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

Class LogicalOperatorAtom

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.LogicalOperatorAtom

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) and or(org.openscience.cdk.isomorphism.matchers.IQueryAtom, org.openscience.cdk.isomorphism.matchers.IQueryAtom).

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
LogicalOperatorAtom(IChemObjectBuilder builder)	Deprecated.

Method Summary

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 given atom 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) or not(org.openscience.cdk.isomorphism.matchers.IQueryAtom).
void	setRight(IQueryAtom right)	Deprecated.

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, 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, 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

LogicalOperatorAtom

public LogicalOperatorAtom(IChemObjectBuilder builder)

Deprecated.

Method Detail

getLeft

@Deprecated
public IQueryAtom getLeft()

Deprecated.

getOperator

@Deprecated
public String getOperator()

Deprecated.

getRight

@Deprecated
public IQueryAtom getRight()

Deprecated.

setLeft

@Deprecated
public void setLeft(IQueryAtom left)

Deprecated.

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) or not(org.openscience.cdk.isomorphism.matchers.IQueryAtom).

setRight

@Deprecated
public void setRight(IQueryAtom right)

Deprecated.

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 SMARTSAtom

Parameters:

atom - IAtom to match against

Returns:

true, if this IQueryAtom matches the given IAtom

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. CDKConstants.ISAROMATIC).

 if(chemObject.getFlag(CDKConstants.ISAROMATIC)){
     // handle aromatic flag on this chem object
 }
 

Specified by:

getFlag in interface IChemObject

Overrides:

getFlag in class QueryChemObject

Parameters:

flagType - flag to retrieve the value of

Returns:

true if the flag flag_type is set

See Also:

IChemObject.setFlag(int, boolean), CDKConstants

and

public static SMARTSAtom and(IQueryAtom left,
                             IQueryAtom right)

Deprecated.

Conjunction the provided expressions.

Parameters:

left - expression

right - expression

Returns:

conjunction of the left and right expressions

or

public static SMARTSAtom or(IQueryAtom left,
                            IQueryAtom right)

Deprecated.

Disjunction the provided expressions.

Parameters:

left - expression

right - expression

Returns:

disjunction of the left and right expressions

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