toxtree.tree.cramer3.rules

Class RuleRingsSMARTSSubstituents

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.RuleRingsSMARTSSubstituents

All Implemented Interfaces:

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

Direct Known Subclasses:

RuleQ11, RuleQ14_A, RuleQ14_B, RuleQ25, RuleQ26

public abstract class RuleRingsSMARTSSubstituents
extends RuleSMARTSSubstructureAmbit

See Also:

Serialized Form

Field Summary

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
RuleRingsSMARTSSubstituents()

Method Summary

Modifier and Type	Method and Description
protected abstract boolean	analyze(org.openscience.cdk.interfaces.IRing r)
String	getImplementationDetails()
protected abstract boolean	process(int allowedSubstituents, int allsubstituents)
boolean	processRings(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
abstract boolean	substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)

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, verifyRule, 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

Constructor Detail

RuleRingsSMARTSSubstituents

public RuleRingsSMARTSSubstituents()

Method Detail

analyze

protected abstract boolean analyze(org.openscience.cdk.interfaces.IRing r)

substituentIsAllowed

public abstract boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a,
                                             int[] place)
                                      throws DecisionMethodException

Throws:

DecisionMethodException

processRings

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

Throws:

DecisionMethodException

process

protected abstract boolean process(int allowedSubstituents,
                                   int allsubstituents)

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails

Overrides:

getImplementationDetails in class AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>