Package org.openscience.cdk.isomorphism.matchers.smarts

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 SMARTS R<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

Modifier and Type	Method	Description
boolean	matches(IAtom atom)	Deprecated. Returns true of the given atom 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 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