org.openscience.cdk.pharmacophore

Class PharmacophoreAtom

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.PharmacophoreAtom

All Implemented Interfaces:

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

public class PharmacophoreAtom
extends Atom

A representation of a pharmacophore group. In general this class is used internally for pharmacophore matchin and does not be instantiated by the user. However after a successful match the user will get access to objects of this class which match parts of a query. The main features of a pharmacophore group are the SMARTS pattern defining what the group is meant to identify and the atoms of a molecule that correspond to the SMARTS pattern.

Author:

Rajarshi Guha

See Also:

PharmacophoreMatcher, PharmacophoreBond, Serialized Form

Source code:

master

Belongs to CDK module:

pcore

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.Atom

charge, fractionalPoint3d, hydrogenCount, point2d, point3d, stereoParity

Fields inherited from class org.openscience.cdk.AtomType

electronValency, formalCharge, formalNeighbourCount, hybridization

Fields inherited from class org.openscience.cdk.Isotope

exactMass, naturalAbundance

Fields inherited from class org.openscience.cdk.Element

atomicNumber, symbol

Constructor Summary

Constructors

Constructor and Description
PharmacophoreAtom(PharmacophoreAtom pharmacophoreAtom) Create a pharmacophore group.
PharmacophoreAtom(String smarts, String symbol, javax.vecmath.Point3d coordinates) Create a pharmacophore group.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
int[]	getMatchingAtoms() Get the atoms of a target molecule that correspond to this group.
String	getSmarts() Get the SMARTS for the group.
int	hashCode()
void	setMatchingAtoms(int[] atomIndices) Set the atoms of a target molecule that correspond to this group.
void	setSmarts(String smarts) Set the SMARTS for the group.

Methods inherited from class org.openscience.cdk.Atom

clone, compare, getCharge, getFractionalPoint3d, getImplicitHydrogenCount, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setPoint2d, setPoint3d, setStereoParity, toString

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, 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.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, 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.ICDKObject

getBuilder

Constructor Detail

PharmacophoreAtom

public PharmacophoreAtom(String smarts,
                 String symbol,
                 javax.vecmath.Point3d coordinates)

Create a pharmacophore group.

Parameters:

smarts - The SMARTS pattern for the group

symbol - The label for this group.

coordinates - The coordinates for the group. Note that since a pharmacophore group may match multiple atoms (say a c1ccccc1 group), the coordinates for the group are the effective coordinates of all the atoms for the group. In effect this means that for multi-atom groups, the coordinate is simply the mean of the coordinates of the individual atoms for the group.

PharmacophoreAtom

public PharmacophoreAtom(PharmacophoreAtom pharmacophoreAtom)

Create a pharmacophore group.

Parameters:

pharmacophoreAtom - A previously created pharmacophore group

Method Detail

setSmarts

public void setSmarts(String smarts)

Set the SMARTS for the group.

Parameters:

smarts - The SMARTS pattern

getSmarts

public String getSmarts()

Get the SMARTS for the group.

Returns:

The SMARTS pattern

See Also:

setSmarts(String)

setMatchingAtoms

public void setMatchingAtoms(int[] atomIndices)

Set the atoms of a target molecule that correspond to this group. This method is generally only useful in the context of pharmacophore matching

Parameters:

atomIndices - The indicies of the atoms in a molecule that match the pattern for this group.

See Also:

getMatchingAtoms(), PharmacophoreMatcher

getMatchingAtoms

public int[] getMatchingAtoms()

Get the atoms of a target molecule that correspond to this group. This method is generally only useful in the context of pharmacophore matching

Returns:

The indices of the atoms, in a molecule, that match the pattern for this group.

See Also:

setMatchingAtoms(int[]), PharmacophoreMatcher

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object