mic.rules

Class SA2

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

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

toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK

toxTree.tree.rules.StructureAlertCDK

mic.rules.SA2

All Implemented Interfaces:

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

public class SA2
extends StructureAlertCDK

SA2

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>	prescreenPhosphonic
protected ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>	prescreenSulphonic
static String	SA2_phosphonic
static String	SA2_sulphonic
static String[][]	substituents

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
SA2() Alkyl (C<5) or benzyl ester of sulphonic or phosphonic acid.

Method Summary

Modifier and Type	Method and Description
protected boolean	isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject) Simple prescreening

Methods inherited from class toxTree.tree.rules.StructureAlertCDK

getImplementationDetails, incrementCounter, verifyRule

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

createSmartsPattern, getObjectToVerify

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

addSubstructure, addSubstructure, addSubstructure, clearSubstructures, containsAllSubstructures, deleteSubstructure, equals, getSelector, getSmartsPatterns, getSubstructure, initSingleSMARTS, 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

Field Detail

SA2_sulphonic

public static String SA2_sulphonic

SA2_phosphonic

public static String SA2_phosphonic

prescreenSulphonic

protected ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer> prescreenSulphonic

prescreenPhosphonic

protected ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer> prescreenPhosphonic

substituents

public static String[][] substituents

Constructor Detail

SA2

public SA2()

Alkyl (C<5) or benzyl ester of sulphonic or phosphonic acid.

Method Detail

isAPossibleHit

protected boolean isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol,
                                 org.openscience.cdk.interfaces.IAtomContainer processedObject)
                          throws DecisionMethodException

Simple prescreening

Overrides:

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

Returns:

true if possibly a hit

Throws:

DecisionMethodException