mutant.rules
Class SA31a_nogen

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.SA31a_nogen
All Implemented Interfaces:
ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.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
static java.lang.Object[][] exclusion_rules
           
static java.lang.String[][] exclusion_rules_Hal
           
static java.lang.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 java.lang.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
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
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 java.lang.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 java.lang.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 java.lang.String[][] exclusion_rules_Hal

exclusion_rules

public static java.lang.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


Copyright © 2004-2012 Ideaconsult Ltd.. All Rights Reserved.