Package org.openscience.cdk.pharmacophore

Class PharmacophoreQueryAngleBond

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ElectronContainer

org.openscience.cdk.Bond

org.openscience.cdk.pharmacophore.PharmacophoreQueryAngleBond

All Implemented Interfaces:

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

public class PharmacophoreQueryAngleBond
extends Bond
implements IQueryBond

Represents a pharmacophore query angle 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

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

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

Constructor Summary

Constructors

Constructor	Description
PharmacophoreQueryAngleBond()
PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, PharmacophoreQueryAtom atom3, double angle)	Create a query angle constraint between three query groups.
PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1, PharmacophoreQueryAtom atom2, PharmacophoreQueryAtom atom3, double lower, double upper)	Create a query angle constraint between three query groups.

Method Summary

Modifier and Type	Method	Description
double	getLower()
double	getUpper()
boolean	matches(IBond bond)	Checks whether the query angle constraint matches a target distance.
String	toString()	String representation of an angle 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, 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 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, 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, 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 org.openscience.cdk.interfaces.IElectronContainer

getElectronCount, setElectronCount

Constructor Detail

PharmacophoreQueryAngleBond

public PharmacophoreQueryAngleBond()

PharmacophoreQueryAngleBond

public PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1,
                                   PharmacophoreQueryAtom atom2,
                                   PharmacophoreQueryAtom atom3,
                                   double lower,
                                   double upper)

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

Parameters:

atom1 - The first pharmacophore group

atom2 - The second pharmacophore group

atom3 - The third pharmacophore group

lower - The lower bound of the angle between the three groups

upper - The upper bound of the angle between the three groups

PharmacophoreQueryAngleBond

public PharmacophoreQueryAngleBond(PharmacophoreQueryAtom atom1,
                                   PharmacophoreQueryAtom atom2,
                                   PharmacophoreQueryAtom atom3,
                                   double angle)

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

Parameters:

atom1 - The first pharmacophore group

atom2 - The second pharmacophore group

atom3 - The third pharmacophore group

angle - The exact angle between the two groups

Method Detail

matches

public boolean matches(IBond bond)

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

Specified by:

matches in interface IQueryBond

Parameters:

bond - The angle relationship in a target molecule

Returns:

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

getUpper

public double getUpper()

getLower

public double getLower()

toString

public String toString()

String representation of an angle constraint.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Bond

Returns:

String representation of and angle constraint