Package 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:

main

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

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

Ac, Ag, Al, Am, Ar, As, At, Au, B, Ba, Be, Bh, Bi, Bk, Br, C, Ca, Cd, Ce, Cf, Cl, Cm, Cn, Co, Cr, Cs, Cu, Db, Ds, Dy, Er, Es, Eu, F, Fe, Fl, Fm, Fr, Ga, Gd, Ge, H, He, Hf, Hg, Ho, Hs, I, In, Ir, K, Kr, La, Li, Lr, Lu, Lv, Mc, Md, Mg, Mn, Mo, Mt, N, Na, Nb, Nd, Ne, Nh, Ni, No, Np, O, Og, Os, P, Pa, Pb, Pd, Pm, Po, Pr, Pt, Pu, Ra, Rb, Re, Rf, Rg, Rh, Rn, Ru, S, Sb, Sc, Se, Sg, Si, Sm, Sn, Sr, Ta, Tb, Tc, Te, Th, Ti, Tl, Tm, Ts, U, V, W, Wildcard, Xe, Y, Yb, Zn, Zr

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
static PharmacophoreAtom	get(IAtom atom)
int[]	getMatchingAtoms()	Get the atoms of a target molecule that correspond to this group.
String	getSmarts()	Get the SMARTS for the group.
String	getSymbol()	Returns the element symbol of this element.
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.
void	setSymbol(String symbol)	Sets the element symbol of this element.

Methods inherited from class org.openscience.cdk.Atom

bonds, clone, compare, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, 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, setAtomicNumber

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.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.IElement

getAtomicNumber, setAtomicNumber

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

getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

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

get

public static PharmacophoreAtom get(IAtom atom)

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)

setSymbol

public void setSymbol(String symbol)

Description copied from class: Element

Sets the element symbol of this element.

Specified by:

setSymbol in interface IElement

Overrides:

setSymbol in class Element

Parameters:

symbol - The element symbol to be assigned to this atom

See Also:

Element.getSymbol()

getSymbol

public String getSymbol()

Description copied from class: Element

Returns the element symbol of this element.

Specified by:

getSymbol in interface IElement

Overrides:

getSymbol in class Element

Returns:

The element symbol of this element. Null if unset.

See Also:

Element.setSymbol(java.lang.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()

Description copied from class: Atom

Overrides:

hashCode in class Atom

equals

public boolean equals(Object o)

Description copied from class: Atom

Overrides:

equals in class Atom