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PREV NEXT | FRAMES NO FRAMES |
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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