Uses of Class
toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit

Packages that use RuleSMARTSSubstructureAmbit

Package	Description
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.moa.rules
toxtree.plugins.proteinbinding.rules
toxtree.plugins.skinsensitisation.rules
toxTree.tree.cramer	Class CramerRules is the implementation of Cramer rules [Cramer et al,78].
toxtree.tree.cramer3.rules
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.

Uses of RuleSMARTSSubstructureAmbit in com.molecularnetworks.start.rules

Subclasses of RuleSMARTSSubstructureAmbit in com.molecularnetworks.start.rules

Modifier and Type	Class and Description
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	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 RuleSMARTSSubstructureAmbit in cramer2.rules

Subclasses of RuleSMARTSSubstructureAmbit in cramer2.rules

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	RuleUnchargedOrganophosphates Uncharged Organophosph(othion)ates Modified Dec, 2008

Uses of RuleSMARTSSubstructureAmbit in eye.rules

Subclasses of RuleSMARTSSubstructureAmbit in eye.rules

Modifier and Type	Class and Description
class	Rule22 Substituted indoles
class	Rule39

Uses of RuleSMARTSSubstructureAmbit in mic.rules

Subclasses of RuleSMARTSSubstructureAmbit in mic.rules

Modifier and Type	Class and Description
class	PB29
class	PB30
class	SA12 Quinones
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	SA21
class	SA3
class	SA30
class	SA32
class	SA33
class	SA34
class	SA35
class	SA36
class	SA5
class	SA6
class	SA7
class	SA8
class	SA9

Uses of RuleSMARTSSubstructureAmbit in michaelacceptors.rules

Subclasses of RuleSMARTSSubstructureAmbit in michaelacceptors.rules

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	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 RuleSMARTSSubstructureAmbit in mutant.rules

Subclasses of RuleSMARTSSubstructureAmbit in mutant.rules

Modifier and Type	Class and Description
class	RuleAromaticAmineNoSulfonicGroup
class	SA12_gen Quinones
class	SA14_gen
class	SA15_gen
class	SA16_gen
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	SA21_gen
class	SA26_gen Aromatic ring N-oxide.
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	SA3_gen
class	SA30_gen
class	SA31b_nogen
class	SA31c_nogen
class	SA5_gen
class	SA6_gen
class	SA7_gen
class	SA8_gen
class	SA9_gen

Uses of RuleSMARTSSubstructureAmbit in sicret.rules

Subclasses of RuleSMARTSSubstructureAmbit in sicret.rules

Modifier and Type	Class and Description
class	RuleA_Lactams A Lactams
class	RuleAcidImides Acid imides.
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	RuleBenzylHalides Benwyl halides. SMARTS pattern [ClX1,BrX1]Cc1ccccc1
class	RuleBetaLactones Beta lactones. SMARTS pattern [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
class	RuleEpoxides Epoxides. SMARTS pattern OX2r3]1[#6r3][#6r3]1
class	RuleEthyleneGlycolEthers Ethylene Glycol Ethers SMARTS pattern [OX2H][CX4;$([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	RuleHydroPeroxides HydroPeroxides. SMARTS pattern [OX2H][OX2]
class	RuleKetenes Ketenes. SMARTS pattern [CX3]=[CX2]=[OX1]
class	RuleKetones Ketones. SMARTS pattern [#6][CX3](=[OX1])[#6]

Uses of RuleSMARTSSubstructureAmbit in structurefeatures.rules

Subclasses of RuleSMARTSSubstructureAmbit in structurefeatures.rules

Modifier and Type	Class and Description
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 RuleSMARTSSubstructureAmbit in toxtree.plugins.dnabinding.rules

Subclasses of RuleSMARTSSubstructureAmbit in toxtree.plugins.dnabinding.rules

Modifier and Type	Class and Description
class	AcylTransferRule Acyl transfer
class	DNABindingRule Parent class for all skin sens rules
class	MichaelAcceptorRule Michael acceptors
class	ShiffBaseRule Shiff base
class	SN1Rule SNAR
class	SN2Rule SN2

Uses of RuleSMARTSSubstructureAmbit in toxtree.plugins.func.rules

Subclasses of RuleSMARTSSubstructureAmbit in toxtree.plugins.func.rules

Modifier and Type	Class and Description
class	FG
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

Uses of RuleSMARTSSubstructureAmbit in toxtree.plugins.kroes.rules

Subclasses of RuleSMARTSSubstructureAmbit in toxtree.plugins.kroes.rules

Modifier and Type	Class and Description
class	KroesRule3 Is the chemical an aflatoxin-like, azoxy-, or N-nitroso compound
class	KroesRule6 Is the compound an organophosphate?

Uses of RuleSMARTSSubstructureAmbit in toxtree.plugins.moa.rules

Subclasses of RuleSMARTSSubstructureAmbit in toxtree.plugins.moa.rules

Modifier and Type	Class and Description
class	RuleAlertsNarcosis1_1_1
class	RuleAlertsNarcosis1_1_1_1
class	RuleAlertsNarcosis1_1_2_1
class	RuleAlertsNarcosis1_1_2_3

Uses of RuleSMARTSSubstructureAmbit in toxtree.plugins.proteinbinding.rules

Subclasses of RuleSMARTSSubstructureAmbit in toxtree.plugins.proteinbinding.rules

Modifier and Type	Class and Description
class	ProteinBindingRule Parent class for all skin sens rules
class	SNARRule SNAR

Uses of RuleSMARTSSubstructureAmbit in toxtree.plugins.skinsensitisation.rules

Subclasses of RuleSMARTSSubstructureAmbit in toxtree.plugins.skinsensitisation.rules

Modifier and Type	Class and Description
class	SkinSensitisationRule Parent class for all skin sens rules

Uses of RuleSMARTSSubstructureAmbit in toxTree.tree.cramer

Subclasses of RuleSMARTSSubstructureAmbit in toxTree.tree.cramer

Modifier and Type	Class and Description
class	RuleHeteroaromatic Rule 12 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

Uses of RuleSMARTSSubstructureAmbit in toxtree.tree.cramer3.rules

Subclasses of RuleSMARTSSubstructureAmbit in toxtree.tree.cramer3.rules

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	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	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 RuleSMARTSSubstructureAmbit in toxTree.tree.rules

Subclasses of RuleSMARTSSubstructureAmbit in toxTree.tree.rules

Modifier and Type	Class and Description
class	RuleAromatic Verifies if the molecule is aromatic by applying the Hueckel rule
class	StructureAlert
class	StructureAlertAmbit

Uses of RuleSMARTSSubstructureAmbit in toxTree.tree.rules.smarts

Subclasses of RuleSMARTSSubstructureAmbit in toxTree.tree.rules.smarts

Modifier and Type	Class and Description
class	RuleSMARTSubstructure For backward compatibility

Uses of RuleSMARTSSubstructureAmbit in verhaar.rules

Subclasses of RuleSMARTSSubstructureAmbit in verhaar.rules

Modifier and Type	Class and Description
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	Rule171 Halogenated compounds that comply with rule Rule15 but not alpha-, beta- halogen substituted compounds.
class	Rule24 Primary alkyl amines (containing only C,H,N).
class	Rule31 Possess alylic/propargylic activation.
class	Rule32 Possess benzylic 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.