ambit2.smarts.query

Class SmartsPatternAmbit

java.lang.Object

ambit2.smarts.query.AbstractSmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>

ambit2.smarts.query.SmartsPatternAmbit

All Implemented Interfaces:

ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>, Serializable

public class SmartsPatternAmbit
extends AbstractSmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>

Encapsulates Ambit SMARTS parser.

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected SMARTSPropertiesReader	reader
protected SmartsManager	sman
protected boolean	useCDKIsomorphism

Fields inherited from class ambit2.smarts.query.AbstractSmartsPattern

hint, logger, name, negate, smarts

Constructor Summary

Constructors

Constructor and Description
SmartsPatternAmbit()
SmartsPatternAmbit(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
SmartsPatternAmbit(String smarts)
SmartsPatternAmbit(String smarts, boolean negate, org.openscience.cdk.interfaces.IChemObjectBuilder builder)
SmartsPatternAmbit(String smarts, org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
String	getImplementationDetails()
org.openscience.cdk.interfaces.IAtomContainer	getMatchingStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainer	getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	getQuery()
int	hasSMARTSPattern(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	isUseCDKIsomorphism()
void	setSmarts(String smarts)
void	setUseCDKIsomorphism(boolean useCDKIsomorphism)
void	useMOEvPrimitive(boolean flag)

Methods inherited from class ambit2.smarts.query.AbstractSmartsPattern

equals, getHint, getName, getSmarts, getUniqueMatchingAtoms, isNegate, match, setHint, setName, setNegate, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

sman

protected transient SmartsManager sman

reader

protected transient SMARTSPropertiesReader reader

useCDKIsomorphism

protected boolean useCDKIsomorphism

Constructor Detail

SmartsPatternAmbit

public SmartsPatternAmbit()
                   throws SMARTSException

Throws:

SMARTSException

SmartsPatternAmbit

public SmartsPatternAmbit(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                   throws SMARTSException

Throws:

SMARTSException

SmartsPatternAmbit

public SmartsPatternAmbit(String smarts)
                   throws SMARTSException

Throws:

SMARTSException

SmartsPatternAmbit

public SmartsPatternAmbit(String smarts,
                          org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                   throws SMARTSException

Throws:

SMARTSException

SmartsPatternAmbit

public SmartsPatternAmbit(String smarts,
                          boolean negate,
                          org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                   throws SMARTSException

Throws:

SMARTSException

Method Detail

isUseCDKIsomorphism

public boolean isUseCDKIsomorphism()

setUseCDKIsomorphism

public void setUseCDKIsomorphism(boolean useCDKIsomorphism)

getQuery

public org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer getQuery()

getObjectToVerify

public org.openscience.cdk.interfaces.IAtomContainer getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)

getMatchingStructure

public org.openscience.cdk.interfaces.IAtomContainer getMatchingStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                   throws SMARTSException

Throws:

SMARTSException

hasSMARTSPattern

public int hasSMARTSPattern(org.openscience.cdk.interfaces.IAtomContainer mol)
                     throws SMARTSException

Throws:

SMARTSException

getImplementationDetails

public String getImplementationDetails()

setSmarts

public void setSmarts(String smarts)
               throws SMARTSException

Specified by:

setSmarts in interface ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>

Overrides:

setSmarts in class AbstractSmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>

Throws:

SMARTSException

useMOEvPrimitive

public void useMOEvPrimitive(boolean flag)
                      throws UnsupportedOperationException

Throws:

UnsupportedOperationException