SMARTSAtom (cdk 2.9 API)

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
```
@Deprecated
public abstract class SMARTSAtom
extends QueryAtom
implements IQueryAtom
```
Deprecated.

Abstract smarts atom.

Source code:
main

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
- 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

SMARTSAtom(IChemObjectBuilder builder)
Deprecated.

Method Summary

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

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

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

Methods inherited from interface org.openscience.cdk.interfaces.IAtom
bonds, clone, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, isAromatic, isInRing, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, 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.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, toString

Methods inherited from interface org.openscience.cdk.interfaces.IElement
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol

Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance

- Constructor Detail
  - SMARTSAtom
```
public SMARTSAtom(IChemObjectBuilder builder)
```
    Deprecated.
- Method Detail
  - 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 QueryAtom
    
    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)
```
    Deprecated.
    
    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)