ambit2.smarts.query

Class SmartsPatternCDK

java.lang.Object

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

ambit2.smarts.query.SmartsPatternCDK

All Implemented Interfaces:

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

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

Encapsulates CDK SMARTS parser.

Author:

Nina Jeliazkova nina@acad.bg

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.smiles.smarts.SMARTSQueryTool	sqt

Fields inherited from class ambit2.smarts.query.AbstractSmartsPattern

hint, logger, name, negate, smarts

Constructor Summary

Constructors

Constructor and Description
SmartsPatternCDK()
SmartsPatternCDK(String smarts)
SmartsPatternCDK(String smarts, boolean negate)

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()
String	getSmarts()
List<List<Integer>>	getUniqueMatchingAtoms() For backward compatibility
List<List<Integer>>	getUniqueMatchingAtoms(org.openscience.cdk.interfaces.IAtomContainer mol)
int	hasSMARTSPattern(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setSmarts(String smarts)
void	useMOEvPrimitive(boolean flag)

Methods inherited from class ambit2.smarts.query.AbstractSmartsPattern

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

Methods inherited from class java.lang.Object

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

Field Detail

sqt

protected transient org.openscience.cdk.smiles.smarts.SMARTSQueryTool sqt

Constructor Detail

SmartsPatternCDK

public SmartsPatternCDK()

SmartsPatternCDK

public SmartsPatternCDK(String smarts)
                 throws SMARTSException

Throws:

SMARTSException

SmartsPatternCDK

public SmartsPatternCDK(String smarts,
                        boolean negate)
                 throws SMARTSException

Throws:

SMARTSException

Method Detail

getQuery

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

getSmarts

public String getSmarts()

Specified by:

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

Overrides:

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

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

hasSMARTSPattern

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

Throws:

SMARTSException

getObjectToVerify

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

getImplementationDetails

public String getImplementationDetails()

getMatchingStructure

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

Throws:

SMARTSException

getUniqueMatchingAtoms

public List<List<Integer>> getUniqueMatchingAtoms(org.openscience.cdk.interfaces.IAtomContainer mol)
                                           throws SMARTSException

Throws:

SMARTSException

useMOEvPrimitive

public void useMOEvPrimitive(boolean flag)
                      throws UnsupportedOperationException

Throws:

UnsupportedOperationException

getUniqueMatchingAtoms

public List<List<Integer>> getUniqueMatchingAtoms()
                                           throws SMARTSException

For backward compatibility

Specified by:

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

Overrides:

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

Returns:

Throws:

SMARTSException