org.openscience.cdk.isomorphism.matchers.smarts

Class SMARTSAtom

java.lang.Object

org.openscience.cdk.isomorphism.matchers.QueryChemObject

org.openscience.cdk.isomorphism.matchers.QueryAtom

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

All Implemented Interfaces:

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

Direct Known Subclasses:

AliphaticAtom, AliphaticSymbolAtom, AnyAtom, AromaticAtom, AromaticSymbolAtom, AtomicNumberAtom, ChiralityAtom, ExplicitConnectionAtom, FormalChargeAtom, HybridizationNumberAtom, HydrogenAtom, ImplicitHCountAtom, LogicalOperatorAtom, MassAtom, NonCHHeavyAtom, PeriodicGroupNumberAtom, ReactionRoleQueryAtom, RecursiveSmartsAtom, RingIdentifierAtom, RingMembershipAtom, SmallestRingAtom, TotalConnectionAtom, TotalHCountAtom, TotalRingConnectionAtom, TotalValencyAtom

public abstract class SMARTSAtom
extends QueryAtom
implements IQueryAtom

Abstract smarts atom.

Source code:

master

Belongs to CDK module:

smarts

Keywords:

SMARTS

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.isomorphism.matchers.QueryAtom

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

Constructor Summary

Constructors

Constructor and Description
SMARTSAtom(IChemObjectBuilder builder)

Method Summary

Methods

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

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryAtom

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

Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject

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

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

clone, getCharge, getFractionalPoint3d, getImplicitHydrogenCount, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, 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, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

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

getBuilder

Constructor Detail

SMARTSAtom

public SMARTSAtom(IChemObjectBuilder builder)

Method Detail

matches

public boolean matches(IAtom atom)

Description copied from interface: IQueryAtom

Returns true of the given atom matches this IQueryAtom.

Specified by:

matches in interface IQueryAtom

Overrides:

matches in class QueryChemObject

Parameters:

atom - IAtom to match against

Returns:

true, if this IQueryAtom matches the given IAtom

chiralityMatches

public boolean chiralityMatches(IAtom target,
                       int tParity,
                       int permParity)

Check if the atom-based chirality of the target matches. This check is done post-matching and should only be checked on atoms which are know to have already been matched (matches(IAtom). Currently the only atom-based chirality allowed is tetrahedral stereo- chemistry. The

Parameters:

target - the matched target (required to verify 'OR' conditions)

tParity - the parity (winding) of the target centre, 0=unspecified, 1=clockwise and -1=anticlockwise

permParity - permutation parity of the query neighbors (will be multiplied by the query parity)