toxtree.tree.cramer3.rules

Class RuleSMARTSSubstructureTagged

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.RuleSMARTSSubstructureTagged

All Implemented Interfaces:

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

Direct Known Subclasses:

RuleQ16, RuleQ18_AI, RuleQ18_JM, RuleQ4, RuleQ6

public class RuleSMARTSSubstructureTagged
extends RuleSMARTSSubstructureAmbit

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected String	tag

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
RuleSMARTSSubstructureTagged()

Method Summary

Modifier and Type	Method and Description
Map<String,Integer>	tagAtoms(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected, Map<String,ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>> smartsPatterns)
protected boolean	uniqueGroup(int allatoms, String key, Map<String,Integer> histogram)

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, getImplementationDetails, 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

Field Detail

tag

protected String tag

Constructor Detail

RuleSMARTSSubstructureTagged

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

Throws:

ambit2.smarts.query.SMARTSException

Method Detail

tagAtoms

public Map<String,Integer> tagAtoms(org.openscience.cdk.interfaces.IAtomContainer mol,
                                    org.openscience.cdk.interfaces.IAtomContainer selected,
                                    Map<String,ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>> smartsPatterns)
                             throws DecisionMethodException

Throws:

DecisionMethodException

uniqueGroup

protected boolean uniqueGroup(int allatoms,
                              String key,
                              Map<String,Integer> histogram)