mic.rules

Class SA28

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.SA28

All Implemented Interfaces:

ambit2.smarts.query.ISmartsPatternFactory, Serializable, 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

Fields

Modifier and Type	Field and Description
static String	amine_and_SO3H
static String[][]	amines
static 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 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

Constructors

Constructor and Description
SA28()

Method Summary

Modifier and Type	Method and Description
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 String SA28_title

amine_and_SO3H

public static 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 String[][] amines

exclusion_rules

public static 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