SA31a_nogen (Toxtree 3.1.0 API)

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
        
        mutant.rules.SA31a_nogen

All Implemented Interfaces:

ambit2.smarts.query.ISmartsPatternFactory, Serializable, Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IAlertCounter, IRuleSMARTSubstructures
```
public class SA31a_nogen
extends StructureAlertCDK
```
TODO Verify how many level of recursive smarts are supported TODO verify what's wrong with matching c;R

Author:

Nina Jeliazkova nina@acad.bg Modified Jan 5, 2008

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static Object[][]`	`exclusion_rules`
`static String[][]`	`exclusion_rules_Hal`
`static String`	`hydroxyl` Overlaps are accepted, except with the following alerts: NA_27, NA_28s (NA_28, NA_28bis, NA_28ter) and NA_29.
`static int`	`index_biphenyl`
`static int`	`index_diazo`
`static int`	`index_diphenyl1`
`static int`	`index_diphenyl2`
`static int`	`index_hydroxyl_amine`
`static int`	`index_hydroxyl_amineester`
`static int`	`index_monodialkylamine1`
`static int`	`index_monodialkylamine2`
`static int`	`index_monodialkylamine3`
`static int`	`index_nacymamine`
`static int`	`index_nitro_aromatic`
`static int`	`index_primary_aromatic_amine`
`static int`	`index_singlering`
`static String`	`SA31a_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
`SA31a_nogen()` The generated string is: [c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@!@c1ccccc1);!$(c!@!@!@c1ccccc1)]1[c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@!@c1ccccc1);!$(c!@!@!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@!@c1ccccc1);!$(c!@!@!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@!@c1ccccc1);!$(c!@!@!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@!@c1ccccc1);!$(c!@!@*!@c1ccccc1)][c]1([Cl,Br,F,I;!$([Cl,Br,I,F]cc[Cl,Br,I,F]);!$([Cl,Br,I,F]ccc[Cl,Br,I,F])])

Method Summary

All Methods Instance Methods Concrete Methods
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
  - SA31a_title
```
public static String SA31a_title
```
  - index_singlering
```
public static int index_singlering
```
  - index_nitro_aromatic
```
public static int index_nitro_aromatic
```
  - index_primary_aromatic_amine
```
public static int index_primary_aromatic_amine
```
  - index_hydroxyl_amine
```
public static int index_hydroxyl_amine
```
  - index_hydroxyl_amineester
```
public static int index_hydroxyl_amineester
```
  - index_monodialkylamine1
```
public static int index_monodialkylamine1
```
  - index_monodialkylamine2
```
public static int index_monodialkylamine2
```
  - index_monodialkylamine3
```
public static int index_monodialkylamine3
```
  - index_nacymamine
```
public static int index_nacymamine
```
  - index_diazo
```
public static int index_diazo
```
  - index_biphenyl
```
public static int index_biphenyl
```
  - index_diphenyl1
```
public static int index_diphenyl1
```
  - index_diphenyl2
```
public static int index_diphenyl2
```
  - hydroxyl
```
public static String hydroxyl
```
    Overlaps are accepted, except with the following alerts: NA_27, NA_28s (NA_28, NA_28bis, NA_28ter) and NA_29. This alert contains the exclusion of diphenyls and biphenyls. This imply that if in the same molecule there is a diphenyl or a biphenyl and a halogenated benzene, the latter will not be detected.
  - exclusion_rules_Hal
```
public static String[][] exclusion_rules_Hal
```
  - exclusion_rules
```
public static Object[][] exclusion_rules
```
- Constructor Detail
  - SA31a_nogen
```
public SA31a_nogen()
            throws ambit2.smarts.query.SMARTSException
```
    The generated string is: [c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)]1[c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)][c]1([Cl,Br,F,I;!$([Cl,Br,I,F]cc[Cl,Br,I,F]);!$([Cl,Br,I,F]ccc[Cl,Br,I,F])])
    
    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

Class SA31a_nogen

Field Summary

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

Fields inherited from class toxTree.tree.AbstractRule

Fields inherited from interface toxTree.core.XMLSerializable

Constructor Summary

Method Summary

Methods inherited from class toxTree.tree.rules.StructureAlertCDK

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

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

Methods inherited from class toxTree.tree.AbstractRule

Methods inherited from class java.util.Observable

Methods inherited from class java.lang.Object

Field Detail

SA31a_title

index_singlering

index_nitro_aromatic

index_primary_aromatic_amine

index_hydroxyl_amine

index_hydroxyl_amineester

index_monodialkylamine1

index_monodialkylamine2

index_monodialkylamine3

index_nacymamine

index_diazo

index_biphenyl

index_diphenyl1

index_diphenyl2

hydroxyl

exclusion_rules_Hal

exclusion_rules

Constructor Detail

SA31a_nogen

Method Detail

isAPossibleHit