Class AromaticAtom

java.lang.Object

org.openscience.cdk.isomorphism.matchers.QueryChemObject

org.openscience.cdk.isomorphism.matchers.QueryAtom

org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom

org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom

All Implemented Interfaces:

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

@Deprecated
public class AromaticAtom
extends SMARTSAtom

Deprecated.

This matcher any aromatic atom. This assumes that aromaticity in the molecule has been perceived.

Keywords:

SMARTS

Nested Class Summary

Nested classes/interfaces inherited from interface IAtomType

IAtomType.Hybridization

Modifier and Type	Interface	Description
static enum	IAtomType.Hybridization	An enum for the different hybridization states.

Field Summary

Fields inherited from class QueryAtom

atomicNumber, charge, electronValency, exactMass, formalCharge, formalNeighbourCount, fractionalPoint3d, hybridization, hydrogenCount, naturalAbundance, point2d, point3d, stereoParity, symbol

Modifier and Type	Field	Description
protected Integer	atomicNumber	The atomic number for this element giving their position in the periodic table.
protected Double	charge	The partial charge of the atom.
protected Integer	electronValency	The electron Valency of this atom with CDKConstants.UNSET as default.
Double	exactMass	Exact mass of this isotope.
protected Integer	formalCharge	The formal charge of the atom with CDKConstants.UNSET as default.
protected Integer	formalNeighbourCount	The formal number of neighbours this atom type can have with CDKConstants_UNSET as default.
protected javax.vecmath.Point3d	fractionalPoint3d	A 3 point specifying the location of this atom in a crystal unit cell.
protected IAtomType.Hybridization	hybridization	The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
protected Integer	hydrogenCount	The number of implicitly bound hydrogen atoms for this atom.
Double	naturalAbundance	Natural abundance of this isotope.
protected javax.vecmath.Point2d	point2d	A 2D point specifying the location of this atom in a 2D coordinate space.
protected javax.vecmath.Point3d	point3d	A 3 point specifying the location of this atom in a 3D coordinate space.
protected Integer	stereoParity	A stereo parity descriptor for the stereochemistry of this atom.
protected String	symbol	The element symbol for this element as listed in the periodic table.

Fields inherited from interface IChemObject

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

Modifier and Type	Field	Description
static final int	ALIPHATIC	Flag that is set if a ChemObject is part of an aliphatic chain.
static final int	AROMATIC	Flag is set if ChemObject is part of an aromatic system.
static final int	CONJUGATED	Flag is set if ChemObject is part of a conjugated system.
static final int	HIDDEN	This flag can be used when depicted structures to hide certain parts, for example the things are abbreviated (display shortcuts).
static final int	HYDROGEN_BOND_ACCEPTOR	Sets to true if the atom is a hydrogen bond acceptor.
static final int	HYDROGEN_BOND_DONOR	Sets to true if the atom is a hydrogen bond donor.
static final int	IN_RING	Flag that is set when the ChemObject is part of a ring.
static final int	MAPPED	Flag is set if a ChemObject is mapped to another ChemObject.
static final int	MARKUSH	Flag to indicate a flattened molecule holds a Markush structure, you can work on it as is or it might make more sense to repack into something sensible like a RGroupQuery.
static final int	NOT_IN_RING	Flag that is set when the ChemObject is part of a ring.
static final int	PLACED	Flag that is set if the ChemObject is placed when calculating 2D/3D layouts.
static final int	REACTIVE_CENTER	Flag is set if a ChemObject has reactive center.
static final int	SINGLE_OR_DOUBLE	Flag used for marking uncertainty of the bond order.
static final int	TYPEABLE	Flag is set if an atom could be typed.
static final int	VISITED	Flag is set if ChemObject has been visited.

Fields inherited from interface 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

Modifier and Type	Field	Description
static final int	Ac
static final int	Ag
static final int	Al
static final int	Am
static final int	Ar
static final int	As
static final int	At
static final int	Au
static final int	B
static final int	Ba
static final int	Be
static final int	Bh
static final int	Bi
static final int	Bk
static final int	Br
static final int	C	Carbon atomic number
static final int	Ca
static final int	Cd
static final int	Ce
static final int	Cf
static final int	Cl
static final int	Cm
static final int	Cn
static final int	Co
static final int	Cr
static final int	Cs
static final int	Cu
static final int	Db
static final int	Ds
static final int	Dy
static final int	Er
static final int	Es
static final int	Eu
static final int	F
static final int	Fe
static final int	Fl
static final int	Fm
static final int	Fr
static final int	Ga
static final int	Gd
static final int	Ge
static final int	H	Hydrogen atomic number
static final int	He
static final int	Hf
static final int	Hg
static final int	Ho
static final int	Hs
static final int	I
static final int	In
static final int	Ir
static final int	K
static final int	Kr
static final int	La
static final int	Li
static final int	Lr
static final int	Lu
static final int	Lv
static final int	Mc
static final int	Md
static final int	Mg
static final int	Mn
static final int	Mo
static final int	Mt
static final int	N	Nitrogen atomic number
static final int	Na
static final int	Nb
static final int	Nd
static final int	Ne
static final int	Nh
static final int	Ni
static final int	No
static final int	Np
static final int	O	Oxygen atomic number
static final int	Og
static final int	Os
static final int	P
static final int	Pa
static final int	Pb
static final int	Pd
static final int	Pm
static final int	Po
static final int	Pr
static final int	Pt
static final int	Pu
static final int	Ra
static final int	Rb
static final int	Re
static final int	Rf
static final int	Rg
static final int	Rh
static final int	Rn
static final int	Ru
static final int	S
static final int	Sb
static final int	Sc
static final int	Se
static final int	Sg
static final int	Si
static final int	Sm
static final int	Sn
static final int	Sr
static final int	Ta
static final int	Tb
static final int	Tc
static final int	Te
static final int	Th
static final int	Ti
static final int	Tl
static final int	Tm
static final int	Ts
static final int	U
static final int	V
static final int	W
static final int	Wildcard	Wildcard atom is atomic number 0
static final int	Xe
static final int	Y
static final int	Yb
static final int	Zn
static final int	Zr

Constructor Summary

Constructors

Constructor	Description
AromaticAtom(IChemObjectBuilder builder)	Deprecated. Creates a new instance

Method Summary

Modifier and Type	Method	Description
boolean	matches(IAtom atom)	Deprecated. Returns true of the given atom matches this IQueryAtom.
String	toString()	Deprecated. Returns a one line description of this IChemObject.

Methods inherited from class SMARTSAtom

chiralityMatches

Modifier and Type	Method	Description
boolean	chiralityMatches(IAtom target, int tParity, int permParity)	Deprecated. Check if the atom-based chirality of the target matches.

Methods inherited from class QueryAtom

bonds, clone, equals, getAtomicNumber, getAtomTypeName, getBond, getBondCount, getBondOrderSum, getCharge, getContainer, getCovalentRadius, getExactMass, getExpression, getFormalCharge, getFormalNeighbourCount, getFractionalPoint3d, getHybridization, getImplicitHydrogenCount, getIndex, getMapIdx, getMassNumber, getMaxBondOrder, getNaturalAbundance, getPoint2d, getPoint3d, getStereoParity, getSymbol, getValency, hashCode, isAromatic, isInRing, setAtomicNumber, setAtomTypeName, setBondOrderSum, setCharge, setCovalentRadius, setExactMass, setExpression, setFormalCharge, setFormalNeighbourCount, setFractionalPoint3d, setHybridization, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setMassNumber, setMaxBondOrder, setNaturalAbundance, setPoint2d, setPoint3d, setStereoParity, setSymbol, setValency

Modifier and Type	Method	Description
Iterable<IBond>	bonds()	Returns the bonds connected to this atom.
IAtom	clone()	Returns a deep clone of this IChemObject.
boolean	equals(Object obj)
Integer	getAtomicNumber()	Returns the atomic number of this element.
String	getAtomTypeName()	Gets the id attribute of the AtomType object.
IBond	getBond(IAtom atom)	Returns the bond connecting 'this' atom to the provided atom.
int	getBondCount()	Get the number of explicit bonds connected to this atom.
Double	getBondOrderSum()	Gets the bondOrderSum attribute of the AtomType object.
Double	getCharge()	Returns the partial charge of this atom.
IAtomContainer	getContainer()	Access the IAtomContainer of which this atom is a member of.
Double	getCovalentRadius()	Returns the covalent radius for this AtomType.
Double	getExactMass()	Gets the ExactMass attribute of the Isotope object.
Expr	getExpression()	Get the atom-expression predicate for this query atom.
Integer	getFormalCharge()	Returns the formal charge of this atom.
Integer	getFormalNeighbourCount()	Returns the formal neighbour count of this atom.
javax.vecmath.Point3d	getFractionalPoint3d()	Returns a point specifying the location of this atom in a Crystal unit cell.
IAtomType.Hybridization	getHybridization()	Returns the hybridization of this atom.
Integer	getImplicitHydrogenCount()	Returns the hydrogen count of this atom.
int	getIndex()	Acces the index of an atom in the context of an IAtomContainer.
int	getMapIdx()	Access the map index for this atom.
Integer	getMassNumber()	Returns the atomic mass of this element.
IBond.Order	getMaxBondOrder()	Gets the MaxBondOrder attribute of the AtomType object.
Double	getNaturalAbundance()	Gets the NaturalAbundance attribute of the Isotope object.
javax.vecmath.Point2d	getPoint2d()	Returns a point specifying the location of this atom in a 2D space.
javax.vecmath.Point3d	getPoint3d()	Returns a point specifying the location of this atom in a 3D space.
Integer	getStereoParity()	Returns the stereo parity of this atom.
String	getSymbol()	Returns the element symbol of this element.
Integer	getValency()	Gets the the exact electron valency of the AtomType object.
int	hashCode()
boolean	isAromatic()	Access whether this atom has been marked as aromatic.
boolean	isInRing()	Access whether this atom has been flagged as in a ring.
void	setAtomicNumber(Integer atomicNumber)	Sets the atomic number of this element.
void	setAtomTypeName(String identifier)	Sets the if attribute of the AtomType object.
void	setBondOrderSum(Double bondOrderSum)	Sets the the exact bond order sum attribute of the AtomType object.
void	setCharge(Double charge)	Sets the partial charge of this atom.
void	setCovalentRadius(Double radius)	Sets the covalent radius for this AtomType.
void	setExactMass(Double exactMass)	Sets the ExactMass attribute of the Isotope object.
void	setExpression(Expr expr)	Set the atom-expression predicate for this query atom.
void	setFormalCharge(Integer charge)	Sets the formal charge of this atom.
void	setFormalNeighbourCount(Integer count)	Sets the formal neighbour count of this atom.
void	setFractionalPoint3d(javax.vecmath.Point3d point3d)	Sets a point specifying the location of this atom in a Crystal unit cell.
void	setHybridization(IAtomType.Hybridization hybridization)	Sets the hybridization of this atom.
void	setImplicitHydrogenCount(Integer hydrogenCount)	Sets the number of implicit hydrogen count of this atom.
void	setIsAromatic(boolean arom)	Mark this atom as being aromatic.
void	setIsInRing(boolean ring)	Mark this atom as being in a ring.
void	setMapIdx(int mapidx)	Set the map index for this atom.
void	setMassNumber(Integer massNumber)	Sets the atomic mass of this element.
void	setMaxBondOrder(IBond.Order maxBondOrder)	Sets the MaxBondOrder attribute of the AtomType object.
void	setNaturalAbundance(Double naturalAbundance)	Sets the NaturalAbundance attribute of the Isotope object.
void	setPoint2d(javax.vecmath.Point2d point2d)	Sets a point specifying the location of this atom in a 2D space.
void	setPoint3d(javax.vecmath.Point3d point3d)	Sets a point specifying the location of this atom in 3D space.
void	setStereoParity(Integer stereoParity)	Sets the stereo parity for this atom.
void	setSymbol(String symbol)	Sets the element symbol of this element.
void	setValency(Integer valency)	Sets the the exact electron valency of the AtomType object.

Methods inherited from class QueryChemObject

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

Modifier and Type	Method	Description
void	addListener(IChemObjectListener col)	Use this to add yourself to this IChemObject as a listener.
void	addProperties(Map<Object,Object> properties)	Sets the properties of this object.
void	clear(int flags)	Clear the provided flags.
int	flags()	Access the current value of the flags for this ChemObject.
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
boolean	getFlag(int mask)	Returns the value of a given flag.
boolean[]	getFlags()	Returns the whole set of flags.
Integer	getFlagValue()	Access the internal value used to store the flags.
String	getID()	Returns the identifier (ID) of this object.
int	getListenerCount()	Returns the number of ChemObjectListeners registered with this object.
boolean	getNotification()	Returns the flag that indicates whether notification messages are sent around.
Map<Object,Object>	getProperties()	Returns a Map with the IChemObject's properties.
<T> T	getProperty(Object description)	Returns a property for the IChemObject.
<T> T	getProperty(Object description, Class<T> c)	Access a property of the given description and cast the specified class.
boolean	is(int flags)	Test if a flag(s) are set on this ChemObject.
void	notifyChanged()	This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
void	notifyChanged(IChemObjectChangeEvent evt)	This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.
void	removeListener(IChemObjectListener col)	Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.
void	removeProperty(Object description)	Removes a property for a IChemObject.
void	set(int flags)	Set the provided flags.
void	setFlag(int mask, boolean value)	Sets the value of some flag.
void	setFlags(boolean[] flagsNew)	Sets the whole set of flags.
void	setID(String identifier)	Sets the identifier (ID) of this object.
void	setNotification(boolean bool)	Set a flag to use or not use notification.
void	setProperties(Map<Object,Object> properties)	Set the properties of this object to the provided map (shallow copy).
void	setProperty(Object description, Object property)	Sets a property for a IChemObject.

Methods inherited from class Object

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

Methods inherited from interface IAtom

getTotalHydrogenCount, neighbors

Modifier and Type	Method	Description
default Integer	getTotalHydrogenCount()	Calculates the total number of hydrogens connected to this atom.
default Iterable<IAtom>	neighbors()	Iterable over the atoms connected to this atom (the neighbors).

Constructor Details

AromaticAtom

public AromaticAtom(IChemObjectBuilder builder)

Deprecated.

Creates a new instance

Method Details

matches

public boolean matches(IAtom atom)

Deprecated.

Description copied from class: QueryAtom

Returns true of the given atom matches this IQueryAtom.

Specified by:

matches in interface IQueryAtom

Overrides:

matches in class SMARTSAtom

Parameters:

atom - IAtom to match against

Returns:

true, if this IQueryAtom matches the given IAtom

toString

public String toString()

Deprecated.

Description copied from interface: IChemObject

Returns a one line description of this IChemObject.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

Returns:

a String representation of this object