)	Create a query distance constraint between two query groups.
PharmacophoreQueryBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, double lower, double upper)	Create a query distance constraint between two query groups.

Method Summary

Modifier and Type	Method	Description
double	getLower()
double	getUpper()
boolean	matches(IBond bond)	Checks whether the query distance constraint matches a target distance.
String	toString()	String representation of a distance constraint.

Methods inherited from class org.openscience.cdk.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

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

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

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

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

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

getBuilder

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.IElectronContainer

getElectronCount, setElectronCount

Constructor Details

PharmacophoreQueryBond

public PharmacophoreQueryBond()

PharmacophoreQueryBond

public PharmacophoreQueryBond(PharmacophoreQueryAtom atom1,
 PharmacophoreQueryAtom atom2,
 double lower,
 double upper)

Create a query distance constraint between two query groups. Note that the distance is only considered upto 2 decimal places.

Parameters:

atom1 - The first pharmacophore group

atom2 - The second pharmacophore group

lower - The lower bound of the distance between the two groups

upper - The upper bound of the distance between the two groups

See Also:

• PharmacophoreQueryBond(PharmacophoreQueryAtom,PharmacophoreQueryAtom,double)

PharmacophoreQueryBond

public PharmacophoreQueryBond(PharmacophoreQueryAtom atom1,
 PharmacophoreQueryAtom atom2,
 double distance)

Create a query distance constraint between two query groups. This constructor allows you to define a query distance constraint such that the distance between the two query groups is exact (i.e., not a range). Note that the distance is only considered upto 2 decimal places.

Parameters:

atom1 - The first pharmacophore group

atom2 - The second pharmacophore group

distance - The exact distance between the two groups

See Also:

• PharmacophoreQueryBond(PharmacophoreQueryAtom, PharmacophoreQueryAtom, double, double)

Method Details

matches

public boolean matches(IBond bond)

Checks whether the query distance constraint matches a target distance. This method checks whether a query constraint is satisfied by an observed distance (represented by a PharmacophoreBond in the target molecule. Note that distance are compared upto 2 decimal places.

Specified by:

matches in interface IQueryBond

Parameters:

bond - The distance relationship in a target molecule

Returns:

true if the target distance lies within the range of the query constraint

getUpper

public double getUpper()

getLower

public double getLower()

toString

public String toString()

String representation of a distance constraint.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Bond

Returns:

String representation of a distance constraint