toxtree.tree.cramer3.rules

Class RuleLactone

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>

toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit

toxtree.tree.cramer3.rules.RuleSMARTSSubstructureHydrolysis

toxtree.tree.cramer3.rules.RuleLactone

All Implemented Interfaces:

ambit2.smarts.query.ISmartsPatternFactory, Serializable, Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IRuleSMARTS, IRuleSMARTSubstructures

Direct Known Subclasses:

RuleQ9_C, RuleQ9_D

public abstract class RuleLactone
extends RuleSMARTSSubstructureHydrolysis

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	tag
protected String	tag_ring

Fields inherited from class toxtree.tree.cramer3.rules.RuleSMARTSSubstructureHydrolysis

reactor

Fields inherited from class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure

containsAllSubstructures, final_and_patch, smartsPatterns

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

Constructor Summary

Constructors

Constructor and Description
RuleLactone()

Method Summary

Modifier and Type	Method and Description
protected boolean	allowedRingsOfAtom(org.openscience.cdk.interfaces.IRingSet allrings, org.openscience.cdk.interfaces.IAtom atom)
String[][]	getSMARTS()
protected boolean	isFused(org.openscience.cdk.interfaces.IAtomContainer mol, String tag_ring, org.openscience.cdk.interfaces.IRingSet rings) if we have fused rings, the tag_ring will appear in more than one ring
protected org.openscience.cdk.interfaces.IRingSet	tagRings(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Methods inherited from class toxtree.tree.cramer3.rules.RuleSMARTSSubstructureHydrolysis

extraTest, getImplementationDetails, getReactor, getSmirks, verifyRule

Methods inherited from class toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit

createSmartsPattern, getObjectToVerify, hasRingsToProcess

Methods inherited from class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure

addSubstructure, addSubstructure, addSubstructure, clearSubstructures, containsAllSubstructures, deleteSubstructure, equals, getSelector, getSmartsPatterns, getSubstructure, initSingleSMARTS, isAPossibleHit, isImplemented, removeSingleSMARTS, setContainsAllSubstructures, setSmartsPatterns, setSubstructure, setSubstructure

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

Field Detail

tag

protected static final String tag

tag_ring

protected String tag_ring

Constructor Detail

RuleLactone

public RuleLactone()
            throws ambit2.smarts.query.SMARTSException

Throws:

ambit2.smarts.query.SMARTSException

Method Detail

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
                          org.openscience.cdk.interfaces.IAtomContainer selected)
                   throws DecisionMethodException

Overrides:

verifyRule in class RuleSMARTSSubstructureHydrolysis

Throws:

DecisionMethodException

getSMARTS

public String[][] getSMARTS()

tagRings

protected org.openscience.cdk.interfaces.IRingSet tagRings(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                    throws DecisionMethodException

Throws:

DecisionMethodException

allowedRingsOfAtom

protected boolean allowedRingsOfAtom(org.openscience.cdk.interfaces.IRingSet allrings,
                                     org.openscience.cdk.interfaces.IAtom atom)

isFused

protected boolean isFused(org.openscience.cdk.interfaces.IAtomContainer mol,
                          String tag_ring,
                          org.openscience.cdk.interfaces.IRingSet rings)
                   throws DecisionMethodException

if we have fused rings, the tag_ring will appear in more than one ring

Parameters:

mol -

tag_ring -

Returns:

Throws:

DecisionMethodException