mutant.rules
Class SA2_gen

java.lang.Object
  extended by java.util.Observable
      extended by toxTree.tree.AbstractRule
          extended by toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
              extended by toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK
                  extended by toxTree.tree.rules.StructureAlertCDK
                      extended by mutant.rules.SA2_gen
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IAlertCounter, IRuleSMARTSubstructures

public class SA2_gen
extends StructureAlertCDK

SA2_gen

Author:
nina
See Also:
Serialized Form

Field Summary
protected  ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer> prescreenPhosphonic
           
protected  ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer> prescreenSulphonic
           
static java.lang.String SA2_phosphonic
           
static java.lang.String SA2_sulphonic
           
static java.lang.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
SA2_gen()
          Alkyl (C<5) or benzyl ester of sulphonic or phosphonic acid.
 
Method Summary
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 java.lang.String SA2_sulphonic

SA2_phosphonic

public static java.lang.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 java.lang.String[][] substituents
Constructor Detail

SA2_gen

public SA2_gen()
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


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