mic.rules
Class SA28

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 mic.rules.SA28
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IAlertCounter, IRuleSMARTSubstructures

public class SA28
extends StructureAlertCDK

TODO - this is same as mutant.rules.SA28 -to reuse instead of copy

 [a;!$(a(a[A;!#1])(a[A;!#1]));!$(aa[CX3](=O)[OX2H1]);!$(aa[SX4](=[OX1])(=[OX1])([O-]));!$(aaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]))]!@[$([NX3;v3]([#1,CX4,CX3])([#1,CX4,CX3])),$([NX3;v3]([OX2H])([#1,CX4,CX3])),$([NX3;v3]([#1,CX4])OC=O)]
 

Author:
nina
See Also:
Serialized Form

Field Summary
static java.lang.String amine_and_SO3H
           
static java.lang.String[][] amines
           
static java.lang.Object[][] exclusion_rules
           
static int index_ortho_carboxylicacid
           
static int index_ortho_disubstitution
           
static int index_so3h_1
           
static int index_so3h_2
           
static int index_so3h_3
           
static int index_so3h_4
           
static java.lang.String SA28_title
           
 
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
SA28()
           
 
Method Summary
protected  boolean isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
          Returns true always.
 
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

SA28_title

public static java.lang.String SA28_title

amine_and_SO3H

public static java.lang.String amine_and_SO3H

index_ortho_disubstitution

public static int index_ortho_disubstitution

index_ortho_carboxylicacid

public static int index_ortho_carboxylicacid

index_so3h_1

public static int index_so3h_1

index_so3h_2

public static int index_so3h_2

index_so3h_3

public static int index_so3h_3

index_so3h_4

public static int index_so3h_4

amines

public static java.lang.String[][] amines

exclusion_rules

public static java.lang.Object[][] exclusion_rules
Constructor Detail

SA28

public SA28()
     throws ambit2.smarts.query.SMARTSException
Throws:
ambit2.smarts.query.SMARTSException
Method Detail

isAPossibleHit

protected boolean isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol,
                                 org.openscience.cdk.interfaces.IAtomContainer processedObject)
                          throws DecisionMethodException
Description copied from class: AbstractRuleSmartSubstructure
Returns true always. Override to apply simple prescreening for the rule;

Overrides:
isAPossibleHit in class AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
Returns:
Throws:
DecisionMethodException


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