Class RingMembershipAtom
- 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.RingMembershipAtom
-
- All Implemented Interfaces:
Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IIsotope
,IQueryAtom
@Deprecated public class RingMembershipAtom extends SMARTSAtom
Deprecated.This query is found in a specified number of ring. The ring membership is specified with the SMARTSR<NUMBER>
. The membership depends on the ring set used and as such is not a portable term. If the Smallest Set of Smallest Rings (SSSR) is used then changing the order of atoms may change which atoms match in a pattern.- 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 RingMembershipAtom(int num, IChemObjectBuilder builder)
Deprecated.Ring membership query atom.
-
Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description boolean
matches(IAtom atom)
Deprecated.Returns true of the givenatom
matches this IQueryAtom.-
Methods inherited from class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
chiralityMatches
-
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
-
RingMembershipAtom
public RingMembershipAtom(int num, IChemObjectBuilder builder)
Deprecated.Ring membership query atom. Check if the an atom belongs to num of rings. To specify any ring membership, num should be specified as < 0. Generally in SMARTS it's better negate ring membership with[!R]
however for legacy reasons[R0]
was accepted and checks this atoms belongs to 0 rings.- Parameters:
num
- number of rings which this atom belongs to, < 0 any ring.
-
-
Method Detail
-
matches
public boolean matches(IAtom atom)
Deprecated.Returns true of the givenatom
matches this IQueryAtom.- Specified by:
matches
in interfaceIQueryAtom
- Overrides:
matches
in classSMARTSAtom
- Parameters:
atom
- IAtom to match against- Returns:
- true, if this IQueryAtom matches the given IAtom
-
-