toxTree.tree.rules.smarts
Class RuleSMARTSubstructureCDK
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK
- All Implemented Interfaces:
- ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IRuleSMARTSubstructures
- Direct Known Subclasses:
- QSAR6Applicable, Rule14Aliphatic_glycerol_monoethers, Rule15, Rule16, Rule17, Rule18, Rule19, Rule20, Rule21, Rule23, Rule24, Rule25, Rule26, Rule27, Rule28, Rule29, Rule31, Rule32, Rule34, Rule35, Rule36, Rule37, RuleABUnsaturatedAldehyde, RuleAromaticDiazo, RuleDerivedAromaticAmines, RulePhenols, StructureAlertCDK
public class RuleSMARTSubstructureCDK
- extends AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
An IDecisionRule, making use of CDK SMARTS parser.
- Author:
- Nina Jeliazkova nina@acad.bg
- See Also:
- Serialized Form
Fields inherited from class toxTree.tree.AbstractRule |
changes, editable, ERR_STRUCTURENOTPREPROCESSED, examples, explanation, id, logger, MSG_NO, MSG_YES, no, residueIDHidden, title |
Fields inherited from interface toxTree.core.XMLSerializable |
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 |
Method Summary |
ambit2.smarts.query.ISmartsPattern |
createSmartsPattern(java.lang.String smarts,
boolean negate)
|
protected org.openscience.cdk.interfaces.IAtomContainer |
getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
|
boolean |
verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
This is the core of a IDecisionRule behaviour. |
Methods inherited from class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure |
addSubstructure, addSubstructure, addSubstructure, clearSubstructures, containsAllSubstructures, deleteSubstructure, equals, getImplementationDetails, getSelector, getSmartsPatterns, getSubstructure, initSingleSMARTS, isAPossibleHit, isImplemented, removeSingleSMARTS, setContainsAllSubstructures, setSmartsPatterns, setSubstructure, setSubstructure, verifyRule |
Methods inherited from class toxTree.tree.AbstractRule |
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 |
addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged |
Methods inherited from class java.lang.Object |
finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
RuleSMARTSubstructureCDK
public RuleSMARTSubstructureCDK()
createSmartsPattern
public ambit2.smarts.query.ISmartsPattern createSmartsPattern(java.lang.String smarts,
boolean negate)
throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
getObjectToVerify
protected org.openscience.cdk.interfaces.IAtomContainer getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
- Specified by:
getObjectToVerify
in class AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
throws DecisionMethodException
- Description copied from interface:
IDecisionRule
- This is the core of a
IDecisionRule
behaviour. The method returns true
if the answer of the rule is YES for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer
and FALSE
if the answer of the rule is NO for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer
??
- Specified by:
verifyRule
in interface IDecisionRule
- Overrides:
verifyRule
in class AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
- Parameters:
mol
- org.openscience.cdk.interfaces.AtomContainer
- Returns:
- rule result, boolean
- Throws:
DecisionMethodException
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