|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectjava.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
public class SA31a_nogen
TODO Verify how many level of recursive smarts are supported TODO verify what's wrong with matching c;R
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 |
---|
public static java.lang.String SA31a_title
public static int index_singlering
public static int index_nitro_aromatic
public static int index_primary_aromatic_amine
public static int index_hydroxyl_amine
public static int index_hydroxyl_amineester
public static int index_monodialkylamine1
public static int index_monodialkylamine2
public static int index_monodialkylamine3
public static int index_nacymamine
public static int index_diazo
public static int index_biphenyl
public static int index_diphenyl1
public static int index_diphenyl2
public static java.lang.String hydroxyl
public static java.lang.String[][] exclusion_rules_Hal
public static java.lang.Object[][] exclusion_rules
Constructor Detail |
---|
public SA31a_nogen() throws ambit2.smarts.query.SMARTSException
ambit2.smarts.query.SMARTSException
Method Detail |
---|
protected boolean isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject) throws DecisionMethodException
AbstractRuleSmartSubstructure
isAPossibleHit
in class AbstractRuleSmartSubstructure<org.openscience.cdk.interfaces.IAtomContainer>
DecisionMethodException
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |