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java.lang.Objectjava.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit
public class RuleSMARTSSubstructureAmbit
An IDecisionRule, making use of Ambit SMARTS parser. http://ambit.sourceforge.net/AMBIT2-LIBS/ambit2-smarts/index.html http://onlinelibrary.wiley.com/doi/10.1002/minf.201100028/abstract
Field Summary |
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Fields inherited from class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure |
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containsAllSubstructures, final_and_patch, smartsPatterns |
Fields inherited from class toxTree.tree.AbstractRule |
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changes, editable, ERR_STRUCTURENOTPREPROCESSED, examples, explanation, id, logger, MSG_NO, MSG_YES, no, residueIDHidden, title |
Fields inherited from interface toxTree.core.XMLSerializable |
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xmltag_CATEGORIES, xmltag_CATEGORY, xmltag_CATEGORYTHRESHOLD, xmltag_CLASS, xmltag_EXPLANATION, xmltag_ID, xmltag_METHOD, xmltag_METHODPARAMETER, xmltag_METHODS, xmltag_NAME, xmltag_RULE, xmltag_RULEEXAMPLE, xmltag_RULES, xmltag_TREEROOT |
Constructor Summary | |
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RuleSMARTSSubstructureAmbit()
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Method Summary | |
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ambit2.smarts.query.ISmartsPattern |
createSmartsPattern(java.lang.String smarts,
boolean negate)
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protected org.openscience.cdk.interfaces.IAtomContainer |
getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
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Methods inherited from class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure |
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addSubstructure, addSubstructure, addSubstructure, clearSubstructures, containsAllSubstructures, deleteSubstructure, equals, getImplementationDetails, getSelector, getSmartsPatterns, getSubstructure, initSingleSMARTS, isAPossibleHit, isImplemented, removeSingleSMARTS, setContainsAllSubstructures, setSmartsPatterns, setSubstructure, setSubstructure, verifyRule, verifyRule |
Methods inherited from class toxTree.tree.AbstractRule |
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addPropertyChangeListener, clearFlags, clone, createRule, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getTitle, hideResiduesID, isEditable, isResidueIDHidden, log, log, log, makeMolecule, removePropertyChangeListener, setEditable, setExampleMolecule, setExamples, setExplanation, setID, setNum, setTitle, toShallowXML, toString, toXML |
Methods inherited from class java.util.Observable |
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addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged |
Methods inherited from class java.lang.Object |
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finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public RuleSMARTSSubstructureAmbit()
Method Detail |
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protected org.openscience.cdk.interfaces.IAtomContainer getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
getObjectToVerify
in class AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
public ambit2.smarts.query.ISmartsPattern createSmartsPattern(java.lang.String smarts, boolean negate) throws ambit2.smarts.query.SMARTSException
ambit2.smarts.query.SMARTSException
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