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

Packages that use RuleSMARTSSubstructureAmbit
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.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
 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
 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
 class Rule22
          Substituted indoles
 class Rule39
           
 

Uses of RuleSMARTSSubstructureAmbit in mic.rules
 

Subclasses of RuleSMARTSSubstructureAmbit in mic.rules
 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
 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
 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
 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
 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
 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
 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
 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
 class RuleAlertsNarcosis1_1_1
           
 class RuleAlertsNarcosis1_1_1_1
           
 class RuleAlertsNarcosis1_1_2
           
 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
 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
 class SkinSensitisationRule
          Parent class for all skin sens rules
 

Uses of RuleSMARTSSubstructureAmbit in toxTree.tree.cramer
 

Subclasses of RuleSMARTSSubstructureAmbit in toxTree.tree.cramer
 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.rules
 

Subclasses of RuleSMARTSSubstructureAmbit in toxTree.tree.rules
 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
 class RuleSMARTSubstructure
          For backward compatibility
 

Uses of RuleSMARTSSubstructureAmbit in verhaar.rules
 

Subclasses of RuleSMARTSSubstructureAmbit in verhaar.rules
 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.
 



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