toxTree.tree.rules.smarts
Class SmartsPattern
java.lang.Object
ambit2.smarts.query.AbstractSmartsPattern<joelib.molecule.JOEMol>
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
Fields inherited from class ambit2.smarts.query.AbstractSmartsPattern |
hint, name, negate, smarts |
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 |
joeSmartsPatern
protected transient joelib.smarts.JOESmartsPattern joeSmartsPatern
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
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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