Class LogicalOperatorAtom
- java.lang.Object
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- org.openscience.cdk.isomorphism.matchers.QueryChemObject
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- org.openscience.cdk.isomorphism.matchers.QueryAtom
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- org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
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- org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom
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- All Implemented Interfaces:
Cloneable
,IAtom
,IAtomType
,ICDKObject
,IChemObject
,IElement
,IIsotope
,IQueryAtom
@Deprecated public class LogicalOperatorAtom extends SMARTSAtom
Deprecated.This class matches a logical operator that connects two query atoms. Logical matchers are created with,and(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom)
,not(org.openscience.cdk.isomorphism.matchers.IQueryAtom)
andor(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom)
.- Source code:
- main
- Belongs to CDK module:
- smarts
- Keywords:
- SMARTS
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IAtomType
IAtomType.Hybridization
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Field Summary
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Fields inherited from class org.openscience.cdk.isomorphism.matchers.QueryAtom
atomicNumber, charge, electronValency, exactMass, formalCharge, formalNeighbourCount, fractionalPoint3d, hybridization, hydrogenCount, naturalAbundance, point2d, point3d, stereoParity, symbol
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Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
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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
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Constructor Summary
Constructors Constructor Description LogicalOperatorAtom(IChemObjectBuilder builder)
Deprecated.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description static SMARTSAtom
and(IQueryAtom left, IQueryAtom right)
Deprecated.Conjunction the provided expressions.boolean
getFlag(int flagType)
Deprecated.IQueryAtom
getLeft()
Deprecated.String
getOperator()
Deprecated.IQueryAtom
getRight()
Deprecated.boolean
matches(IAtom atom)
Deprecated.Returns true of the givenatom
matches this IQueryAtom.static SMARTSAtom
not(IQueryAtom expr)
Deprecated.Negate the provided expression.static SMARTSAtom
or(IQueryAtom left, IQueryAtom right)
Deprecated.Disjunction the provided expressions.void
setLeft(IQueryAtom left)
Deprecated.void
setOperator(String name)
Deprecated.use static utility methods to create logical atom matcher,and(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom)
,or(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom)
ornot(org.openscience.cdk.isomorphism.matchers.IQueryAtom)
.void
setRight(IQueryAtom right)
Deprecated.-
Methods inherited from class org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
chiralityMatches
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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
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Methods inherited from class org.openscience.cdk.isomorphism.matchers.QueryChemObject
addListener, addProperties, clear, flags, getBuilder, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty
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Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IAtom
bonds, clone, getBond, getBondCount, getCharge, getContainer, getFractionalPoint3d, getImplicitHydrogenCount, getIndex, getMapIdx, getPoint2d, getPoint3d, getStereoParity, getTotalHydrogenCount, isAromatic, isInRing, neighbors, setCharge, setFractionalPoint3d, setImplicitHydrogenCount, setIsAromatic, setIsInRing, setMapIdx, setPoint2d, setPoint3d, setStereoParity
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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
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, clear, flags, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
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Methods inherited from interface org.openscience.cdk.interfaces.IElement
getAtomicNumber, getSymbol, setAtomicNumber, setSymbol
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Methods inherited from interface org.openscience.cdk.interfaces.IIsotope
getExactMass, getMassNumber, getNaturalAbundance, setExactMass, setMassNumber, setNaturalAbundance
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Constructor Detail
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LogicalOperatorAtom
public LogicalOperatorAtom(IChemObjectBuilder builder)
Deprecated.
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Method Detail
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getLeft
@Deprecated public IQueryAtom getLeft()
Deprecated.
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getOperator
@Deprecated public String getOperator()
Deprecated.
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getRight
@Deprecated public IQueryAtom getRight()
Deprecated.
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setLeft
@Deprecated public void setLeft(IQueryAtom left)
Deprecated.
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setOperator
@Deprecated public void setOperator(String name)
Deprecated.use static utility methods to create logical atom matcher,and(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom)
,or(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom)
ornot(org.openscience.cdk.isomorphism.matchers.IQueryAtom)
.
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setRight
@Deprecated public void setRight(IQueryAtom right)
Deprecated.
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matches
public boolean matches(IAtom atom)
Deprecated.Description copied from class:QueryAtom
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
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getFlag
@Deprecated public boolean getFlag(int flagType)
Deprecated.Description copied from class:QueryChemObject
Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g.IChemObject.AROMATIC
).if(chemObject.getFlag(CDKConstants.ISAROMATIC)){ // handle aromatic flag on this chem object }
- Specified by:
getFlag
in interfaceIChemObject
- Overrides:
getFlag
in classQueryChemObject
- Parameters:
flagType
- flag to retrieve the value of- Returns:
- true if the flag
flag_type
is set - See Also:
IChemObject.setFlag(int, boolean)
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and
public static SMARTSAtom and(IQueryAtom left, IQueryAtom right)
Deprecated.Conjunction the provided expressions.- Parameters:
left
- expressionright
- expression- Returns:
- conjunction of the left and right expressions
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or
public static SMARTSAtom or(IQueryAtom left, IQueryAtom right)
Deprecated.Disjunction the provided expressions.- Parameters:
left
- expressionright
- expression- Returns:
- disjunction of the left and right expressions
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not
public static SMARTSAtom not(IQueryAtom expr)
Deprecated.Negate the provided expression.- Parameters:
expr
- expression to negate- Returns:
- a SMARTS atom which is the negation of the expression
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