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Uses of IDecisionRule in com.molecularnetworks.start.rules |
---|
Classes in com.molecularnetworks.start.rules that implement IDecisionRule | |
---|---|
class |
RuleAlcohols
Biodegradation rule for alcohols. |
class |
RuleAldehyde
Biodegradation rule for aldehydes. |
class |
RuleAliphaticCyclicNoBranches
Biodegradation rule for aliphatic cyclic chemicals with no branches. |
class |
RuleAliphaticEther
Biodegradation rule for aliphatic ethers. |
class |
RuleAliphaticFusedRingsNonBranched
Biodegradation rule for aliphatic compounds consisting of fused rings and no branches. |
class |
RuleAlyphaticSulphonicAcids
Biodegradation rule for aliphatic sulphonic acids. |
class |
RuleAminoAcids
Biodegradation rule for amino acids. |
class |
RuleAromaticHalogen
Biodegradation rule for chemicals with and Iodine, Chlorine, or Fluorine atom attached to an aromatic atom. |
class |
RuleAromaticNGroups
Biodegradation rule for chemicals with an NO2, NH2, or NH attached to an aromatic atom. |
class |
RuleAromaticSulphonicAcid
Biodegradation rule for aromatic sulphonic acids. |
class |
RuleAzoGroup
Biodegradation rule for chemicals containing an azo group. |
class |
RuleCyanoGroupOnMoreThanEightAtomsChain
Biodegradation rule for chemicals containing a cyano group that is attached to a more than 8 atoms chain. |
class |
RuleEpoxide
Biodegradation rule for chemicals containing an epoxide functional group. |
class |
RuleEsters
Biodegradation rule for esters. |
class |
RuleFormaldehyde
Biodegradation rule for formaldehyde. |
class |
RuleHalogenSubstitutedBranched
Biodegradation rule for branched, halogen substituted chemicals. |
class |
RuleKetone
Biodegradation rule for ketones. |
class |
RuleMoreThanTwoHydroxyOnAromaticRing
Biodegradation rule for chemicals with more than two hydroxy substituents on an aromatic ring. |
class |
RuleNitrile
Biodegradation rule for nitriles. |
class |
RuleNNitroso
Biodegradation rule for chemicals with an N-Nitroso (-N-N=0) group. |
class |
RuleOneHalogenOnUnbranched
Biodegradation rule for unbranched chemicals with one halogen substituent. |
class |
RulePhosphateEsters
Biodegradation rule for phosphoric esters. |
class |
RulePyridineRing
Biodegradation rule for pyridines. |
class |
RuleTerminalIsopropylNonCyclic
Biodegradation rule for a non-cyclic chemical with at least two terminal isopropyl groups. |
class |
RuleTerminalTertButyl
Biodegradation rule for chemicals with a terminal tert-butyl branch. |
class |
RuleTertiaryAmine
Biodegradation rule for tertiary amines. |
class |
RuleTriazineRing
Biodegradation rule for chemicals containing triazine ring. |
class |
RuleTrifluoromethyl
Biodegradation rule for chemicals containing trifluoromethyl group (-CF3). |
class |
RuleTwoHalogensOnUnbranchedNonCyclic
Biodegradation rule for unbranched, non-cyclic chemicals with two halogen substituents. |
class |
RuleTwoOrMoreRings
Biodegradation rule for chemicals with two or more rings. |
class |
RuleTwoTerminalDiaminoGroupsOnNonCyclic
Biodegradation rule for chemicals with two terminal diamino groups that are not attached to a cycle. |
class |
RuleTwoTerminalDoubleBondsOnUnbranched
Biodegradation rule for unbranched chemicals with two terminal double-bonded carbons. |
Uses of IDecisionRule in cramer2.categories |
---|
Methods in cramer2.categories with parameters of type IDecisionRule | |
---|---|
void |
CramerTreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in cramer2.rules |
---|
Classes in cramer2.rules that implement IDecisionRule | |
---|---|
class |
RuleBenzeneAnalogues
benzene analogues, with 0-6 substituents that consist of at most 1 heavy atom. |
class |
RuleDivalentSulphur
Many kinds of divalent sulphurs, *-S-*, are synthetic and outside the scope of the Cramer dataset. |
class |
RuleFreeABUnsaturatedHetero
free a,b-unsaturates heteroatoms (allyl amine), where free implies that the b carbon has 2 H's. |
class |
RuleReadilyHydrolysedPO4
cleaves PO4's from compounds, and analyses the remaining fragments Modified Dec, 2008 |
class |
RuleUnchargedOrganophosphates
Uncharged Organophosph(othion)ates Modified Dec, 2008 |
Uses of IDecisionRule in eye.rules |
---|
Classes in eye.rules that implement IDecisionRule | |
---|---|
class |
Rule13_AliphaticMonoalcohols
A Lactams |
class |
Rule14Aliphatic_glycerol_monoethers
LipidSolubility < 4.0 |
class |
Rule39
|
class |
RuleAqueousSolubility_10_2
AqueousSolubility < 0.1 |
class |
RuleAqueousSolubility_10_5
AqueousSolubility < 0.001 |
class |
RuleAqueousSolubility_11_7
|
class |
RuleAqueousSolubility_8_3
|
class |
RuleAqueousSolubility_8_4
|
class |
RuleAqueousSolubility_9_3
AqueousSolubility < 0.0001 |
class |
RuleAqueousSolubility1
|
class |
RuleLipidSolubility_10_4
LipidSolubility < 400.0 |
class |
RuleLipidSolubility_9_1
|
class |
RuleLogP_10_1
LogKow > 3.8 |
class |
RuleLogP_11_4
LogKow < -2 |
class |
RuleLogP_11_5
LogKow > 3.6 |
class |
RuleLogP_11_6
|
class |
RuleLogP_12_4
LogP > 4.5 |
class |
RuleLogP_9_4
LogKow > 5.5 |
class |
RuleLogP1
|
class |
RuleMelting_Point_11_3
MeltingPoint > 200.0 |
class |
RuleMeltingPoint_11_2
MeltingPoint > 200.0 |
class |
RuleMeltingPoint_12_3
MeltingPoint > 65.0 |
class |
RuleMeltingPoint_8_1
|
class |
RuleMolWeight_10_3
Molecular Weight > 370.0 |
class |
RuleMolWeight_11_1
Molecular Weight > 620 |
class |
RuleMolweight_12_1
MoleculWeight > 370 |
class |
RuleMolWeight_12_2
Molecular Weight > 280 |
class |
RuleMolWeight_8_2
|
class |
RuleMolWeight_9_2
MoleculWeight > 290.0 |
Uses of IDecisionRule in mic.rules |
---|
Classes in mic.rules that implement IDecisionRule | |
---|---|
class |
PB29
|
class |
PB30
|
class |
RuleAlertsForMIC
|
class |
SA1
|
class |
SA10
|
class |
SA11
Aliphatic and aromatic aldehydes. |
class |
SA12
Quinones |
class |
SA13
|
class |
SA14
|
class |
SA15
|
class |
SA16
|
class |
SA18
TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic) |
class |
SA19
If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic rings, the rule returns true. |
class |
SA2
SA2 |
class |
SA21
|
class |
SA22
|
class |
SA23
|
class |
SA24
|
class |
SA25
|
class |
SA26
Aromatic ring N-oxide. |
class |
SA27
Nitro aromatic (and more). |
class |
SA28
TODO - this is same as mutant.rules.SA28 -to reuse instead of copy |
class |
SA28bis
Aromatic mono- and dialkylamine (with exceptions). |
class |
SA28ter
Aromatic N-acyl amine. |
class |
SA29
|
class |
SA3
|
class |
SA30
|
class |
SA32
|
class |
SA33
|
class |
SA34
|
class |
SA35
|
class |
SA36
|
class |
SA4
|
class |
SA5
|
class |
SA6
|
class |
SA7
|
class |
SA8
|
class |
SA9
|
Methods in mic.rules with parameters of type IDecisionRule | |
---|---|
void |
MICTreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in michaelacceptors |
---|
Methods in michaelacceptors with parameters of type IDecisionRule | |
---|---|
void |
MATreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in michaelacceptors.rules |
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Classes in michaelacceptors.rules that implement IDecisionRule | |
---|---|
class |
Rule1
TODO with StructureAlertAmbit [CH]#CC=O doesn't match COC(=O)C#C while C#CC=O matches COC(=O)C#C |
class |
Rule10A
|
class |
Rule10B
|
class |
Rule12A
|
class |
Rule12B
|
class |
Rule13A
|
class |
Rule13B
|
class |
Rule2
|
class |
Rule3
|
class |
Rule4A
|
class |
Rule4B
|
class |
Rule5
|
class |
Rule6
|
class |
Rule7
|
class |
Rule9A
|
class |
Rule9B
|
Uses of IDecisionRule in mutant.rules |
---|
Classes in mutant.rules that implement IDecisionRule | |
---|---|
class |
QSAR6Applicable
|
class |
RuleABUnsaturatedAldehyde
Hits alfa-beta unsaturated aldehydes, exclude cyclic alfa-beta unsaturated aldehydes. |
class |
RuleAlertsForCarcinogenicity
|
class |
RuleAlertsForGenotoxicCarcinogenicity
|
class |
RuleAlertsNongenotoxicCarcinogenicity
|
class |
RuleAromaticAmineNoSulfonicGroup
|
class |
RuleAromaticDiazo
|
class |
RuleDACancerogenicityAromaticAmines
|
class |
RuleDAMutagenicityABUnsaturatedAldehydes
Returns true if structure is predicted as mutagen , based on linear discriminant analysis over descriptors MR, LogP, LUMO. |
class |
RuleDAMutagenicityAromaticAmines
Returns true if structure is predicted as mutagen , based on linear discriminant analysis. |
class |
RuleDerivedAromaticAmines
|
class |
SA1_gen
|
class |
SA10_gen
|
class |
SA11_gen
Aliphatic and aromatic aldehydes. |
class |
SA12_gen
Quinones |
class |
SA13_gen
|
class |
SA14_gen
|
class |
SA15_gen
|
class |
SA16_gen
|
class |
SA17_nogen
|
class |
SA18_gen
TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic) |
class |
SA19_gen
If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic rings, the rule returns true. |
class |
SA2_gen
SA2_gen |
class |
SA20_nogen
|
class |
SA21_gen
|
class |
SA22_gen
|
class |
SA23_gen
|
class |
SA24_gen
|
class |
SA25_gen
|
class |
SA26_gen
Aromatic ring N-oxide. |
class |
SA27_gen
Nitro aromatic (and more). |
class |
SA28_gen
[a;!$(a(a[A;!#1])(a[A;!#1]));!$(aa[CX3](=O)[OX2H1]);!$(aa[SX4](=[OX1])(=[OX1])([O-]));!$(aaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]))]!@[$([NX3;v3]([#1,CX4,CX3])([#1,CX4,CX3])),$([NX3;v3]([OX2H])([#1,CX4,CX3])),$([NX3;v3]([#1,CX4])OC=O)] |
class |
SA28bis_gen
Aromatic mono- and dialkylamine (with exceptions). |
class |
SA28ter_gen
Aromatic N-acyl amine. |
class |
SA29_gen
|
class |
SA3_gen
|
class |
SA30_gen
|
class |
SA31a_nogen
TODO Verify how many level of recursive smarts are supported TODO verify what's wrong with matching c;R |
class |
SA31b_nogen
|
class |
SA31c_nogen
|
class |
SA37_gen
|
class |
SA38_gen
|
class |
SA39_gen_and_nogen
|
class |
SA4_gen
|
class |
SA40_nogen
|
class |
SA41_nogen
|
class |
SA42_nogen
|
class |
SA43_nogen
|
class |
SA44_nogen
|
class |
SA45_nogen
|
class |
SA46_nogen
|
class |
SA47_nogen
|
class |
SA48_nogen
|
class |
SA49_nogen
|
class |
SA5_gen
|
class |
SA50_nogen
|
class |
SA51_nogen
|
class |
SA52_nogen
|
class |
SA53_nogen
|
class |
SA54_nogen
|
class |
SA55_nogen
|
class |
SA56_nogen
|
class |
SA6_gen
|
class |
SA7_gen
|
class |
SA8_gen
|
class |
SA9_gen
|
class |
UserInputABUnsaturatedAldehyde
|
class |
UserInputAromaticAmine
|
class |
VerifyAlertsGenotoxic
|
class |
VerifyAlertsNongenotoxic
|
Methods in mutant.rules with parameters of type IDecisionRule | |
---|---|
void |
MutantTreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in sicret.rules |
---|
Classes in sicret.rules that implement IDecisionRule | |
---|---|
class |
Rule12
VapourPressure < 0.0001 |
class |
Rule18
AqueousSolubility < 0.1 |
class |
Rule19
MoleculWeight > 370.0 |
class |
Rule20
LipidSolubility < 400.0 |
class |
Rule26
SurfaceTension > 62.0 |
class |
Rule27
MeltingPoint > 120.0 |
class |
Rule28
LogKow < 0.5 |
class |
Rule29
Molecular Weight > 370.0 |
class |
Rule30
Molecular Weight > 280.0 |
class |
Rule8
LipidSolubility < 0.4 |
class |
Rule9
MoleculWeight > 290.0 |
class |
RuleA_Lactams
A Lactams |
class |
RuleAcidAnhydrides
Acid anhydrides. |
class |
RuleAcidImides
Acid imides. |
class |
RuleAcrylicAcids
Acrylic acids. |
class |
RuleAcrylicAndMethacrylicEsters
Acrylic and methacrylic esters. SMARTS pattern [CX3](=[CX3])[CX3](=[OX1])[OX2]C. |
class |
RuleAldehydes
Aldehydes. SMARTS pattern [$([CX3H][#6]),$([CX3H2])]=[OX1]. |
class |
RuleAliphaticSaturatedAcidsAndHalogenatedAcids
Aliphatic Saturated Acids and Halogenated Acids. SMARTS pattern [AR0][CX3](=O)[OX2H1] [ClX1,BrX1][C;H2][CX3](=O)[OX2H1] |
class |
RuleAlkylAlkanolAmines
Alkyl Alkanol Amines. SMARTS pattern [OX2H][CX4][CX4][NX3;H2,H1;!$(NC=O)] |
class |
RuleAlphaAlkynes
Alpha alkynes. SMARTS pattern [CX4][CX2]#[CX2] |
class |
RuleAlphaHalogenatedAmidesAndThioamides
Alpha Halogenated Amides And Thioamides SMARTS pattern [CX3;$([R0][#6]Cl)](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] [#6](Cl)[CX3;!R](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] |
class |
RuleAqueousSolubility
AqueousSolubility < 0.1. |
class |
RuleAromaticAmines
Aromatic Amines. SMARTS pattern [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])] |
class |
RuleBenzylHalides
Benwyl halides. SMARTS pattern [ClX1,BrX1]Cc1ccccc1 |
class |
RuleBetaLactones
Beta lactones. SMARTS pattern [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])] |
class |
RuleC10_C20AliphaticAlcohols
C10-C20 Aliphatic Alcohols. SMARTS pattern [AR0][OH] |
class |
RuleCarbamoylHalide
Carbamoyl Halide. |
class |
RuleCatecholsResorcinolsHydroquinones
Catechols, Resorcinols Hydroquinones. |
class |
RuleDi_Tri_Nitrobenzenes
Di & Tri-Nitrobenzenes. |
class |
RuleEpoxides
Epoxides. SMARTS pattern OX2r3]1[#6r3][#6r3]1 |
class |
RuleEthyleneGlycolEthers
Ethylene Glycol Ethers SMARTS pattern [OX2H][CX4;$([H1]),$(C[#6])][CX4;$([H1]),$(C[#6])][OX2H] |
class |
RuleHalogenatedAlkanesAndAlkenes
Halogenated Alkanes And Alkenes SMARTS patterns [FX1,ClX1,BrX1,IX1][CX4H3] [FX1,ClX1,BrX1,IX1][CX4H2][#6] [FX1,ClX1,BrX1,IX1][CX3]=[CX3] |
class |
RuleHalonitrobenzene
Halonitrobenzene. |
class |
RuleHasOnlyC_H_O
Contains only these elements C,O. |
class |
RuleHasOnlyC_H_O_Halogen
Contains only these elements C,O,Halogen. |
class |
RuleHasOnlyC_H_O_N
Contains only these elements C,O,N. |
class |
RuleHasOnlyC_H_O_N_Halogen
Contains only these elements C,O,N,Halogen. |
class |
RuleHasOnlyC_H_O_N_S
Contains only these elements C,O,N,S,Halogen. |
class |
RuleHydroPeroxides
HydroPeroxides. SMARTS pattern [OX2H][OX2] |
class |
RuleKetenes
Ketenes. SMARTS pattern [CX3]=[CX2]=[OX1] |
class |
RuleKetones
Ketones. SMARTS pattern [#6][CX3](=[OX1])[#6] |
class |
RuleLipidSolubility
LipidSolubility < 0.01. |
class |
RuleLogP
LogP < 3.1. Expects property to be read from IMolecule.getProperty( RuleLogP.LogKow ). |
class |
RuleMeltingPoint
MeltingPoint < 200. |
class |
RuleMolWeight
Molecular weight > 350. |
class |
RuleOandPQuinones
O and P Quinones. Substructures O=C1C=CC=CC1(=O) O=C1C=CC(=O)C=C1 |
class |
RulePhenols
Phenols. Substructure c1ccccc1O[H] |
class |
RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts
Rule Quaternary Organic Ammonium And Phosphonium Salts |
class |
RuleSurfaceTension
SurfaceTension > 62.0. |
class |
RuleTriAndTetraHalogenatedBenzenes
Tri And Tetra Halogenated Benzenes. Substructure ClC1=CC(Cl)C(Cl)C(Cl)C1 ClC1C=CC(Cl)C(Cl)C1(Cl) ClC1C=CCC(Cl)C1(Cl) |
class |
RuleVapourPressure
VapourPressure < 0.0001. |
Uses of IDecisionRule in structurefeatures.rules |
---|
Classes in structurefeatures.rules that implement IDecisionRule | |
---|---|
class |
RuleAlcohol
|
class |
RuleAlkylAldehyde
|
class |
RuleAlkylHydrazine
|
class |
RuleAlkylPhosphonate
|
class |
RuleAmine
|
class |
RuleAromaticAldehyde
|
class |
RuleAromaticAzo
|
class |
RuleAromaticNitro
|
class |
RuleArylMethylHalide
|
class |
RuleAziridine
|
class |
RuleAzo
|
class |
RuleBenzene
|
class |
RuleEther
|
class |
RuleFuran
|
class |
RuleHalide
|
class |
RuleHeterocycle
|
class |
RuleHydrazine
|
class |
RuleIminomethyl
|
class |
RuleNChloramine
|
class |
RuleNHydroxy
|
class |
RuleNitro
|
class |
RuleNitrogenMustard
|
class |
RuleNitrosamine
|
class |
RuleNitroso
|
class |
RuleNMethylol
|
class |
RuleNOxide
|
class |
RuleNucleosides
|
class |
RulePhosphoricGroups
|
class |
RuleprimaryAlkylHalide
|
class |
RulePropiolactone
|
class |
RuleUrethaneDerivatives
|
Uses of IDecisionRule in toxTree.core |
---|
Subinterfaces of IDecisionRule in toxTree.core | |
---|---|
interface |
IRuleRange
|
interface |
IRuleSubstructures
An interface to support substructure rules |
interface |
IRuleValue
|
Methods in toxTree.core that return IDecisionRule | |
---|---|
IDecisionRule |
IDecisionRuleEditor.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
IDecisionTransition.getBranch(boolean answer)
|
IDecisionRule |
IDecisionMethod.getBranch(IDecisionRule rule,
boolean answer)
|
IDecisionRule |
IDecisionRuleEditor.getRule()
|
IDecisionRule |
IDecisionRuleList.getRule(int index)
|
IDecisionRule |
IDecisionResult.getRule(int index)
|
IDecisionRule |
IDecisionMethod.getRule(int id)
|
IDecisionRule |
IDecisionMethod.getRule(java.lang.String name)
|
IDecisionRule |
IDecisionMethod.getTopRule()
|
Methods in toxTree.core with parameters of type IDecisionRule | |
---|---|
void |
IDecisionMethod.addDecisionRule(IDecisionRule rule)
|
void |
IDecisionRuleList.addRule(IDecisionRule rule)
|
void |
IDecisionResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
IDecisionRule |
IDecisionRuleEditor.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
IDecisionMethod.getBranch(IDecisionRule rule,
boolean answer)
|
IDecisionCategory |
IDecisionMethod.getCategory(IDecisionRule rule,
boolean answer)
|
void |
IDecisionResult.hilightAlert(IDecisionRule rule)
|
java.lang.Object |
IProcessRule.process(IDecisionMethod method,
IDecisionRule rule)
|
void |
IDecisionMethod.setDecisionRule(IDecisionRule rule)
|
void |
IDecisionRuleEditor.setRule(IDecisionRule rule)
|
void |
IDecisionMethod.walkRules(IDecisionRule rule,
IProcessRule processor)
|
Uses of IDecisionRule in toxtree.plugins.dnabinding.rules |
---|
Classes in toxtree.plugins.dnabinding.rules that implement IDecisionRule | |
---|---|
class |
DNABindingRule
Parent class for all skin sens rules |
class |
RuleDNABindingAlerts
|
class |
SN1Rule
SNAR |
class |
VerifyAlertsDNABinding
|
Methods in toxtree.plugins.dnabinding.rules with parameters of type IDecisionRule | |
---|---|
void |
DNABindingTreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in toxtree.plugins.func.rules |
---|
Classes in toxtree.plugins.func.rules that implement IDecisionRule | |
---|---|
class |
FG
|
class |
FG1
|
class |
FG10
|
class |
FG11
|
class |
FG12
|
class |
FG13
|
class |
FG14
|
class |
FG15
|
class |
FG16
|
class |
FG17
|
class |
FG18
|
class |
FG19
|
class |
FG2
|
class |
FG20
|
class |
FG21
|
class |
FG22
|
class |
FG23_1
|
class |
FG23_2
|
class |
FG23_3
|
class |
FG23_4
|
class |
FG23_5
|
class |
FG23_6
|
class |
FG23_7
|
class |
FG23_8
|
class |
FG23_LS
|
class |
FG24_1
|
class |
FG24_2
|
class |
FG24_3
|
class |
FG24_LS
|
class |
FG25
|
class |
FG26
|
class |
FG27
|
class |
FG28
|
class |
FG29
|
class |
FG3_1
|
class |
FG3_2
|
class |
FG3_LS
|
class |
FG30
|
class |
FG31_1
|
class |
FG31_2
|
class |
FG31_3
|
class |
FG31_4
|
class |
FG31_5
|
class |
FG31_6
|
class |
FG31_7
|
class |
FG31_8
|
class |
FG31_9
|
class |
FG31_LS
|
class |
FG32
|
class |
FG33_1
|
class |
FG33_2
|
class |
FG33_3
|
class |
FG33_4
|
class |
FG33_5
|
class |
FG33_6
|
class |
FG33_7
|
class |
FG33_8
|
class |
FG33_LS
|
class |
FG34_1
|
class |
FG34_2
|
class |
FG34_LS
|
class |
FG35_1
|
class |
FG35_10
|
class |
FG35_11
|
class |
FG35_12
|
class |
FG35_13
|
class |
FG35_2
|
class |
FG35_3
|
class |
FG35_4
|
class |
FG35_5
|
class |
FG35_6
|
class |
FG35_7
|
class |
FG35_8
|
class |
FG35_9
|
class |
FG35_LS
|
class |
FG36
|
class |
FG37_1
|
class |
FG37_2
|
class |
FG37_3
|
class |
FG37_4
|
class |
FG37_LS
|
class |
FG38
|
class |
FG39
|
class |
FG4
|
class |
FG4_1
|
class |
FG4_2
|
class |
FG4_LS
|
class |
FG40
|
class |
FG41_1
|
class |
FG41_2
|
class |
FG41_3
|
class |
FG41_4
|
class |
FG41_5
|
class |
FG41_LS
|
class |
FG42
|
class |
FG43
|
class |
FG44
|
class |
FG45
|
class |
FG46_1
|
class |
FG46_2
|
class |
FG46_LS
|
class |
FG47
|
class |
FG48_1
|
class |
FG48_2
|
class |
FG48_LS
|
class |
FG49
|
class |
FG5
|
class |
FG50_1
|
class |
FG50_2
|
class |
FG50_3
|
class |
FG50_LS
|
class |
FG51_1
|
class |
FG51_2
|
class |
FG51_3
|
class |
FG51_LS
|
class |
FG52_1
|
class |
FG52_2
|
class |
FG52_3
|
class |
FG52_LS
|
class |
FG53_1
|
class |
FG53_2
|
class |
FG53_3
|
class |
FG53_LS
|
class |
FG54
|
class |
FG55
|
class |
FG56
|
class |
FG57
|
class |
FG58
|
class |
FG59
|
class |
FG6
|
class |
FG60
|
class |
FG61
|
class |
FG62
|
class |
FG63
|
class |
FG64
|
class |
FG65
|
class |
FG66
|
class |
FG67
|
class |
FG68
|
class |
FG69
|
class |
FG7
|
class |
FG70
|
class |
FG71
|
class |
FG72
|
class |
FG73
|
class |
FG74_1
|
class |
FG74_2
|
class |
FG74_3
|
class |
FG74_4
|
class |
FG74_5
|
class |
FG74_6
|
class |
FG74_7
|
class |
FG74_LS
|
class |
FG75_1
|
class |
FG75_2
|
class |
FG75_3
|
class |
FG75_4
|
class |
FG75_LS
|
class |
FG76
|
class |
FG77
|
class |
FG78_1
|
class |
FG78_2
|
class |
FG78_3
|
class |
FG78_4
|
class |
FG78_LS
|
class |
FG79_1
|
class |
FG79_2
|
class |
FG79_3
|
class |
FG79_4
|
class |
FG79_LS
|
class |
FG8
|
class |
FG80_1
|
class |
FG80_2
|
class |
FG80_LS
|
class |
FG81_1
|
class |
FG81_2
|
class |
FG81_3
|
class |
FG81_4
|
class |
FG81_LS
|
class |
FG82_1
|
class |
FG82_2
|
class |
FG82_3
|
class |
FG82_4
|
class |
FG82_LS
|
class |
FG83_1
|
class |
FG83_2
|
class |
FG83_3
|
class |
FG83_4
|
class |
FG83_LS
|
class |
FG84_1
|
class |
FG84_2
|
class |
FG84_LS
|
class |
FG85
|
class |
FG86
|
class |
FG87
|
class |
FG88
|
class |
FG89
|
class |
FG9
|
class |
FG90
|
class |
RuleAlertsForFunc
|
Methods in toxtree.plugins.func.rules with parameters of type IDecisionRule | |
---|---|
void |
FuncTreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in toxtree.plugins.kroes.rules |
---|
Classes in toxtree.plugins.kroes.rules that implement IDecisionRule | |
---|---|
class |
KroesRule10
|
class |
KroesRule11
|
class |
KroesRule12
Does estimated intake exceed 1800 µg/day ? |
class |
KroesRule2
Are there structural alerts that raise concern for potential genotoxicity? |
class |
KroesRule3
Is the chemical an aflatoxin-like, azoxy-, or N-nitroso compound |
class |
KroesRule4
Does estimated intake exceed TTC of 0.15 µg/day ? |
class |
KroesRule5
Does estimated intake exceed TTC of 1.5 mcg/day ? |
class |
KroesRule6
Is the compound an organophosphate? |
class |
KroesRule7
Does estimated intake exceed TTC of 18µg/day ? |
class |
KroesRule8
Is the compound in Cramer structural class III? |
class |
KroesRule9
|
class |
RuleKroesFig1Q1
TODO refactor with SMARTS |
class |
RuleVerifyIntake
|
Uses of IDecisionRule in toxtree.plugins.lewis.rules |
---|
Classes in toxtree.plugins.lewis.rules that implement IDecisionRule | |
---|---|
class |
Rule_areadepthratio
|
class |
Rule_high_AreaDepthRatio
|
class |
Rule_high_pKa
|
class |
Rule_highLogP
|
class |
Rule_highVolume
|
class |
Rule_lowVolume
|
class |
Rule_volume
|
Uses of IDecisionRule in toxtree.plugins.moa.rules |
---|
Classes in toxtree.plugins.moa.rules that implement IDecisionRule | |
---|---|
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 IDecisionRule in toxtree.plugins.proteinbinding.rules |
---|
Classes in toxtree.plugins.proteinbinding.rules that implement IDecisionRule | |
---|---|
class |
ProteinBindingRule
Parent class for all skin sens rules |
class |
RuleProteinBindingAlerts
|
class |
VerifyAlertsProteinBinding
|
Methods in toxtree.plugins.proteinbinding.rules with parameters of type IDecisionRule | |
---|---|
void |
ProteinBindingTreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in toxtree.plugins.search.rules |
---|
Classes in toxtree.plugins.search.rules that implement IDecisionRule | |
---|---|
class |
Find
Compound lookup |
Uses of IDecisionRule in toxtree.plugins.skinsensitisation.rules |
---|
Classes in toxtree.plugins.skinsensitisation.rules that implement IDecisionRule | |
---|---|
class |
AcylTransferRule
Acyl transfer |
class |
MichaelAcceptorRule
Michael acceptors |
class |
RuleSkinSensitisationAlerts
|
class |
ShiffBaseRule
Shiff base |
class |
SkinSensitisationRule
Parent class for all skin sens rules |
class |
SN2Rule
SN2 |
class |
SNARRule
SNAR |
class |
VerifyAlertsSkinSensitisation
|
Methods in toxtree.plugins.skinsensitisation.rules with parameters of type IDecisionRule | |
---|---|
void |
SkinSensitisationTreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in toxtree.plugins.smartcyp.rules |
---|
Classes in toxtree.plugins.smartcyp.rules that implement IDecisionRule | |
---|---|
class |
MetaboliteGenerator
|
class |
SMARTCYPRuleHigherRank
|
class |
SMARTCYPRuleRank1
|
class |
SMARTCYPRuleRank2
|
class |
SMARTCYPRuleRank3
|
Uses of IDecisionRule in toxTree.qsar |
---|
Classes in toxTree.qsar that implement IDecisionRule | |
---|---|
class |
LinearDiscriminantRule
Uses LinearQSARModel and returns true if LinearQSARModel.predict(IAtomContainer) is >= LinearDiscriminantRule.getThreshold() and false otherwise. |
Uses of IDecisionRule in toxTree.tree |
---|
Classes in toxTree.tree that implement IDecisionRule | |
---|---|
class |
AbstractRule
An abstract class implementing IDecisionRule interface. |
class |
AbstractRuleHilightHits
|
class |
DecisionNode
A decision node to be used in UserDefinedTree . |
class |
MultiLabelDecisionNode
|
Fields in toxTree.tree declared as IDecisionRule | |
---|---|
protected IDecisionRule |
RuleResult.rule
|
protected IDecisionRule |
DecisionNode.rule
|
Fields in toxTree.tree with type parameters of type IDecisionRule | |
---|---|
protected java.util.ArrayList<IDecisionRule> |
RulesList.list
|
protected java.util.ArrayList<IDecisionRule> |
DecisionNodesList.list
|
Methods in toxTree.tree that return IDecisionRule | |
---|---|
static IDecisionRule |
AbstractRule.createRule(java.lang.String className)
|
IDecisionRule |
RulesList.get(int arg0)
|
IDecisionRule |
DecisionNodesList.get(int arg0)
|
IDecisionRule |
DecisionNode.getBranch(boolean answer)
returns the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true |
IDecisionRule |
UserDefinedTree.getBranch(IDecisionRule rule,
boolean answer)
|
IDecisionRule |
BatchDecisionResultsList.getBranch(IDecisionRule rule,
boolean answer)
|
IDecisionRule |
UserDefinedTree.getBranch(int ruleId,
boolean answer)
|
IDecisionRule |
RuleResult.getRule()
|
IDecisionRule |
DecisionNode.getRule()
|
IDecisionRule |
UserDefinedTree.getRule(int id)
|
IDecisionRule |
TreeResult.getRule(int index)
|
IDecisionRule |
RulesList.getRule(int index)
returns a rule IDecisionRule |
IDecisionRule |
DecisionNodesList.getRule(int index)
|
IDecisionRule |
BatchDecisionResultsList.getRule(int id)
|
IDecisionRule |
AbstractTree.getRule(int id)
|
IDecisionRule |
BatchDecisionResultsList.getRule(java.lang.String name)
|
IDecisionRule |
AbstractTree.getRule(java.lang.String name)
|
IDecisionRule |
BatchDecisionResultsList.getTopRule()
|
IDecisionRule |
AbstractTree.getTopRule()
|
IDecisionRule |
RulesList.remove(int arg0)
|
IDecisionRule |
DecisionNodesList.remove(int arg0)
|
IDecisionRule |
RulesList.set(int arg0,
IDecisionRule arg1)
|
IDecisionRule |
DecisionNodesList.set(int arg0,
IDecisionRule arg1)
|
Methods in toxTree.tree that return types with arguments of type IDecisionRule | |
---|---|
java.util.ArrayList<IDecisionRule> |
DecisionNodesList.getList()
|
java.util.Iterator<IDecisionRule> |
DecisionNodesList.iterator()
|
java.util.ListIterator<IDecisionRule> |
DecisionNodesList.listIterator()
|
java.util.ListIterator<IDecisionRule> |
DecisionNodesList.listIterator(int arg0)
|
java.util.List<IDecisionRule> |
DecisionNodesList.subList(int arg0,
int arg1)
|
Methods in toxTree.tree with parameters of type IDecisionRule | |
---|---|
boolean |
RulesList.add(IDecisionRule arg0)
Adds an object only if it is a rule IDecisionRule
otherwise returns false |
boolean |
DecisionNodesList.add(IDecisionRule arg0)
|
void |
RulesList.add(int arg0,
IDecisionRule arg1)
not implemented |
void |
DecisionNodesList.add(int arg0,
IDecisionRule arg1)
|
void |
BatchDecisionResultsList.addDecisionRule(IDecisionRule rule)
|
void |
AbstractTree.addDecisionRule(IDecisionRule rule)
|
void |
RulesList.addRule(IDecisionRule rule)
adds a rule IDecisionRule |
void |
MultiLabelDecisionNodesList.addRule(IDecisionRule rule)
|
void |
DecisionNodesList.addRule(IDecisionRule rule)
|
void |
TreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
void |
BatchDecisionResultsList.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
IDecisionRule |
UserDefinedTree.getBranch(IDecisionRule rule,
boolean answer)
|
IDecisionRule |
BatchDecisionResultsList.getBranch(IDecisionRule rule,
boolean answer)
|
IDecisionCategory |
UserDefinedTree.getCategory(IDecisionRule rule,
boolean answer)
|
IDecisionCategory |
BatchDecisionResultsList.getCategory(IDecisionRule rule,
boolean answer)
|
void |
TreeResult.hilightAlert(IDecisionRule rule)
|
void |
BatchDecisionResultsList.hilightAlert(IDecisionRule rule)
|
java.lang.Object |
Tree2PrefuseGraph.process(IDecisionMethod method,
IDecisionRule rule)
|
java.lang.Object |
SimpleTreePrinter.process(IDecisionMethod method,
IDecisionRule rule)
|
java.lang.Object |
ReportTreePrinter.process(IDecisionMethod method,
IDecisionRule rule)
|
java.lang.Object |
PDFTreePrinter.process(IDecisionMethod method,
IDecisionRule rule)
|
IDecisionRule |
RulesList.set(int arg0,
IDecisionRule arg1)
|
IDecisionRule |
DecisionNodesList.set(int arg0,
IDecisionRule arg1)
|
void |
MultiLabelDecisionNode.setBranch(boolean answer,
IDecisionRule node)
|
void |
DecisionNode.setBranch(boolean answer,
IDecisionRule node)
Sets the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true |
void |
BatchDecisionResultsList.setDecisionRule(IDecisionRule rule)
|
void |
AbstractTree.setDecisionRule(IDecisionRule rule)
|
void |
RuleResult.setRule(IDecisionRule rule)
|
void |
DecisionNode.setRule(IDecisionRule rule)
Sets rule |
protected boolean |
AbstractTree.verifyResidues(org.openscience.cdk.interfaces.IAtomContainerSet mols,
IDecisionResult result,
IDecisionRule rule)
|
protected boolean |
UserDefinedTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol,
IDecisionResult result,
IDecisionRule topRule)
|
protected abstract boolean |
AbstractTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol,
IDecisionResult result,
IDecisionRule rule)
abstract method, to be implemented in the child class |
protected prefuse.data.Node |
Tree2PrefuseGraph.walkRules(IDecisionMethod tree,
IDecisionRule rule,
java.util.ArrayList<java.lang.Integer> visited)
|
protected void |
AbstractTree.walkRules(IDecisionRule rule,
java.util.ArrayList<java.lang.Integer> visited,
IProcessRule processor)
|
void |
BatchDecisionResultsList.walkRules(IDecisionRule rule,
IProcessRule processor)
|
void |
AbstractTree.walkRules(IDecisionRule rule,
IProcessRule processor)
|
protected java.lang.String |
ReportTreePrinter.writeMolecule(IDecisionRule rule,
boolean answer)
|
protected void |
AbstractTreePrinter.writeMolecule(IDecisionRule rule,
boolean answer,
java.io.OutputStream out)
|
Method parameters in toxTree.tree with type arguments of type IDecisionRule | |
---|---|
void |
DecisionNodesList.setList(java.util.ArrayList<IDecisionRule> list)
|
Constructors in toxTree.tree with parameters of type IDecisionRule | |
---|---|
DecisionNode(IDecisionRule rule)
Constructs a decision node with rule, null next nodes. |
|
DecisionNode(IDecisionRule rule,
DecisionNode nodeNo,
DecisionNode nodeYes)
Constructs a decision node with rule, nodeNo at branch NO and nodeYes at branch YES. |
|
DecisionNode(IDecisionRule rule,
DecisionNode nodeNo,
DecisionNode nodeYes,
IDecisionCategory categoryNo,
IDecisionCategory categoryYes)
|
|
MultiLabelDecisionNode(IDecisionRule rule)
Constructs a decision node with rule, null next nodes. |
|
RuleResult(IDecisionRule rule,
boolean result)
|
|
RuleResult(IDecisionRule rule,
boolean result,
IDecisionCategory category)
|
Uses of IDecisionRule in toxTree.tree.cramer |
---|
Classes in toxTree.tree.cramer that implement IDecisionRule | |
---|---|
class |
Rule32
Rule 32 of the Cramer scheme (see CramerRules ) |
class |
Rule3FuncGroups
Rule 21 of the Cramer scheme (see CramerRules ) |
class |
Rule3MemberedHeterocycle
3-membered heterocycle. |
class |
RuleAcyclicAcetalEsterOfQ30
Rule 31 of the Cramer scheme (see CramerRules ) |
class |
RuleAliphaticWithSomeFuncGroups
Rule 20 of the Cramer scheme (see CramerRules ) |
class |
RuleCommonComponentOfFood
Rule 22 of the Cramer scheme (see CramerRules ) |
class |
RuleCyclopropaneEtc
Rule 25 of the Cramer scheme (see CramerRules ) |
class |
RuleHasOnlySaltSulphonateSulphate
Rule 4 of the Cramer scheme (see CramerRules ) |
class |
RuleHasOtherThanC_H_O_N_S2
Rule 3 of the Cramer scheme (see CramerRules ) |
class |
RuleHeteroaromatic
Rule 12 of the Cramer scheme (see CramerRules ) |
class |
RuleHeterocyclicComplexSubstituents
Rule 11 of the Cramer scheme (see CramerRules ) |
class |
RuleIsAromatic
Rule 23 of the Cramer scheme (see CramerRules )
Note this is descendant of RuleAromatic and therefore
follows the Hueckel rule, rather than verifying for the presence of
benzene, furan, thiophene, pyridine or pyrrole ring |
class |
RuleIsCommonTerpene
Rule 16 of the Cramer scheme (see CramerRules )
Verifies if the substance is a terpene |
class |
RuleIsHeterocyclic
Rule 7 of the Cramer scheme (see CramerRules ) |
class |
RuleIsOpenChain
Rule 19 of the Cramer scheme (see CramerRules ) |
class |
RuleKetoneAlcoholEtc
Rule 18 of the Cramer scheme (see CramerRules ) |
class |
RuleLactoneOrCyclicDiester
Rule 8 of the Cramer scheme (see CramerRules ) |
class |
RuleLactonesFusedOrUnsaturated
Rule 9 of the Cramer scheme (see CramerRules ) |
class |
RuleManyAromaticRings14
Rule 14 of the Cramer scheme (see CramerRules ) |
class |
RuleManyAromaticRings28
Rule 28 of the Cramer scheme (see CramerRules ) |
class |
RuleMonocarbocyclic
Rule 24 of the Cramer scheme (see CramerRules ) |
class |
RuleMonocycloalkanoneEtc
Rule 26 of the Cramer scheme (see CramerRules ) |
class |
RuleNormalBodyConstituent
Rule 1 of the Cramer scheme (see CramerRules ) |
class |
RuleOnlyFuncGroupsQ30
Rule 32 of the Cramer scheme (see CramerRules ) |
class |
RuleReadilyHydrolysed29
Rule 29 of the Cramer scheme (see CramerRules ) |
class |
RuleReadilyHydrolysedMononuclear
Rule 15 of the Cramer scheme (see CramerRules ) |
class |
RuleReadilyHydrolysedToCommonterpene
Rule 17 of the Cramer scheme (see CramerRules ) |
class |
RuleRingComplexSubstituents30
Rule 30 of the Cramer scheme (see CramerRules ) |
class |
RuleRingsWithSubstituents
Rule 27 of the Cramer scheme (see CramerRules ) |
class |
RuleRingWithSubstituents
Rule 13 of the Cramer scheme (see CramerRules ) |
class |
RuleSimplyBranchedAliphaticHydrocarbon
Implementation of Cramer rule No.5 Simply branched aliphatic or a common carbohydrate A descendant of RuleCarbohydrate |
class |
RuleSomeBenzeneDerivatives
Rule 6 of the Cramer scheme (see CramerRules ) |
class |
RuleSufficientSulphonateGroups
Rule 33 of the Cramer scheme (see CramerRules ) |
class |
RuleToxicFunctionalGroups
Rule 2 of the Cramer scheme (see CramerRules ) |
Methods in toxTree.tree.cramer with parameters of type IDecisionRule | |
---|---|
void |
CramerTreeResult.addRuleResult(IDecisionRule rule,
boolean value,
org.openscience.cdk.interfaces.IAtomContainer molecule)
|
Uses of IDecisionRule in toxTree.tree.rules |
---|
Classes in toxTree.tree.rules that implement IDecisionRule | |
---|---|
class |
RuleAllAllowedElements
|
class |
RuleAllSubstructures
Verifies if all of the fragments are a substructure of moleclue |
class |
RuleAnySubstituents
Verifies if the molecule consists of only allowed substituents |
class |
RuleAnySubstructure
Verifies if the molecule has at least one substructure of the list |
class |
RuleAromatic
Verifies if the molecule is aromatic by applying the Hueckel rule |
class |
RuleCarbohydrate
Verifies if the molecule is a carbohydrate |
class |
RuleCommonTerpene
Verifies if the molecule is a common terpene |
class |
RuleDescriptor
An abstract class to allow for descriptor analysis |
class |
RuleDescriptorRange
Verifies if the descriptor is within a range |
class |
RuleElements
Verifies if the molecule consists of only allowed elements |
class |
RuleHeterocyclic
Verifies if the molecule is heterocyclic |
class |
RuleInitAlertCounter
|
class |
RuleLipinski5
Returns true if all Lipinski Rule of Five are true |
class |
RuleManyAromaticRings
Verifies if there are many aromatic rings |
class |
RuleMolecularMassRange
Molecular mass in [ RuleDescriptorRange.getMinValue() ,RuleDescriptorRange.getMaxValue() ]
TODO add description |
class |
RuleOnlyAllowedSubstructures
Verifies if the structure contains only allowed substructures |
class |
RuleOpenChain
Verifies if the moleucle is open chain |
class |
RuleReadilyHydrolised
Verifies if a compound is readily hydrolised |
class |
RuleRingAllowedSubstituents
A rule to analyze ring substituents |
class |
RuleRingOtherThanAllowedSubstituents
A rule to analyze ring substituents |
class |
RuleRings
|
class |
RuleRingSubstituents
A rule to analyze ring substituents |
class |
RuleStructuresList
A rule, which returns true if the query is isomorphic to one of the structures read from a preconfigured file of a type SDF, SMI, CSV |
class |
RuleSubstructures
An abstract class to implement substructure rules |
class |
RuleVerifyAlertsCounter
|
class |
RuleVerifyProperty
Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value. |
class |
StructureAlert
|
class |
StructureAlertAmbit
|
class |
StructureAlertCDK
|
class |
UserInputRule
|
Uses of IDecisionRule in toxTree.tree.rules.smarts |
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Classes in toxTree.tree.rules.smarts that implement IDecisionRule | |
---|---|
class |
AbstractRuleSmartSubstructure<T>
|
class |
RuleSMARTSSubstructureAmbit
An IDecisionRule, making use of Ambit SMARTS parser. |
class |
RuleSMARTSubstructure
For backward compatibility |
class |
RuleSMARTSubstructureCDK
An IDecisionRule, making use of CDK SMARTS parser. |
Uses of IDecisionRule in toxTree.ui |
---|
Methods in toxTree.ui with parameters of type IDecisionRule | |
---|---|
IDecisionRuleEditor |
IEditorFactory.createEditor(IDecisionRule rule)
|
IDecisionRuleEditor |
EditorFactory.createEditor(IDecisionRule rule)
|
Uses of IDecisionRule in toxtree.ui.editors |
---|
Methods in toxtree.ui.editors with parameters of type IDecisionRule | |
---|---|
IDecisionRuleEditor |
SwingEditorFactory.createEditor(IDecisionRule rule)
|
Uses of IDecisionRule in toxtree.ui.tree |
---|
Methods in toxtree.ui.tree that return IDecisionRule | |
---|---|
static IDecisionRule |
SelectListDialog.selectNewRule(java.awt.Component parent,
java.lang.ClassLoader classLoader)
Provides a list of names of the classes implementing IDecisionRule
If the user selects an object, the rule is created and returned Uses Introspection.getAvailableRuleTypes(ClassLoader) |
Methods in toxtree.ui.tree with parameters of type IDecisionRule | |
---|---|
protected boolean |
TreeLayout.isVisited(IDecisionRule node)
|
void |
TreeDrawing.setNode(IDecisionRule node)
|
protected void |
TreeEditorPanel.setRule(IDecisionRule rule)
|
void |
EditTreeActions.setRule(IDecisionRule rule)
|
protected void |
TreeLayout.setVisited(IDecisionRule node,
boolean value)
|
Constructors in toxtree.ui.tree with parameters of type IDecisionRule | |
---|---|
QueryAtomContainersModel(java.util.List list,
IDecisionRule rule)
|
|
QueryAtomContainersModel(QueryAtomContainers list,
IDecisionRule rule)
|
Uses of IDecisionRule in toxtree.ui.tree.actions |
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Fields in toxtree.ui.tree.actions declared as IDecisionRule | |
---|---|
protected IDecisionRule |
EditRuleAction.rule
|
protected IDecisionRule |
AbstractRuleAction.rule
|
Methods in toxtree.ui.tree.actions that return IDecisionRule | |
---|---|
IDecisionRule |
IRuleAction.getRule()
|
IDecisionRule |
EditRuleAction.getRule()
|
IDecisionRule |
AbstractRuleAction.getRule()
|
Methods in toxtree.ui.tree.actions with parameters of type IDecisionRule | |
---|---|
void |
IRuleAction.setRule(IDecisionRule rule)
|
void |
EditRuleAction.setRule(IDecisionRule rule)
|
void |
AbstractRuleAction.setRule(IDecisionRule rule)
|
static IDecisionMethod |
NewRuleAction.treeFromRule(IDecisionRule rule)
|
Constructors in toxtree.ui.tree.actions with parameters of type IDecisionRule | |
---|---|
AbstractRuleAction(IDecisionRule rule)
|
|
AbstractRuleAction(IDecisionRule rule,
java.lang.String arg0)
|
|
AbstractRuleAction(IDecisionRule rule,
java.lang.String arg0,
javax.swing.Icon arg1)
|
|
SubstructureFromListAction(IDecisionRule rule)
|
|
SubstructureFromListAction(IDecisionRule rule,
java.lang.String arg0)
|
|
SubstructureFromListAction(IDecisionRule rule,
java.lang.String arg0,
javax.swing.Icon arg1)
|
|
SubstructuresFromFileAction(IDecisionRule rule)
|
|
SubstructuresFromFileAction(IDecisionRule rule,
java.lang.String arg0)
|
|
SubstructuresFromFileAction(IDecisionRule rule,
java.lang.String arg0,
javax.swing.Icon arg1)
|
Uses of IDecisionRule in toxtree.ui.tree.rules |
---|
Fields in toxtree.ui.tree.rules declared as IDecisionRule | |
---|---|
protected IDecisionRule |
RulePanel.rule
|
protected IDecisionRule |
RuleMoleculeEditAction.rule
|
protected IDecisionRule |
RuleEditor.rule
|
Methods in toxtree.ui.tree.rules that return IDecisionRule | |
---|---|
IDecisionRule |
SubstructureRulePanel.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
SMARTSRuleEditor.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
RulePanel.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
RuleEditor.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
SubstructureRulePanel.getRule()
|
IDecisionRule |
RulePanel.getRule()
|
IDecisionRule |
RuleMoleculeEditAction.getRule()
|
IDecisionRule |
RuleEditor.getRule()
|
Methods in toxtree.ui.tree.rules with parameters of type IDecisionRule | |
---|---|
IDecisionRule |
SubstructureRulePanel.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
SMARTSRuleEditor.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
RulePanel.edit(java.awt.Container owner,
IDecisionRule rule)
|
IDecisionRule |
RuleEditor.edit(java.awt.Container owner,
IDecisionRule rule)
|
void |
SubstructureRulePanel.setRule(IDecisionRule rule)
|
void |
RuleStructuresPanel.setRule(IDecisionRule rule)
|
void |
RulePanel.setRule(IDecisionRule rule)
|
void |
RuleMoleculeEditAction.setRule(IDecisionRule rule)
|
void |
RuleEditor.setRule(IDecisionRule rule)
|
Constructors in toxtree.ui.tree.rules with parameters of type IDecisionRule | |
---|---|
RuleEditor(IDecisionRule object)
|
|
RuleExampleEditAction(IDecisionRule rule,
boolean answer)
|
|
RuleExampleEditAction(IDecisionRule rule,
boolean answer,
java.lang.String arg0)
|
|
RuleExampleEditAction(IDecisionRule rule,
boolean answer,
java.lang.String arg0,
javax.swing.Icon arg1)
|
|
RulePanel(IDecisionRule rule)
|
Uses of IDecisionRule in verhaar.rules |
---|
Classes in verhaar.rules that implement IDecisionRule | |
---|---|
class |
Rule01
Consists only of C,H,N,O,S,halogens (exluding I). |
class |
Rule03
Have a molecular mass (MW) not more than 600 Daltons. |
class |
Rule11
Does not contain I. |
class |
Rule13
Contain only C&H. |
class |
Rule14
Contain only C,H and halogen. |
class |
Rule141
Acyclic compound NOT containing halogen at beta-positions from unsaturations (e.g. |
class |
Rule142
Monocyclic compounds substituted with halogens. |
class |
Rule143
Monocyclic compounds that are unsubstituted or substituted with acyclic structures containing only C&H or complying with rule Rule141 . |
class |
Rule144
Polycyclic compounds that are unsubstituted or substituted with acyclic structures containing only C&H or complying with Rule141 . |
class |
Rule15
Contain only C,H,O. |
class |
Rule151
Linear ethers or monocyclic mono ethers, but not epoxides or peroxides. |
class |
Rule152
Aliphatic alcohols but not allylic/propargylic alcohols. |
class |
Rule153
Alcohols with aromatic moieties, but NOT phenols or benzylic alcohols. |
class |
Rule154
Ketones, but not alpha-, beta unsaturated ketones (e.g. |
class |
Rule16
Contain only C,H,N. |
class |
Rule161
Aliphatic secondary or tertiary amines. |
class |
Rule17
Contain only C,H,O and halogen. |
class |
Rule171
Halogenated compounds that comply with rule Rule15 but not alpha-, beta- halogen substituted compounds. |
class |
Rule21
Non- or weakly acidic phenols. |
class |
Rule22
Anilines with one nitro substituent and/or one to three chlorine substituents, and/or alkyl substituents. |
class |
Rule23
Be mononitroaromatics with one or two chlorine substituents and/or alkyl substituents. |
class |
Rule24
Primary alkyl amines (containing only C,H,N). |
class |
Rule25
Pyridines with one or two chlorine substituents and/or alkyl substituents. |
class |
Rule31
Possess alylic/propargylic activation. |
class |
Rule33
Be other compound with a (good) leaving group at an alpha position of a double or triple bond fragment. |
class |
Rule34
Possess a three-membered heterocyclic ring. |
class |
Rule35
Possess activated C-C double/triple bonds. |
class |
Rule36
Hydrazines or other compounds with a single , double or triple N-N linkage. |
class |
Rule37
Activated nitriles like alpha hydroxynitriles (cyanohidrins) or allylic /propargylic nitriles. |
class |
Rule38
Contain one of the following structural entities: |
class |
Rule4
Compounds acting by a specific mechanism. |
class |
RuleAlertsClass1
|
class |
RuleAlertsClass2
|
class |
RuleAlertsClass3
|
class |
RuleIonicGroups
Uses QueryAssociationBond ro verify if the query compound
has an ionic bond. |
class |
RuleLogPRange
0 <= LogP <= 6. |
class |
RuleRingMainStrucSubstituents
|
class |
RuleVerifyClass1Alerts
|
class |
RuleVerifyClass2Alerts
|
class |
RuleVerifyClass3Alerts
|
Uses of IDecisionRule in verhaar.rules.helper |
---|
Classes in verhaar.rules.helper that implement IDecisionRule | |
---|---|
class |
RuleAnySubstructureCounter
|
class |
RuleElementsCounter
|
class |
RuleOnlyAllowedSubstructuresCounter
|
|
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