toxTree.tree.rules.smarts
Class SmartsPattern

java.lang.Object
  extended by ambit2.smarts.query.AbstractSmartsPattern<joelib.molecule.JOEMol>
      extended by toxTree.tree.rules.smarts.SmartsPattern
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPattern<joelib.molecule.JOEMol>, java.io.Serializable

public class SmartsPattern
extends ambit2.smarts.query.AbstractSmartsPattern<joelib.molecule.JOEMol>

Encapsulates Joelib SMARTS parser. JoeSmartsPattern is hidden, mainly to avoid some problems in XML serialization.

Author:
Nina Jeliazkova
See Also:
Serialized Form

Field Summary
protected  joelib.smarts.JOESmartsPattern joeSmartsPatern
           
 
Fields inherited from class ambit2.smarts.query.AbstractSmartsPattern
hint, name, negate, smarts
 
Constructor Summary
SmartsPattern()
           
SmartsPattern(java.lang.String smarts)
           
SmartsPattern(java.lang.String smarts, boolean negate)
           
 
Method Summary
 java.lang.String getImplementationDetails()
           
 org.openscience.cdk.interfaces.IAtomContainer getMatchingStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 joelib.molecule.JOEMol getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 org.openscience.cdk.isomorphism.matchers.QueryAtomContainer getQuery()
           
 java.lang.String getSmarts()
           
 java.util.List<java.util.List<java.lang.Integer>> getUniqueMatchingAtoms()
           
 int hasSMARTSPattern(joelib.molecule.JOEMol mol)
           
 void setSmarts(java.lang.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

joeSmartsPatern

protected transient joelib.smarts.JOESmartsPattern joeSmartsPatern
Constructor Detail

SmartsPattern

public SmartsPattern()
              throws ambit2.smarts.query.SMARTSException
Throws:
ambit2.smarts.query.SMARTSException

SmartsPattern

public SmartsPattern(java.lang.String smarts)
              throws ambit2.smarts.query.SMARTSException
Throws:
ambit2.smarts.query.SMARTSException

SmartsPattern

public SmartsPattern(java.lang.String smarts,
                     boolean negate)
              throws ambit2.smarts.query.SMARTSException
Throws:
ambit2.smarts.query.SMARTSException
Method Detail

getSmarts

public java.lang.String getSmarts()
Specified by:
getSmarts in interface ambit2.smarts.query.ISmartsPattern<joelib.molecule.JOEMol>
Overrides:
getSmarts in class ambit2.smarts.query.AbstractSmartsPattern<joelib.molecule.JOEMol>

setSmarts

public void setSmarts(java.lang.String smarts)
               throws ambit2.smarts.query.SMARTSException
Specified by:
setSmarts in interface ambit2.smarts.query.ISmartsPattern<joelib.molecule.JOEMol>
Overrides:
setSmarts in class ambit2.smarts.query.AbstractSmartsPattern<joelib.molecule.JOEMol>
Throws:
ambit2.smarts.query.SMARTSException

hasSMARTSPattern

public int hasSMARTSPattern(joelib.molecule.JOEMol mol)
                     throws ambit2.smarts.query.SMARTSException
Throws:
ambit2.smarts.query.SMARTSException

getObjectToVerify

public joelib.molecule.JOEMol getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)

getImplementationDetails

public java.lang.String getImplementationDetails()

getUniqueMatchingAtoms

public java.util.List<java.util.List<java.lang.Integer>> getUniqueMatchingAtoms()
                                                                         throws ambit2.smarts.query.SMARTSException
Specified by:
getUniqueMatchingAtoms in interface ambit2.smarts.query.ISmartsPattern<joelib.molecule.JOEMol>
Overrides:
getUniqueMatchingAtoms in class ambit2.smarts.query.AbstractSmartsPattern<joelib.molecule.JOEMol>
Throws:
ambit2.smarts.query.SMARTSException

getMatchingStructure

public org.openscience.cdk.interfaces.IAtomContainer getMatchingStructure(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                   throws java.lang.UnsupportedOperationException,
                                                                          ambit2.smarts.query.SMARTSException
Throws:
java.lang.UnsupportedOperationException
ambit2.smarts.query.SMARTSException

getQuery

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

useMOEvPrimitive

public void useMOEvPrimitive(boolean flag)
                      throws java.lang.UnsupportedOperationException
Throws:
java.lang.UnsupportedOperationException


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