toxTree.core
Interface IDecisionRule

All Superinterfaces:
java.lang.Cloneable, java.io.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, 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, RuleAcidAnhydrides, RuleAcidImides, RuleAcrylicAcids, RuleAcrylicAndMethacrylicEsters, RuleAcyclicAcetalEsterOfQ30, RuleAlcohol, RuleAlcohols, RuleAldehyde, RuleAldehyde, RuleAldehydes, RuleAlertsAche, RuleAlertsClass1, RuleAlertsClass2, RuleAlertsClass3, RuleAlertsCNS, RuleAlertsForCarcinogenicity, RuleAlertsForFunc, RuleAlertsForGenotoxicCarcinogenicity, RuleAlertsForMIC, RuleAlertsNarcosis1_1_1, RuleAlertsNarcosis1_1_1_1, RuleAlertsNarcosis1_1_2, 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, RuleAromaticAmines, RuleAromaticAzo, RuleAromaticDiazo, RuleAromaticHalogen, RuleAromaticNGroups, RuleAromaticNitro, RuleAromaticSulphonicAcid, RuleArylMethylHalide, RuleAziridine, RuleAzo, RuleAzoGroup, RuleBenzene, RuleBenzeneAnalogues, RuleBenzylHalides, RuleBetaLactones, RuleC10_C20AliphaticAlcohols, RuleCarbamoylHalide, RuleCarbohydrate, RuleCatecholsResorcinolsHydroquinones, RuleCommonComponentOfFood, RuleCommonTerpene, RuleCyanoGroupOnMoreThanEightAtomsChain, RuleCyclopropaneEtc, RuleDACancerogenicityAromaticAmines, RuleDAMutagenicityABUnsaturatedAldehydes, RuleDAMutagenicityAromaticAmines, 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, 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, RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts, RuleReadilyHydrolised, RuleReadilyHydrolysed29, RuleReadilyHydrolysedMononuclear, RuleReadilyHydrolysedPO4, RuleReadilyHydrolysedToCommonterpene, RuleRingAllowedSubstituents, RuleRingComplexSubstituents30, RuleRingMainStrucSubstituents, RuleRingOtherThanAllowedSubstituents, RuleRings, RuleRingSubstituents, RuleRingsWithSubstituents, RuleRingWithSubstituents, RuleSimplyBranchedAliphaticHydrocarbon, RuleSkinSensitisationAlerts, RuleSMARTSSubstructureAmbit, 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, SA10, SA10_gen, SA11, SA11_gen, SA12, SA12_gen, SA13, SA13_gen, SA14, SA14_gen, SA15, SA15_gen, SA16, SA16_gen, SA17_nogen, SA18, SA18_gen, SA19, SA19_gen, SA2, SA2_gen, SA20_nogen, SA21, SA21_gen, SA22, SA22_gen, SA23, SA23_gen, SA24, SA24_gen, SA25, SA25_gen, SA26, SA26_gen, SA27, SA27_gen, SA28, SA28_gen, SA28bis, SA28bis_gen, SA28ter, SA28ter_gen, SA29, SA29_gen, SA3, SA3_gen, SA30, SA30_gen, SA31a_nogen, SA31b_nogen, SA31c_nogen, SA32, SA33, SA34, SA35, SA36, SA37_gen, SA38_gen, SA39_gen_and_nogen, SA4, 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, SA50_nogen, SA51_nogen, SA52_nogen, SA53_nogen, SA54_nogen, SA55_nogen, SA56_nogen, SA6, SA6_gen, SA7, SA7_gen, SA8, SA8_gen, SA9, SA9_gen, ShiffBaseRule, ShiffBaseRule, ShiffBaseRule, SkinSensitisationRule, SMARTCYPRuleHigherRank, SMARTCYPRuleRank1, SMARTCYPRuleRank2, SMARTCYPRuleRank3, SN1Rule, SN2Rule, SN2Rule, SN2Rule, SNARRule, SNARRule, StructureAlert, StructureAlertAmbit, StructureAlertCDK, UserInputABUnsaturatedAldehyde, UserInputAromaticAmine, UserInputRule, VerifyAlertsAche, VerifyAlertsCNS, VerifyAlertsDNABinding, VerifyAlertsGenotoxic, VerifyAlertsNarcosis1, VerifyAlertsNarcosis2, VerifyAlertsNarcosis3, VerifyAlertsNongenotoxic, VerifyAlertsProteinBinding, VerifyAlertsReactive, VerifyAlertsSkinSensitisation, VerifyAlertsUncouplers

public interface IDecisionRule
extends java.io.Serializable, java.lang.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
 void addPropertyChangeListener(java.beans.PropertyChangeListener l)
           
 void clearFlags(org.openscience.cdk.interfaces.IAtomContainer mol)
          When rules analyze a molecule, a set of properties are set.
 java.lang.Object clone()
           
 IDecisionRuleEditor getEditor()
          Each rule provides an editor, which is a class implementing IDecisionRuleEditor.
 org.openscience.cdk.interfaces.IMolecule 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
 java.lang.String getExplanation()
          Rule explanation is an arbitrary text, could be multiline and may contain html tags.
 java.lang.String getID()
          Rule identifier is an arbitrary string, preferably short one
 int getNum()
           
 ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
           
 java.lang.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(java.beans.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(java.lang.String message)
          Sets rule explanation
 void setID(java.lang.String id)
          Sets rule identifier
 void setNum(int no)
           
 void setTitle(java.lang.String name)
          Sets rule name
 java.lang.String toString()
           
 boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          This is the core of a IDecisionRule behaviour.
 

Method Detail

getID

java.lang.String getID()
Rule identifier is an arbitrary string, preferably short one

Returns:
the rule identifier

setID

void setID(java.lang.String id)
Sets rule identifier

Parameters:
id -

getNum

int getNum()

setNum

void setNum(int no)

getTitle

java.lang.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(java.lang.String name)
Sets rule name

Parameters:
name -

getExplanation

java.lang.String getExplanation()
Rule explanation is an arbitrary text, could be multiline and may contain html tags.

Returns:
explanation

setExplanation

void setExplanation(java.lang.String message)
Sets rule explanation

Parameters:
message -

getExampleMolecule

org.openscience.cdk.interfaces.IMolecule 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

java.lang.String toString()
Overrides:
toString in class java.lang.Object

addPropertyChangeListener

void addPropertyChangeListener(java.beans.PropertyChangeListener l)

removePropertyChangeListener

void removePropertyChangeListener(java.beans.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

java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException
Throws:
java.lang.CloneNotSupportedException

isEditable

boolean isEditable()

setEditable

void setEditable(boolean value)

getSelector

ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()


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