Uses of Class
toxTree.tree.AbstractRule

Packages that use AbstractRule
com.molecularnetworks.start.rules   
cramer2.rules   
eye.rules The package contains implementations of IDecisionRule rules for SicretRules decision tree. 
mic.rules   
michaelacceptors.rules   
mutant.rules   
sicret.rules The package contains implementations of IDecisionRule rules for SicretRules decision tree. 
structurefeatures.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 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.rules The package contains several generic implementations of IDecisionRule rules 
toxTree.tree.rules.smarts SMARTS support. 
verhaar.rules The package contains implementations of IDecisionRule rules for VerhaarScheme decision tree. 
verhaar.rules.helper   
 

Uses of AbstractRule in com.molecularnetworks.start.rules
 

Subclasses of AbstractRule in com.molecularnetworks.start.rules
 class RuleAlcohols
          Biodegradation rule for alcohols.
 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 RuleEsters
          Biodegradation rule for esters.
 class RuleFormaldehyde
          Biodegradation rule for formaldehyde.
 class RuleHalogenSubstitutedBranched
          Biodegradation rule for branched, halogen substituted chemicals.
 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 AbstractRule in cramer2.rules
 

Subclasses of AbstractRule in cramer2.rules
 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 AbstractRule in eye.rules
 

Subclasses of AbstractRule in eye.rules
 class Rule13_AliphaticMonoalcohols
          A Lactams
 class Rule14Aliphatic_glycerol_monoethers
          LipidSolubility < 4.0
 class Rule15
          Acid anhydrides.
 class Rule16
          Halogen benzenes with substituents containing carboxylic acid groups
SMARTS pattern [CX3](=[OX1])[NX3H][CX3](=[OX1]).
 class Rule17
          Aliphatic esters of chloro formic acid
 class Rule18
          Chlorinated aliphatic alcohols
 class Rule19
          Diphenyl iodonium salts
 class Rule20
          Derivatives of alpha amino benzene
 class Rule26
          Thiazoles and thiazolidines
 class Rule27
           
 class Rule28
           
 class Rule29
           
 class Rule30
          TODO Aliphatic monoalcohols
 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 AbstractRule in mic.rules
 

Subclasses of AbstractRule in mic.rules
 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
           
 

Uses of AbstractRule in michaelacceptors.rules
 

Subclasses of AbstractRule in michaelacceptors.rules
 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 Rule11
           
 class Rule12A
           
 class Rule12B
           
 class Rule13A
           
 class Rule13B
           
 class Rule14
           
 class Rule2
           
 class Rule3
           
 class Rule4A
           
 class Rule4B
           
 class Rule5
           
 class Rule6
           
 class Rule7
           
 class Rule8
           
 class Rule9A
           
 class Rule9B
           
 

Uses of AbstractRule in mutant.rules
 

Subclasses of AbstractRule in mutant.rules
 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
           
 

Uses of AbstractRule in sicret.rules
 

Subclasses of AbstractRule in sicret.rules
 class Rule12
          VapourPressure < 0.0001
 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 AbstractRule in structurefeatures.rules
 

Subclasses of AbstractRule in structurefeatures.rules
 class RuleAlcohol
           
 class RuleAldehyde
           
 class RuleAlkylAldehyde
           
 class RuleAlkylHydrazine
           
 class RuleAlkylPhosphonate
           
 class RuleAmine
           
 class RuleAromaticAldehyde
           
 class RuleAromaticAzo
           
 class RuleAromaticNitro
           
 class RuleArylMethylHalide
           
 class RuleAziridine
           
 class RuleAzo
           
 class RuleBenzene
           
 class RuleEpoxide
           
 class RuleEther
           
 class RuleFuran
           
 class RuleHalide
           
 class RuleHeterocycle
           
 class RuleHydrazine
           
 class RuleIminomethyl
           
 class RuleKetone
           
 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 AbstractRule in toxtree.plugins.dnabinding.rules
 

Subclasses of AbstractRule in toxtree.plugins.dnabinding.rules
 class AcylTransferRule
          Acyl transfer
 class DNABindingRule
          Parent class for all skin sens rules
 class MichaelAcceptorRule
          Michael acceptors
 class RuleDNABindingAlerts
           
 class ShiffBaseRule
          Shiff base
 class SN1Rule
          SNAR
 class SN2Rule
          SN2
 class VerifyAlertsDNABinding
           
 

Uses of AbstractRule in toxtree.plugins.func.rules
 

Subclasses of AbstractRule in toxtree.plugins.func.rules
 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
           
 

Uses of AbstractRule in toxtree.plugins.kroes.rules
 

Subclasses of AbstractRule in toxtree.plugins.kroes.rules
 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 AbstractRule in toxtree.plugins.lewis.rules
 

Subclasses of AbstractRule in toxtree.plugins.lewis.rules
 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 AbstractRule in toxtree.plugins.moa.rules
 

Subclasses of AbstractRule in toxtree.plugins.moa.rules
 class RuleAlertsAche
           
 class RuleAlertsCNS
           
 class RuleAlertsNarcosis1_1_1
           
 class RuleAlertsNarcosis1_1_1_1
           
 class RuleAlertsNarcosis1_1_2
           
 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 AbstractRule in toxtree.plugins.proteinbinding.rules
 

Subclasses of AbstractRule in toxtree.plugins.proteinbinding.rules
 class ProteinBindingRule
          Parent class for all skin sens rules
 class RuleProteinBindingAlerts
           
 class SNARRule
          SNAR
 class VerifyAlertsProteinBinding
           
 

Uses of AbstractRule in toxtree.plugins.search.rules
 

Subclasses of AbstractRule in toxtree.plugins.search.rules
 class Find
          Compound lookup
 

Uses of AbstractRule in toxtree.plugins.skinsensitisation.rules
 

Subclasses of AbstractRule in toxtree.plugins.skinsensitisation.rules
 class RuleSkinSensitisationAlerts
           
 class SkinSensitisationRule
          Parent class for all skin sens rules
 class VerifyAlertsSkinSensitisation
           
 

Uses of AbstractRule in toxtree.plugins.smartcyp.rules
 

Subclasses of AbstractRule in toxtree.plugins.smartcyp.rules
 class MetaboliteGenerator
           
 class SMARTCYPRuleHigherRank
           
 class SMARTCYPRuleRank1
           
 class SMARTCYPRuleRank2
           
 class SMARTCYPRuleRank3
           
 

Uses of AbstractRule in toxTree.qsar
 

Subclasses of AbstractRule in toxTree.qsar
 class LinearDiscriminantRule
          Uses LinearQSARModel and returns true if LinearQSARModel.predict(IAtomContainer) is >= LinearDiscriminantRule.getThreshold() and false otherwise.
 

Uses of AbstractRule in toxTree.tree
 

Subclasses of AbstractRule in toxTree.tree
 class AbstractRuleHilightHits
           
 

Uses of AbstractRule in toxTree.tree.cramer
 

Subclasses of AbstractRule in toxTree.tree.cramer
 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)
 

Uses of AbstractRule in toxTree.tree.rules
 

Subclasses of AbstractRule in toxTree.tree.rules
 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 AbstractRule in toxTree.tree.rules.smarts
 

Subclasses of AbstractRule in toxTree.tree.rules.smarts
 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 AbstractRule in verhaar.rules
 

Subclasses of AbstractRule in verhaar.rules
 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 Rule13
          Contain only C&H.
 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 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 Rule161
          Aliphatic secondary or tertiary amines.
 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 AbstractRule in verhaar.rules.helper
 

Subclasses of AbstractRule in verhaar.rules.helper
 class RuleAnySubstructureCounter
           
 class RuleElementsCounter
           
 class RuleOnlyAllowedSubstructuresCounter
           
 



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