toxtree.plugins.ames.rules

Class SA18_gen

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.rules.RuleAromatic

toxtree.plugins.ames.rules.SA18_gen

All Implemented Interfaces:

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

Direct Known Subclasses:

SA19_gen

public class SA18_gen
extends RuleAromatic
implements IAlertCounter

TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic)

Author:

nina

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
SA18_gen()

Method Summary

Modifier and Type	Method and Description
protected boolean	acceptRingSet(org.openscience.cdk.interfaces.IRingSet ringset, int heteroaromaticrings, int aromaticrings)
String	getImplementationDetails()
protected int	getNumberOfAromaticAtoms(org.openscience.cdk.interfaces.IRing ring)
void	incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
protected boolean	isAromaticRing(int aromaticAtoms, int allAtoms)
protected boolean	isHeterocyclic(org.openscience.cdk.interfaces.IRing ring)
boolean	isImplemented()
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Find essential rings through SSSRFinder.findEssentialRings.

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, 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

Constructor Detail

SA18_gen

public SA18_gen()

Method Detail

incrementCounter

public void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

incrementCounter in interface IAlertCounter

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails

Overrides:

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

isImplemented

public boolean isImplemented()

Specified by:

isImplemented in interface IDecisionRule

Overrides:

isImplemented in class RuleAromatic

Returns:

false if the rule is not implemented and true if it is

verifyRule

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

Find essential rings through SSSRFinder.findEssentialRings. This set of rings is uniquely defined. Split into set of fused rings. For each set of fused rings verify for each ring if it is composed of aromatic atoms only. If yes, the ring is considered aromatic and the counter for aromatic rings within this set of fused rings is incremented. If the ring is aromatic, it is verified if it contains an heteroaromatic atoms, and if yes, the counter for heteroaromatic rings is incremented. If the set of fused rings contains > 2 aromatic rings and no heteroaromatic rings, the rule returns true.

Specified by:

verifyRule in interface IDecisionRule

Overrides:

verifyRule in class RuleAromatic

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

isAromaticRing

protected boolean isAromaticRing(int aromaticAtoms,
                                 int allAtoms)

acceptRingSet

protected boolean acceptRingSet(org.openscience.cdk.interfaces.IRingSet ringset,
                                int heteroaromaticrings,
                                int aromaticrings)

getNumberOfAromaticAtoms

protected int getNumberOfAromaticAtoms(org.openscience.cdk.interfaces.IRing ring)

isHeterocyclic

protected boolean isHeterocyclic(org.openscience.cdk.interfaces.IRing ring)