org.openscience.cdk.pharmacophore

Class PharmacophoreQueryAtom

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.Element

org.openscience.cdk.Isotope

org.openscience.cdk.AtomType

org.openscience.cdk.Atom

org.openscience.cdk.pharmacophore.PharmacophoreQueryAtom

All Implemented Interfaces:

Serializable, Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IIsotope, IQueryAtom

@TestClass(value="org.openscience.cdk.pharmacophore.PharmacophoreQueryAtomTest")
public class PharmacophoreQueryAtom
extends Atom
implements IQueryAtom

Represents a query pharmacophore group.

This class is meant to be used to construct pharmacophore queries in conjunction with PharmacophoreQueryBond and an QueryAtomContainer.

Author:

Rajarshi Guha

See Also:

PharmacophoreQueryBond, QueryAtomContainer, PharmacophoreMatcher, Serialized Form

Keywords:

pharmacophore, 3D isomorphism

Nested Class Summary

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

IAtomType.Hybridization

Field Summary

Fields inherited from class org.openscience.cdk.Isotope

exactMass, naturalAbundance

Constructor Summary

Constructors

Constructor and Description
PharmacophoreQueryAtom(String symbol, String smarts) Creat a new query pharmacophore group

Method Summary

Methods

Modifier and Type	Method and Description
String	getSmarts() Get the SMARTS pattern for this pharmacophore group.
boolean	matches(IAtom atom) Checks whether this query atom matches a target atom.
void	setOperator(String ID)
String	toString() String representation of this pharmacophore group.

Methods inherited from class org.openscience.cdk.Atom

clone, compare, getCharge, getFractionalPoint3d, getImplicitHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setPoint2d, setPoint3d, setStereoParity

Methods inherited from class org.openscience.cdk.AtomType

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency

Methods inherited from class org.openscience.cdk.Isotope

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

Methods inherited from class org.openscience.cdk.Element

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from class org.openscience.cdk.ChemObject

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

Methods inherited from class java.lang.Object

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

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

getCharge, getFractionalPoint3d, getImplicitHydrogenCount, getPoint2d, getPoint3d, getStereoParity, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setPoint2d, setPoint3d, setStereoParity

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

getAtomTypeName, getBondOrderSum, getCovalentRadius, getFormalCharge, getFormalNeighbourCount, getHybridization, getMaxBondOrder, getValency, setAtomTypeName, setBondOrderSum, setCovalentRadius, setFormalCharge, setFormalNeighbourCount, setHybridization, setMaxBondOrder, setValency

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

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

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

getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

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

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

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

getBuilder

Constructor Detail

PharmacophoreQueryAtom

public PharmacophoreQueryAtom(String symbol,
                      String smarts)

Creat a new query pharmacophore group

Parameters:

symbol - The symbol for the group

smarts - The SMARTS pattern to be used for matching

Method Detail

getSmarts

@TestMethod(value="testGetSmarts")
public String getSmarts()

Get the SMARTS pattern for this pharmacophore group.

Returns:

The SMARTS pattern

matches

@TestMethod(value="testMatches")
public boolean matches(IAtom atom)

Checks whether this query atom matches a target atom.

Currently a query pharmacophore atom will match a target pharmacophore group if the symbols of the two groups match. This is based on the assumption that pharmacophore groups with the same symbol will have the same SMARTS pattern.

Specified by:

matches in interface IQueryAtom

Parameters:

atom - A target pharmacophore group

Returns:

true if the current query group has the same symbol as the target group

setOperator

@TestMethod(value="testSetOperator")
public void setOperator(String ID)

toString

@TestMethod(value="testToString")
public String toString()

String representation of this pharmacophore group.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Atom

Returns:

String representation of this pharmacophore group