Uses of Interface
toxTree.core.IDecisionRule

Packages that use IDecisionRule

Package	Description
com.molecularnetworks.start.rules
cramer2.categories
cramer2.rules
eye.rules	The package contains implementations of IDecisionRule rules for SicretRules decision tree.
mic.rules
michaelacceptors
michaelacceptors.rules
mutant.rules
sicret.rules	The package contains implementations of IDecisionRule rules for SicretRules decision tree.
structurefeatures.rules
toxTree.core	This packages contains only interface definitions, defining essential classes in toxTree application.
toxtree.plugins.ames.rules
toxtree.plugins.dnabinding.rules
toxtree.plugins.func.rules
toxtree.plugins.kroes.rules
toxtree.plugins.lewis.rules
toxtree.plugins.moa.rules
toxtree.plugins.proteinbinding.rules
toxtree.plugins.search.rules
toxtree.plugins.skinsensitisation.rules
toxtree.plugins.smartcyp.rules
toxTree.qsar
toxtree.tree
toxTree.tree	This packages contains abstract and default classes implementing the interfaces defined in toxTree.core package.
toxTree.tree.cramer	Class CramerRules is the implementation of Cramer rules [Cramer et al,78].
toxtree.tree.cramer3
toxtree.tree.cramer3.rules
toxTree.tree.rules	The package contains several generic implementations of IDecisionRule rules
toxTree.tree.rules.smarts	SMARTS support.
toxTree.ui
toxtree.ui.editors
toxtree.ui.tree	User interface for viewing and editing a decision tree IDecisionMethod
toxtree.ui.tree.actions	Actions (derived from AbstractAction for the decision tree user interface toxTree.ui.tree
toxtree.ui.tree.rules
verhaar.rules	The package contains implementations of IDecisionRule rules for VerhaarScheme decision tree.
verhaar.rules.helper

Uses of IDecisionRule in com.molecularnetworks.start.rules

Classes in com.molecularnetworks.start.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	RuleAlcohols Biodegradation rule for alcohols.
class	RuleAldehyde Biodegradation rule for aldehydes.
class	RuleAliphaticCyclicNoBranches Biodegradation rule for aliphatic cyclic chemicals with no branches.
class	RuleAliphaticEther Biodegradation rule for aliphatic ethers.
class	RuleAliphaticFusedRingsNonBranched Biodegradation rule for aliphatic compounds consisting of fused rings and no branches.
class	RuleAlyphaticSulphonicAcids Biodegradation rule for aliphatic sulphonic acids.
class	RuleAminoAcids Biodegradation rule for amino acids.
class	RuleAromaticHalogen Biodegradation rule for chemicals with and Iodine, Chlorine, or Fluorine atom attached to an aromatic atom.
class	RuleAromaticNGroups Biodegradation rule for chemicals with an NO2, NH2, or NH attached to an aromatic atom.
class	RuleAromaticSulphonicAcid Biodegradation rule for aromatic sulphonic acids.
class	RuleAzoGroup Biodegradation rule for chemicals containing an azo group.
class	RuleCyanoGroupOnMoreThanEightAtomsChain Biodegradation rule for chemicals containing a cyano group that is attached to a more than 8 atoms chain.
class	RuleEpoxide Biodegradation rule for chemicals containing an epoxide functional group.
class	RuleEsters Biodegradation rule for esters.
class	RuleFormaldehyde Biodegradation rule for formaldehyde.
class	RuleHalogenSubstitutedBranched Biodegradation rule for branched, halogen substituted chemicals.
class	RuleKetone Biodegradation rule for ketones.
class	RuleMoreThanTwoHydroxyOnAromaticRing Biodegradation rule for chemicals with more than two hydroxy substituents on an aromatic ring.
class	RuleNitrile Biodegradation rule for nitriles.
class	RuleNNitroso Biodegradation rule for chemicals with an N-Nitroso (-N-N=0) group.
class	RuleOneHalogenOnUnbranched Biodegradation rule for unbranched chemicals with one halogen substituent.
class	RulePhosphateEsters Biodegradation rule for phosphoric esters.
class	RulePyridineRing Biodegradation rule for pyridines.
class	RuleTerminalIsopropylNonCyclic Biodegradation rule for a non-cyclic chemical with at least two terminal isopropyl groups.
class	RuleTerminalTertButyl Biodegradation rule for chemicals with a terminal tert-butyl branch.
class	RuleTertiaryAmine Biodegradation rule for tertiary amines.
class	RuleTriazineRing Biodegradation rule for chemicals containing triazine ring.
class	RuleTrifluoromethyl Biodegradation rule for chemicals containing trifluoromethyl group (-CF3).
class	RuleTwoHalogensOnUnbranchedNonCyclic Biodegradation rule for unbranched, non-cyclic chemicals with two halogen substituents.
class	RuleTwoOrMoreRings Biodegradation rule for chemicals with two or more rings.
class	RuleTwoTerminalDiaminoGroupsOnNonCyclic Biodegradation rule for chemicals with two terminal diamino groups that are not attached to a cycle.
class	RuleTwoTerminalDoubleBondsOnUnbranched Biodegradation rule for unbranched chemicals with two terminal double-bonded carbons.

Uses of IDecisionRule in cramer2.categories

Methods in cramer2.categories with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	CramerTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in cramer2.rules

Classes in cramer2.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	RuleBenzeneAnalogues benzene analogues, with 0-6 substituents that consist of at most 1 heavy atom.
class	RuleDivalentSulphur Many kinds of divalent sulphurs, *-S-*, are synthetic and outside the scope of the Cramer dataset.
class	RuleFreeABUnsaturatedHetero free a,b-unsaturates heteroatoms (allyl amine), where free implies that the b carbon has 2 H's.
class	RuleReadilyHydrolysedPO4 cleaves PO4's from compounds, and analyses the remaining fragments Modified Dec, 2008
class	RuleUnchargedOrganophosphates Uncharged Organophosph(othion)ates Modified Dec, 2008

Uses of IDecisionRule in eye.rules

Classes in eye.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	Rule13_AliphaticMonoalcohols A Lactams
class	Rule14Aliphatic_glycerol_monoethers LipidSolubility < 4.0
class	Rule39
class	RuleAqueousSolubility_10_2 AqueousSolubility < 0.1
class	RuleAqueousSolubility_10_5 AqueousSolubility < 0.001
class	RuleAqueousSolubility_11_7
class	RuleAqueousSolubility_8_3
class	RuleAqueousSolubility_8_4
class	RuleAqueousSolubility_9_3 AqueousSolubility < 0.0001
class	RuleAqueousSolubility1
class	RuleLipidSolubility_10_4 LipidSolubility < 400.0
class	RuleLipidSolubility_9_1
class	RuleLogP_10_1 LogKow > 3.8
class	RuleLogP_11_4 LogKow < -2
class	RuleLogP_11_5 LogKow > 3.6
class	RuleLogP_11_6
class	RuleLogP_12_4 LogP > 4.5
class	RuleLogP_9_4 LogKow > 5.5
class	RuleLogP1
class	RuleMelting_Point_11_3 MeltingPoint > 200.0
class	RuleMeltingPoint_11_2 MeltingPoint > 200.0
class	RuleMeltingPoint_12_3 MeltingPoint > 65.0
class	RuleMeltingPoint_8_1
class	RuleMolWeight_10_3 Molecular Weight > 370.0
class	RuleMolWeight_11_1 Molecular Weight > 620
class	RuleMolweight_12_1 MoleculWeight > 370
class	RuleMolWeight_12_2 Molecular Weight > 280
class	RuleMolWeight_8_2
class	RuleMolWeight_9_2 MoleculWeight > 290.0

Uses of IDecisionRule in mic.rules

Classes in mic.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	PB29
class	PB30
class	RuleAlertsForMIC
class	SA1
class	SA10
class	SA11 Aliphatic and aromatic aldehydes.
class	SA12 Quinones
class	SA13
class	SA14
class	SA15
class	SA16
class	SA18 TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic)
class	SA19 If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic rings, the rule returns true.
class	SA2 SA2
class	SA21
class	SA22
class	SA23
class	SA24
class	SA25
class	SA26 Aromatic ring N-oxide.
class	SA27 Nitro aromatic (and more).
class	SA28 TODO - this is same as mutant.rules.SA28 -to reuse instead of copy
class	SA28bis Aromatic mono- and dialkylamine (with exceptions).
class	SA28ter Aromatic N-acyl amine.
class	SA29
class	SA3
class	SA30
class	SA32
class	SA33
class	SA34
class	SA35
class	SA36
class	SA4
class	SA5
class	SA6
class	SA7
class	SA8
class	SA9

Methods in mic.rules with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	MICTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in michaelacceptors

Methods in michaelacceptors with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	MATreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in michaelacceptors.rules

Classes in michaelacceptors.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	Rule1 TODO with StructureAlertAmbit [CH]#CC=O doesn't match COC(=O)C#C while C#CC=O matches COC(=O)C#C
class	Rule10A
class	Rule10B
class	Rule12A
class	Rule12B
class	Rule13A
class	Rule13B
class	Rule2
class	Rule3
class	Rule4A
class	Rule4B
class	Rule5
class	Rule6
class	Rule7
class	Rule9A
class	Rule9B

Uses of IDecisionRule in mutant.rules

Classes in mutant.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	QSAR6Applicable
class	RuleABUnsaturatedAldehyde Hits alfa-beta unsaturated aldehydes, exclude cyclic alfa-beta unsaturated aldehydes.
class	RuleAlertsForCarcinogenicity
class	RuleAlertsForGenotoxicCarcinogenicity
class	RuleAlertsNongenotoxicCarcinogenicity
class	RuleAromaticAmineNoSulfonicGroup
class	RuleAromaticDiazo
class	RuleDACancerogenicityAromaticAmines
class	RuleDAMutagenicityABUnsaturatedAldehydes Returns true if structure is predicted as mutagen , based on linear discriminant analysis over descriptors MR, LogP, LUMO.
class	RuleDAMutagenicityAromaticAmines Returns true if structure is predicted as mutagen , based on linear discriminant analysis.
class	RuleDerivedAromaticAmines
class	SA1_gen
class	SA10_gen
class	SA11_gen Aliphatic and aromatic aldehydes.
class	SA12_gen Quinones
class	SA13_gen
class	SA14_gen
class	SA15_gen
class	SA16_gen
class	SA17_nogen
class	SA18_gen TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic)
class	SA19_gen If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic rings, the rule returns true.
class	SA2_gen SA2_gen
class	SA20_nogen
class	SA21_gen
class	SA22_gen
class	SA23_gen
class	SA24_gen
class	SA25_gen
class	SA26_gen Aromatic ring N-oxide.
class	SA27_gen Nitro aromatic (and more).
class	SA28_gen [a;!$(a(a[A;!#1])(a[A;!#1]));!$(aa[CX3](=O)[OX2H1]);!$(aa[SX4](=[OX1])(=[OX1])([O-]));!$(aaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]))]!@[$([NX3;v3]([#1,CX4,CX3])([#1,CX4,CX3])),$([NX3;v3]([OX2H])([#1,CX4,CX3])),$([NX3;v3]([#1,CX4])OC=O)]
class	SA28bis_gen Aromatic mono- and dialkylamine (with exceptions).
class	SA28ter_gen Aromatic N-acyl amine.
class	SA29_gen
class	SA3_gen
class	SA30_gen
class	SA31a_nogen TODO Verify how many level of recursive smarts are supported TODO verify what's wrong with matching c;R
class	SA31b_nogen
class	SA31c_nogen
class	SA37_gen
class	SA38_gen
class	SA39_gen_and_nogen
class	SA4_gen
class	SA40_nogen
class	SA41_nogen
class	SA42_nogen
class	SA43_nogen
class	SA44_nogen
class	SA45_nogen
class	SA46_nogen
class	SA47_nogen
class	SA48_nogen
class	SA49_nogen
class	SA5_gen
class	SA50_nogen
class	SA51_nogen
class	SA52_nogen
class	SA53_nogen
class	SA54_nogen
class	SA55_nogen
class	SA56_nogen
class	SA6_gen
class	SA7_gen
class	SA8_gen
class	SA9_gen
class	UserInputABUnsaturatedAldehyde
class	UserInputAromaticAmine
class	VerifyAlertsGenotoxic
class	VerifyAlertsNongenotoxic

Methods in mutant.rules with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	MutantTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in sicret.rules

Classes in sicret.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	Rule12 VapourPressure < 0.0001
class	Rule18 AqueousSolubility < 0.1
class	Rule19 MoleculWeight > 370.0
class	Rule20 LipidSolubility < 400.0
class	Rule26 SurfaceTension > 62.0
class	Rule27 MeltingPoint > 120.0
class	Rule28 LogKow < 0.5
class	Rule29 Molecular Weight > 370.0
class	Rule30 Molecular Weight > 280.0
class	Rule8 LipidSolubility < 0.4
class	Rule9 MoleculWeight > 290.0
class	RuleA_Lactams A Lactams
class	RuleAcidAnhydrides Acid anhydrides.
class	RuleAcidImides Acid imides.
class	RuleAcrylicAcids Acrylic acids.
class	RuleAcrylicAndMethacrylicEsters Acrylic and methacrylic esters. SMARTS pattern [CX3](=[CX3])[CX3](=[OX1])[OX2]C.
class	RuleAldehydes Aldehydes. SMARTS pattern [$([CX3H][#6]),$([CX3H2])]=[OX1].
class	RuleAliphaticSaturatedAcidsAndHalogenatedAcids Aliphatic Saturated Acids and Halogenated Acids. SMARTS pattern [AR0][CX3](=O)[OX2H1] [ClX1,BrX1][C;H2][CX3](=O)[OX2H1]
class	RuleAlkylAlkanolAmines Alkyl Alkanol Amines. SMARTS pattern [OX2H][CX4][CX4][NX3;H2,H1;!$(NC=O)]
class	RuleAlphaAlkynes Alpha alkynes. SMARTS pattern [CX4][CX2]#[CX2]
class	RuleAlphaHalogenatedAmidesAndThioamides Alpha Halogenated Amides And Thioamides SMARTS pattern [CX3;$([R0][#6]Cl)](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] [#6](Cl)[CX3;!R](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
class	RuleAqueousSolubility AqueousSolubility < 0.1.
class	RuleAromaticAmines Aromatic Amines. SMARTS pattern [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
class	RuleBenzylHalides Benwyl halides. SMARTS pattern [ClX1,BrX1]Cc1ccccc1
class	RuleBetaLactones Beta lactones. SMARTS pattern [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
class	RuleC10_C20AliphaticAlcohols C10-C20 Aliphatic Alcohols. SMARTS pattern [AR0][OH]
class	RuleCarbamoylHalide Carbamoyl Halide.
class	RuleCatecholsResorcinolsHydroquinones Catechols, Resorcinols Hydroquinones.
class	RuleDi_Tri_Nitrobenzenes Di & Tri-Nitrobenzenes.
class	RuleEpoxides Epoxides. SMARTS pattern OX2r3]1[#6r3][#6r3]1
class	RuleEthyleneGlycolEthers Ethylene Glycol Ethers SMARTS pattern [OX2H][CX4;$([H1]),$(C[#6])][CX4;$([H1]),$(C[#6])][OX2H]
class	RuleHalogenatedAlkanesAndAlkenes Halogenated Alkanes And Alkenes SMARTS patterns [FX1,ClX1,BrX1,IX1][CX4H3] [FX1,ClX1,BrX1,IX1][CX4H2][#6] [FX1,ClX1,BrX1,IX1][CX3]=[CX3]
class	RuleHalonitrobenzene Halonitrobenzene.
class	RuleHasOnlyC_H_O Contains only these elements C,O.
class	RuleHasOnlyC_H_O_Halogen Contains only these elements C,O,Halogen.
class	RuleHasOnlyC_H_O_N Contains only these elements C,O,N.
class	RuleHasOnlyC_H_O_N_Halogen Contains only these elements C,O,N,Halogen.
class	RuleHasOnlyC_H_O_N_S Contains only these elements C,O,N,S,Halogen.
class	RuleHydroPeroxides HydroPeroxides. SMARTS pattern [OX2H][OX2]
class	RuleKetenes Ketenes. SMARTS pattern [CX3]=[CX2]=[OX1]
class	RuleKetones Ketones. SMARTS pattern [#6][CX3](=[OX1])[#6]
class	RuleLipidSolubility LipidSolubility < 0.01.
class	RuleLogP LogP < 3.1. Expects property to be read from IMolecule.getProperty(RuleLogP.LogKow).
class	RuleMeltingPoint MeltingPoint < 200.
class	RuleMolWeight Molecular weight > 350.
class	RuleOandPQuinones O and P Quinones. Substructures O=C1C=CC=CC1(=O) O=C1C=CC(=O)C=C1
class	RulePhenols Phenols. Substructure c1ccccc1O[H]
class	RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts Rule Quaternary Organic Ammonium And Phosphonium Salts
class	RuleSurfaceTension SurfaceTension > 62.0.
class	RuleTriAndTetraHalogenatedBenzenes Tri And Tetra Halogenated Benzenes. Substructure ClC1=CC(Cl)C(Cl)C(Cl)C1 ClC1C=CC(Cl)C(Cl)C1(Cl) ClC1C=CCC(Cl)C1(Cl)
class	RuleVapourPressure VapourPressure < 0.0001.

Uses of IDecisionRule in structurefeatures.rules

Classes in structurefeatures.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	RuleAlcohol
class	RuleAlkylAldehyde
class	RuleAlkylHydrazine
class	RuleAlkylPhosphonate
class	RuleAmine
class	RuleAromaticAldehyde
class	RuleAromaticAzo
class	RuleAromaticNitro
class	RuleArylMethylHalide
class	RuleAziridine
class	RuleAzo
class	RuleBenzene
class	RuleEther
class	RuleFuran
class	RuleHalide
class	RuleHeterocycle
class	RuleHydrazine
class	RuleIminomethyl
class	RuleNChloramine
class	RuleNHydroxy
class	RuleNitro
class	RuleNitrogenMustard
class	RuleNitrosamine
class	RuleNitroso
class	RuleNMethylol
class	RuleNOxide
class	RuleNucleosides
class	RulePhosphoricGroups
class	RuleprimaryAlkylHalide
class	RulePropiolactone
class	RuleUrethaneDerivatives

Uses of IDecisionRule in toxTree.core

Subinterfaces of IDecisionRule in toxTree.core

Modifier and Type	Interface and Description
interface	IRuleRange
interface	IRuleSubstructures An interface to support substructure rules
interface	IRuleValue

Methods in toxTree.core that return IDecisionRule

Modifier and Type	Method and Description
IDecisionRule	IDecisionRuleEditor.edit(Container owner, IDecisionRule rule)
IDecisionRule	IDecisionTransition.getBranch(boolean answer)
IDecisionRule	IDecisionMethod.getBranch(IDecisionRule rule, boolean answer)
IDecisionRule	IDecisionRuleEditor.getRule()
IDecisionRule	IDecisionRuleList.getRule(int index)
IDecisionRule	IDecisionMethod.getRule(int id)
IDecisionRule	IDecisionResult.getRule(int index)
IDecisionRule	IDecisionMethod.getRule(String name)
IDecisionRule	IDecisionMethod.getTopRule()

Methods in toxTree.core with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	IDecisionMethod.addDecisionRule(IDecisionRule rule)
void	IDecisionRuleList.addRule(IDecisionRule rule)
void	IDecisionResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)
IDecisionRule	IDecisionRuleEditor.edit(Container owner, IDecisionRule rule)
IDecisionRule	IDecisionMethod.getBranch(IDecisionRule rule, boolean answer)
IDecisionCategory	IDecisionMethod.getCategory(IDecisionRule rule, boolean answer)
void	IDecisionResult.hilightAlert(IDecisionRule rule)
Object	IProcessRule.process(IDecisionMethod method, IDecisionRule rule)
void	IDecisionMethod.setDecisionRule(IDecisionRule rule)
void	IDecisionRuleEditor.setRule(IDecisionRule rule)
void	IDecisionMethod.walkRules(IDecisionRule rule, IProcessRule processor)

Uses of IDecisionRule in toxtree.plugins.ames.rules

Classes in toxtree.plugins.ames.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	RuleAlertsAmes
class	RuleAlertsForAmesMutagenicity
class	RuleAlertsForNewAmesMutagenicity
class	SA57_Ames
class	SA58_Ames
class	SA59_Ames
class	SA60_Ames
class	SA61_Ames
class	SA62_Ames
class	SA63_Ames
class	SA64_Ames
class	SA65_Ames
class	SA66_Ames
class	SA67_Ames
class	SA68_Ames
class	SA69_Ames
class	VerifyAlertsAmes
class	VerifyAlertsNewAmes

Methods in toxtree.plugins.ames.rules with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	AmesMutagenicityTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in toxtree.plugins.dnabinding.rules

Classes in toxtree.plugins.dnabinding.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	DNABindingRule Parent class for all skin sens rules
class	RuleDNABindingAlerts
class	SN1Rule SNAR
class	VerifyAlertsDNABinding

Methods in toxtree.plugins.dnabinding.rules with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	DNABindingTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in toxtree.plugins.func.rules

Classes in toxtree.plugins.func.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	FG
class	FG1
class	FG10
class	FG11
class	FG12
class	FG13
class	FG14
class	FG15
class	FG16
class	FG17
class	FG18
class	FG19
class	FG2
class	FG20
class	FG21
class	FG22
class	FG23_1
class	FG23_2
class	FG23_3
class	FG23_4
class	FG23_5
class	FG23_6
class	FG23_7
class	FG23_8
class	FG23_LS
class	FG24_1
class	FG24_2
class	FG24_3
class	FG24_LS
class	FG25
class	FG26
class	FG27
class	FG28
class	FG29
class	FG3_1
class	FG3_2
class	FG3_LS
class	FG30
class	FG31_1
class	FG31_2
class	FG31_3
class	FG31_4
class	FG31_5
class	FG31_6
class	FG31_7
class	FG31_8
class	FG31_9
class	FG31_LS
class	FG32
class	FG33_1
class	FG33_2
class	FG33_3
class	FG33_4
class	FG33_5
class	FG33_6
class	FG33_7
class	FG33_8
class	FG33_LS
class	FG34_1
class	FG34_2
class	FG34_LS
class	FG35_1
class	FG35_10
class	FG35_11
class	FG35_12
class	FG35_13
class	FG35_2
class	FG35_3
class	FG35_4
class	FG35_5
class	FG35_6
class	FG35_7
class	FG35_8
class	FG35_9
class	FG35_LS
class	FG36
class	FG37_1
class	FG37_2
class	FG37_3
class	FG37_4
class	FG37_LS
class	FG38
class	FG39
class	FG4
class	FG4_1
class	FG4_2
class	FG4_LS
class	FG40
class	FG41_1
class	FG41_2
class	FG41_3
class	FG41_4
class	FG41_5
class	FG41_LS
class	FG42
class	FG43
class	FG44
class	FG45
class	FG46_1
class	FG46_2
class	FG46_LS
class	FG47
class	FG48_1
class	FG48_2
class	FG48_LS
class	FG49
class	FG5
class	FG50_1
class	FG50_2
class	FG50_3
class	FG50_LS
class	FG51_1
class	FG51_2
class	FG51_3
class	FG51_LS
class	FG52_1
class	FG52_2
class	FG52_3
class	FG52_LS
class	FG53_1
class	FG53_2
class	FG53_3
class	FG53_LS
class	FG54
class	FG55
class	FG56
class	FG57
class	FG58
class	FG59
class	FG6
class	FG60
class	FG61
class	FG62
class	FG63
class	FG64
class	FG65
class	FG66
class	FG67
class	FG68
class	FG69
class	FG7
class	FG70
class	FG71
class	FG72
class	FG73
class	FG74_1
class	FG74_2
class	FG74_3
class	FG74_4
class	FG74_5
class	FG74_6
class	FG74_7
class	FG74_LS
class	FG75_1
class	FG75_2
class	FG75_3
class	FG75_4
class	FG75_LS
class	FG76
class	FG77
class	FG78_1
class	FG78_2
class	FG78_3
class	FG78_4
class	FG78_LS
class	FG79_1
class	FG79_2
class	FG79_3
class	FG79_4
class	FG79_LS
class	FG8
class	FG80_1
class	FG80_2
class	FG80_LS
class	FG81_1
class	FG81_2
class	FG81_3
class	FG81_4
class	FG81_LS
class	FG82_1
class	FG82_2
class	FG82_3
class	FG82_4
class	FG82_LS
class	FG83_1
class	FG83_2
class	FG83_3
class	FG83_4
class	FG83_LS
class	FG84_1
class	FG84_2
class	FG84_LS
class	FG85
class	FG86
class	FG87
class	FG88
class	FG89
class	FG9
class	FG90
class	RuleAlertsForFunc

Methods in toxtree.plugins.func.rules with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	FuncTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in toxtree.plugins.kroes.rules

Classes in toxtree.plugins.kroes.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	KroesRule10
class	KroesRule11
class	KroesRule12 Does estimated intake exceed 1800 µg/day ?
class	KroesRule2 Are there structural alerts that raise concern for potential genotoxicity?
class	KroesRule3 Is the chemical an aflatoxin-like, azoxy-, or N-nitroso compound
class	KroesRule4 Does estimated intake exceed TTC of 0.15 µg/day ?
class	KroesRule5 Does estimated intake exceed TTC of 1.5 mcg/day ?
class	KroesRule6 Is the compound an organophosphate?
class	KroesRule7 Does estimated intake exceed TTC of 18µg/day ?
class	KroesRule8 Is the compound in Cramer structural class III?
class	KroesRule9
class	RuleKroesFig1Q1 TODO refactor with SMARTS
class	RuleVerifyIntake

Uses of IDecisionRule in toxtree.plugins.lewis.rules

Classes in toxtree.plugins.lewis.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	Rule_areadepthratio
class	Rule_high_AreaDepthRatio
class	Rule_high_pKa
class	Rule_highLogP
class	Rule_highVolume
class	Rule_lowVolume
class	Rule_volume

Uses of IDecisionRule in toxtree.plugins.moa.rules

Classes in toxtree.plugins.moa.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	RuleAlertsAche
class	RuleAlertsCNS
class	RuleAlertsNarcosis1_1_1
class	RuleAlertsNarcosis1_1_1_1
class	RuleAlertsNarcosis1_1_2_1
class	RuleAlertsNarcosis1_1_2_3
class	RuleAlertsNarcosis2_2_1
class	RuleAlertsNarcosis3
class	RuleAlertsReactive
class	RuleAlertsUncouplers
class	VerifyAlertsAche
class	VerifyAlertsCNS
class	VerifyAlertsNarcosis1
class	VerifyAlertsNarcosis2
class	VerifyAlertsNarcosis3
class	VerifyAlertsReactive
class	VerifyAlertsUncouplers

Uses of IDecisionRule in toxtree.plugins.proteinbinding.rules

Classes in toxtree.plugins.proteinbinding.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	ProteinBindingRule Parent class for all skin sens rules
class	RuleProteinBindingAlerts
class	VerifyAlertsProteinBinding

Methods in toxtree.plugins.proteinbinding.rules with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	ProteinBindingTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in toxtree.plugins.search.rules

Classes in toxtree.plugins.search.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	Find Compound lookup

Uses of IDecisionRule in toxtree.plugins.skinsensitisation.rules

Classes in toxtree.plugins.skinsensitisation.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	AcylTransferRule Acyl transfer
class	MichaelAcceptorRule Michael acceptors
class	RuleSkinSensitisationAlerts
class	ShiffBaseRule Shiff base
class	SkinSensitisationRule Parent class for all skin sens rules
class	SN2Rule SN2
class	SNARRule SNAR
class	VerifyAlertsSkinSensitisation

Methods in toxtree.plugins.skinsensitisation.rules with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	SkinSensitisationTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in toxtree.plugins.smartcyp.rules

Classes in toxtree.plugins.smartcyp.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	MetaboliteGenerator
class	SMARTCYPRuleHigherRank
class	SMARTCYPRuleRank1
class	SMARTCYPRuleRank2
class	SMARTCYPRuleRank3

Uses of IDecisionRule in toxTree.qsar

Classes in toxTree.qsar that implement IDecisionRule

Modifier and Type	Class and Description
class	LinearDiscriminantRule Uses LinearQSARModel and returns true if LinearQSARModel.predict(IAtomContainer) is >= LinearDiscriminantRule.getThreshold() and false otherwise.

Uses of IDecisionRule in toxtree.tree

Methods in toxtree.tree with parameters of type IDecisionRule

Modifier and Type	Method and Description
static void	BundleRuleResource.retrieveStrings(IDecisionRule rule, String[] examples)
static void	BundleRuleResource.retrieveStrings(IDecisionRule rule, String resourceBundle, String[] examples)

Uses of IDecisionRule in toxTree.tree

Classes in toxTree.tree that implement IDecisionRule

Modifier and Type	Class and Description
class	AbstractRule An abstract class implementing IDecisionRule interface.
class	AbstractRuleHilightHits
class	DecisionNode A decision node to be used in UserDefinedTree.
class	MultiLabelDecisionNode

Fields in toxTree.tree declared as IDecisionRule

Modifier and Type	Field and Description
protected IDecisionRule	DecisionNode.rule
protected IDecisionRule	RuleResult.rule

Fields in toxTree.tree with type parameters of type IDecisionRule

Modifier and Type	Field and Description
protected ArrayList<IDecisionRule>	RulesList.list
protected ArrayList<IDecisionRule>	DecisionNodesList.list

Methods in toxTree.tree that return IDecisionRule

Modifier and Type	Method and Description
static IDecisionRule	AbstractRule.createRule(String className)
IDecisionRule	RulesList.get(int arg0)
IDecisionRule	DecisionNodesList.get(int arg0)
IDecisionRule	DecisionNode.getBranch(boolean answer) returns the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true
IDecisionRule	UserDefinedTree.getBranch(IDecisionRule rule, boolean answer)
IDecisionRule	BatchDecisionResultsList.getBranch(IDecisionRule rule, boolean answer)
IDecisionRule	UserDefinedTree.getBranch(int ruleId, boolean answer)
IDecisionRule	DecisionNode.getRule()
IDecisionRule	RuleResult.getRule()
IDecisionRule	RulesList.getRule(int index) returns a rule IDecisionRule
IDecisionRule	DecisionNodesList.getRule(int index)
IDecisionRule	AbstractTree.getRule(int id)
IDecisionRule	TreeResult.getRule(int index)
IDecisionRule	UserDefinedTree.getRule(int id)
IDecisionRule	BatchDecisionResultsList.getRule(int id)
IDecisionRule	AbstractTree.getRule(String name)
IDecisionRule	BatchDecisionResultsList.getRule(String name)
IDecisionRule	AbstractTree.getTopRule()
IDecisionRule	BatchDecisionResultsList.getTopRule()
IDecisionRule	RulesList.remove(int arg0)
IDecisionRule	DecisionNodesList.remove(int arg0)
IDecisionRule	RulesList.set(int arg0, IDecisionRule arg1)
IDecisionRule	DecisionNodesList.set(int arg0, IDecisionRule arg1)

Methods in toxTree.tree that return types with arguments of type IDecisionRule

Modifier and Type	Method and Description
ArrayList<IDecisionRule>	DecisionNodesList.getList()
Iterator<IDecisionRule>	DecisionNodesList.iterator()
ListIterator<IDecisionRule>	DecisionNodesList.listIterator()
ListIterator<IDecisionRule>	DecisionNodesList.listIterator(int arg0)
List<IDecisionRule>	DecisionNodesList.subList(int arg0, int arg1)

Methods in toxTree.tree with parameters of type IDecisionRule

Modifier and Type	Method and Description
boolean	RulesList.add(IDecisionRule arg0) Adds an object only if it is a rule IDecisionRule otherwise returns false
boolean	DecisionNodesList.add(IDecisionRule arg0)
void	RulesList.add(int arg0, IDecisionRule arg1) not implemented
void	DecisionNodesList.add(int arg0, IDecisionRule arg1)
void	AbstractTree.addDecisionRule(IDecisionRule rule)
void	BatchDecisionResultsList.addDecisionRule(IDecisionRule rule)
void	RulesList.addRule(IDecisionRule rule) adds a rule IDecisionRule
void	DecisionNodesList.addRule(IDecisionRule rule)
void	MultiLabelDecisionNodesList.addRule(IDecisionRule rule)
void	TreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)
void	BatchDecisionResultsList.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)
IDecisionRule	UserDefinedTree.getBranch(IDecisionRule rule, boolean answer)
IDecisionRule	BatchDecisionResultsList.getBranch(IDecisionRule rule, boolean answer)
IDecisionCategory	UserDefinedTree.getCategory(IDecisionRule rule, boolean answer)
IDecisionCategory	BatchDecisionResultsList.getCategory(IDecisionRule rule, boolean answer)
void	TreeResult.hilightAlert(IDecisionRule rule)
void	BatchDecisionResultsList.hilightAlert(IDecisionRule rule)
Object	Tree2PrefuseGraph.process(IDecisionMethod method, IDecisionRule rule)
Object	ReportTreePrinter.process(IDecisionMethod method, IDecisionRule rule)
Object	PDFTreePrinter.process(IDecisionMethod method, IDecisionRule rule)
Object	SimpleTreePrinter.process(IDecisionMethod method, IDecisionRule rule)
IDecisionRule	RulesList.set(int arg0, IDecisionRule arg1)
IDecisionRule	DecisionNodesList.set(int arg0, IDecisionRule arg1)
void	MultiLabelDecisionNode.setBranch(boolean answer, IDecisionRule node)
void	DecisionNode.setBranch(boolean answer, IDecisionRule node) Sets the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true
void	AbstractTree.setDecisionRule(IDecisionRule rule)
void	BatchDecisionResultsList.setDecisionRule(IDecisionRule rule)
void	DecisionNode.setRule(IDecisionRule rule) Sets rule
void	RuleResult.setRule(IDecisionRule rule)
protected boolean	AbstractTree.verifyResidues(org.openscience.cdk.interfaces.IAtomContainerSet mols, IDecisionResult result, IDecisionRule rule)
protected abstract boolean	AbstractTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result, IDecisionRule rule) abstract method, to be implemented in the child class
protected boolean	UserDefinedTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result, IDecisionRule topRule)
protected prefuse.data.Node	Tree2PrefuseGraph.walkRules(IDecisionMethod tree, IDecisionRule rule, ArrayList<Integer> visited)
protected void	AbstractTree.walkRules(IDecisionRule rule, ArrayList<Integer> visited, IProcessRule processor)
void	AbstractTree.walkRules(IDecisionRule rule, IProcessRule processor)
void	BatchDecisionResultsList.walkRules(IDecisionRule rule, IProcessRule processor)
protected String	ReportTreePrinter.writeMolecule(IDecisionMethod tree, IDecisionRule rule, boolean answer)
protected void	AbstractTreePrinter.writeMolecule(IDecisionMethod tree, IDecisionRule rule, boolean answer, OutputStream out)

Method parameters in toxTree.tree with type arguments of type IDecisionRule

Modifier and Type	Method and Description
void	DecisionNodesList.setList(ArrayList<IDecisionRule> list)

Constructors in toxTree.tree with parameters of type IDecisionRule

Constructor and Description
DecisionNode(IDecisionRule rule) Constructs a decision node with rule, null next nodes.
DecisionNode(IDecisionRule rule, DecisionNode nodeNo, DecisionNode nodeYes) Constructs a decision node with rule, nodeNo at branch NO and nodeYes at branch YES.
DecisionNode(IDecisionRule rule, DecisionNode nodeNo, DecisionNode nodeYes, IDecisionCategory categoryNo, IDecisionCategory categoryYes)
MultiLabelDecisionNode(IDecisionRule rule) Constructs a decision node with rule, null next nodes.
RuleResult(IDecisionRule rule, boolean result)
RuleResult(IDecisionRule rule, boolean result, IDecisionCategory category)

Uses of IDecisionRule in toxTree.tree.cramer

Classes in toxTree.tree.cramer that implement IDecisionRule

Modifier and Type	Class and Description
class	Rule32 Rule 32 of the Cramer scheme (see CramerRules)
class	Rule3FuncGroups Rule 21 of the Cramer scheme (see CramerRules)
class	Rule3MemberedHeterocycle 3-membered heterocycle.
class	RuleAcyclicAcetalEsterOfQ30 Rule 31 of the Cramer scheme (see CramerRules)
class	RuleAliphaticWithSomeFuncGroups Rule 20 of the Cramer scheme (see CramerRules)
class	RuleCommonComponentOfFood Rule 22 of the Cramer scheme (see CramerRules)
class	RuleCyclopropaneEtc Rule 25 of the Cramer scheme (see CramerRules)
class	RuleHasOnlySaltSulphonateSulphate Rule 4 of the Cramer scheme (see CramerRules)
class	RuleHasOtherThanC_H_O_N_S2 Rule 3 of the Cramer scheme (see CramerRules)
class	RuleHeteroaromatic Rule 12 of the Cramer scheme (see CramerRules)
class	RuleHeterocyclicComplexSubstituents Rule 11 of the Cramer scheme (see CramerRules)
class	RuleIsAromatic Rule 23 of the Cramer scheme (see CramerRules) Note this is descendant of RuleAromatic and therefore follows the Hueckel rule, rather than verifying for the presence of benzene, furan, thiophene, pyridine or pyrrole ring
class	RuleIsCommonTerpene Rule 16 of the Cramer scheme (see CramerRules) Verifies if the substance is a terpene
class	RuleIsHeterocyclic Rule 7 of the Cramer scheme (see CramerRules)
class	RuleIsOpenChain Rule 19 of the Cramer scheme (see CramerRules)
class	RuleKetoneAlcoholEtc Rule 18 of the Cramer scheme (see CramerRules)
class	RuleLactoneOrCyclicDiester Rule 8 of the Cramer scheme (see CramerRules)
class	RuleLactonesFusedOrUnsaturated Rule 9 of the Cramer scheme (see CramerRules)
class	RuleManyAromaticRings14 Rule 14 of the Cramer scheme (see CramerRules)
class	RuleManyAromaticRings28 Rule 28 of the Cramer scheme (see CramerRules)
class	RuleMonocarbocyclic Rule 24 of the Cramer scheme (see CramerRules)
class	RuleMonocycloalkanoneEtc Rule 26 of the Cramer scheme (see CramerRules)
class	RuleNormalBodyConstituent Rule 1 of the Cramer scheme (see CramerRules)
class	RuleOnlyFuncGroupsQ30 Rule 32 of the Cramer scheme (see CramerRules)
class	RuleReadilyHydrolysed29 Rule 29 of the Cramer scheme (see CramerRules)
class	RuleReadilyHydrolysedMononuclear Rule 15 of the Cramer scheme (see CramerRules)
class	RuleReadilyHydrolysedToCommonterpene Rule 17 of the Cramer scheme (see CramerRules)
class	RuleRingComplexSubstituents30 Rule 30 of the Cramer scheme (see CramerRules)
class	RuleRingsWithSubstituents Rule 27 of the Cramer scheme (see CramerRules)
class	RuleRingWithSubstituents Rule 13 of the Cramer scheme (see CramerRules)
class	RuleSimplyBranchedAliphaticHydrocarbon Implementation of Cramer rule No.5 Simply branched aliphatic or a common carbohydrate A descendant of RuleCarbohydrate
class	RuleSomeBenzeneDerivatives Rule 6 of the Cramer scheme (see CramerRules)
class	RuleSufficientSulphonateGroups Rule 33 of the Cramer scheme (see CramerRules)
class	RuleToxicFunctionalGroups Rule 2 of the Cramer scheme (see CramerRules)

Methods in toxTree.tree.cramer with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	CramerTreeResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in toxtree.tree.cramer3

Methods in toxtree.tree.cramer3 with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	CDTResult.addRuleResult(IDecisionRule rule, boolean value, org.openscience.cdk.interfaces.IAtomContainer molecule)

Uses of IDecisionRule in toxtree.tree.cramer3.rules

Classes in toxtree.tree.cramer3.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	RuleLactone
class	RuleQ1 Looks like similar to RuleAcyclicAcetalEsterOfQ30, although not specified as such by the rule authors.
class	RuleQ10 Very similar to Cramer Rules Q10 Rule3MemberedHeterocycle TODO Check if there are differences!
class	RuleQ11
class	RuleQ12 Identical to Cramer rules Q12 RuleHeteroaromatic
class	RuleQ13
class	RuleQ14_A Similar to Cramer rules Q14 RuleManyAromaticRings14
class	RuleQ14_B
class	RuleQ15 Identical to Cramer Rule Q19 RuleIsOpenChain
class	RuleQ16 For this question, if A or B or C is true, then Q16 = YES If A and B and C are false, then Q16 = NO
class	RuleQ17 This rule considers ALL possible functional groups, not only the ones listed! based on toxTree.tree.cramer.Rule3FuncGroups
class	RuleQ18_AI Very similar to Cramer rule Q18 @{link RuleKetoneAlcoholEtc} with additions
class	RuleQ18_JM
class	RuleQ19
class	RuleQ2
class	RuleQ20
class	RuleQ21
class	RuleQ22
class	RuleQ23 Identical to Cramer rules Q27 RuleRingsWithSubstituents
class	RuleQ24 Identical to Cramer rules Q28 RuleManyAromaticRings28
class	RuleQ25 Similar to Cramer rules Q30 RuleRingComplexSubstituents30 with addtions and changes
class	RuleQ26 Similar to Cramer rules Q6 RuleSomeBenzeneDerivatives with addtions
class	RuleQ27
class	RuleQ28
class	RuleQ29 Similar to Cramer rules Q33 RuleSufficientSulphonateGroups with addtions
class	RuleQ3 Derived from Cramer Q2 RuleToxicFunctionalGroups with additions and changes
class	RuleQ4 Derived from Cramer Rules Q3 RuleHasOtherThanC_H_O_N_S2 with additions and changes
class	RuleQ4A
class	RuleQ5 Derived from Q4 RuleHasOnlySaltSulphonateSulphate with additions and changes
class	RuleQ6 Derived from Cramer rules Q5 RuleSimplyBranchedAliphaticHydrocarbon with addition
class	RuleQ7 Identical to Cramer rules Q7 RuleHeterocyclic
class	RuleQ8
class	RuleQ9_A Identical to Cramer rules Q8 RuleLactoneOrCyclicDiester
class	RuleQ9_B
class	RuleQ9_C
class	RuleQ9_D
class	RuleRingsSMARTSSubstituents
class	RuleSMARTSSubstructureHydrolysis
class	RuleSMARTSSubstructureTagged

Uses of IDecisionRule in toxTree.tree.rules

Classes in toxTree.tree.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	RuleAllAllowedElements
class	RuleAllSubstructures Verifies if all of the fragments are a substructure of moleclue
class	RuleAnySubstituents Verifies if the molecule consists of only allowed substituents
class	RuleAnySubstructure Verifies if the molecule has at least one substructure of the list
class	RuleAromatic Verifies if the molecule is aromatic by applying the Hueckel rule
class	RuleCarbohydrate Verifies if the molecule is a carbohydrate
class	RuleCommonTerpene Verifies if the molecule is a common terpene
class	RuleDescriptor An abstract class to allow for descriptor analysis
class	RuleDescriptorRange Verifies if the descriptor is within a range
class	RuleElements Verifies if the molecule consists of only allowed elements
class	RuleHeterocyclic Verifies if the molecule is heterocyclic
class	RuleInitAlertCounter
class	RuleLipinski5 Returns true if all Lipinski Rule of Five are true
class	RuleManyAromaticRings Verifies if there are many aromatic rings
class	RuleMolecularMassRange Molecular mass in [RuleDescriptorRange.getMinValue(),RuleDescriptorRange.getMaxValue()] TODO add description
class	RuleOnlyAllowedSubstructures Verifies if the structure contains only allowed substructures
class	RuleOpenChain Verifies if the moleucle is open chain
class	RuleReadilyHydrolised Verifies if a compound is readily hydrolised
class	RuleRingAllowedSubstituents A rule to analyze ring substituents
class	RuleRingOtherThanAllowedSubstituents A rule to analyze ring substituents
class	RuleRings
class	RuleRingSubstituents A rule to analyze ring substituents
class	RuleStructuresList A rule, which returns true if the query is isomorphic to one of the structures read from a preconfigured file of a type SDF, SMI, CSV
class	RuleSubstructures An abstract class to implement substructure rules
class	RuleVerifyAlertsCounter
class	RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
class	StructureAlert
class	StructureAlertAmbit
class	StructureAlertCDK
class	UserInputRule

Uses of IDecisionRule in toxTree.tree.rules.smarts

Classes in toxTree.tree.rules.smarts that implement IDecisionRule

Modifier and Type	Class and Description
class	AbstractRuleSmartSubstructure<T>
class	RuleSMARTSSubstructureAmbit An IDecisionRule, making use of Ambit SMARTS parser.
class	RuleSMARTSubstructure For backward compatibility
class	RuleSMARTSubstructureCDK An IDecisionRule, making use of CDK SMARTS parser.

Uses of IDecisionRule in toxTree.ui

Methods in toxTree.ui with parameters of type IDecisionRule

Modifier and Type	Method and Description
IDecisionRuleEditor	IEditorFactory.createEditor(IDecisionRule rule)
IDecisionRuleEditor	EditorFactory.createEditor(IDecisionRule rule)

Uses of IDecisionRule in toxtree.ui.editors

Methods in toxtree.ui.editors with parameters of type IDecisionRule

Modifier and Type	Method and Description
IDecisionRuleEditor	SwingEditorFactory.createEditor(IDecisionRule rule)

Uses of IDecisionRule in toxtree.ui.tree

Methods in toxtree.ui.tree that return IDecisionRule

Modifier and Type	Method and Description
static IDecisionRule	SelectListDialog.selectNewRule(Component parent, ClassLoader classLoader) Provides a list of names of the classes implementing IDecisionRule If the user selects an object, the rule is created and returned Uses Introspection.getAvailableRuleTypes(ClassLoader)

Methods in toxtree.ui.tree with parameters of type IDecisionRule

Modifier and Type	Method and Description
protected boolean	TreeLayout.isVisited(IDecisionRule node)
void	TreeDrawing.setNode(IDecisionRule node)
protected void	TreeEditorPanel.setRule(IDecisionRule rule)
void	EditTreeActions.setRule(IDecisionRule rule)
protected void	TreeLayout.setVisited(IDecisionRule node, boolean value)

Constructors in toxtree.ui.tree with parameters of type IDecisionRule

Constructor and Description
QueryAtomContainersModel(List list, IDecisionRule rule)
QueryAtomContainersModel(QueryAtomContainers list, IDecisionRule rule)

Uses of IDecisionRule in toxtree.ui.tree.actions

Fields in toxtree.ui.tree.actions declared as IDecisionRule

Modifier and Type	Field and Description
protected IDecisionRule	AbstractRuleAction.rule
protected IDecisionRule	EditRuleAction.rule

Methods in toxtree.ui.tree.actions that return IDecisionRule

Modifier and Type	Method and Description
IDecisionRule	AbstractRuleAction.getRule()
IDecisionRule	EditRuleAction.getRule()
IDecisionRule	IRuleAction.getRule()

Methods in toxtree.ui.tree.actions with parameters of type IDecisionRule

Modifier and Type	Method and Description
void	AbstractRuleAction.setRule(IDecisionRule rule)
void	EditRuleAction.setRule(IDecisionRule rule)
void	IRuleAction.setRule(IDecisionRule rule)
static IDecisionMethod	NewRuleAction.treeFromRule(IDecisionRule rule)

Constructors in toxtree.ui.tree.actions with parameters of type IDecisionRule

Constructor and Description
AbstractRuleAction(IDecisionRule rule)
AbstractRuleAction(IDecisionRule rule, String arg0)
AbstractRuleAction(IDecisionRule rule, String arg0, Icon arg1)
SubstructureFromListAction(IDecisionRule rule)
SubstructureFromListAction(IDecisionRule rule, String arg0)
SubstructureFromListAction(IDecisionRule rule, String arg0, Icon arg1)
SubstructuresFromFileAction(IDecisionRule rule)
SubstructuresFromFileAction(IDecisionRule rule, String arg0)
SubstructuresFromFileAction(IDecisionRule rule, String arg0, Icon arg1)

Uses of IDecisionRule in toxtree.ui.tree.rules

Fields in toxtree.ui.tree.rules declared as IDecisionRule

Modifier and Type	Field and Description
protected IDecisionRule	RuleMoleculeEditAction.rule
protected IDecisionRule	RulePanel.rule
protected IDecisionRule	RuleEditor.rule

Methods in toxtree.ui.tree.rules that return IDecisionRule

Modifier and Type	Method and Description
IDecisionRule	RulePanel.edit(Container owner, IDecisionRule rule)
IDecisionRule	SubstructureRulePanel.edit(Container owner, IDecisionRule rule)
IDecisionRule	RuleEditor.edit(Container owner, IDecisionRule rule)
IDecisionRule	SMARTSRuleEditor.edit(Container owner, IDecisionRule rule)
IDecisionRule	RuleMoleculeEditAction.getRule()
IDecisionRule	RulePanel.getRule()
IDecisionRule	SubstructureRulePanel.getRule()
IDecisionRule	RuleEditor.getRule()

Methods in toxtree.ui.tree.rules with parameters of type IDecisionRule

Modifier and Type	Method and Description
IDecisionRule	RulePanel.edit(Container owner, IDecisionRule rule)
IDecisionRule	SubstructureRulePanel.edit(Container owner, IDecisionRule rule)
IDecisionRule	RuleEditor.edit(Container owner, IDecisionRule rule)
IDecisionRule	SMARTSRuleEditor.edit(Container owner, IDecisionRule rule)
void	RuleMoleculeEditAction.setRule(IDecisionRule rule)
void	RuleStructuresPanel.setRule(IDecisionRule rule)
void	RulePanel.setRule(IDecisionRule rule)
void	SubstructureRulePanel.setRule(IDecisionRule rule)
void	RuleEditor.setRule(IDecisionRule rule)

Constructors in toxtree.ui.tree.rules with parameters of type IDecisionRule

Constructor and Description
RuleEditor(IDecisionRule object)
RuleExampleEditAction(IDecisionRule rule, boolean answer)
RuleExampleEditAction(IDecisionRule rule, boolean answer, String arg0)
RuleExampleEditAction(IDecisionRule rule, boolean answer, String arg0, Icon arg1)
RulePanel(IDecisionRule rule)

Uses of IDecisionRule in verhaar.rules

Classes in verhaar.rules that implement IDecisionRule

Modifier and Type	Class and Description
class	Rule01 Consists only of C,H,N,O,S,halogens (exluding I).
class	Rule03 Have a molecular mass (MW) not more than 600 Daltons.
class	Rule11 Does not contain I.
class	Rule13 Contain only C&H.
class	Rule14 Contain only C,H and halogen.
class	Rule141 Acyclic compound NOT containing halogen at beta-positions from unsaturations (e.g.
class	Rule142 Monocyclic compounds substituted with halogens.
class	Rule143 Monocyclic compounds that are unsubstituted or substituted with acyclic structures containing only C&H or complying with rule Rule141.
class	Rule144 Polycyclic compounds that are unsubstituted or substituted with acyclic structures containing only C&H or complying with Rule141.
class	Rule15 Contain only C,H,O.
class	Rule151 Linear ethers or monocyclic mono ethers, but not epoxides or peroxides.
class	Rule152 Aliphatic alcohols but not allylic/propargylic alcohols.
class	Rule153 Alcohols with aromatic moieties, but NOT phenols or benzylic alcohols.
class	Rule154 Ketones, but not alpha-, beta unsaturated ketones (e.g.
class	Rule16 Contain only C,H,N.
class	Rule161 Aliphatic secondary or tertiary amines.
class	Rule17 Contain only C,H,O and halogen.
class	Rule171 Halogenated compounds that comply with rule Rule15 but not alpha-, beta- halogen substituted compounds.
class	Rule21 Non- or weakly acidic phenols.
class	Rule22 Anilines with one nitro substituent and/or one to three chlorine substituents, and/or alkyl substituents.
class	Rule23 Be mononitroaromatics with one or two chlorine substituents and/or alkyl substituents.
class	Rule24 Primary alkyl amines (containing only C,H,N).
class	Rule25 Pyridines with one or two chlorine substituents and/or alkyl substituents.
class	Rule31 Possess alylic/propargylic activation.
class	Rule33 Be other compound with a (good) leaving group at an alpha position of a double or triple bond fragment.
class	Rule34 Possess a three-membered heterocyclic ring.
class	Rule35 Possess activated C-C double/triple bonds.
class	Rule36 Hydrazines or other compounds with a single , double or triple N-N linkage.
class	Rule37 Activated nitriles like alpha hydroxynitriles (cyanohidrins) or allylic /propargylic nitriles.
class	Rule38 Contain one of the following structural entities:
class	Rule4 Compounds acting by a specific mechanism.
class	RuleAlertsClass1
class	RuleAlertsClass2
class	RuleAlertsClass3
class	RuleIonicGroups Uses QueryAssociationBond ro verify if the query compound has an ionic bond.
class	RuleLogPRange 0 <= LogP <= 6.
class	RuleRingMainStrucSubstituents
class	RuleVerifyClass1Alerts
class	RuleVerifyClass2Alerts
class	RuleVerifyClass3Alerts

Uses of IDecisionRule in verhaar.rules.helper

Classes in verhaar.rules.helper that implement IDecisionRule

Modifier and Type	Class and Description
class	RuleAnySubstructureCounter
class	RuleElementsCounter
class	RuleOnlyAllowedSubstructuresCounter