IDecisionRule (Toxtree 3.1.0 API)

All Superinterfaces:

Cloneable, Serializable

All Known Subinterfaces:

IRuleRange, IRuleSubstructures, IRuleValue

All Known Implementing Classes:

AbstractRule, AbstractRuleHilightHits, AbstractRuleSmartSubstructure, AcylTransferRule, AcylTransferRule, AcylTransferRule, DecisionNode, DNABindingRule, FG, FG1, FG10, FG11, FG12, FG13, FG14, FG15, FG16, FG17, FG18, FG19, FG2, FG20, FG21, FG22, FG23_1, FG23_2, FG23_3, FG23_4, FG23_5, FG23_6, FG23_7, FG23_8, FG23_LS, FG24_1, FG24_2, FG24_3, FG24_LS, FG25, FG26, FG27, FG28, FG29, FG3_1, FG3_2, FG3_LS, FG30, FG31_1, FG31_2, FG31_3, FG31_4, FG31_5, FG31_6, FG31_7, FG31_8, FG31_9, FG31_LS, FG32, FG33_1, FG33_2, FG33_3, FG33_4, FG33_5, FG33_6, FG33_7, FG33_8, FG33_LS, FG34_1, FG34_2, FG34_LS, FG35_1, FG35_10, FG35_11, FG35_12, FG35_13, FG35_2, FG35_3, FG35_4, FG35_5, FG35_6, FG35_7, FG35_8, FG35_9, FG35_LS, FG36, FG37_1, FG37_2, FG37_3, FG37_4, FG37_LS, FG38, FG39, FG4, FG4_1, FG4_2, FG4_LS, FG40, FG41_1, FG41_2, FG41_3, FG41_4, FG41_5, FG41_LS, FG42, FG43, FG44, FG45, FG46_1, FG46_2, FG46_LS, FG47, FG48_1, FG48_2, FG48_LS, FG49, FG5, FG50_1, FG50_2, FG50_3, FG50_LS, FG51_1, FG51_2, FG51_3, FG51_LS, FG52_1, FG52_2, FG52_3, FG52_LS, FG53_1, FG53_2, FG53_3, FG53_LS, FG54, FG55, FG56, FG57, FG58, FG59, FG6, FG60, FG61, FG62, FG63, FG64, FG65, FG66, FG67, FG68, FG69, FG7, FG70, FG71, FG72, FG73, FG74_1, FG74_2, FG74_3, FG74_4, FG74_5, FG74_6, FG74_7, FG74_LS, FG75_1, FG75_2, FG75_3, FG75_4, FG75_LS, FG76, FG77, FG78_1, FG78_2, FG78_3, FG78_4, FG78_LS, FG79_1, FG79_2, FG79_3, FG79_4, FG79_LS, FG8, FG80_1, FG80_2, FG80_LS, FG81_1, FG81_2, FG81_3, FG81_4, FG81_LS, FG82_1, FG82_2, FG82_3, FG82_4, FG82_LS, FG83_1, FG83_2, FG83_3, FG83_4, FG83_LS, FG84_1, FG84_2, FG84_LS, FG85, FG86, FG87, FG88, FG89, FG9, FG90, Find, KroesRule10, KroesRule11, KroesRule12, KroesRule2, KroesRule3, KroesRule4, KroesRule5, KroesRule6, KroesRule7, KroesRule8, KroesRule9, LinearDiscriminantRule, MetaboliteGenerator, MichaelAcceptorRule, MichaelAcceptorRule, MichaelAcceptorRule, MultiLabelDecisionNode, PB29, PB30, ProteinBindingRule, QSAR6Applicable, QSAR6Applicable, Rule_areadepthratio, Rule_high_AreaDepthRatio, Rule_high_pKa, Rule_highLogP, Rule_highVolume, Rule_lowVolume, Rule_volume, Rule01, Rule03, Rule1, Rule1, Rule10A, Rule10B, Rule11, Rule11, Rule11, Rule12, Rule12A, Rule12B, Rule13, Rule13, Rule13_AliphaticMonoalcohols, Rule13A, Rule13B, Rule14, Rule14, Rule14, Rule141, Rule142, Rule143, Rule144, Rule14Aliphatic_glycerol_monoethers, Rule15, Rule15, Rule15, Rule151, Rule152, Rule153, Rule154, Rule16, Rule16, Rule16, Rule161, Rule17, Rule17, Rule17, Rule171, Rule18, Rule18, Rule19, Rule19, Rule2, Rule20, Rule20, Rule21, Rule21, Rule21, Rule22, Rule22, Rule22, Rule23, Rule23, Rule23, Rule24, Rule24, Rule24, Rule25, Rule25, Rule25, Rule26, Rule26, Rule27, Rule27, Rule28, Rule28, Rule29, Rule29, Rule3, Rule30, Rule30, Rule31, Rule31, Rule32, Rule32, Rule32, Rule33, Rule33, Rule34, Rule34, Rule35, Rule35, Rule36, Rule36, Rule37, Rule37, Rule38, Rule38, Rule39, Rule3FuncGroups, Rule3MemberedHeterocycle, Rule4, Rule4, Rule4A, Rule4B, Rule5, Rule6, Rule7, Rule8, Rule8, Rule9, Rule9A, Rule9B, RuleA_Lactams, RuleABUnsaturatedAldehyde, RuleABUnsaturatedAldehyde, RuleAcidAnhydrides, RuleAcidImides, RuleAcrylicAcids, RuleAcrylicAndMethacrylicEsters, RuleAcyclicAcetalEsterOfQ30, RuleAlcohol, RuleAlcohols, RuleAldehyde, RuleAldehyde, RuleAldehydes, RuleAlertsAche, RuleAlertsAmes, RuleAlertsClass1, RuleAlertsClass2, RuleAlertsClass3, RuleAlertsCNS, RuleAlertsForAmesMutagenicity, RuleAlertsForCarcinogenicity, RuleAlertsForFunc, RuleAlertsForGenotoxicCarcinogenicity, RuleAlertsForGenotoxicCarcinogenicity, RuleAlertsForMIC, RuleAlertsForNewAmesMutagenicity, RuleAlertsNarcosis1_1_1, RuleAlertsNarcosis1_1_1_1, RuleAlertsNarcosis1_1_2_1, RuleAlertsNarcosis1_1_2_3, RuleAlertsNarcosis2_2_1, RuleAlertsNarcosis3, RuleAlertsNongenotoxicCarcinogenicity, RuleAlertsReactive, RuleAlertsUncouplers, RuleAliphaticCyclicNoBranches, RuleAliphaticEther, RuleAliphaticFusedRingsNonBranched, RuleAliphaticSaturatedAcidsAndHalogenatedAcids, RuleAliphaticWithSomeFuncGroups, RuleAlkylAldehyde, RuleAlkylAlkanolAmines, RuleAlkylHydrazine, RuleAlkylPhosphonate, RuleAllAllowedElements, RuleAllSubstructures, RuleAlphaAlkynes, RuleAlphaHalogenatedAmidesAndThioamides, RuleAlyphaticSulphonicAcids, RuleAmine, RuleAminoAcids, RuleAnySubstituents, RuleAnySubstructure, RuleAnySubstructureCounter, RuleAqueousSolubility, RuleAqueousSolubility, RuleAqueousSolubility_10_2, RuleAqueousSolubility_10_5, RuleAqueousSolubility_11_7, RuleAqueousSolubility_8_3, RuleAqueousSolubility_8_4, RuleAqueousSolubility_9_3, RuleAqueousSolubility1, RuleAromatic, RuleAromaticAldehyde, RuleAromaticAmineNoSulfonicGroup, RuleAromaticAmineNoSulfonicGroup, RuleAromaticAmines, RuleAromaticAzo, RuleAromaticDiazo, RuleAromaticDiazo, RuleAromaticHalogen, RuleAromaticNGroups, RuleAromaticNitro, RuleAromaticSulphonicAcid, RuleArylMethylHalide, RuleAziridine, RuleAzo, RuleAzoGroup, RuleBenzene, RuleBenzeneAnalogues, RuleBenzylHalides, RuleBetaLactones, RuleC10_C20AliphaticAlcohols, RuleCarbamoylHalide, RuleCarbohydrate, RuleCatecholsResorcinolsHydroquinones, RuleCommonComponentOfFood, RuleCommonTerpene, RuleCyanoGroupOnMoreThanEightAtomsChain, RuleCyclopropaneEtc, RuleDACancerogenicityAromaticAmines, RuleDAMutagenicityABUnsaturatedAldehydes, RuleDAMutagenicityABUnsaturatedAldehydes, RuleDAMutagenicityAromaticAmines, RuleDAMutagenicityAromaticAmines, RuleDerivedAromaticAmines, RuleDerivedAromaticAmines, RuleDescriptor, RuleDescriptorRange, RuleDi_Tri_Nitrobenzenes, RuleDivalentSulphur, RuleDNABindingAlerts, RuleElements, RuleElementsCounter, RuleEpoxide, RuleEpoxide, RuleEpoxides, RuleEsters, RuleEther, RuleEthyleneGlycolEthers, RuleFormaldehyde, RuleFreeABUnsaturatedHetero, RuleFuran, RuleHalide, RuleHalogenatedAlkanesAndAlkenes, RuleHalogenSubstitutedBranched, RuleHalonitrobenzene, RuleHasOnlyC_H_O, RuleHasOnlyC_H_O, RuleHasOnlyC_H_O_Halogen, RuleHasOnlyC_H_O_Halogen, RuleHasOnlyC_H_O_N, RuleHasOnlyC_H_O_N, RuleHasOnlyC_H_O_N_Halogen, RuleHasOnlyC_H_O_N_Halogen, RuleHasOnlyC_H_O_N_S, RuleHasOnlyC_H_O_N_S, RuleHasOnlySaltSulphonateSulphate, RuleHasOnlySaltSulphonateSulphate, RuleHasOtherThanC_H_O_N_S2, RuleHeteroaromatic, RuleHeterocycle, RuleHeterocyclic, RuleHeterocyclicComplexSubstituents, RuleHydrazine, RuleHydroPeroxides, RuleIminomethyl, RuleInitAlertCounter, RuleIonicGroups, RuleIsAromatic, RuleIsCommonTerpene, RuleIsHeterocyclic, RuleIsOpenChain, RuleKetenes, RuleKetone, RuleKetone, RuleKetoneAlcoholEtc, RuleKetones, RuleKroesFig1Q1, RuleLactone, RuleLactoneOrCyclicDiester, RuleLactonesFusedOrUnsaturated, RuleLactonesFusedOrUnsaturated, RuleLipidSolubility, RuleLipidSolubility, RuleLipidSolubility_10_4, RuleLipidSolubility_9_1, RuleLipinski5, RuleLogP, RuleLogP, RuleLogP_10_1, RuleLogP_11_4, RuleLogP_11_5, RuleLogP_11_6, RuleLogP_12_4, RuleLogP_9_4, RuleLogP1, RuleLogPRange, RuleManyAromaticRings, RuleManyAromaticRings14, RuleManyAromaticRings28, RuleMelting_Point_11_3, RuleMeltingPoint, RuleMeltingPoint_11_2, RuleMeltingPoint_12_3, RuleMeltingPoint_8_1, RuleMolecularMassRange, RuleMolWeight, RuleMolWeight, RuleMolWeight_10_3, RuleMolWeight_11_1, RuleMolweight_12_1, RuleMolWeight_12_2, RuleMolWeight_8_2, RuleMolWeight_9_2, RuleMonocarbocyclic, RuleMonocycloalkanoneEtc, RuleMoreThanTwoHydroxyOnAromaticRing, RuleNChloramine, RuleNHydroxy, RuleNitrile, RuleNitro, RuleNitrogenMustard, RuleNitrosamine, RuleNitroso, RuleNMethylol, RuleNNitroso, RuleNormalBodyConstituent, RuleNormalBodyConstituent, RuleNOxide, RuleNucleosides, RuleOandPQuinones, RuleOneHalogenOnUnbranched, RuleOnlyAllowedSubstructures, RuleOnlyAllowedSubstructuresCounter, RuleOnlyFuncGroupsQ30, RuleOpenChain, RulePhenols, RulePhosphateEsters, RulePhosphoricGroups, RuleprimaryAlkylHalide, RulePropiolactone, RuleProteinBindingAlerts, RulePyridineRing, RuleQ1, RuleQ10, RuleQ11, RuleQ12, RuleQ13, RuleQ14_A, RuleQ14_B, RuleQ15, RuleQ16, RuleQ17, RuleQ18_AI, RuleQ18_JM, RuleQ19, RuleQ2, RuleQ20, RuleQ21, RuleQ22, RuleQ23, RuleQ24, RuleQ25, RuleQ26, RuleQ27, RuleQ28, RuleQ29, RuleQ3, RuleQ4, RuleQ4A, RuleQ5, RuleQ6, RuleQ7, RuleQ8, RuleQ9_A, RuleQ9_B, RuleQ9_C, RuleQ9_D, RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts, RuleReadilyHydrolised, RuleReadilyHydrolysed29, RuleReadilyHydrolysedMononuclear, RuleReadilyHydrolysedPO4, RuleReadilyHydrolysedToCommonterpene, RuleRingAllowedSubstituents, RuleRingComplexSubstituents30, RuleRingMainStrucSubstituents, RuleRingOtherThanAllowedSubstituents, RuleRings, RuleRingsSMARTSSubstituents, RuleRingSubstituents, RuleRingsWithSubstituents, RuleRingWithSubstituents, RuleSimplyBranchedAliphaticHydrocarbon, RuleSkinSensitisationAlerts, RuleSMARTSSubstructureAmbit, RuleSMARTSSubstructureHydrolysis, RuleSMARTSSubstructureTagged, RuleSMARTSubstructure, RuleSMARTSubstructureCDK, RuleSomeBenzeneDerivatives, RuleStructuresList, RuleSubstructures, RuleSufficientSulphonateGroups, RuleSurfaceTension, RuleTerminalIsopropylNonCyclic, RuleTerminalTertButyl, RuleTertiaryAmine, RuleToxicFunctionalGroups, RuleTriAndTetraHalogenatedBenzenes, RuleTriazineRing, RuleTrifluoromethyl, RuleTwoHalogensOnUnbranchedNonCyclic, RuleTwoOrMoreRings, RuleTwoTerminalDiaminoGroupsOnNonCyclic, RuleTwoTerminalDoubleBondsOnUnbranched, RuleUnchargedOrganophosphates, RuleUrethaneDerivatives, RuleVapourPressure, RuleVerifyAlertsCounter, RuleVerifyClass1Alerts, RuleVerifyClass2Alerts, RuleVerifyClass3Alerts, RuleVerifyIntake, RuleVerifyProperty, SA1, SA1_gen, SA1_gen, SA10, SA10_gen, SA10_gen, SA11, SA11_gen, SA11_gen, SA12, SA12_gen, SA12_gen, SA13, SA13_gen, SA13_gen, SA14, SA14_gen, SA14_gen, SA15, SA15_gen, SA15_gen, SA16, SA16_gen, SA16_gen, SA17_nogen, SA18, SA18_gen, SA18_gen, SA19, SA19_gen, SA19_gen, SA2, SA2_gen, SA2_gen, SA20_nogen, SA21, SA21_gen, SA21_gen, SA22, SA22_gen, SA22_gen, SA23, SA23_gen, SA23_gen, SA24, SA24_gen, SA24_gen, SA25, SA25_gen, SA25_gen, SA26, SA26_gen, SA26_gen, SA27, SA27_gen, SA27_gen, SA28, SA28_gen, SA28_gen, SA28bis, SA28bis_gen, SA28bis_gen, SA28ter, SA28ter_gen, SA28ter_gen, SA29, SA29_gen, SA29_gen, SA3, SA3_gen, SA3_gen, SA30, SA30_gen, SA30_gen, SA31a_nogen, SA31b_nogen, SA31c_nogen, SA32, SA33, SA34, SA35, SA36, SA37_gen, SA37_gen, SA38_gen, SA38_gen, SA39_gen_and_nogen, SA39_gen_and_nogen, SA4, SA4_gen, SA4_gen, SA40_nogen, SA41_nogen, SA42_nogen, SA43_nogen, SA44_nogen, SA45_nogen, SA46_nogen, SA47_nogen, SA48_nogen, SA49_nogen, SA5, SA5_gen, SA5_gen, SA50_nogen, SA51_nogen, SA52_nogen, SA53_nogen, SA54_nogen, SA55_nogen, SA56_nogen, SA57_Ames, SA58_Ames, SA59_Ames, SA6, SA6_gen, SA6_gen, SA60_Ames, SA61_Ames, SA62_Ames, SA63_Ames, SA64_Ames, SA65_Ames, SA66_Ames, SA67_Ames, SA68_Ames, SA69_Ames, SA7, SA7_gen, SA7_gen, SA8, SA8_gen, SA8_gen, SA9, SA9_gen, SA9_gen, ShiffBaseRule, ShiffBaseRule, ShiffBaseRule, SkinSensitisationRule, SMARTCYPRuleHigherRank, SMARTCYPRuleRank1, SMARTCYPRuleRank2, SMARTCYPRuleRank3, SN1Rule, SN2Rule, SN2Rule, SN2Rule, SNARRule, SNARRule, StructureAlert, StructureAlertAmbit, StructureAlertCDK, UserInputABUnsaturatedAldehyde, UserInputABUnsaturatedAldehyde, UserInputAromaticAmine, UserInputAromaticAmine, UserInputRule, VerifyAlertsAche, VerifyAlertsAmes, VerifyAlertsCNS, VerifyAlertsDNABinding, VerifyAlertsGenotoxic, VerifyAlertsGenotoxic, VerifyAlertsNarcosis1, VerifyAlertsNarcosis2, VerifyAlertsNarcosis3, VerifyAlertsNewAmes, VerifyAlertsNongenotoxic, VerifyAlertsNongenotoxic, VerifyAlertsProteinBinding, VerifyAlertsReactive, VerifyAlertsSkinSensitisation, VerifyAlertsUncouplers
```
public interface IDecisionRule
extends Serializable, Cloneable
```
An interface definition to represent a rule, that will be used in a IDecisionMethod. All classes, implementing a rule to be used in toxTree application should implement this interface.

Version:

0.1, 2005-5-2

Author:

Nina Jeliazkova nina@acad.bg

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`void`	`addPropertyChangeListener(PropertyChangeListener l)`
`void`	`clearFlags(org.openscience.cdk.interfaces.IAtomContainer mol)` When rules analyze a molecule, a set of properties are set.
`Object`	`clone()`
`IDecisionRuleEditor`	`getEditor()` Each rule provides an editor, which is a class implementing `IDecisionRuleEditor`.
`org.openscience.cdk.interfaces.IAtomContainer`	`getExampleMolecule(boolean ruleResult)` if ruleResult is TRUE, returns the example molecule if the rule is answered YES if ruleResult is FALSE, returns the example molecule if the rule is answered NO
`String`	`getExplanation()` Rule explanation is an arbitrary text, could be multiline and may contain html tags.
`String`	`getID()` Rule identifier is an arbitrary string, preferably short one
`int`	`getNum()`
`ambit2.rendering.IAtomContainerHighlights`	`getSelector()`
`String`	`getTitle()` Rule name is an arbitrary string, preferably one line, reflecting the essence of the rule (e.g.
`void`	`hideResiduesID(boolean hide)`
`boolean`	`isEditable()`
`boolean`	`isImplemented()`
`boolean`	`isResidueIDHidden()`
`void`	`removePropertyChangeListener(PropertyChangeListener l)`
`void`	`setEditable(boolean value)`
`void`	`setExampleMolecule(org.openscience.cdk.interfaces.IAtomContainer mol, boolean ruleResult)` Sets example molecule for the YES or NO answer of the rule
`void`	`setExplanation(String message)` Sets rule explanation
`void`	`setID(String id)` Sets rule identifier
`void`	`setNum(int no)`
`void`	`setTitle(String name)` Sets rule name
`String`	`toString()`
`boolean`	`verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)` This is the core of a `IDecisionRule` behaviour.

- Method Detail
  - getID
```
String getID()
```
    Rule identifier is an arbitrary string, preferably short one
    
    Returns:
    
    the rule identifier
  - setID
```
void setID(String id)
```
    Sets rule identifier
    
    Parameters:
    
    id -
  - getNum
```
int getNum()
```
  - setNum
```
void setNum(int no)
```
  - getTitle
```
String getTitle()
```
    Rule name is an arbitrary string, preferably one line, reflecting the essence of the rule
    (e.g. "Is aromatic")
    
    Returns:
    
    rule name
  - setTitle
```
void setTitle(String name)
```
    Sets rule name
    
    Parameters:
    
    name -
  - getExplanation
```
String getExplanation()
```
    Rule explanation is an arbitrary text, could be multiline and may contain html tags.
    
    Returns:
    
    explanation
  - setExplanation
```
void setExplanation(String message)
```
    Sets rule explanation
    
    Parameters:
    
    message -
  - getExampleMolecule
```
org.openscience.cdk.interfaces.IAtomContainer getExampleMolecule(boolean ruleResult)
                                                          throws DecisionMethodException
```
    if ruleResult is TRUE, returns the example molecule if the rule is answered YES if ruleResult is FALSE, returns the example molecule if the rule is answered NO
    
    Parameters:
    
    ruleResult -
    
    Returns:
    
    org.openscience.cdk.interfaces.Molecule
    
    Throws:
    
    {@link - DecisionMethodException}
    
    DecisionMethodException
  - setExampleMolecule
```
void setExampleMolecule(org.openscience.cdk.interfaces.IAtomContainer mol,
                        boolean ruleResult)
```
    Sets example molecule for the YES or NO answer of the rule
    
    Parameters:
    
    mol - org.openscience.cdk.interfaces.Molecule
    
    ruleResult -
  - clearFlags
```
void clearFlags(org.openscience.cdk.interfaces.IAtomContainer mol)
```
    When rules analyze a molecule, a set of properties are set. This method provides a way to clear the properties. Could be moved in a different class in a later release
    
    Parameters:
    
    mol - org.openscience.cdk.interfaces.Molecule
  - verifyRule
```
boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
            throws DecisionMethodException
```
    This is the core of a IDecisionRule behaviour. The method returns true if the answer of the rule is YES for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer and FALSE if the answer of the rule is NO for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer??
    
    Parameters:
    
    mol - org.openscience.cdk.interfaces.AtomContainer
    
    Returns:
    
    rule result, boolean
    
    Throws:
    
    {@link - DecisionMethodException}
    
    DecisionMethodException
  - toString
```
String toString()
```
    Overrides:
    
    toString in class Object
  - addPropertyChangeListener
```
void addPropertyChangeListener(PropertyChangeListener l)
```
  - removePropertyChangeListener
```
void removePropertyChangeListener(PropertyChangeListener l)
```
  - isImplemented
```
boolean isImplemented()
```
    Returns:
    
    false if the rule is not implemented and true if it is
  - hideResiduesID
```
void hideResiduesID(boolean hide)
```
  - isResidueIDHidden
```
boolean isResidueIDHidden()
```
  - getEditor
```
IDecisionRuleEditor getEditor()
```
    Each rule provides an editor, which is a class implementing IDecisionRuleEditor. The editor shall provide user interface for visualization and modification of various rule settings.
    
    Returns:
    
    IDecisionRuleEditor
  - clone
```
Object clone()
      throws CloneNotSupportedException
```
    Throws:
    
    CloneNotSupportedException
  - isEditable
```
boolean isEditable()
```
  - setEditable
```
void setEditable(boolean value)
```
  - getSelector
```
ambit2.rendering.IAtomContainerHighlights getSelector()
```

Interface IDecisionRule

Method Summary

Method Detail

getID

setID

getNum

setNum

getTitle

setTitle

getExplanation

setExplanation

getExampleMolecule

setExampleMolecule

clearFlags

verifyRule

toString

addPropertyChangeListener

removePropertyChangeListener

isImplemented

hideResiduesID

isResidueIDHidden

getEditor

clone

isEditable

setEditable

getSelector