- C - Static variable in class toxTree.query.FunctionalGroups
-
- c_categories - Static variable in class verhaar.VerhaarScheme
-
- c_rules - Static variable in class com.molecularnetworks.start.BiodgeradationRules
-
- c_rules - Static variable in class cramer2.CramerRulesWithExtensions
-
- c_rules - Static variable in class eye.EyeIrritationRules
-
- c_rules - Static variable in class mic.MICRules
-
- c_rules - Static variable in class michaelacceptors.MichaelAcceptorRules
-
- c_rules - Static variable in class mutant.BB_CarcMutRules
-
- c_rules - Static variable in class sicret.SicretRules
-
- c_rules - Static variable in class toxtree.plugins.ames.AmesMutagenicityRules
-
- c_rules - Static variable in class toxtree.plugins.dnabinding.DNABindingPlugin
-
- c_rules - Static variable in class toxtree.plugins.func.FuncRules
-
- c_rules - Static variable in class toxtree.plugins.kroes.Kroes1Tree
-
- c_rules - Static variable in class toxtree.plugins.lewis.LewisTree
-
- c_rules - Static variable in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
-
- c_rules - Static variable in class toxtree.plugins.search.CompoundLookup
-
- c_rules - Static variable in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- c_rules - Static variable in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- c_rules - Static variable in class toxTree.tree.cramer.CramerRules
-
- c_rules_normal - Static variable in class verhaar.VerhaarScheme
-
- c_rules_reversed - Static variable in class verhaar.VerhaarScheme
-
- calculate(IAtomContainer) - Method in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
-
- calculate(IAtomContainerSet, String) - Method in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
-
- calculate(IAtomContainer) - Method in class mutant.descriptors.DescriptorIDist
-
- calculate(IAtomContainer) - Method in class mutant.descriptors.DescriptorIsAniline
-
- calculate(IAtomContainer) - Method in class mutant.descriptors.DescriptorMolarRefractivity
-
- calculate(IAtomContainer) - Method in class mutant.descriptors.DescriptorStructurePresence
-
- calculate(IAtomContainer) - Method in class mutant.descriptors.SubstituentsDescriptor
-
- calculate(IAtomContainerSet, String) - Method in class mutant.descriptors.SubstituentsDescriptor
-
- calculate(IAtomContainer) - Method in class toxTree.core.ToxTreeDescriptor
-
- calculate(IAtomContainer) - Method in class toxtree.plugins.ames.descriptors.AromaticAmineSubstituentsDescriptor
-
- calculate(IAtomContainerSet, String) - Method in class toxtree.plugins.ames.descriptors.AromaticAmineSubstituentsDescriptor
-
- calculate(IAtomContainer) - Method in class toxtree.plugins.ames.descriptors.DescriptorIDist
-
- calculate(IAtomContainer) - Method in class toxtree.plugins.ames.descriptors.DescriptorIsAniline
-
- calculate(IAtomContainer) - Method in class toxtree.plugins.ames.descriptors.DescriptorMolarRefractivity
-
- calculate(IAtomContainer) - Method in class toxtree.plugins.ames.descriptors.DescriptorStructurePresence
-
- calculate(IAtomContainer) - Method in class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- calculate(IAtomContainerSet, String) - Method in class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- calculate(IAtomContainer) - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
-
- calculate(IAtomContainer) - Method in class toxTree.tree.UserDefinedTree
-
- calculated - Variable in class toxTree.qsar.QSARDescriptor
-
- calculateSize(Object, int, int) - Method in class toxtree.ui.tree.TreeLayout
-
- cancel() - Method in class toxTree.io.batch.BatchProcessing
-
- cancel() - Method in interface toxTree.io.batch.IBatchProcessing
-
- cancelAction() - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
-
- cancelAction() - Method in class toxtree.ui.batch.BatchProcessingDialog
-
- cancelButton - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
-
- cancelPressed - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
-
- canMetabolize(IAtomContainer, boolean) - Method in class toxTree.query.SimpleReactions
-
- canMetabolize(IAtomContainer, boolean, IChemObjectBuilder) - Method in class toxTree.query.SimpleReactions
-
Checks if 4 predefined metabolic reactions can be applied to Molecule mol
- carbohydrate - Variable in class toxtree.tree.cramer3.rules.RuleQ6
-
Is the substance a simply branched
(I) acyclic hydrocarbon containing alkane and/or alkene moieties (but
not alkyne moieties),
(II) a monocyclic or terpene bicyclic, or
(III) a simple carbohydrate?
- CARBONATE - Static variable in class toxTree.query.FunctionalGroups
-
- carbonate() - Static method in class toxTree.query.FunctionalGroups
-
- carbonate_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
-
- CARBONYL - Static variable in class toxTree.query.FunctionalGroups
-
- carbonyl() - Static method in class toxTree.query.FunctionalGroups
-
- CARBONYL_ABUNSATURATED - Static variable in class toxTree.query.FunctionalGroups
-
- CARBOXYLIC_ACID - Static variable in class toxTree.query.FunctionalGroups
-
- CARBOXYLIC_ACID_SALT - Static variable in class toxTree.query.FunctionalGroups
-
- carboxylicAcid() - Static method in class toxTree.query.FunctionalGroups
-
- carboxylicacid_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
-
- categories - Variable in class toxTree.tree.AbstractTree
-
- categories - Variable in class toxtree.tree.cramer3.TreeSpecification
-
- categories - Variable in class toxTree.tree.DecisionNode
-
- categories - Variable in class toxtree.ui.tree.categories.CategoriesPanel
-
- CategoriesList - Class in toxTree.tree
-
- CategoriesList() - Constructor for class toxTree.tree.CategoriesList
-
- CategoriesList(IDecisionCategory[]) - Constructor for class toxTree.tree.CategoriesList
-
- CategoriesList(IDecisionCategory[], boolean) - Constructor for class toxTree.tree.CategoriesList
-
- CategoriesList(String[]) - Constructor for class toxTree.tree.CategoriesList
-
- CategoriesList(String[], boolean) - Constructor for class toxTree.tree.CategoriesList
-
- categoriesListPanel - Variable in class toxtree.ui.wizard.DecisionNodeWizard
-
- CategoriesPanel - Class in toxtree.ui.tree.categories
-
Displays categories in a coloured list.
- CategoriesPanel(IDecisionCategories, IDecisionResult) - Constructor for class toxtree.ui.tree.categories.CategoriesPanel
-
- categoriesPanel - Variable in class toxtree.ui.tree.TreeEditorPanel
-
- categoriesRenderer - Static variable in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
-
- categoriesRenderer - Variable in class toxtree.ui.tree.categories.CategoriesPanel
-
- CategoriesRenderer - Class in toxTree.ui.tree.categories
-
Used mainly to provide an unique color per a category.
- CategoriesRenderer() - Constructor for class toxTree.ui.tree.categories.CategoriesRenderer
-
- CategoriesRenderer(int, int) - Constructor for class toxTree.ui.tree.categories.CategoriesRenderer
-
- CategoriesRenderer(IDecisionCategories) - Constructor for class toxTree.ui.tree.categories.CategoriesRenderer
-
- CategoriesRenderer(int) - Constructor for class toxTree.ui.tree.categories.CategoriesRenderer
-
- categoriesRenderer - Variable in class toxtree.ui.tree.TreeLayout
-
- CategoriesTableModel - Class in toxtree.ui.tree.categories
-
- CategoriesTableModel(IDecisionCategories, int) - Constructor for class toxtree.ui.tree.categories.CategoriesTableModel
-
- CategoriesTableModel(IDecisionCategories) - Constructor for class toxtree.ui.tree.categories.CategoriesTableModel
-
- category - Variable in class toxtree.plugins.kroes.rules.KroesRule8
-
- category - Variable in class toxTree.tree.RuleResult
-
- category - Variable in class toxTree.tree.TreeResult
-
- category - Variable in class toxtree.ui.tree.actions.EditCategoryAction
-
- category - Variable in class toxtree.ui.tree.categories.CategoryPanel
-
- category2assign - Variable in exception toxTree.exceptions.DRuleException
-
- CategoryAcetylcholinesteraseInhibitors - Class in toxtree.plugins.moa.categories
-
- CategoryAcetylcholinesteraseInhibitors() - Constructor for class toxtree.plugins.moa.categories.CategoryAcetylcholinesteraseInhibitors
-
- categoryActions - Variable in class toxtree.ui.tree.actions.SetBranchAction
-
- categoryActions - Variable in class toxtree.ui.tree.EditTreeActions
-
- CategoryBiodegradable - Class in com.molecularnetworks.start.categories
-
Class 1 (easily biodegradable chemical).
- CategoryBiodegradable() - Constructor for class com.molecularnetworks.start.categories.CategoryBiodegradable
-
Default constructor
- CategoryCarcinogen - Class in mutant.categories
-
- CategoryCarcinogen() - Constructor for class mutant.categories.CategoryCarcinogen
-
- CategoryCentralNervousSystemSeizureAgents - Class in toxtree.plugins.moa.categories
-
- CategoryCentralNervousSystemSeizureAgents() - Constructor for class toxtree.plugins.moa.categories.CategoryCentralNervousSystemSeizureAgents
-
- CategoryCorrosive - Class in sicret.categories
-
Assigned when compound is estimated to be corrosive to skin.
- CategoryCorrosive() - Constructor for class sicret.categories.CategoryCorrosive
-
- CategoryCorrosiveEye - Class in eye.categories
-
Assigned when compound is estimated to be corrosive to skin.
- CategoryCorrosiveEye() - Constructor for class eye.categories.CategoryCorrosiveEye
-
- CategoryCorrosiveSkin - Class in eye.categories
-
- CategoryCorrosiveSkin() - Constructor for class eye.categories.CategoryCorrosiveSkin
-
- CategoryElectrophileProelectrophileReactivity - Class in toxtree.plugins.moa.categories
-
- CategoryElectrophileProelectrophileReactivity() - Constructor for class toxtree.plugins.moa.categories.CategoryElectrophileProelectrophileReactivity
-
- CategoryError - Class in mutant.categories
-
- CategoryError() - Constructor for class mutant.categories.CategoryError
-
- CategoryError(String) - Constructor for class mutant.categories.CategoryError
-
- CategoryError - Class in toxtree.plugins.ames.categories
-
- CategoryError() - Constructor for class toxtree.plugins.ames.categories.CategoryError
-
- CategoryError(String) - Constructor for class toxtree.plugins.ames.categories.CategoryError
-
- CategoryFilter - Class in toxTree.data
-
- CategoryFilter(Object, IDecisionCategory) - Constructor for class toxTree.data.CategoryFilter
-
- CategoryFilter(Object, String) - Constructor for class toxTree.data.CategoryFilter
-
- CategoryIrritating - Class in sicret.categories
-
Assigned when compound is estimated to be irritating to skin.
- CategoryIrritating() - Constructor for class sicret.categories.CategoryIrritating
-
- CategoryIrritatingOrCorrosive - Class in sicret.categories
-
Assigned when compound is estimated to be irritating or corrosive to skin.
- CategoryIrritatingOrCorrosive() - Constructor for class sicret.categories.CategoryIrritatingOrCorrosive
-
- CategoryMichaelAcceptor - Class in michaelacceptors.categories
-
- CategoryMichaelAcceptor() - Constructor for class michaelacceptors.categories.CategoryMichaelAcceptor
-
- CategoryModerateIrritation2Eye - Class in eye.categories
-
- CategoryModerateIrritation2Eye() - Constructor for class eye.categories.CategoryModerateIrritation2Eye
-
- CategoryMutagenTA100 - Class in mutant.categories
-
- CategoryMutagenTA100() - Constructor for class mutant.categories.CategoryMutagenTA100
-
- CategoryMutagenTA100 - Class in toxtree.plugins.ames.categories
-
- CategoryMutagenTA100() - Constructor for class toxtree.plugins.ames.categories.CategoryMutagenTA100
-
- CategoryNarcosis1 - Class in toxtree.plugins.moa.categories
-
Assigned when compound is estimated to be corrosive to skin.
- CategoryNarcosis1() - Constructor for class toxtree.plugins.moa.categories.CategoryNarcosis1
-
- CategoryNarcosis2 - Class in toxtree.plugins.moa.categories
-
- CategoryNarcosis2() - Constructor for class toxtree.plugins.moa.categories.CategoryNarcosis2
-
- CategoryNarcosis3 - Class in toxtree.plugins.moa.categories
-
- CategoryNarcosis3() - Constructor for class toxtree.plugins.moa.categories.CategoryNarcosis3
-
- CategoryNoAlertAmes - Class in toxtree.plugins.ames.categories
-
- CategoryNoAlertAmes() - Constructor for class toxtree.plugins.ames.categories.CategoryNoAlertAmes
-
- CategoryNoGenotoxicAlert - Class in mutant.categories
-
- CategoryNoGenotoxicAlert() - Constructor for class mutant.categories.CategoryNoGenotoxicAlert
-
- CategoryNonMutagen - Class in mutant.categories
-
- CategoryNonMutagen() - Constructor for class mutant.categories.CategoryNonMutagen
-
- CategoryNonMutagen - Class in toxtree.plugins.ames.categories
-
- CategoryNonMutagen() - Constructor for class toxtree.plugins.ames.categories.CategoryNonMutagen
-
- CategoryNoNongenotoxicAlert - Class in mutant.categories
-
- CategoryNoNongenotoxicAlert() - Constructor for class mutant.categories.CategoryNoNongenotoxicAlert
-
- CategoryNotCarcinogen - Class in mutant.categories
-
- CategoryNotCarcinogen() - Constructor for class mutant.categories.CategoryNotCarcinogen
-
- CategoryNotCorrosive - Class in sicret.categories
-
Assigned when compound is estimated to be not corrosive to skin.
- CategoryNotCorrosive() - Constructor for class sicret.categories.CategoryNotCorrosive
-
- CategoryNotCorrosive2Eye - Class in eye.categories
-
- CategoryNotCorrosive2Eye() - Constructor for class eye.categories.CategoryNotCorrosive2Eye
-
- CategoryNotCorrosive2Skin - Class in eye.categories
-
Assigned when compound is estimated to be not corrosive to skin.
- CategoryNotCorrosive2Skin() - Constructor for class eye.categories.CategoryNotCorrosive2Skin
-
- CategoryNotCorrosive2SkinAndIrritating2Eye - Class in eye.categories
-
- CategoryNotCorrosive2SkinAndIrritating2Eye() - Constructor for class eye.categories.CategoryNotCorrosive2SkinAndIrritating2Eye
-
- CategoryNotCorrosive2SkinEye - Class in eye.categories
-
- CategoryNotCorrosive2SkinEye() - Constructor for class eye.categories.CategoryNotCorrosive2SkinEye
-
- CategoryNotCorrosive2SkinOrIrritating2Eye - Class in eye.categories
-
- CategoryNotCorrosive2SkinOrIrritating2Eye() - Constructor for class eye.categories.CategoryNotCorrosive2SkinOrIrritating2Eye
-
- CategoryNotIrritating - Class in sicret.categories
-
Assigned when compound is estimated to be not irritating to skin.
- CategoryNotIrritating() - Constructor for class sicret.categories.CategoryNotIrritating
-
- CategoryNotIrritating2Eye - Class in eye.categories
-
Assigned when compound is estimated to be not irritating to skin.
- CategoryNotIrritating2Eye() - Constructor for class eye.categories.CategoryNotIrritating2Eye
-
- CategoryNotIrritatingOrCorrosive - Class in sicret.categories
-
Assigned when compound is estimated to be not Irritating or corrosive to skin.
- CategoryNotIrritatingOrCorrosive() - Constructor for class sicret.categories.CategoryNotIrritatingOrCorrosive
-
- CategoryNotIrritatingOrCorrosive2Eye - Class in eye.categories
-
Assigned when compound is estimated to be not Irritating or corrosive to skin.
- CategoryNotIrritatingOrCorrosive2Eye() - Constructor for class eye.categories.CategoryNotIrritatingOrCorrosive2Eye
-
- CategoryOxidativePhosphorylationUncouplers - Class in toxtree.plugins.moa.categories
-
- CategoryOxidativePhosphorylationUncouplers() - Constructor for class toxtree.plugins.moa.categories.CategoryOxidativePhosphorylationUncouplers
-
- CategoryPanel - Class in toxtree.ui.tree.categories
-
- CategoryPanel(IDecisionCategory) - Constructor for class toxtree.ui.tree.categories.CategoryPanel
-
- CategoryPanel() - Constructor for class toxtree.ui.tree.categories.CategoryPanel
-
- CategoryPersistent - Class in com.molecularnetworks.start.categories
-
Class 2 (persistent chemical).
- CategoryPersistent() - Constructor for class com.molecularnetworks.start.categories.CategoryPersistent
-
Default constructor
- CategoryPositiveAlertAmes - Class in toxtree.plugins.ames.categories
-
- CategoryPositiveAlertAmes() - Constructor for class toxtree.plugins.ames.categories.CategoryPositiveAlertAmes
-
- CategoryPositiveAlertGenotoxic - Class in mutant.categories
-
- CategoryPositiveAlertGenotoxic() - Constructor for class mutant.categories.CategoryPositiveAlertGenotoxic
-
- CategoryPositiveAlertNongenotoxic - Class in mutant.categories
-
- CategoryPositiveAlertNongenotoxic() - Constructor for class mutant.categories.CategoryPositiveAlertNongenotoxic
-
- CategoryUnknown - Class in com.molecularnetworks.start.categories
-
Class 3 (unknown biodegradability).
- CategoryUnknown() - Constructor for class com.molecularnetworks.start.categories.CategoryUnknown
-
Default constructor
- CategoryUnknown - Class in eye.categories
-
Assigned when
EyeIrritationRules are not able to estimate eye irritation or corrosive potential.
- CategoryUnknown() - Constructor for class eye.categories.CategoryUnknown
-
- CategoryUnknown - Class in michaelacceptors.categories
-
- CategoryUnknown() - Constructor for class michaelacceptors.categories.CategoryUnknown
-
- CategoryUnknown - Class in sicret.categories
-
Assigned when
SicretRules are not able to estimate skin irritation or corrosive potential.
- CategoryUnknown() - Constructor for class sicret.categories.CategoryUnknown
-
- CategoryUnknown - Class in toxtree.plugins.moa.categories
-
- CategoryUnknown() - Constructor for class toxtree.plugins.moa.categories.CategoryUnknown
-
- categoryURL - Static variable in class toxTree.tree.RuleResult
-
- CDTResult - Class in toxtree.tree.cramer3
-
- CDTResult() - Constructor for class toxtree.tree.cramer3.CDTResult
-
- cell - Variable in class toxTree.io.PDFWriter
-
- cells - Variable in class toxtree.ui.tree.TreeLayout
-
- centerScreen() - Method in class toxTree.apps.AbstractApplication
-
- centerScreen() - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
-
- centerScreen(Component) - Method in class toxtree.ui.wizard.WizardWrapper
-
- CH - Static variable in class toxTree.query.FunctionalGroups
-
- CH2 - Static variable in class toxTree.query.FunctionalGroups
-
- CH3 - Static variable in class toxTree.query.FunctionalGroups
-
- CH6SubstituentAtBetaCarbon(IAtomContainer) - Method in class mic.rules.SA10
-
- CH6SubstituentAtBetaCarbon(IAtomContainer) - Method in class mutant.rules.SA10_gen
-
- CH6SubstituentAtBetaCarbon(IAtomContainer) - Method in class toxtree.plugins.ames.rules.SA10_gen
-
- changeExtension(File, MolFileFilter) - Static method in class toxtree.data.ActionList
-
- changes - Variable in class toxTree.tree.AbstractRule
-
- changes - Variable in class toxTree.tree.AbstractTree
-
- changes - Variable in class toxTree.tree.TreeResult
-
- checkAromaticity - Variable in class toxTree.tree.rules.LookupFile
-
- chemObject - Variable in class toxTree.io.batch.ChemObjectBatchProcessing
-
- ChemObjectBatchProcessing - Class in toxTree.io.batch
-
Implements batch processing of chemical files
- ChemObjectBatchProcessing() - Constructor for class toxTree.io.batch.ChemObjectBatchProcessing
-
- ChemObjectBatchProcessing(String, String) - Constructor for class toxTree.io.batch.ChemObjectBatchProcessing
-
- ChemObjectBatchProcessing(File, File) - Constructor for class toxTree.io.batch.ChemObjectBatchProcessing
-
- chIDs - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
-
- CHQueryAtom - Class in toxTree.query
-
This is to match a hydrocarbon atom in subgraph query
Molecule should be preprocessed with FunctionalGroups.markCHn(), otherwise results will not be correct
- CHQueryAtom(IChemObjectBuilder) - Constructor for class toxTree.query.CHQueryAtom
-
- CHQueryAtom(IAtom) - Constructor for class toxTree.query.CHQueryAtom
-
- Class1BaselineToxicity - Class in verhaar.categories
-
Class 1 (narcosis or baseline toxicity).
- Class1BaselineToxicity() - Constructor for class verhaar.categories.Class1BaselineToxicity
-
- Class2LessInertCompounds - Class in verhaar.categories
-
Class 2 (less inert compounds).
- Class2LessInertCompounds() - Constructor for class verhaar.categories.Class2LessInertCompounds
-
- Class3UnspecificReactivity - Class in verhaar.categories
-
Class 3 (unspecific reactivity).
- Class3UnspecificReactivity() - Constructor for class verhaar.categories.Class3UnspecificReactivity
-
- Class3UnspecificReactivity(String, int) - Constructor for class verhaar.categories.Class3UnspecificReactivity
-
- Class4SpecificMechanism - Class in verhaar.categories
-
Class 4 (compounds and groups of compounds acting by a specific mechanism).
- Class4SpecificMechanism() - Constructor for class verhaar.categories.Class4SpecificMechanism
-
- Class4SpecificMechanism(String, int) - Constructor for class verhaar.categories.Class4SpecificMechanism
-
- Class5Unknown - Class in verhaar.categories
-
Class 5 Not possible to classify according to these rules.
- Class5Unknown() - Constructor for class verhaar.categories.Class5Unknown
-
- Class5Unknown(String, int) - Constructor for class verhaar.categories.Class5Unknown
-
- classify(IDecisionResult) - Method in class toxTree.apps.toxForest.ToxForestData
-
- classify() - Method in class toxTree.apps.toxForest.ToxForestDataModule
-
- classify(IAtomContainer, IDecisionResult) - Method in interface toxTree.core.IDecisionMethod
-
- classify(IAtomContainer) - Method in interface toxTree.core.IDecisionResult
-
- classify(IDecisionResult) - Method in class toxtree.data.DecisionMethodData
-
- classify() - Method in class toxtree.data.DecisionMethodsDataModule
-
- classify(IAtomContainer, IDecisionResult) - Method in class toxTree.tree.AbstractTree
-
- classify(IAtomContainer, IDecisionResult) - Method in class toxTree.tree.BatchDecisionResultsList
-
- classify(IAtomContainer) - Method in class toxTree.tree.BatchDecisionResultsList
-
- classify(IAtomContainer) - Method in class toxTree.tree.TreeResult
-
- classifyAll(IDecisionMethodsList) - Method in class toxTree.apps.toxForest.ToxForestData
-
- classifyAll() - Method in class toxTree.apps.toxForest.ToxForestDataModule
-
- classifyAll(IDecisionResult) - Method in class toxtree.data.DecisionMethodData
-
- classifyAll(IDecisionMethodsList) - Method in class toxtree.data.DecisionMethodData
-
- classifyAll() - Method in class toxtree.data.DecisionMethodsDataModule
-
- className - Variable in class toxTree.core.ToxTreePackageEntry
-
- cleanPausedBatch() - Method in class toxtree.ui.batch.BatchProcessingDialog
-
- clear() - Method in interface toxTree.core.IDecisionCategories
-
- clear() - Method in interface toxTree.core.IDecisionResult
-
- clear() - Method in interface toxTree.core.IMoleculesIterator
-
- clear() - Method in class toxtree.data.FilteredMoleculesIterator
-
- clear() - Method in class toxTree.data.MoleculesIterator
-
- clear() - Method in class toxTree.data.SortedPropertyList
-
- clear() - Method in class toxTree.query.MolFlags
-
- clear() - Method in class toxTree.tree.CategoriesList
-
- clear() - Method in class toxTree.tree.DecisionMethodsList
-
- clear() - Method in class toxTree.tree.DecisionNodesList
-
- clear() - Method in class toxTree.tree.ProgressStatus
-
- clear() - Method in class toxTree.tree.RulesList
-
- clear() - Method in class toxTree.tree.stats.ConfusionMatrix
-
- clear() - Method in class toxTree.tree.TreeResult
-
- clearChanged() - Method in class toxTree.tree.AbstractTree
-
- ClearFilteredSubsetsAction - Class in toxtree.ui.molecule
-
- ClearFilteredSubsetsAction(DataModule) - Constructor for class toxtree.ui.molecule.ClearFilteredSubsetsAction
-
- ClearFilteredSubsetsAction(DataModule, String) - Constructor for class toxtree.ui.molecule.ClearFilteredSubsetsAction
-
- ClearFilteredSubsetsAction(DataModule, String, Icon) - Constructor for class toxtree.ui.molecule.ClearFilteredSubsetsAction
-
- clearFilters() - Method in class toxtree.data.DataContainer
-
- clearFilters() - Method in class toxtree.data.DecisionMethodsDataModule
-
- clearFlags(IAtomContainer) - Method in interface toxTree.core.IDecisionRule
-
When rules analyze a molecule, a set of properties are set.
- clearFlags(IAtomContainer) - Method in class toxTree.tree.AbstractRule
-
- clearFlags(IAtomContainer) - Method in class toxTree.tree.DecisionNode
-
- clearFlags() - Method in class toxTree.tree.rules.RuleRingSubstituents
-
- clearMark(IAtomContainer, QueryAtomContainer) - Static method in class toxTree.query.FunctionalGroups
-
- clearMark(IAtomContainer, Object) - Static method in class toxTree.query.FunctionalGroups
-
- clearMarks(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
-
- ClearMethodsList - Class in toxtree.ui.tree.actions
-
- ClearMethodsList(DecisionMethodsDataModule) - Constructor for class toxtree.ui.tree.actions.ClearMethodsList
-
- ClearMethodsList(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.tree.actions.ClearMethodsList
-
- ClearMethodsList(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.ClearMethodsList
-
- ClearResultAction - Class in toxtree.ui.actions
-
Clears the result of the current compound
- ClearResultAction(DataModule) - Constructor for class toxtree.ui.actions.ClearResultAction
-
- ClearResultAction(DataModule, String) - Constructor for class toxtree.ui.actions.ClearResultAction
-
- ClearResultAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.ClearResultAction
-
- clearResults() - Method in class toxTree.apps.toxForest.ToxForestDataModule
-
- clearResults() - Method in class toxtree.data.DecisionMethodsDataModule
-
- clearResults() - Method in class toxTree.tree.TreeResult
-
- clearSubstructures() - Method in interface toxTree.core.IRuleSubstructures
-
removes all substructures defined for a rule
- clearSubstructures() - Method in class toxTree.tree.rules.RuleSubstructures
-
- clearSubstructures() - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- clearSubstructures() - Method in interface toxTree.tree.rules.smarts.IRuleSMARTSubstructures
-
- clearVisited() - Method in class toxtree.ui.tree.TreeLayout
-
- clearVisitedFlags(IAtomContainer) - Static method in class toxTree.query.MolAnalyser
-
- clone() - Method in interface toxTree.core.IDecisionRule
-
- clone() - Method in class toxTree.tree.AbstractRule
-
- clone() - Method in class toxTree.tree.DecisionNode
-
- clone() - Method in class toxTree.tree.UserDefinedTree
-
- cloneDiscardRingAtomAndBonds(IAtomContainer, String) - Static method in class mutant.descriptors.SubstituentExtractor
-
- cloneDiscardRingAtomAndBonds(IAtomContainer, String) - Static method in class toxtree.plugins.ames.descriptors.SubstituentExtractor
-
- cloneDiscardRingAtomAndBonds(IAtomContainer, IRing) - Static method in class toxTree.query.FunctionalGroups
-
- close() - Method in class toxTree.data.MoleculesFile
-
- close() - Method in class toxTree.io.batch.BatchProcessing
-
- close() - Method in interface toxTree.io.batch.IBatchProcessing
-
- close() - Method in class toxTree.io.PDFWriter
-
- close() - Method in class toxTree.tree.UserDefinedTree
-
- close(Window) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- closeInputFile() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
-
- closeInputFile() - Method in interface toxTree.io.batch.IBatchProcessing
-
- closeOutputFile() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
-
- closeOutputFile() - Method in interface toxTree.io.batch.IBatchProcessing
-
- cmatrix - Variable in class toxTree.tree.stats.ConfusionMatrix
-
- columnNames - Variable in class toxtree.ui.HashtableModel
-
- columnsno - Variable in class toxtree.ui.tree.categories.CategoriesTableModel
-
- com.molecularnetworks.start - package com.molecularnetworks.start
-
- com.molecularnetworks.start.categories - package com.molecularnetworks.start.categories
-
- com.molecularnetworks.start.rules - package com.molecularnetworks.start.rules
-
- compare(double, double) - Method in class mutant.rules.RuleDACancerogenicityAromaticAmines
-
- compare(double, double) - Method in class mutant.rules.RuleDAMutagenicityABUnsaturatedAldehydes
-
Classified as mutagens if lower than the threshold
- compare(double, double) - Method in class mutant.rules.RuleDAMutagenicityAromaticAmines
-
- compare(double, double) - Method in class toxtree.plugins.ames.rules.RuleDAMutagenicityABUnsaturatedAldehydes
-
Classified as mutagens if lower than the threshold
- compare(double, double) - Method in class toxtree.plugins.ames.rules.RuleDAMutagenicityAromaticAmines
-
- compare(double, double) - Method in class toxTree.qsar.LinearDiscriminantRule
-
- compare(double, double) - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- compareTo(IDecisionCategory) - Method in class mutant.categories.MutantCategory
-
- compareTo(Object) - Method in class toxTree.data.AbstractFilter
-
- compareTo(IDecisionCategory) - Method in class toxtree.plugins.ames.categories.AmesMutagenicityCategory
-
- compareTo(String) - Method in class toxTree.qsar.QSARDescriptor
-
- compareTo(Object) - Method in class toxTree.tree.BatchDecisionResultsList
-
- compareTo(IDecisionCategory) - Method in class toxTree.tree.DefaultCategory
-
- compareTo(Object) - Method in class toxTree.tree.TreeResult
-
- comparison - Static variable in class toxTree.tree.rules.RuleElements
-
- component - Variable in class toxtree.ui.wizard.EditorPanel
-
- CompoundLookup - Class in toxtree.plugins.search
-
- CompoundLookup() - Constructor for class toxtree.plugins.search.CompoundLookup
-
- CompoundMethodApplication - Class in toxTree.apps
-
- CompoundMethodApplication(String, Color, Color) - Constructor for class toxTree.apps.CompoundMethodApplication
-
- compoundPanel - Variable in class toxTree.apps.CompoundMethodApplication
-
- CompoundPanel - Class in toxtree.ui.tree.molecule
-
A
JPanel descendant, displaying 2D structure diagram of the molecule at the bottom
and a table with molecule properties read by
org.openscience.cdk.interfaces.Molecule#getRecordProperties()
- CompoundPanel(DataContainer, Color, Color) - Constructor for class toxtree.ui.tree.molecule.CompoundPanel
-
- condition - Variable in class toxTree.tree.rules.RuleVerifyProperty
-
- condition_equals - Static variable in class toxTree.tree.rules.RuleVerifyProperty
-
- CONDITION_FAILED - Static variable in class toxTree.tree.rules.RuleRingSubstituents
-
- condition_higher - Static variable in class toxTree.tree.rules.RuleVerifyProperty
-
- condition_lower - Static variable in class toxTree.tree.rules.RuleVerifyProperty
-
- conditionBox - Variable in class toxtree.ui.tree.rules.RulePropertyEditor
-
- config - Static variable in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
-
- configFile - Variable in class toxTree.io.batch.BatchProcessing
-
- configure(Template) - Method in class toxtree.plugins.search.rules.Find
-
- configureURLLoader(ClassLoader) - Static method in class toxTree.core.Introspection
-
Adds URLS of jars in default directories to the class loader.
- configureURLLoader(File) - Static method in class toxTree.core.Introspection
-
Adds URLS of jars in specified directory to the class loader.
- configureURLLoader(File[]) - Static method in class toxTree.core.Introspection
-
Adds URLS of jars specified in File[] to the class loader.
- ConfusionMatrix<A,B extends Comparable> - Class in toxTree.tree.stats
-
Performance statistics , similar to confusion matrix
- ConfusionMatrix() - Constructor for class toxTree.tree.stats.ConfusionMatrix
-
- ConnectionMatrix - Class in toxTree.core
-
- ConnectionMatrix() - Constructor for class toxTree.core.ConnectionMatrix
-
- containers - Variable in class toxtree.data.DataContainer
-
- containers - Variable in class toxTree.data.MoleculesIterator
-
- contains(Object) - Method in class toxTree.core.SmartElementsList
-
- contains(Object) - Method in class toxTree.query.QueryAtomContainers
-
- contains(Object) - Method in class toxTree.tree.CategoriesList
-
- contains(Object) - Method in class toxTree.tree.DecisionMethodsList
-
- contains(Object) - Method in class toxTree.tree.DecisionNodesList
-
- contains(String) - Method in class toxTree.tree.rules.RuleElements
-
- contains(Object) - Method in class toxTree.tree.RulesList
-
- containsAll(Collection) - Method in class toxTree.query.QueryAtomContainers
-
- containsAll(Collection) - Method in class toxTree.tree.CategoriesList
-
- containsAll(Collection) - Method in class toxTree.tree.DecisionMethodsList
-
- containsAll(Collection) - Method in class toxTree.tree.DecisionNodesList
-
- containsAll(Collection) - Method in class toxTree.tree.RulesList
-
- containsAllSubstructures - Variable in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- containsAllSubstructures() - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- containsAllSubstructures() - Method in interface toxTree.tree.rules.smarts.IRuleSMARTSubstructures
-
- convert(IAtom) - Static method in class toxTree.tree.rules.smarts.Convertor
-
Converts an org.openscience.cdk.Atom class into a joelib.molecule.JOEAtom
class.
- convert(IAtom, int) - Static method in class toxTree.tree.rules.smarts.Convertor
-
Converts an org.openscience.cdk.Atom class into a joelib.molecule.JOEAtom
class.
- convert(JOEAtom) - Static method in class toxTree.tree.rules.smarts.Convertor
-
Converts an joelib.molecule.JOEAtom class into a org.openscience.cdk.Atom
class.
- convert(IBond) - Static method in class toxTree.tree.rules.smarts.Convertor
-
Converts an org.openscience.cdk.Bond class into a joelib.molecule.JOEBond
class.
- convert(JOEBond) - Static method in class toxTree.tree.rules.smarts.Convertor
-
Converts an joelib.molecule.JOEBond class into a org.openscience.cdk.Bond
class.
- convert(IAtomContainer) - Static method in class toxTree.tree.rules.smarts.Convertor
-
Converts an org.openscience.cdk.Molecule class into a
joelib.molecule.JOEMol class.
- convert(IAtomContainer, int) - Static method in class toxTree.tree.rules.smarts.Convertor
-
Converts an org.openscience.cdk.Molecule class into a
joelib.molecule.JOEMol class.
- convert(JOEMol) - Static method in class toxTree.tree.rules.smarts.Convertor
-
Converts an joelib.molecule.JOEMol class into a
org.openscience.cdk.Molecule class.
- Convertor - Class in toxTree.tree.rules.smarts
-
Abstract class that provides convertor procedures to convert CDK classes to
JOELib classes and visa versa.
- Convertor() - Constructor for class toxTree.tree.rules.smarts.Convertor
-
- COORDINATES_2D - Static variable in class toxTree.tree.rules.smarts.Convertor
-
- COORDINATES_3D - Static variable in class toxTree.tree.rules.smarts.Convertor
-
- copyMolecule(IAtomContainer) - Method in class toxtree.ui.metabolites.MetabolitesFrame
-
- countChain(IAtomContainer) - Method in class eye.rules.Rule13_AliphaticMonoalcohols
-
- cramer2 - package cramer2
-
Class
CramerRules is the implementation of Cramer rules [Cramer et al,78].
- cramer2.categories - package cramer2.categories
-
- cramer2.rules - package cramer2.rules
-
- CramerClass1 - Class in cramer2.categories
-
A
DefaultCategory descendant, implementation of
Cramer class 1 (see
cramer2.CramerRulesExtendedExtended)
- CramerClass1() - Constructor for class cramer2.categories.CramerClass1
-
- CramerClass1 - Class in toxTree.tree.cramer
-
- CramerClass1() - Constructor for class toxTree.tree.cramer.CramerClass1
-
- CramerClass1 - Class in toxtree.tree.cramer3
-
A
DefaultCategory descendant, implementation of
Cramer class 1 (see
toxTree.tree.RevisedCramerDecisionTree.CramerRules)
- CramerClass1() - Constructor for class toxtree.tree.cramer3.CramerClass1
-
- CramerClass2 - Class in cramer2.categories
-
A
DefaultCategory descendant, implementation of
Cramer class 2 (see
cramer2.CramerRulesExtendedExtended)
- CramerClass2() - Constructor for class cramer2.categories.CramerClass2
-
- CramerClass2 - Class in toxTree.tree.cramer
-
- CramerClass2() - Constructor for class toxTree.tree.cramer.CramerClass2
-
- CramerClass2 - Class in toxtree.tree.cramer3
-
A
DefaultCategory descendant, implementation of
Cramer class 2 (see
toxTree.tree.RevisedCramerDecisionTree.CramerRules)
- CramerClass2() - Constructor for class toxtree.tree.cramer3.CramerClass2
-
- CramerClass3 - Class in cramer2.categories
-
A
DefaultCategory descendant, implementation of
Cramer class 3 (see
cramer2.CramerRulesExtendedExtended)
- CramerClass3() - Constructor for class cramer2.categories.CramerClass3
-
- CramerClass3 - Class in toxTree.tree.cramer
-
- CramerClass3() - Constructor for class toxTree.tree.cramer.CramerClass3
-
- CramerClass3 - Class in toxtree.tree.cramer3
-
A
DefaultCategory descendant, implementation of
Cramer class 3 (see
toxTree.tree.RevisedCramerDecisionTree.CramerRules)
- CramerClass3() - Constructor for class toxtree.tree.cramer3.CramerClass3
-
- cramerResults - Variable in class toxtree.plugins.kroes.rules.KroesRule8
-
- cramerRules - Variable in class toxtree.plugins.kroes.rules.KroesRule8
-
- CramerRules - Class in toxTree.tree.cramer
-
An
UserDefinedTree descendant, implementing
the decision tree described in "Cramer G.
- CramerRules() - Constructor for class toxTree.tree.cramer.CramerRules
-
- CramerRulesWithExtensions - Class in cramer2
-
TODO update
An
UserDefinedTree descendant, implementing
the decision tree described in "Cramer G.
- CramerRulesWithExtensions() - Constructor for class cramer2.CramerRulesWithExtensions
-
- CramerTreeResult - Class in cramer2.categories
-
A descendant ot
TreeResult, to be used by
cramer2.CramerRulesExtendedExtended.
- CramerTreeResult() - Constructor for class cramer2.categories.CramerTreeResult
-
- CramerTreeResult - Class in toxTree.tree.cramer
-
- CramerTreeResult() - Constructor for class toxTree.tree.cramer.CramerTreeResult
-
- createAndShowGUI() - Static method in class toxTree.apps.AbstractApplication
-
initLookAndFeel(); JFrame.setDefaultLookAndFeelDecorated(true); new
ToxTreeApp(); Create the GUI and show it.
- createAndShowGUI() - Static method in class toxTree.apps.toxForest.ToxForestApp
-
- createAndShowGUI() - Static method in class toxTree.apps.ToxTreeApp
-
Create the GUI and show it.
- createApplyRuleOptions() - Method in class toxTree.ui.EditorFactory
-
- createApplyRuleOptions() - Method in class toxtree.ui.editors.SwingEditorFactory
-
- createApplyRuleOptions() - Method in interface toxTree.ui.IEditorFactory
-
- createArrayResult(int) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- createArrayResult(int) - Method in class toxTree.tree.UserDefinedTree
-
- createAtomContainer(String, String) - Static method in class toxTree.query.FunctionalGroups
-
- createAtomContainer(String, String, SmilesParserWrapper.SMILES_PARSER) - Static method in class toxTree.query.FunctionalGroups
-
- createAtomContainer(String) - Static method in class toxTree.query.FunctionalGroups
-
- createAtomContainer(String, SmilesParserWrapper.SMILES_PARSER) - Static method in class toxTree.query.FunctionalGroups
-
- createAtomContainer(String, boolean) - Static method in class toxTree.query.FunctionalGroups
-
- createAtomContainer(String, boolean, String) - Static method in class toxTree.query.FunctionalGroups
-
- createAtomContainer(String, boolean, String, SmilesParserWrapper.SMILES_PARSER) - Static method in class toxTree.query.FunctionalGroups
-
- createAutoQueryContainer(String) - Static method in class verhaar.query.FunctionalGroups
-
- createAutoQueryContainer(IAtomContainer) - Static method in class verhaar.query.FunctionalGroups
-
- createButtons(List<T>, List<JRadioButton>, int) - Method in class toxtree.ui.wizard.RadioBoxPanel
-
- createCancerogenicityAromaticAminesModel() - Static method in class mutant.rules.RuleDACancerogenicityAromaticAmines
-
- createCategories() - Static method in class toxtree.plugins.moa.MOARules
-
- createCategoriesPanel(IDecisionCategories) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- createCategoryActions() - Method in class toxtree.ui.tree.EditTreeActions
-
- createCategoryEditor(IDecisionCategory) - Method in class toxTree.ui.EditorFactory
-
- createCategoryEditor(IDecisionCategory) - Method in class toxtree.ui.editors.SwingEditorFactory
-
- createCategoryEditor(IDecisionCategory) - Method in interface toxTree.ui.IEditorFactory
-
- createColumnModel(ListTableModel) - Method in class toxtree.ui.tree.ListPanel
-
- createcolumns(TableModel) - Method in class toxTree.apps.toxForest.ToxForestDataModulePanel
-
- createCompoundPanel(DataContainer, Color, Color) - Method in class toxTree.apps.CompoundMethodApplication
-
- createCompoundPanel(DataContainer, Color, Color) - Method in class toxTree.apps.toxForest.ToxForestApp
-
- createConfigFile() - Method in class toxTree.io.batch.BatchProcessing
-
- createDataContainer(File) - Method in class toxTree.apps.toxForest.ToxForestDataModule
-
- createDataContainer(File) - Method in class toxtree.data.DataModule
-
- createDataContainer(File) - Method in class toxtree.data.DecisionMethodsDataModule
-
- createDataContainer(File) - Method in class toxtree.data.ToxTreeModule
-
- createDataLabel(int) - Method in class toxtree.ui.tree.qsar.DescriptorOptions
-
- createDataLabel(int) - Method in class toxtree.ui.tree.qsar.OptionsPanel
-
- createDataModule() - Method in class toxTree.apps.AbstractApplication
-
- createDataModule() - Method in class toxTree.apps.CompoundMethodApplication
-
- createDataModule() - Method in class toxTree.apps.toxForest.ToxForestApp
-
- createDataModule() - Method in class toxTree.apps.ToxTreeApp
-
- createDataModulePanel(DataModule) - Method in class toxTree.apps.CompoundMethodApplication
-
- createDataModulePanel(DataModule) - Method in class toxTree.apps.toxForest.ToxForestApp
-
- createDataModulePanel(DataModule) - Method in class toxTree.apps.ToxTreeApp
-
- createDataTextField(int) - Method in class toxtree.ui.tree.qsar.DescriptorOptions
-
- createDataTextField(int) - Method in class toxtree.ui.tree.qsar.OptionsPanel
-
- createDecisionResult() - Method in class cramer2.CramerRulesWithExtensions
-
- createDecisionResult() - Method in class mic.MICRules
-
- createDecisionResult() - Method in class michaelacceptors.MichaelAcceptorRules
-
- createDecisionResult() - Method in class mutant.BB_CarcMutRules
-
- createDecisionResult() - Method in interface toxTree.core.IDecisionMethod
-
- createDecisionResult() - Method in class toxtree.plugins.ames.AmesMutagenicityRules
-
- createDecisionResult() - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
-
- createDecisionResult() - Method in class toxtree.plugins.func.FuncRules
-
- createDecisionResult() - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
-
- createDecisionResult() - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- createDecisionResult() - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- createDecisionResult() - Method in class toxTree.tree.AbstractTree
-
- createDecisionResult() - Method in class toxTree.tree.BatchDecisionResultsList
-
- createDecisionResult() - Method in class toxTree.tree.cramer.CramerRules
-
- createDecisionResult() - Method in class toxtree.tree.cramer3.RevisedCramerDecisionTree
-
- createEditor(IDecisionRule) - Method in class toxTree.ui.EditorFactory
-
- createEditor(IDecisionRule) - Method in class toxtree.ui.editors.SwingEditorFactory
-
- createEditor(RuleDescriptorRange) - Method in class toxtree.ui.editors.SwingEditorFactory
-
RuleDescriptorRange
- createEditor(RuleMolecularMassRange) - Method in class toxtree.ui.editors.SwingEditorFactory
-
RuleMolecularMassRange
- createEditor(RuleVerifyProperty) - Method in class toxtree.ui.editors.SwingEditorFactory
-
RuleVerifyProperty
- createEditor(RuleManyAromaticRings) - Method in class toxtree.ui.editors.SwingEditorFactory
-
RuleManyAromaticRings
- createEditor(RuleSubstructures) - Method in class toxtree.ui.editors.SwingEditorFactory
-
RuleSubstructures
- createEditor(RuleStructuresList) - Method in class toxtree.ui.editors.SwingEditorFactory
-
RuleStructuresList
- createEditor(AbstractRuleSmartSubstructure) - Method in class toxtree.ui.editors.SwingEditorFactory
-
- createEditor(IDecisionRule) - Method in interface toxTree.ui.IEditorFactory
-
- createException(QSARModelException) - Method in class mutant.rules.RuleDACancerogenicityAromaticAmines
-
- createException(QSARModelException) - Method in class mutant.rules.RuleDAMutagenicityABUnsaturatedAldehydes
-
- createException(QSARModelException) - Method in class mutant.rules.RuleDAMutagenicityAromaticAmines
-
- createException(QSARModelException) - Method in class toxtree.plugins.ames.rules.RuleDAMutagenicityABUnsaturatedAldehydes
-
- createException(QSARModelException) - Method in class toxtree.plugins.ames.rules.RuleDAMutagenicityAromaticAmines
-
- createException(QSARModelException) - Method in class toxTree.qsar.LinearDiscriminantRule
-
- createFile() - Method in class toxTree.io.batch.FileState
-
- createFromConfig(File) - Static method in class toxTree.io.batch.BatchFactory
-
- createHeaderLabel(int) - Method in class toxtree.ui.tree.qsar.DescriptorOptions
-
- createHeaderLabel(int) - Method in class toxtree.ui.tree.qsar.OptionsPanel
-
- createHeaderTextField(int) - Method in class toxtree.ui.tree.qsar.DescriptorOptions
-
- createHeaderTextField(int) - Method in class toxtree.ui.tree.qsar.OptionsPanel
-
- createLabel(String, String) - Method in class toxtree.ui.molecule.NavigationPanel
-
- createMainPanel() - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
-
- createMainPanel() - Method in class toxtree.ui.batch.BatchProcessingDialog
-
- createMainStructure() - Method in class verhaar.rules.Rule21
-
- createMainStructure() - Method in class verhaar.rules.Rule22
-
- createMainStructure() - Method in class verhaar.rules.Rule23
-
- createMainStructure() - Method in class verhaar.rules.Rule25
-
- createMainStructure() - Method in class verhaar.rules.RuleRingMainStrucSubstituents
-
- createMenu(JMenuBar) - Method in class toxtree.data.ActionList
-
- createMenuBar() - Method in class toxTree.apps.AbstractApplication
-
- createModelEditor(AbstractQSARModel) - Method in class toxTree.ui.EditorFactory
-
- createModelEditor(AbstractQSARModel) - Method in class toxtree.ui.editors.SwingEditorFactory
-
- createModelEditor(AbstractQSARModel) - Method in interface toxTree.ui.IEditorFactory
-
- createMoleculeFromSMILES(String) - Method in class toxtree.ui.molecule.SmilesEntryPanel
-
- createMutagenicityofAldehydesModel() - Static method in class mutant.rules.RuleDAMutagenicityABUnsaturatedAldehydes
-
- createMutagenicityofAldehydesModel() - Static method in class toxtree.plugins.ames.rules.RuleDAMutagenicityABUnsaturatedAldehydes
-
- createMutagenicityofAromaticAminesModel() - Static method in class mutant.rules.RuleDAMutagenicityAromaticAmines
-
- createMutagenicityofAromaticAminesModel() - Static method in class toxtree.plugins.ames.rules.RuleDAMutagenicityAromaticAmines
-
- createNewMolecule - Variable in class toxtree.ui.tree.rules.RuleSubstructuresEditAction
-
- createNodePanel(DecisionNode) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- createNodesList() - Method in class toxTree.tree.DecisionNodesFactory
-
- createNodesList(IDecisionCategories, String[], int[][]) - Method in class toxTree.tree.DecisionNodesFactory
-
- createNodesList() - Method in interface toxTree.tree.IDecisionNodesFactory
-
- createNodesList(IDecisionCategories, String[], int[][]) - Method in interface toxTree.tree.IDecisionNodesFactory
-
- createObject(String) - Static method in class toxTree.core.Introspection
-
Creates object given the class name
- createOptions() - Method in class toxTree.apps.ToxtreeOptions
-
- createOutputFile() - Method in class toxTree.io.batch.BatchProcessing
-
- createOutputFile() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
-
Creates ChemObjectWriter
- createOutputFile() - Method in interface toxTree.io.batch.IBatchProcessing
-
- createPalette(IDecisionMethod) - Method in class toxtree.ui.tree.TreePrefuse
-
- createPanel2DPopupmenu() - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
-
- createPopupmenu() - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
-
- createPropertyInput() - Method in class toxTree.ui.EditorFactory
-
- createPropertyInput() - Method in class toxtree.ui.editors.SwingEditorFactory
-
- createPropertyInput() - Method in interface toxTree.ui.IEditorFactory
-
- createQuery(String) - Static method in class toxTree.query.FunctionalGroups
-
- createQuery(String, String) - Static method in class toxTree.query.FunctionalGroups
-
- createQueryContainer(IAtomContainer) - Static method in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
-
- createQueryContainer(IAtomContainer) - Static method in class toxTree.query.SimpleReactions
-
- createReader(File, IChemObjectBuilder, IReaderListener) - Method in class toxTree.data.MoleculesFile
-
- createRule(String) - Static method in class toxTree.tree.AbstractRule
-
- createRuleActions() - Method in class toxtree.ui.tree.EditTreeActions
-
- createRules() - Static method in class toxtree.plugins.moa.MOARules
-
- createRulesPanel(IDecisionRuleList) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- createSmartsPane() - Method in class toxtree.ui.tree.rules.SMARTSRuleEditor
-
- createSmartsPattern(String, boolean) - Method in class mic.rules.SA34
-
- createSmartsPattern() - Method in class mutant.descriptors.DescriptorBridgedBiphenyl
-
- createSmartsPattern() - Method in class mutant.descriptors.DescriptorHasNO2Group
-
- createSmartsPattern() - Method in class mutant.descriptors.DescriptorIsAniline
-
- createSmartsPattern() - Method in class mutant.descriptors.DescriptorStructurePresence
-
- createSmartsPattern() - Method in class toxtree.plugins.ames.descriptors.DescriptorBridgedBiphenyl
-
- createSmartsPattern() - Method in class toxtree.plugins.ames.descriptors.DescriptorHasNO2Group
-
- createSmartsPattern() - Method in class toxtree.plugins.ames.descriptors.DescriptorIsAniline
-
- createSmartsPattern() - Method in class toxtree.plugins.ames.descriptors.DescriptorStructurePresence
-
- createSmartsPattern(String, boolean) - Method in class toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit
-
- createSmartsPattern(String, boolean) - Method in class toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK
-
- createSplitPanel(int) - Method in class toxTree.apps.CompoundMethodApplication
-
- createSplitPanel(int) - Method in class toxTree.apps.toxForest.ToxForestApp
-
- createStatusBar() - Method in class toxTree.apps.CompoundMethodApplication
-
- createSubmenu(Action) - Static method in class toxtree.data.ActionList
-
- createTransitions() - Static method in class toxtree.plugins.moa.MOARules
-
- createTreeActions() - Method in class toxtree.ui.tree.EditTreeActions
-
- createTreeEditor(IDecisionMethod) - Method in class toxTree.ui.EditorFactory
-
- createTreeEditor(IDecisionMethod) - Method in class toxtree.ui.editors.SwingEditorFactory
-
- createTreeEditor(IDecisionMethod) - Method in interface toxTree.ui.IEditorFactory
-
- createTreeNodeActions() - Method in class toxtree.ui.tree.EditTreeActions
-
- createTreePanel() - Method in class toxtree.ui.tree.TreeEditorPanel
-
- createWizard(Frame, IDecisionMethod, int) - Static method in class toxtree.ui.wizard.DecisionNodeWizard
-
- CSV_INDEX - Static variable in class toxTree.io.batch.ChemObjectBatchProcessing
-
- currentNo - Variable in class toxTree.data.MoleculesIterator
-
- currentRecord - Variable in class toxTree.io.batch.FileState
-
- CYANO - Static variable in class toxTree.query.FunctionalGroups
-
- cyano() - Static method in class toxTree.query.FunctionalGroups
-
SMARTS: C(#N)([C,#1])
- CYCLIC_DIESTER - Static variable in class toxTree.query.FunctionalGroups
-
- CYCLIC_SUBSTITUENT - Static variable in class toxTree.tree.rules.RuleRingSubstituents
-
- CYCLICESTER - Static variable in class verhaar.query.FunctionalGroups
-
- cyclicEster() - Static method in class verhaar.query.FunctionalGroups
-
- CYP1A2 - Class in toxtree.plugins.lewis.categories
-
- CYP1A2() - Constructor for class toxtree.plugins.lewis.categories.CYP1A2
-
- CYP2A - Class in toxtree.plugins.lewis.categories
-
- CYP2A() - Constructor for class toxtree.plugins.lewis.categories.CYP2A
-
- CYP2B - Class in toxtree.plugins.lewis.categories
-
- CYP2B() - Constructor for class toxtree.plugins.lewis.categories.CYP2B
-
- CYP2C - Class in toxtree.plugins.lewis.categories
-
- CYP2C() - Constructor for class toxtree.plugins.lewis.categories.CYP2C
-
- CYP2D - Class in toxtree.plugins.lewis.categories
-
- CYP2D() - Constructor for class toxtree.plugins.lewis.categories.CYP2D
-
- CYP2E - Class in toxtree.plugins.lewis.categories
-
- CYP2E() - Constructor for class toxtree.plugins.lewis.categories.CYP2E
-
- CYP3A4 - Class in toxtree.plugins.lewis.categories
-
- CYP3A4() - Constructor for class toxtree.plugins.lewis.categories.CYP3A4
-
- R - Static variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
-
- R - Static variable in class toxtree.plugins.ames.descriptors.AromaticAmineSubstituentsDescriptor
-
- RadioBoxPanel<T> - Class in toxtree.ui.wizard
-
- RadioBoxPanel() - Constructor for class toxtree.ui.wizard.RadioBoxPanel
-
- RadioBoxPanel(String, List<T>, int) - Constructor for class toxtree.ui.wizard.RadioBoxPanel
-
- rank - Variable in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
-
- reaction - Variable in class toxTree.query.SimpleReactions
-
- ReactionException - Exception in toxTree.exceptions
-
TODO add description
- ReactionException() - Constructor for exception toxTree.exceptions.ReactionException
-
- ReactionException(String) - Constructor for exception toxTree.exceptions.ReactionException
-
- ReactionException(String, Throwable) - Constructor for exception toxTree.exceptions.ReactionException
-
- ReactionException(Throwable) - Constructor for exception toxTree.exceptions.ReactionException
-
- reactor - Variable in class toxtree.tree.cramer3.rules.RuleSMARTSSubstructureHydrolysis
-
- Reactor - Class in toxtree.tree
-
- Reactor() - Constructor for class toxtree.tree.Reactor
-
- Reactor(String[][]) - Constructor for class toxtree.tree.Reactor
-
- reader - Variable in class toxTree.data.MoleculesFile
-
- reader - Variable in class toxTree.io.batch.ChemObjectBatchProcessing
-
- readFile() - Method in class toxTree.tree.rules.InChILookupFile
-
- readFileInchi() - Method in class toxTree.tree.rules.InChILookupFile
-
- readFileSDF(File, InchiProcessor) - Static method in class toxTree.tree.rules.InChILookupFile
-
- readRecord() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
-
- readRecord() - Method in interface toxTree.io.batch.IBatchProcessing
-
- readStream(InputStream, String) - Method in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
-
- ReallyAnyAtom - Class in toxTree.query
-
To be used instead of org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom
until its matcher code is fixed
- ReallyAnyAtom(IChemObjectBuilder) - Constructor for class toxTree.query.ReallyAnyAtom
-
- reference - Variable in class toxtree.ui.tree.TreePanel
-
- RemoteCompoundLookup - Class in toxTree.query.remote
-
- RemoteCompoundLookup() - Constructor for class toxTree.query.remote.RemoteCompoundLookup
-
- RemoteLookup<RESULT> - Class in toxtree.lookup
-
- RemoteLookup() - Constructor for class toxtree.lookup.RemoteLookup
-
- remove() - Method in class toxTree.data.MoleculesIterator
-
- remove(int) - Method in class toxTree.tree.CategoriesList
-
- remove(Object) - Method in class toxTree.tree.CategoriesList
-
- remove(int) - Method in class toxTree.tree.DecisionMethodsList
-
- remove(Object) - Method in class toxTree.tree.DecisionMethodsList
-
- remove(int) - Method in class toxTree.tree.DecisionNodesList
-
- remove(Object) - Method in class toxTree.tree.DecisionNodesList
-
- remove(int) - Method in class toxTree.tree.DecisionResultsList
-
- remove(Object) - Method in class toxTree.tree.DecisionResultsList
-
- remove(int) - Method in class toxTree.tree.RulesList
-
- remove(Object) - Method in class toxTree.tree.RulesList
-
- removeAll(Collection) - Method in class toxTree.tree.CategoriesList
-
- removeAll(Collection) - Method in class toxTree.tree.DecisionMethodsList
-
- removeAll(Collection) - Method in class toxTree.tree.DecisionNodesList
-
- removeAll(Collection) - Method in class toxTree.tree.RulesList
-
- removeAllAtomContainers() - Method in class toxTree.data.ListOfAtomContainers
-
- removeAllAtomContainers() - Method in class toxTree.data.MoleculesFile
-
- removeAtomContainer(IAtomContainer) - Method in class toxTree.data.ListOfAtomContainers
-
- removeAtomContainer(int) - Method in class toxTree.data.ListOfAtomContainers
-
- removeAtomContainer(IAtomContainer) - Method in class toxTree.data.MoleculesFile
-
- removeAtomContainer(int) - Method in class toxTree.data.MoleculesFile
-
- removeCategory(IDecisionCategory) - Method in class mutant.rules.MutantTreeResult
-
- removeCategory(IDecisionCategory) - Method in class toxtree.plugins.ames.rules.AmesMutagenicityTreeResult
-
- removeElement(String) - Method in class toxTree.tree.rules.RuleElements
-
- removeListener() - Method in class mutant.rules.QSAR6Applicable
-
- removeListener() - Method in class mutant.rules.UserInputABUnsaturatedAldehyde
-
- removeListener() - Method in class mutant.rules.UserInputAromaticAmine
-
- removeListener() - Method in interface toxTree.core.IDecisionInteractive
-
- removeListener(IChemObjectListener) - Method in class toxTree.data.ListOfAtomContainers
-
- removeListener() - Method in class toxtree.plugins.ames.rules.QSAR6Applicable
-
- removeListener() - Method in class toxtree.plugins.ames.rules.UserInputABUnsaturatedAldehyde
-
- removeListener() - Method in class toxtree.plugins.ames.rules.UserInputAromaticAmine
-
- removeListener() - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- removeListener() - Method in class toxTree.tree.UserDefinedTree
-
- removeMethod(DecisionResultsList, int) - Method in class toxTree.apps.toxForest.ToxForestDataModulePanel
-
- removeNode(DecisionNode) - Method in class toxTree.tree.DecisionNodesList
-
- removeProperty(String) - Method in class toxTree.data.AbstractFilter
-
- removeProperty(String) - Method in interface toxTree.data.IObjectFilter
-
- removeProperty(Object) - Method in class toxTree.data.ListOfAtomContainers
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class com.molecularnetworks.start.BiodgeradationRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class cramer2.CramerRulesWithExtensions
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class eye.EyeIrritationRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class mic.MICRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class michaelacceptors.MichaelAcceptorRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class mutant.BB_CarcMutRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class sicret.SicretRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in interface toxTree.core.IDecisionMethod
-
- removePropertyChangeListener(PropertyChangeListener) - Method in interface toxTree.core.IDecisionResult
-
- removePropertyChangeListener(PropertyChangeListener) - Method in interface toxTree.core.IDecisionRule
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxTree.data.MoleculesFile
-
- removePropertyChangeListener(String, PropertyChangeListener) - Method in class toxTree.data.MoleculesFile
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.ames.AmesMutagenicityRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.func.FuncRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.AbstractRule
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.AbstractTree
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.BatchDecisionResultsList
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.cramer.CramerRules
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxtree.tree.cramer3.RevisedCramerDecisionTree
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.DecisionNode
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.TreeResult
-
- removeSingleSMARTS(Hashtable, String) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- removeSubstructure(int) - Method in interface toxTree.core.IRuleSubstructures
-
Removes substructure at a given index
- removeSubstructure(int) - Method in class toxTree.tree.rules.RuleSubstructures
-
- removeTreeModelListener(TreeModelListener) - Method in class toxtree.ui.tree.DecisionTreeModel
-
- replaceAtomContainer(int, IAtomContainer) - Method in class toxTree.data.ListOfAtomContainers
-
- replaceAtomContainer(int, IAtomContainer) - Method in class toxTree.data.MoleculesFile
-
- ReportTreePrinter - Class in toxTree.tree
-
- ReportTreePrinter() - Constructor for class toxTree.tree.ReportTreePrinter
-
- ReportTreePrinter(OutputStream) - Constructor for class toxTree.tree.ReportTreePrinter
-
- ReportTreePrinter(File) - Constructor for class toxTree.tree.ReportTreePrinter
-
- RequireCompoundSpecificToxicityData - Class in toxtree.plugins.kroes.categories
-
- RequireCompoundSpecificToxicityData() - Constructor for class toxtree.plugins.kroes.categories.RequireCompoundSpecificToxicityData
-
- RequireCompoundSpecificToxicityData(String, int) - Constructor for class toxtree.plugins.kroes.categories.RequireCompoundSpecificToxicityData
-
- residueIDHidden - Variable in class toxTree.tree.AbstractRule
-
- residues - Variable in class toxTree.query.MolFlags
-
- residuesIDVisible - Variable in class com.molecularnetworks.start.BiodgeradationRules
-
- residuesIDVisible - Variable in class cramer2.CramerRulesWithExtensions
-
- residuesIDVisible - Variable in class eye.EyeIrritationRules
-
- residuesIDVisible - Variable in class mic.MICRules
-
- residuesIDVisible - Variable in class michaelacceptors.MichaelAcceptorRules
-
- residuesIDVisible - Variable in class mutant.BB_CarcMutRules
-
- residuesIDVisible - Variable in class sicret.SicretRules
-
- residuesIDVisible - Variable in class toxtree.plugins.ames.AmesMutagenicityRules
-
- residuesIDVisible - Variable in class toxtree.plugins.dnabinding.DNABindingPlugin
-
- residuesIDVisible - Variable in class toxtree.plugins.func.FuncRules
-
- residuesIDVisible - Variable in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
-
- residuesIDVisible - Variable in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- residuesIDVisible - Variable in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- residuesIDVisible - Variable in class toxTree.tree.cramer.CramerRules
-
- residuesIDVisible - Variable in class toxtree.tree.cramer3.RevisedCramerDecisionTree
-
- resolveClass(ObjectStreamClass) - Method in class toxTree.core.ToxTreeObjectInputStream
-
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6500212
Thus, we highly recommend replacement of this code:
- result - Variable in class toxTree.tree.RuleResult
-
- result - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
-
- result - Variable in class toxtree.ui.tree.categories.CategoriesPanel
-
- resultName - Variable in class mutant.descriptors.DescriptorStructurePresence
-
- resultName - Variable in class toxtree.plugins.ames.descriptors.DescriptorStructurePresence
-
- resultURL - Static variable in class toxTree.tree.RuleResult
-
- retainAll(Collection) - Method in class toxTree.tree.CategoriesList
-
- retainAll(Collection) - Method in class toxTree.tree.DecisionMethodsList
-
- retainAll(Collection) - Method in class toxTree.tree.DecisionNodesList
-
- retainAll(Collection) - Method in class toxTree.tree.RulesList
-
- retrieveExplanation(String) - Method in class toxTree.tree.AbstractTree
-
- retrieveRemote(String) - Method in class toxtree.ui.molecule.SmilesEntryPanel
-
- retrieveStrings(IDecisionRule, String[]) - Static method in class toxtree.tree.BundleRuleResource
-
- retrieveStrings(IDecisionRule, String, String[]) - Static method in class toxtree.tree.BundleRuleResource
-
- reverse_numbers - Variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
-
- reverse_numbers - Variable in class toxtree.plugins.ames.descriptors.AromaticAmineSubstituentsDescriptor
-
- RevisedCramerDecisionTree - Class in toxtree.tree.cramer3
-
Assigns categories:
toxTree.tree.cramer3.CramerClass1
toxTree.tree.cramer3.CramerClass2
toxTree.tree.cramer3.CramerClass2
- RevisedCramerDecisionTree() - Constructor for class toxtree.tree.cramer3.RevisedCramerDecisionTree
-
- RevisedCramerDecisionTree(TreeSpecification) - Constructor for class toxtree.tree.cramer3.RevisedCramerDecisionTree
-
- ring - Variable in class mutant.descriptors.SubstituentPosition
-
- ring - Variable in class toxtree.plugins.ames.descriptors.SubstituentPosition
-
- ring(int) - Static method in class toxTree.query.FunctionalGroups
-
- ring6 - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
-
- RING_NUMBERING - Static variable in class toxTree.query.FunctionalGroups
-
- ringQuery - Variable in class mutant.descriptors.SubstituentExtractor
-
- ringQuery - Variable in class toxtree.plugins.ames.descriptors.SubstituentExtractor
-
- ringset - Variable in class toxTree.query.MolFlags
-
- RINGSUBSTITUTED - Static variable in class verhaar.query.FunctionalGroups
-
- ringSubstituted(String) - Static method in class verhaar.query.FunctionalGroups
-
- rule - Variable in class toxTree.tree.DecisionNode
-
- rule - Variable in class toxTree.tree.RuleResult
-
- rule - Variable in class toxtree.ui.OptionsPanel
-
- rule - Variable in class toxtree.ui.tree.actions.AbstractRuleAction
-
- rule - Variable in class toxtree.ui.tree.actions.EditRuleAction
-
- rule - Variable in class toxtree.ui.tree.rules.RuleEditor
-
- rule - Variable in class toxtree.ui.tree.rules.RuleMoleculeEditAction
-
- rule - Variable in class toxtree.ui.tree.rules.RulePanel
-
- rule - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
-
- Rule01 - Class in verhaar.rules
-
Consists only of C,H,N,O,S,halogens (exluding I).
- Rule01() - Constructor for class verhaar.rules.Rule01
-
- Rule03 - Class in verhaar.rules
-
Have a molecular mass (MW) not more than 600 Daltons.
- Rule03() - Constructor for class verhaar.rules.Rule03
-
- Rule1 - Class in eye.rules
-
- Rule1() - Constructor for class eye.rules.Rule1
-
- Rule1 - Class in michaelacceptors.rules
-
TODO with StructureAlertAmbit [CH]#CC=O doesn't match COC(=O)C#C
while C#CC=O matches COC(=O)C#C
- Rule1() - Constructor for class michaelacceptors.rules.Rule1
-
- Rule10A - Class in michaelacceptors.rules
-
- Rule10A() - Constructor for class michaelacceptors.rules.Rule10A
-
- Rule10B - Class in michaelacceptors.rules
-
- Rule10B() - Constructor for class michaelacceptors.rules.Rule10B
-
- Rule11 - Class in michaelacceptors.rules
-
- Rule11() - Constructor for class michaelacceptors.rules.Rule11
-
- Rule11 - Class in sicret.rules
-
LogKow > 4.5
- Rule11() - Constructor for class sicret.rules.Rule11
-
- Rule11 - Class in verhaar.rules
-
Does not contain I.
- Rule11() - Constructor for class verhaar.rules.Rule11
-
- Rule12 - Class in sicret.rules
-
VapourPressure < 0.0001
- Rule12() - Constructor for class sicret.rules.Rule12
-
- Rule12A - Class in michaelacceptors.rules
-
- Rule12A() - Constructor for class michaelacceptors.rules.Rule12A
-
- Rule12B - Class in michaelacceptors.rules
-
- Rule12B() - Constructor for class michaelacceptors.rules.Rule12B
-
- Rule13 - Class in sicret.rules
-
Molecular Weight > 540.0
- Rule13() - Constructor for class sicret.rules.Rule13
-
- Rule13 - Class in verhaar.rules
-
Contain only C&H.
- Rule13() - Constructor for class verhaar.rules.Rule13
-
- Rule13_AliphaticMonoalcohols - Class in eye.rules
-
A Lactams
- Rule13_AliphaticMonoalcohols() - Constructor for class eye.rules.Rule13_AliphaticMonoalcohols
-
- Rule13A - Class in michaelacceptors.rules
-
- Rule13A() - Constructor for class michaelacceptors.rules.Rule13A
-
- Rule13B - Class in michaelacceptors.rules
-
- Rule13B() - Constructor for class michaelacceptors.rules.Rule13B
-
- Rule14 - Class in michaelacceptors.rules
-
- Rule14() - Constructor for class michaelacceptors.rules.Rule14
-
- Rule14 - Class in sicret.rules
-
MeltingPoint > 180.0
- Rule14() - Constructor for class sicret.rules.Rule14
-
- Rule14 - Class in verhaar.rules
-
Contain only C,H and halogen.
- Rule14() - Constructor for class verhaar.rules.Rule14
-
- Rule141 - Class in verhaar.rules
-
Acyclic compound NOT containing halogen at beta-positions from unsaturations (e.g.
- Rule141() - Constructor for class verhaar.rules.Rule141
-
- Rule142 - Class in verhaar.rules
-
Monocyclic compounds substituted with halogens.
- Rule142() - Constructor for class verhaar.rules.Rule142
-
- Rule143 - Class in verhaar.rules
-
Monocyclic compounds that are unsubstituted or substituted with acyclic
structures containing only C&H or complying with rule
Rule141.
- Rule143() - Constructor for class verhaar.rules.Rule143
-
- Rule144 - Class in verhaar.rules
-
Polycyclic compounds that are unsubstituted or substituted with acyclic structures containing only C&H or complying with
Rule141.
- Rule144() - Constructor for class verhaar.rules.Rule144
-
- Rule14Aliphatic_glycerol_monoethers - Class in eye.rules
-
LipidSolubility < 4.0
- Rule14Aliphatic_glycerol_monoethers() - Constructor for class eye.rules.Rule14Aliphatic_glycerol_monoethers
-
- Rule15 - Class in eye.rules
-
Acid anhydrides.
- Rule15() - Constructor for class eye.rules.Rule15
-
Constructor
- Rule15 - Class in sicret.rules
-
AqueousSolubility < 0.0001
- Rule15() - Constructor for class sicret.rules.Rule15
-
- Rule15 - Class in verhaar.rules
-
Contain only C,H,O.
- Rule15() - Constructor for class verhaar.rules.Rule15
-
- Rule151 - Class in verhaar.rules
-
Linear ethers or monocyclic mono ethers, but not epoxides or peroxides.
- Rule151() - Constructor for class verhaar.rules.Rule151
-
- Rule152 - Class in verhaar.rules
-
Aliphatic alcohols but not allylic/propargylic alcohols.
- Rule152() - Constructor for class verhaar.rules.Rule152
-
- Rule153 - Class in verhaar.rules
-
Alcohols with aromatic moieties, but NOT phenols or benzylic alcohols.
- Rule153() - Constructor for class verhaar.rules.Rule153
-
- Rule154 - Class in verhaar.rules
-
Ketones, but not alpha-, beta unsaturated ketones (e.g.
- Rule154() - Constructor for class verhaar.rules.Rule154
-
- Rule16 - Class in eye.rules
-
Halogen benzenes with substituents containing carboxylic acid groups
SMARTS pattern [CX3](=[OX1])[NX3H][CX3](=[OX1]).
- Rule16() - Constructor for class eye.rules.Rule16
-
- Rule16 - Class in sicret.rules
-
LogKow > 5.5
- Rule16() - Constructor for class sicret.rules.Rule16
-
- Rule16 - Class in verhaar.rules
-
Contain only C,H,N.
- Rule16() - Constructor for class verhaar.rules.Rule16
-
- Rule161 - Class in verhaar.rules
-
Aliphatic secondary or tertiary amines.
- Rule161() - Constructor for class verhaar.rules.Rule161
-
- Rule17 - Class in eye.rules
-
Aliphatic esters of chloro formic acid
- Rule17() - Constructor for class eye.rules.Rule17
-
- Rule17 - Class in sicret.rules
-
LogKow > 3.8
- Rule17() - Constructor for class sicret.rules.Rule17
-
- Rule17 - Class in verhaar.rules
-
Contain only C,H,O and halogen.
- Rule17() - Constructor for class verhaar.rules.Rule17
-
- Rule171 - Class in verhaar.rules
-
Halogenated compounds that comply with rule
Rule15 but not alpha-, beta- halogen substituted compounds.
- Rule171() - Constructor for class verhaar.rules.Rule171
-
- Rule18 - Class in eye.rules
-
Chlorinated aliphatic alcohols
- Rule18() - Constructor for class eye.rules.Rule18
-
- Rule18 - Class in sicret.rules
-
AqueousSolubility < 0.1
- Rule18() - Constructor for class sicret.rules.Rule18
-
- Rule19 - Class in eye.rules
-
Diphenyl iodonium salts
- Rule19() - Constructor for class eye.rules.Rule19
-
- Rule19 - Class in sicret.rules
-
MoleculWeight > 370.0
- Rule19() - Constructor for class sicret.rules.Rule19
-
- Rule2 - Class in michaelacceptors.rules
-
- Rule2() - Constructor for class michaelacceptors.rules.Rule2
-
- Rule20 - Class in eye.rules
-
Derivatives of alpha amino benzene
- Rule20() - Constructor for class eye.rules.Rule20
-
- Rule20 - Class in sicret.rules
-
LipidSolubility < 400.0
- Rule20() - Constructor for class sicret.rules.Rule20
-
- Rule21 - Class in eye.rules
-
Pyrrolidones
- Rule21() - Constructor for class eye.rules.Rule21
-
- Rule21 - Class in sicret.rules
-
MoleculWeight > 380.0
- Rule21() - Constructor for class sicret.rules.Rule21
-
- Rule21 - Class in verhaar.rules
-
Non- or weakly acidic phenols.
- Rule21() - Constructor for class verhaar.rules.Rule21
-
- Rule22 - Class in eye.rules
-
Substituted indoles
- Rule22() - Constructor for class eye.rules.Rule22
-
- Rule22 - Class in sicret.rules
-
LipidSolubility < 4.0
- Rule22() - Constructor for class sicret.rules.Rule22
-
- Rule22 - Class in verhaar.rules
-
Anilines with one nitro substituent and/or one to three chlorine substituents, and/or alkyl substituents.
- Rule22() - Constructor for class verhaar.rules.Rule22
-
- Rule23 - Class in eye.rules
-
Substituted pyrasoles
- Rule23() - Constructor for class eye.rules.Rule23
-
- Rule23 - Class in sicret.rules
-
AqueousSolubility < 0.001
- Rule23() - Constructor for class sicret.rules.Rule23
-
- Rule23 - Class in verhaar.rules
-
Be mononitroaromatics with one or two chlorine substituents and/or alkyl
substituents.
- Rule23() - Constructor for class verhaar.rules.Rule23
-
- Rule24 - Class in eye.rules
-
- Rule24() - Constructor for class eye.rules.Rule24
-
- Rule24 - Class in sicret.rules
-
Molecular Weight > 620.0
- Rule24() - Constructor for class sicret.rules.Rule24
-
- Rule24 - Class in verhaar.rules
-
Primary alkyl amines (containing only C,H,N).
- Rule24() - Constructor for class verhaar.rules.Rule24
-
- Rule25 - Class in eye.rules
-
Organic sulphonic salts
- Rule25() - Constructor for class eye.rules.Rule25
-
- Rule25 - Class in sicret.rules
-
MeltingPoint > 50.0
- Rule25() - Constructor for class sicret.rules.Rule25
-
- Rule25 - Class in verhaar.rules
-
Pyridines with one or two chlorine substituents and/or alkyl substituents.
- Rule25() - Constructor for class verhaar.rules.Rule25
-
- Rule26 - Class in eye.rules
-
Thiazoles and thiazolidines
- Rule26() - Constructor for class eye.rules.Rule26
-
- Rule26 - Class in sicret.rules
-
SurfaceTension > 62.0
- Rule26() - Constructor for class sicret.rules.Rule26
-
- Rule27 - Class in eye.rules
-
- Rule27() - Constructor for class eye.rules.Rule27
-
- Rule27 - Class in sicret.rules
-
MeltingPoint > 120.0
- Rule27() - Constructor for class sicret.rules.Rule27
-
- Rule28 - Class in eye.rules
-
- Rule28() - Constructor for class eye.rules.Rule28
-
- Rule28 - Class in sicret.rules
-
LogKow < 0.5
- Rule28() - Constructor for class sicret.rules.Rule28
-
- Rule29 - Class in eye.rules
-
- Rule29() - Constructor for class eye.rules.Rule29
-
- Rule29 - Class in sicret.rules
-
Molecular Weight > 370.0
- Rule29() - Constructor for class sicret.rules.Rule29
-
- Rule3 - Class in michaelacceptors.rules
-
- Rule3() - Constructor for class michaelacceptors.rules.Rule3
-
- Rule30 - Class in eye.rules
-
TODO
Aliphatic monoalcohols
- Rule30() - Constructor for class eye.rules.Rule30
-
- Rule30 - Class in sicret.rules
-
Molecular Weight > 280.0
- Rule30() - Constructor for class sicret.rules.Rule30
-
- Rule31 - Class in eye.rules
-
- Rule31() - Constructor for class eye.rules.Rule31
-
- Rule31 - Class in verhaar.rules
-
Possess alylic/propargylic activation.
- Rule31() - Constructor for class verhaar.rules.Rule31
-
[*]C=CC(X)[*]
- Rule32 - Class in eye.rules
-
- Rule32() - Constructor for class eye.rules.Rule32
-
- Rule32 - Class in toxTree.tree.cramer
-
- Rule32() - Constructor for class toxTree.tree.cramer.Rule32
-
- Rule32 - Class in verhaar.rules
-
Possess benzylic activation.
- Rule32() - Constructor for class verhaar.rules.Rule32
-
- Rule33 - Class in eye.rules
-
- Rule33() - Constructor for class eye.rules.Rule33
-
doesn't work with CDK smarts parser for some reason...
- Rule33 - Class in verhaar.rules
-
Be other compound with a (good) leaving group at an alpha position of a double or triple bond fragment.
- Rule33() - Constructor for class verhaar.rules.Rule33
-
- Rule34 - Class in eye.rules
-
- Rule34() - Constructor for class eye.rules.Rule34
-
- Rule34 - Class in verhaar.rules
-
Possess a three-membered heterocyclic ring.
- Rule34() - Constructor for class verhaar.rules.Rule34
-
- Rule35 - Class in eye.rules
-
- Rule35() - Constructor for class eye.rules.Rule35
-
- Rule35 - Class in verhaar.rules
-
Possess activated C-C double/triple bonds.
- Rule35() - Constructor for class verhaar.rules.Rule35
-
- Rule36 - Class in eye.rules
-
- Rule36() - Constructor for class eye.rules.Rule36
-
- Rule36 - Class in verhaar.rules
-
Hydrazines or other compounds with a single , double or triple N-N linkage.
- Rule36() - Constructor for class verhaar.rules.Rule36
-
- Rule37 - Class in eye.rules
-
- Rule37() - Constructor for class eye.rules.Rule37
-
- Rule37 - Class in verhaar.rules
-
Activated nitriles like alpha hydroxynitriles (cyanohidrins) or allylic /propargylic nitriles.
- Rule37() - Constructor for class verhaar.rules.Rule37
-
- Rule38 - Class in eye.rules
-
- Rule38() - Constructor for class eye.rules.Rule38
-
- Rule38 - Class in verhaar.rules
-
Contain one of the following structural entities:
- Rule38() - Constructor for class verhaar.rules.Rule38
-
- Rule39 - Class in eye.rules
-
- Rule39() - Constructor for class eye.rules.Rule39
-
- Rule3FuncGroups - Class in toxTree.tree.cramer
-
- Rule3FuncGroups() - Constructor for class toxTree.tree.cramer.Rule3FuncGroups
-
Constructor
- Rule3MemberedHeterocycle - Class in toxTree.tree.cramer
-
3-membered heterocycle.
- Rule3MemberedHeterocycle() - Constructor for class toxTree.tree.cramer.Rule3MemberedHeterocycle
-
Constructor
- Rule4 - Class in sicret.rules
-
MeltingPoint > 55.0
- Rule4() - Constructor for class sicret.rules.Rule4
-
- Rule4 - Class in verhaar.rules
-
Compounds acting by a specific mechanism.
- Rule4() - Constructor for class verhaar.rules.Rule4
-
Finally both databases contain several groups of
chemicals which should fall into Verhaar class 4 (chemicals acting
via a specific (non-covalent) mechanism); typically these include
the weak acid respiratory uncouplers.
- Rule4A - Class in michaelacceptors.rules
-
- Rule4A() - Constructor for class michaelacceptors.rules.Rule4A
-
- Rule4B - Class in michaelacceptors.rules
-
- Rule4B() - Constructor for class michaelacceptors.rules.Rule4B
-
- Rule5 - Class in michaelacceptors.rules
-
- Rule5() - Constructor for class michaelacceptors.rules.Rule5
-
- Rule6 - Class in michaelacceptors.rules
-
- Rule6() - Constructor for class michaelacceptors.rules.Rule6
-
- Rule7 - Class in michaelacceptors.rules
-
- Rule7() - Constructor for class michaelacceptors.rules.Rule7
-
- Rule8 - Class in michaelacceptors.rules
-
- Rule8() - Constructor for class michaelacceptors.rules.Rule8
-
- Rule8 - Class in sicret.rules
-
LipidSolubility < 0.4
- Rule8() - Constructor for class sicret.rules.Rule8
-
- Rule9 - Class in sicret.rules
-
MoleculWeight > 290.0
- Rule9() - Constructor for class sicret.rules.Rule9
-
- Rule9A - Class in michaelacceptors.rules
-
- Rule9A() - Constructor for class michaelacceptors.rules.Rule9A
-
- Rule9B - Class in michaelacceptors.rules
-
- Rule9B() - Constructor for class michaelacceptors.rules.Rule9B
-
- Rule_areadepthratio - Class in toxtree.plugins.lewis.rules
-
- Rule_areadepthratio() - Constructor for class toxtree.plugins.lewis.rules.Rule_areadepthratio
-
- Rule_high_AreaDepthRatio - Class in toxtree.plugins.lewis.rules
-
- Rule_high_AreaDepthRatio() - Constructor for class toxtree.plugins.lewis.rules.Rule_high_AreaDepthRatio
-
- Rule_high_pKa - Class in toxtree.plugins.lewis.rules
-
- Rule_high_pKa() - Constructor for class toxtree.plugins.lewis.rules.Rule_high_pKa
-
- Rule_highLogP - Class in toxtree.plugins.lewis.rules
-
- Rule_highLogP() - Constructor for class toxtree.plugins.lewis.rules.Rule_highLogP
-
- Rule_highVolume - Class in toxtree.plugins.lewis.rules
-
- Rule_highVolume() - Constructor for class toxtree.plugins.lewis.rules.Rule_highVolume
-
- Rule_lowVolume - Class in toxtree.plugins.lewis.rules
-
- Rule_lowVolume() - Constructor for class toxtree.plugins.lewis.rules.Rule_lowVolume
-
- Rule_volume - Class in toxtree.plugins.lewis.rules
-
- Rule_volume() - Constructor for class toxtree.plugins.lewis.rules.Rule_volume
-
- RuleA_Lactams - Class in sicret.rules
-
A Lactams
- RuleA_Lactams() - Constructor for class sicret.rules.RuleA_Lactams
-
- RuleABUnsaturatedAldehyde - Class in mutant.rules
-
Hits alfa-beta unsaturated aldehydes, exclude cyclic alfa-beta unsaturated aldehydes.
- RuleABUnsaturatedAldehyde() - Constructor for class mutant.rules.RuleABUnsaturatedAldehyde
-
- RuleABUnsaturatedAldehyde - Class in toxtree.plugins.ames.rules
-
Hits alfa-beta unsaturated aldehydes, exclude cyclic alfa-beta unsaturated aldehydes.
- RuleABUnsaturatedAldehyde() - Constructor for class toxtree.plugins.ames.rules.RuleABUnsaturatedAldehyde
-
- RuleAcidAnhydrides - Class in sicret.rules
-
Acid anhydrides.
- RuleAcidAnhydrides() - Constructor for class sicret.rules.RuleAcidAnhydrides
-
Constructor
- RuleAcidImides - Class in sicret.rules
-
Acid imides.
- RuleAcidImides() - Constructor for class sicret.rules.RuleAcidImides
-
- RuleAcrylicAcids - Class in sicret.rules
-
Acrylic acids.
- RuleAcrylicAcids() - Constructor for class sicret.rules.RuleAcrylicAcids
-
Constructor
- RuleAcrylicAndMethacrylicEsters - Class in sicret.rules
-
Acrylic and methacrylic esters.
SMARTS pattern [CX3](=[CX3])[CX3](=[OX1])[OX2]C.
- RuleAcrylicAndMethacrylicEsters() - Constructor for class sicret.rules.RuleAcrylicAndMethacrylicEsters
-
- ruleActions - Variable in class toxtree.ui.tree.actions.SetBranchAction
-
- ruleActions - Variable in class toxtree.ui.tree.EditTreeActions
-
- RuleAcyclicAcetalEsterOfQ30 - Class in toxTree.tree.cramer
-
- RuleAcyclicAcetalEsterOfQ30() - Constructor for class toxTree.tree.cramer.RuleAcyclicAcetalEsterOfQ30
-
Constructor
- RuleAlcohol - Class in structurefeatures.rules
-
- RuleAlcohol() - Constructor for class structurefeatures.rules.RuleAlcohol
-
- RuleAlcohols - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for alcohols.
- RuleAlcohols() - Constructor for class com.molecularnetworks.start.rules.RuleAlcohols
-
Default constructor
- RuleAldehyde - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for aldehydes.
- RuleAldehyde() - Constructor for class com.molecularnetworks.start.rules.RuleAldehyde
-
Default constructor
- RuleAldehyde - Class in structurefeatures.rules
-
- RuleAldehyde() - Constructor for class structurefeatures.rules.RuleAldehyde
-
- RuleAldehydes - Class in sicret.rules
-
Aldehydes.
SMARTS pattern [$([CX3H][#6]),$([CX3H2])]=[OX1].
- RuleAldehydes() - Constructor for class sicret.rules.RuleAldehydes
-
- RuleAlertsAche - Class in toxtree.plugins.moa.rules
-
- RuleAlertsAche() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsAche
-
- RuleAlertsAmes - Class in toxtree.plugins.ames.rules
-
- RuleAlertsAmes() - Constructor for class toxtree.plugins.ames.rules.RuleAlertsAmes
-
- RuleAlertsClass1 - Class in verhaar.rules
-
- RuleAlertsClass1() - Constructor for class verhaar.rules.RuleAlertsClass1
-
- RuleAlertsClass2 - Class in verhaar.rules
-
- RuleAlertsClass2() - Constructor for class verhaar.rules.RuleAlertsClass2
-
- RuleAlertsClass3 - Class in verhaar.rules
-
- RuleAlertsClass3() - Constructor for class verhaar.rules.RuleAlertsClass3
-
- RuleAlertsCNS - Class in toxtree.plugins.moa.rules
-
- RuleAlertsCNS() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsCNS
-
- RuleAlertsForAmesMutagenicity - Class in toxtree.plugins.ames.rules
-
- RuleAlertsForAmesMutagenicity() - Constructor for class toxtree.plugins.ames.rules.RuleAlertsForAmesMutagenicity
-
- RuleAlertsForCarcinogenicity - Class in mutant.rules
-
- RuleAlertsForCarcinogenicity() - Constructor for class mutant.rules.RuleAlertsForCarcinogenicity
-
- RuleAlertsForFunc - Class in toxtree.plugins.func.rules
-
- RuleAlertsForFunc() - Constructor for class toxtree.plugins.func.rules.RuleAlertsForFunc
-
- RuleAlertsForGenotoxicCarcinogenicity - Class in mutant.rules
-
- RuleAlertsForGenotoxicCarcinogenicity() - Constructor for class mutant.rules.RuleAlertsForGenotoxicCarcinogenicity
-
- RuleAlertsForGenotoxicCarcinogenicity - Class in toxtree.plugins.ames.rules
-
- RuleAlertsForGenotoxicCarcinogenicity() - Constructor for class toxtree.plugins.ames.rules.RuleAlertsForGenotoxicCarcinogenicity
-
- RuleAlertsForMIC - Class in mic.rules
-
- RuleAlertsForMIC() - Constructor for class mic.rules.RuleAlertsForMIC
-
- RuleAlertsForNewAmesMutagenicity - Class in toxtree.plugins.ames.rules
-
- RuleAlertsForNewAmesMutagenicity() - Constructor for class toxtree.plugins.ames.rules.RuleAlertsForNewAmesMutagenicity
-
- RuleAlertsNarcosis1_1_1 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis1_1_1() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_1
-
- RuleAlertsNarcosis1_1_1_1 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis1_1_1_1() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_1_1
-
- RuleAlertsNarcosis1_1_2_1 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis1_1_2_1() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_2_1
-
- RuleAlertsNarcosis1_1_2_3 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis1_1_2_3() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_2_3
-
- RuleAlertsNarcosis1_1_3_1 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis1_1_3_1() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_3_1
-
- RuleAlertsNarcosis1_1_4_1 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis1_1_4_1() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_4_1
-
- RuleAlertsNarcosis1_1_4_2 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis1_1_4_2() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_4_2
-
- RuleAlertsNarcosis2_2_1 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis2_2_1() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis2_2_1
-
- RuleAlertsNarcosis3 - Class in toxtree.plugins.moa.rules
-
- RuleAlertsNarcosis3() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis3
-
- RuleAlertsNongenotoxicCarcinogenicity - Class in mutant.rules
-
- RuleAlertsNongenotoxicCarcinogenicity() - Constructor for class mutant.rules.RuleAlertsNongenotoxicCarcinogenicity
-
- RuleAlertsReactive - Class in toxtree.plugins.moa.rules
-
- RuleAlertsReactive() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsReactive
-
- RuleAlertsUncouplers - Class in toxtree.plugins.moa.rules
-
- RuleAlertsUncouplers() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsUncouplers
-
- RuleAliphaticCyclicNoBranches - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for aliphatic cyclic chemicals with no branches.
- RuleAliphaticCyclicNoBranches() - Constructor for class com.molecularnetworks.start.rules.RuleAliphaticCyclicNoBranches
-
Default constructor
- RuleAliphaticEther - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for aliphatic ethers.
- RuleAliphaticEther() - Constructor for class com.molecularnetworks.start.rules.RuleAliphaticEther
-
Default constructor
- RuleAliphaticFusedRingsNonBranched - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for aliphatic compounds consisting of fused rings and no
branches.
- RuleAliphaticFusedRingsNonBranched() - Constructor for class com.molecularnetworks.start.rules.RuleAliphaticFusedRingsNonBranched
-
Default constructor
- RuleAliphaticSaturatedAcidsAndHalogenatedAcids - Class in sicret.rules
-
Aliphatic Saturated Acids and Halogenated Acids.
SMARTS pattern
[AR0][CX3](=O)[OX2H1]
[ClX1,BrX1][C;H2][CX3](=O)[OX2H1]
- RuleAliphaticSaturatedAcidsAndHalogenatedAcids() - Constructor for class sicret.rules.RuleAliphaticSaturatedAcidsAndHalogenatedAcids
-
- RuleAliphaticWithSomeFuncGroups - Class in toxTree.tree.cramer
-
- RuleAliphaticWithSomeFuncGroups() - Constructor for class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
-
Constructor
- RuleAlkylAldehyde - Class in structurefeatures.rules
-
- RuleAlkylAldehyde() - Constructor for class structurefeatures.rules.RuleAlkylAldehyde
-
- RuleAlkylAlkanolAmines - Class in sicret.rules
-
Alkyl Alkanol Amines.
SMARTS pattern
[OX2H][CX4][CX4][NX3;H2,H1;!$(NC=O)]
- RuleAlkylAlkanolAmines() - Constructor for class sicret.rules.RuleAlkylAlkanolAmines
-
- RuleAlkylHydrazine - Class in structurefeatures.rules
-
- RuleAlkylHydrazine() - Constructor for class structurefeatures.rules.RuleAlkylHydrazine
-
- RuleAlkylPhosphonate - Class in structurefeatures.rules
-
- RuleAlkylPhosphonate() - Constructor for class structurefeatures.rules.RuleAlkylPhosphonate
-
- RuleAllAllowedElements - Class in toxTree.tree.rules
-
- RuleAllAllowedElements() - Constructor for class toxTree.tree.rules.RuleAllAllowedElements
-
- RuleAllSubstructures - Class in toxTree.tree.rules
-
Verifies if all of the fragments are a substructure of moleclue
- RuleAllSubstructures() - Constructor for class toxTree.tree.rules.RuleAllSubstructures
-
- RuleAlphaAlkynes - Class in sicret.rules
-
Alpha alkynes.
SMARTS pattern
[CX4][CX2]#[CX2]
- RuleAlphaAlkynes() - Constructor for class sicret.rules.RuleAlphaAlkynes
-
- RuleAlphaHalogenatedAmidesAndThioamides - Class in sicret.rules
-
Alpha Halogenated Amides And Thioamides
SMARTS pattern
[CX3;$([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])])]
- RuleAlphaHalogenatedAmidesAndThioamides() - Constructor for class sicret.rules.RuleAlphaHalogenatedAmidesAndThioamides
-
- RuleAlyphaticSulphonicAcids - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for aliphatic sulphonic acids.
- RuleAlyphaticSulphonicAcids() - Constructor for class com.molecularnetworks.start.rules.RuleAlyphaticSulphonicAcids
-
Default constructor
- RuleAmine - Class in structurefeatures.rules
-
- RuleAmine() - Constructor for class structurefeatures.rules.RuleAmine
-
- RuleAminoAcids - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for amino acids.
- RuleAminoAcids() - Constructor for class com.molecularnetworks.start.rules.RuleAminoAcids
-
Default constructor
- RuleAnySubstituents - Class in toxTree.tree.rules
-
Verifies if the molecule consists of only allowed substituents
- RuleAnySubstituents() - Constructor for class toxTree.tree.rules.RuleAnySubstituents
-
- RuleAnySubstructure - Class in toxTree.tree.rules
-
Verifies if the molecule has at least one substructure of the list
- RuleAnySubstructure() - Constructor for class toxTree.tree.rules.RuleAnySubstructure
-
- RuleAnySubstructureCounter - Class in verhaar.rules.helper
-
- RuleAnySubstructureCounter() - Constructor for class verhaar.rules.helper.RuleAnySubstructureCounter
-
- RuleAqueousSolubility - Class in eye.rules
-
- RuleAqueousSolubility() - Constructor for class eye.rules.RuleAqueousSolubility
-
- RuleAqueousSolubility(String, String, String, double) - Constructor for class eye.rules.RuleAqueousSolubility
-
- RuleAqueousSolubility - Class in sicret.rules
-
AqueousSolubility < 0.1.
- RuleAqueousSolubility() - Constructor for class sicret.rules.RuleAqueousSolubility
-
- RuleAqueousSolubility(String, String, String, double) - Constructor for class sicret.rules.RuleAqueousSolubility
-
- RuleAqueousSolubility1 - Class in eye.rules
-
- RuleAqueousSolubility1() - Constructor for class eye.rules.RuleAqueousSolubility1
-
- RuleAqueousSolubility1(String, String, String, double) - Constructor for class eye.rules.RuleAqueousSolubility1
-
- RuleAqueousSolubility_10_2 - Class in eye.rules
-
AqueousSolubility < 0.1
- RuleAqueousSolubility_10_2() - Constructor for class eye.rules.RuleAqueousSolubility_10_2
-
- RuleAqueousSolubility_10_5 - Class in eye.rules
-
AqueousSolubility < 0.001
- RuleAqueousSolubility_10_5() - Constructor for class eye.rules.RuleAqueousSolubility_10_5
-
- RuleAqueousSolubility_11_7 - Class in eye.rules
-
- RuleAqueousSolubility_11_7() - Constructor for class eye.rules.RuleAqueousSolubility_11_7
-
- RuleAqueousSolubility_8_3 - Class in eye.rules
-
- RuleAqueousSolubility_8_3() - Constructor for class eye.rules.RuleAqueousSolubility_8_3
-
- RuleAqueousSolubility_8_3(String, String, String, double) - Constructor for class eye.rules.RuleAqueousSolubility_8_3
-
- RuleAqueousSolubility_8_4 - Class in eye.rules
-
- RuleAqueousSolubility_8_4() - Constructor for class eye.rules.RuleAqueousSolubility_8_4
-
- RuleAqueousSolubility_8_4(String, String, String, double) - Constructor for class eye.rules.RuleAqueousSolubility_8_4
-
- RuleAqueousSolubility_9_3 - Class in eye.rules
-
AqueousSolubility < 0.0001
- RuleAqueousSolubility_9_3() - Constructor for class eye.rules.RuleAqueousSolubility_9_3
-
- RuleAromatic - Class in toxTree.tree.rules
-
Verifies if the molecule is aromatic by applying the Hueckel rule
- RuleAromatic() - Constructor for class toxTree.tree.rules.RuleAromatic
-
- RuleAromaticAldehyde - Class in structurefeatures.rules
-
- RuleAromaticAldehyde() - Constructor for class structurefeatures.rules.RuleAromaticAldehyde
-
- RuleAromaticAmineNoSulfonicGroup - Class in mutant.rules
-
- RuleAromaticAmineNoSulfonicGroup() - Constructor for class mutant.rules.RuleAromaticAmineNoSulfonicGroup
-
- RuleAromaticAmineNoSulfonicGroup - Class in toxtree.plugins.ames.rules
-
- RuleAromaticAmineNoSulfonicGroup() - Constructor for class toxtree.plugins.ames.rules.RuleAromaticAmineNoSulfonicGroup
-
- RuleAromaticAmines - Class in sicret.rules
-
Aromatic Amines.
SMARTS pattern
[NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
- RuleAromaticAmines() - Constructor for class sicret.rules.RuleAromaticAmines
-
- RuleAromaticAzo - Class in structurefeatures.rules
-
- RuleAromaticAzo() - Constructor for class structurefeatures.rules.RuleAromaticAzo
-
- RuleAromaticDiazo - Class in mutant.rules
-
- RuleAromaticDiazo() - Constructor for class mutant.rules.RuleAromaticDiazo
-
- RuleAromaticDiazo - Class in toxtree.plugins.ames.rules
-
- RuleAromaticDiazo() - Constructor for class toxtree.plugins.ames.rules.RuleAromaticDiazo
-
- RuleAromaticHalogen - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals with and Iodine, Chlorine,
or Fluorine atom attached to an aromatic atom.
- RuleAromaticHalogen() - Constructor for class com.molecularnetworks.start.rules.RuleAromaticHalogen
-
Default constructor
- RuleAromaticNGroups - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals with an NO2, NH2, or NH attached to an
aromatic atom.
- RuleAromaticNGroups() - Constructor for class com.molecularnetworks.start.rules.RuleAromaticNGroups
-
Default constructor
- RuleAromaticNitro - Class in structurefeatures.rules
-
- RuleAromaticNitro() - Constructor for class structurefeatures.rules.RuleAromaticNitro
-
- RuleAromaticSulphonicAcid - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for aromatic sulphonic acids.
- RuleAromaticSulphonicAcid() - Constructor for class com.molecularnetworks.start.rules.RuleAromaticSulphonicAcid
-
Default constructor
- RuleArylMethylHalide - Class in structurefeatures.rules
-
- RuleArylMethylHalide() - Constructor for class structurefeatures.rules.RuleArylMethylHalide
-
- RuleAziridine - Class in structurefeatures.rules
-
- RuleAziridine() - Constructor for class structurefeatures.rules.RuleAziridine
-
- RuleAzo - Class in structurefeatures.rules
-
- RuleAzo() - Constructor for class structurefeatures.rules.RuleAzo
-
- RuleAzoGroup - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals containing an azo group.
- RuleAzoGroup() - Constructor for class com.molecularnetworks.start.rules.RuleAzoGroup
-
Default constructor
- RuleBenzene - Class in structurefeatures.rules
-
- RuleBenzene() - Constructor for class structurefeatures.rules.RuleBenzene
-
- RuleBenzeneAnalogues - Class in cramer2.rules
-
benzene analogues, with 0-6 substituents that consist of at most 1 heavy atom.
- RuleBenzeneAnalogues() - Constructor for class cramer2.rules.RuleBenzeneAnalogues
-
- RuleBenzylHalides - Class in sicret.rules
-
Benwyl halides.
SMARTS pattern
[ClX1,BrX1]Cc1ccccc1
- RuleBenzylHalides() - Constructor for class sicret.rules.RuleBenzylHalides
-
- RuleBetaLactones - Class in sicret.rules
-
Beta lactones.
SMARTS pattern
[#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
- RuleBetaLactones() - Constructor for class sicret.rules.RuleBetaLactones
-
- RuleC10_C20AliphaticAlcohols - Class in sicret.rules
-
C10-C20 Aliphatic Alcohols.
SMARTS pattern
[AR0][OH]
- RuleC10_C20AliphaticAlcohols() - Constructor for class sicret.rules.RuleC10_C20AliphaticAlcohols
-
Constructor
- RuleCarbamoylHalide - Class in sicret.rules
-
Carbamoyl Halide.
- RuleCarbamoylHalide() - Constructor for class sicret.rules.RuleCarbamoylHalide
-
- RuleCarbohydrate - Class in toxTree.tree.rules
-
Verifies if the molecule is a carbohydrate
- RuleCarbohydrate() - Constructor for class toxTree.tree.rules.RuleCarbohydrate
-
- RuleCatecholsResorcinolsHydroquinones - Class in sicret.rules
-
Catechols, Resorcinols Hydroquinones.
- RuleCatecholsResorcinolsHydroquinones() - Constructor for class sicret.rules.RuleCatecholsResorcinolsHydroquinones
-
Constructor
- RuleCommonComponentOfFood - Class in toxTree.tree.cramer
-
- RuleCommonComponentOfFood() - Constructor for class toxTree.tree.cramer.RuleCommonComponentOfFood
-
Constructor
- RuleCommonComponentOfFood(File) - Constructor for class toxTree.tree.cramer.RuleCommonComponentOfFood
-
- RuleCommonTerpene - Class in toxTree.tree.rules
-
Verifies if the molecule is a common terpene
- RuleCommonTerpene() - Constructor for class toxTree.tree.rules.RuleCommonTerpene
-
Constructor
- RuleCyanoGroupOnMoreThanEightAtomsChain - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals containing a cyano group that is attached
to a more than 8 atoms chain.
- RuleCyanoGroupOnMoreThanEightAtomsChain() - Constructor for class com.molecularnetworks.start.rules.RuleCyanoGroupOnMoreThanEightAtomsChain
-
Default constructor
- RuleCyclopropaneEtc - Class in toxTree.tree.cramer
-
- RuleCyclopropaneEtc() - Constructor for class toxTree.tree.cramer.RuleCyclopropaneEtc
-
Constructor
- RuleDACancerogenicityAromaticAmines - Class in mutant.rules
-
- RuleDACancerogenicityAromaticAmines() - Constructor for class mutant.rules.RuleDACancerogenicityAromaticAmines
-
- RuleDAMutagenicityABUnsaturatedAldehydes - Class in mutant.rules
-
Returns true if structure is predicted as mutagen , based on linear discriminant analysis over descriptors MR, LogP, LUMO.
- RuleDAMutagenicityABUnsaturatedAldehydes() - Constructor for class mutant.rules.RuleDAMutagenicityABUnsaturatedAldehydes
-
- RuleDAMutagenicityABUnsaturatedAldehydes - Class in toxtree.plugins.ames.rules
-
Returns true if structure is predicted as mutagen , based on linear discriminant analysis over descriptors MR, LogP, LUMO.
- RuleDAMutagenicityABUnsaturatedAldehydes() - Constructor for class toxtree.plugins.ames.rules.RuleDAMutagenicityABUnsaturatedAldehydes
-
- RuleDAMutagenicityAromaticAmines - Class in mutant.rules
-
Returns true if structure is predicted as mutagen , based on linear discriminant analysis.
- RuleDAMutagenicityAromaticAmines() - Constructor for class mutant.rules.RuleDAMutagenicityAromaticAmines
-
- RuleDAMutagenicityAromaticAmines - Class in toxtree.plugins.ames.rules
-
Returns true if structure is predicted as mutagen , based on linear
discriminant analysis.
- RuleDAMutagenicityAromaticAmines() - Constructor for class toxtree.plugins.ames.rules.RuleDAMutagenicityAromaticAmines
-
- RuleDeleteSubstructureAction - Class in toxtree.ui.tree.rules
-
- RuleDeleteSubstructureAction(IAtomContainer) - Constructor for class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
-
- RuleDeleteSubstructureAction(IAtomContainer, String) - Constructor for class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
-
- RuleDeleteSubstructureAction(IAtomContainer, String, Icon) - Constructor for class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
-
- RuleDerivedAromaticAmines - Class in mutant.rules
-
- RuleDerivedAromaticAmines() - Constructor for class mutant.rules.RuleDerivedAromaticAmines
-
- RuleDerivedAromaticAmines - Class in toxtree.plugins.ames.rules
-
- RuleDerivedAromaticAmines() - Constructor for class toxtree.plugins.ames.rules.RuleDerivedAromaticAmines
-
- RuleDescriptor - Class in toxTree.tree.rules
-
An abstract class to allow for descriptor analysis
- RuleDescriptor() - Constructor for class toxTree.tree.rules.RuleDescriptor
-
- RuleDescriptorRange - Class in toxTree.tree.rules
-
Verifies if the descriptor is within a range
- RuleDescriptorRange() - Constructor for class toxTree.tree.rules.RuleDescriptorRange
-
- RuleDi_Tri_Nitrobenzenes - Class in sicret.rules
-
Di & Tri-Nitrobenzenes.
- RuleDi_Tri_Nitrobenzenes() - Constructor for class sicret.rules.RuleDi_Tri_Nitrobenzenes
-
Constructor
- RuleDivalentSulphur - Class in cramer2.rules
-
Many kinds of divalent sulphurs, *-S-*, are synthetic and outside the scope of the Cramer dataset.
- RuleDivalentSulphur() - Constructor for class cramer2.rules.RuleDivalentSulphur
-
- RuleDNABindingAlerts - Class in toxtree.plugins.dnabinding.rules
-
- RuleDNABindingAlerts() - Constructor for class toxtree.plugins.dnabinding.rules.RuleDNABindingAlerts
-
- RuleEditor - Class in toxtree.ui.tree.rules
-
- RuleEditor(IDecisionRule) - Constructor for class toxtree.ui.tree.rules.RuleEditor
-
- RuleEditor() - Constructor for class toxtree.ui.tree.rules.RuleEditor
-
- RuleElements - Class in toxTree.tree.rules
-
Verifies if the molecule consists of only allowed elements
- RuleElements() - Constructor for class toxTree.tree.rules.RuleElements
-
- RuleElementsCounter - Class in verhaar.rules.helper
-
- RuleElementsCounter() - Constructor for class verhaar.rules.helper.RuleElementsCounter
-
- RuleEpoxide - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals containing an epoxide functional group.
- RuleEpoxide() - Constructor for class com.molecularnetworks.start.rules.RuleEpoxide
-
Default constructor
- RuleEpoxide - Class in structurefeatures.rules
-
- RuleEpoxide() - Constructor for class structurefeatures.rules.RuleEpoxide
-
- RuleEpoxides - Class in sicret.rules
-
Epoxides.
SMARTS pattern
OX2r3]1[#6r3][#6r3]1
- RuleEpoxides() - Constructor for class sicret.rules.RuleEpoxides
-
- RuleEsters - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for esters.
- RuleEsters() - Constructor for class com.molecularnetworks.start.rules.RuleEsters
-
Default constructor
- RuleEther - Class in structurefeatures.rules
-
- RuleEther() - Constructor for class structurefeatures.rules.RuleEther
-
- RuleEthyleneGlycolEthers - Class in sicret.rules
-
Ethylene Glycol Ethers
SMARTS pattern
[OX2H][CX4;$([H1]),$(C[#6])][CX4;$([H1]),$(C[#6])][OX2H]
- RuleEthyleneGlycolEthers() - Constructor for class sicret.rules.RuleEthyleneGlycolEthers
-
- RuleExampleEditAction - Class in toxtree.ui.tree.rules
-
An action to edit the example molecule of a rule
- RuleExampleEditAction(IDecisionRule, boolean) - Constructor for class toxtree.ui.tree.rules.RuleExampleEditAction
-
- RuleExampleEditAction(IDecisionRule, boolean, String) - Constructor for class toxtree.ui.tree.rules.RuleExampleEditAction
-
- RuleExampleEditAction(IDecisionRule, boolean, String, Icon) - Constructor for class toxtree.ui.tree.rules.RuleExampleEditAction
-
- RuleFormaldehyde - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for formaldehyde.
- RuleFormaldehyde() - Constructor for class com.molecularnetworks.start.rules.RuleFormaldehyde
-
Default constructor
- RuleFreeABUnsaturatedHetero - Class in cramer2.rules
-
free a,b-unsaturates heteroatoms (allyl amine), where free implies that the b carbon has 2 H's.
- RuleFreeABUnsaturatedHetero() - Constructor for class cramer2.rules.RuleFreeABUnsaturatedHetero
-
- RuleFuran - Class in structurefeatures.rules
-
- RuleFuran() - Constructor for class structurefeatures.rules.RuleFuran
-
- RuleHalide - Class in structurefeatures.rules
-
- RuleHalide() - Constructor for class structurefeatures.rules.RuleHalide
-
- RuleHalogenatedAlkanesAndAlkenes - Class in sicret.rules
-
Halogenated Alkanes And Alkenes
SMARTS patterns
[FX1,ClX1,BrX1,IX1][CX4H3]
[FX1,ClX1,BrX1,IX1][CX4H2][#6]
[FX1,ClX1,BrX1,IX1][CX3]=[CX3]
- RuleHalogenatedAlkanesAndAlkenes() - Constructor for class sicret.rules.RuleHalogenatedAlkanesAndAlkenes
-
- RuleHalogenSubstitutedBranched - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for branched, halogen substituted chemicals.
- RuleHalogenSubstitutedBranched() - Constructor for class com.molecularnetworks.start.rules.RuleHalogenSubstitutedBranched
-
Default constructor
- RuleHalonitrobenzene - Class in sicret.rules
-
Halonitrobenzene.
- RuleHalonitrobenzene() - Constructor for class sicret.rules.RuleHalonitrobenzene
-
- RuleHasOnlyC_H_O - Class in eye.rules
-
Contains only these elements C,O,H
- RuleHasOnlyC_H_O() - Constructor for class eye.rules.RuleHasOnlyC_H_O
-
- RuleHasOnlyC_H_O - Class in sicret.rules
-
Contains only these elements C,O.
- RuleHasOnlyC_H_O() - Constructor for class sicret.rules.RuleHasOnlyC_H_O
-
- RuleHasOnlyC_H_O_Halogen - Class in eye.rules
-
Contains only these elements C,O,Halogen.
- RuleHasOnlyC_H_O_Halogen() - Constructor for class eye.rules.RuleHasOnlyC_H_O_Halogen
-
- RuleHasOnlyC_H_O_Halogen - Class in sicret.rules
-
Contains only these elements C,O,Halogen.
- RuleHasOnlyC_H_O_Halogen() - Constructor for class sicret.rules.RuleHasOnlyC_H_O_Halogen
-
- RuleHasOnlyC_H_O_N - Class in eye.rules
-
Contains only these elements C,O,N.
- RuleHasOnlyC_H_O_N() - Constructor for class eye.rules.RuleHasOnlyC_H_O_N
-
- RuleHasOnlyC_H_O_N - Class in sicret.rules
-
Contains only these elements C,O,N.
- RuleHasOnlyC_H_O_N() - Constructor for class sicret.rules.RuleHasOnlyC_H_O_N
-
- RuleHasOnlyC_H_O_N_Halogen - Class in eye.rules
-
Contains only these elements C,O,N,Halogen.
- RuleHasOnlyC_H_O_N_Halogen() - Constructor for class eye.rules.RuleHasOnlyC_H_O_N_Halogen
-
- RuleHasOnlyC_H_O_N_Halogen - Class in sicret.rules
-
Contains only these elements C,O,N,Halogen.
- RuleHasOnlyC_H_O_N_Halogen() - Constructor for class sicret.rules.RuleHasOnlyC_H_O_N_Halogen
-
- RuleHasOnlyC_H_O_N_S - Class in eye.rules
-
Contains only these elements C,O,N,S,Halogen.
- RuleHasOnlyC_H_O_N_S() - Constructor for class eye.rules.RuleHasOnlyC_H_O_N_S
-
Constructor
- RuleHasOnlyC_H_O_N_S - Class in sicret.rules
-
Contains only these elements C,O,N,S,Halogen.
- RuleHasOnlyC_H_O_N_S() - Constructor for class sicret.rules.RuleHasOnlyC_H_O_N_S
-
Constructor
- RuleHasOnlySaltSulphonateSulphate - Class in cramer2.rules
-
Rule 4 of the Cramer scheme (see cramer2.CramerRulesExtendedExtended)
- RuleHasOnlySaltSulphonateSulphate() - Constructor for class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
-
- RuleHasOnlySaltSulphonateSulphate - Class in toxTree.tree.cramer
-
- RuleHasOnlySaltSulphonateSulphate() - Constructor for class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
-
- RuleHasOtherThanC_H_O_N_S2 - Class in toxTree.tree.cramer
-
- RuleHasOtherThanC_H_O_N_S2() - Constructor for class toxTree.tree.cramer.RuleHasOtherThanC_H_O_N_S2
-
Constructor
- RuleHeteroaromatic - Class in toxTree.tree.cramer
-
- RuleHeteroaromatic() - Constructor for class toxTree.tree.cramer.RuleHeteroaromatic
-
Constructor
- RuleHeterocycle - Class in structurefeatures.rules
-
- RuleHeterocycle() - Constructor for class structurefeatures.rules.RuleHeterocycle
-
- RuleHeterocyclic - Class in toxTree.tree.rules
-
Verifies if the molecule is heterocyclic
- RuleHeterocyclic() - Constructor for class toxTree.tree.rules.RuleHeterocyclic
-
- RuleHeterocyclicComplexSubstituents - Class in toxTree.tree.cramer
-
- RuleHeterocyclicComplexSubstituents() - Constructor for class toxTree.tree.cramer.RuleHeterocyclicComplexSubstituents
-
Constructor
- RuleHydrazine - Class in structurefeatures.rules
-
- RuleHydrazine() - Constructor for class structurefeatures.rules.RuleHydrazine
-
- RuleHydroPeroxides - Class in sicret.rules
-
HydroPeroxides.
SMARTS pattern
[OX2H][OX2]
- RuleHydroPeroxides() - Constructor for class sicret.rules.RuleHydroPeroxides
-
- RuleIminomethyl - Class in structurefeatures.rules
-
- RuleIminomethyl() - Constructor for class structurefeatures.rules.RuleIminomethyl
-
- RuleInitAlertCounter - Class in toxTree.tree.rules
-
- RuleInitAlertCounter() - Constructor for class toxTree.tree.rules.RuleInitAlertCounter
-
- RuleInitAlertCounter(String, String, String, double) - Constructor for class toxTree.tree.rules.RuleInitAlertCounter
-
- RuleIonicGroups - Class in verhaar.rules
-
- RuleIonicGroups() - Constructor for class verhaar.rules.RuleIonicGroups
-
- RuleIsAromatic - Class in toxTree.tree.cramer
-
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
- RuleIsAromatic() - Constructor for class toxTree.tree.cramer.RuleIsAromatic
-
Constructor
- RuleIsCommonTerpene - Class in toxTree.tree.cramer
-
Rule 16 of the Cramer scheme (see
CramerRules)
Verifies if the substance is a terpene
- RuleIsCommonTerpene() - Constructor for class toxTree.tree.cramer.RuleIsCommonTerpene
-
- RuleIsHeterocyclic - Class in toxTree.tree.cramer
-
- RuleIsHeterocyclic() - Constructor for class toxTree.tree.cramer.RuleIsHeterocyclic
-
Constructor
- RuleIsOpenChain - Class in toxTree.tree.cramer
-
- RuleIsOpenChain() - Constructor for class toxTree.tree.cramer.RuleIsOpenChain
-
- RuleKetenes - Class in sicret.rules
-
Ketenes.
SMARTS pattern
[CX3]=[CX2]=[OX1]
- RuleKetenes() - Constructor for class sicret.rules.RuleKetenes
-
- RuleKetone - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for ketones.
- RuleKetone() - Constructor for class com.molecularnetworks.start.rules.RuleKetone
-
Default constructor
- RuleKetone - Class in structurefeatures.rules
-
- RuleKetone() - Constructor for class structurefeatures.rules.RuleKetone
-
- RuleKetoneAlcoholEtc - Class in toxTree.tree.cramer
-
- RuleKetoneAlcoholEtc() - Constructor for class toxTree.tree.cramer.RuleKetoneAlcoholEtc
-
Constructor
- RuleKetones - Class in sicret.rules
-
Ketones.
SMARTS pattern
[#6][CX3](=[OX1])[#6]
- RuleKetones() - Constructor for class sicret.rules.RuleKetones
-
- RuleKroesFig1Q1 - Class in toxtree.plugins.kroes.rules
-
TODO refactor with SMARTS
- RuleKroesFig1Q1() - Constructor for class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
-
- RuleKroesFig1Q1(InputStream, String) - Constructor for class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
-
- RuleKroesFig1Q1(File) - Constructor for class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
-
- RuleLactone - Class in toxtree.tree.cramer3.rules
-
- RuleLactone() - Constructor for class toxtree.tree.cramer3.rules.RuleLactone
-
- RuleLactoneOrCyclicDiester - Class in toxTree.tree.cramer
-
- RuleLactoneOrCyclicDiester() - Constructor for class toxTree.tree.cramer.RuleLactoneOrCyclicDiester
-
Constructor
- RuleLactonesFusedOrUnsaturated - Class in sicret.rules
-
RuleLactonesFusedOrUnsaturated.
- RuleLactonesFusedOrUnsaturated() - Constructor for class sicret.rules.RuleLactonesFusedOrUnsaturated
-
Constructor
- RuleLactonesFusedOrUnsaturated - Class in toxTree.tree.cramer
-
- RuleLactonesFusedOrUnsaturated() - Constructor for class toxTree.tree.cramer.RuleLactonesFusedOrUnsaturated
-
- RuleLipidSolubility - Class in eye.rules
-
LipidSolubility < 0.01.
- RuleLipidSolubility() - Constructor for class eye.rules.RuleLipidSolubility
-
- RuleLipidSolubility - Class in sicret.rules
-
LipidSolubility < 0.01.
- RuleLipidSolubility() - Constructor for class sicret.rules.RuleLipidSolubility
-
- RuleLipidSolubility_10_4 - Class in eye.rules
-
LipidSolubility < 400.0
- RuleLipidSolubility_10_4() - Constructor for class eye.rules.RuleLipidSolubility_10_4
-
- RuleLipidSolubility_9_1 - Class in eye.rules
-
- RuleLipidSolubility_9_1() - Constructor for class eye.rules.RuleLipidSolubility_9_1
-
- RuleLipinski5 - Class in toxTree.tree.rules
-
Returns true if all Lipinski Rule of Five are true
- RuleLipinski5() - Constructor for class toxTree.tree.rules.RuleLipinski5
-
- RuleLogP - Class in eye.rules
-
LogP > 9.0
Expects property to be read from IMolecule.getProperty(
RuleLogP.LogKow).
- RuleLogP() - Constructor for class eye.rules.RuleLogP
-
- RuleLogP(String, String, String, double) - Constructor for class eye.rules.RuleLogP
-
- RuleLogP - Class in sicret.rules
-
LogP < 3.1.
Expects property to be read from IMolecule.getProperty(
RuleLogP.LogKow).
- RuleLogP() - Constructor for class sicret.rules.RuleLogP
-
- RuleLogP(String, String, String, double) - Constructor for class sicret.rules.RuleLogP
-
- RuleLogP1 - Class in eye.rules
-
- RuleLogP1() - Constructor for class eye.rules.RuleLogP1
-
- RuleLogP1(String, String, String, double) - Constructor for class eye.rules.RuleLogP1
-
- RuleLogP_10_1 - Class in eye.rules
-
LogKow > 3.8
- RuleLogP_10_1() - Constructor for class eye.rules.RuleLogP_10_1
-
- RuleLogP_11_4 - Class in eye.rules
-
LogKow < -2
- RuleLogP_11_4() - Constructor for class eye.rules.RuleLogP_11_4
-
- RuleLogP_11_5 - Class in eye.rules
-
LogKow > 3.6
- RuleLogP_11_5() - Constructor for class eye.rules.RuleLogP_11_5
-
- RuleLogP_11_6 - Class in eye.rules
-
- RuleLogP_11_6() - Constructor for class eye.rules.RuleLogP_11_6
-
- RuleLogP_12_4 - Class in eye.rules
-
LogP > 4.5
- RuleLogP_12_4() - Constructor for class eye.rules.RuleLogP_12_4
-
- RuleLogP_9_4 - Class in eye.rules
-
LogKow > 5.5
- RuleLogP_9_4() - Constructor for class eye.rules.RuleLogP_9_4
-
- RuleLogPRange - Class in verhaar.rules
-
0 <= LogP <= 6.
- RuleLogPRange() - Constructor for class verhaar.rules.RuleLogPRange
-
- RuleManyAromaticRings - Class in toxTree.tree.rules
-
Verifies if there are many aromatic rings
- RuleManyAromaticRings() - Constructor for class toxTree.tree.rules.RuleManyAromaticRings
-
- RuleManyAromaticRings14 - Class in toxTree.tree.cramer
-
- RuleManyAromaticRings14() - Constructor for class toxTree.tree.cramer.RuleManyAromaticRings14
-
Constructor
- RuleManyAromaticRings28 - Class in toxTree.tree.cramer
-
- RuleManyAromaticRings28() - Constructor for class toxTree.tree.cramer.RuleManyAromaticRings28
-
- RuleMelting_Point_11_3 - Class in eye.rules
-
MeltingPoint > 200.0
- RuleMelting_Point_11_3() - Constructor for class eye.rules.RuleMelting_Point_11_3
-
- RuleMeltingPoint - Class in sicret.rules
-
MeltingPoint < 200.
- RuleMeltingPoint(String, String, String, double) - Constructor for class sicret.rules.RuleMeltingPoint
-
- RuleMeltingPoint() - Constructor for class sicret.rules.RuleMeltingPoint
-
- RuleMeltingPoint_11_2 - Class in eye.rules
-
MeltingPoint > 200.0
- RuleMeltingPoint_11_2() - Constructor for class eye.rules.RuleMeltingPoint_11_2
-
- RuleMeltingPoint_12_3 - Class in eye.rules
-
MeltingPoint > 65.0
- RuleMeltingPoint_12_3() - Constructor for class eye.rules.RuleMeltingPoint_12_3
-
- RuleMeltingPoint_8_1 - Class in eye.rules
-
- RuleMeltingPoint_8_1() - Constructor for class eye.rules.RuleMeltingPoint_8_1
-
- RuleMolecularMassRange - Class in toxTree.tree.rules
-
- RuleMolecularMassRange() - Constructor for class toxTree.tree.rules.RuleMolecularMassRange
-
- RuleMoleculeEditAction - Class in toxtree.ui.tree.rules
-
Launches JChemPaint for a molecule associated with the rule
- RuleMoleculeEditAction(IAtomContainer) - Constructor for class toxtree.ui.tree.rules.RuleMoleculeEditAction
-
- RuleMoleculeEditAction(IAtomContainer, String) - Constructor for class toxtree.ui.tree.rules.RuleMoleculeEditAction
-
- RuleMoleculeEditAction(IAtomContainer, String, Icon) - Constructor for class toxtree.ui.tree.rules.RuleMoleculeEditAction
-
- RuleMolWeight - Class in eye.rules
-
Molecular weight > 350.
- RuleMolWeight() - Constructor for class eye.rules.RuleMolWeight
-
- RuleMolWeight - Class in sicret.rules
-
Molecular weight > 350.
- RuleMolWeight() - Constructor for class sicret.rules.RuleMolWeight
-
- RuleMolWeight_10_3 - Class in eye.rules
-
Molecular Weight > 370.0
- RuleMolWeight_10_3() - Constructor for class eye.rules.RuleMolWeight_10_3
-
- RuleMolWeight_11_1 - Class in eye.rules
-
Molecular Weight > 620
- RuleMolWeight_11_1() - Constructor for class eye.rules.RuleMolWeight_11_1
-
- RuleMolweight_12_1 - Class in eye.rules
-
MoleculWeight > 370
- RuleMolweight_12_1() - Constructor for class eye.rules.RuleMolweight_12_1
-
- RuleMolWeight_12_2 - Class in eye.rules
-
Molecular Weight > 280
- RuleMolWeight_12_2() - Constructor for class eye.rules.RuleMolWeight_12_2
-
- RuleMolWeight_8_2 - Class in eye.rules
-
- RuleMolWeight_8_2() - Constructor for class eye.rules.RuleMolWeight_8_2
-
- RuleMolWeight_9_2 - Class in eye.rules
-
MoleculWeight > 290.0
- RuleMolWeight_9_2() - Constructor for class eye.rules.RuleMolWeight_9_2
-
- RuleMonocarbocyclic - Class in toxTree.tree.cramer
-
- RuleMonocarbocyclic() - Constructor for class toxTree.tree.cramer.RuleMonocarbocyclic
-
- RuleMonocycloalkanoneEtc - Class in toxTree.tree.cramer
-
- RuleMonocycloalkanoneEtc() - Constructor for class toxTree.tree.cramer.RuleMonocycloalkanoneEtc
-
Constructor
- RuleMoreThanTwoHydroxyOnAromaticRing - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals with more than two hydroxy substituents on
an aromatic ring.
- RuleMoreThanTwoHydroxyOnAromaticRing() - Constructor for class com.molecularnetworks.start.rules.RuleMoreThanTwoHydroxyOnAromaticRing
-
Default constructor
- RuleNChloramine - Class in structurefeatures.rules
-
- RuleNChloramine() - Constructor for class structurefeatures.rules.RuleNChloramine
-
- RuleNHydroxy - Class in structurefeatures.rules
-
- RuleNHydroxy() - Constructor for class structurefeatures.rules.RuleNHydroxy
-
- RuleNitrile - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for nitriles.
- RuleNitrile() - Constructor for class com.molecularnetworks.start.rules.RuleNitrile
-
Default constructor
- RuleNitro - Class in structurefeatures.rules
-
- RuleNitro() - Constructor for class structurefeatures.rules.RuleNitro
-
- RuleNitrogenMustard - Class in structurefeatures.rules
-
- RuleNitrogenMustard() - Constructor for class structurefeatures.rules.RuleNitrogenMustard
-
- RuleNitrosamine - Class in structurefeatures.rules
-
- RuleNitrosamine() - Constructor for class structurefeatures.rules.RuleNitrosamine
-
- RuleNitroso - Class in structurefeatures.rules
-
- RuleNitroso() - Constructor for class structurefeatures.rules.RuleNitroso
-
- RuleNMethylol - Class in structurefeatures.rules
-
- RuleNMethylol() - Constructor for class structurefeatures.rules.RuleNMethylol
-
- RuleNNitroso - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals with an N-Nitroso (-N-N=0) group.
- RuleNNitroso() - Constructor for class com.molecularnetworks.start.rules.RuleNNitroso
-
Default constructor
- RuleNormalBodyConstituent - Class in cramer2.rules
-
Rule 1 of the Cramer scheme (see cramer2.CramerRulesExtendedExtended)
- RuleNormalBodyConstituent() - Constructor for class cramer2.rules.RuleNormalBodyConstituent
-
Constructor
- RuleNormalBodyConstituent - Class in toxTree.tree.cramer
-
- RuleNormalBodyConstituent() - Constructor for class toxTree.tree.cramer.RuleNormalBodyConstituent
-
Constructor
- RuleNOxide - Class in structurefeatures.rules
-
- RuleNOxide() - Constructor for class structurefeatures.rules.RuleNOxide
-
- RuleNucleosides - Class in structurefeatures.rules
-
- RuleNucleosides() - Constructor for class structurefeatures.rules.RuleNucleosides
-
- RuleOandPQuinones - Class in sicret.rules
-
O and P Quinones.
Substructures
O=C1C=CC=CC1(=O)
O=C1C=CC(=O)C=C1
- RuleOandPQuinones() - Constructor for class sicret.rules.RuleOandPQuinones
-
Constructor
- RuleOneHalogenOnUnbranched - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for unbranched chemicals with one halogen substituent.
- RuleOneHalogenOnUnbranched() - Constructor for class com.molecularnetworks.start.rules.RuleOneHalogenOnUnbranched
-
Default constructor
- RuleOnlyAllowedSubstructures - Class in toxTree.tree.rules
-
Verifies if the structure contains only allowed substructures
- RuleOnlyAllowedSubstructures() - Constructor for class toxTree.tree.rules.RuleOnlyAllowedSubstructures
-
- RuleOnlyAllowedSubstructuresCounter - Class in verhaar.rules.helper
-
- RuleOnlyAllowedSubstructuresCounter() - Constructor for class verhaar.rules.helper.RuleOnlyAllowedSubstructuresCounter
-
- RuleOnlyFuncGroupsQ30 - Class in toxTree.tree.cramer
-
- RuleOnlyFuncGroupsQ30() - Constructor for class toxTree.tree.cramer.RuleOnlyFuncGroupsQ30
-
Constructor
- RuleOpenChain - Class in toxTree.tree.rules
-
Verifies if the moleucle is open chain
- RuleOpenChain() - Constructor for class toxTree.tree.rules.RuleOpenChain
-
Constructor
- RulePanel - Class in toxtree.ui.tree.rules
-
- RulePanel(IDecisionRule) - Constructor for class toxtree.ui.tree.rules.RulePanel
-
- rulePanel - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
-
- rulePanel - Variable in class toxtree.ui.tree.TreeDrawing
-
- rulePanel - Variable in class toxtree.ui.tree.TreeEditorPanel
-
- rulePanel - Variable in class toxtree.ui.tree.TreePanel
-
- RulePhenols - Class in sicret.rules
-
Phenols.
Substructure
c1ccccc1O[H]
- RulePhenols() - Constructor for class sicret.rules.RulePhenols
-
Constructor
- RulePhosphateEsters - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for phosphoric esters.
- RulePhosphateEsters() - Constructor for class com.molecularnetworks.start.rules.RulePhosphateEsters
-
Default constructor
- RulePhosphoricGroups - Class in structurefeatures.rules
-
- RulePhosphoricGroups() - Constructor for class structurefeatures.rules.RulePhosphoricGroups
-
- RuleprimaryAlkylHalide - Class in structurefeatures.rules
-
- RuleprimaryAlkylHalide() - Constructor for class structurefeatures.rules.RuleprimaryAlkylHalide
-
- RulePropertyEditor - Class in toxtree.ui.tree.rules
-
- RulePropertyEditor(RuleVerifyProperty) - Constructor for class toxtree.ui.tree.rules.RulePropertyEditor
-
- RulePropertyEditor() - Constructor for class toxtree.ui.tree.rules.RulePropertyEditor
-
- RulePropiolactone - Class in structurefeatures.rules
-
- RulePropiolactone() - Constructor for class structurefeatures.rules.RulePropiolactone
-
- RuleProteinBindingAlerts - Class in toxtree.plugins.proteinbinding.rules
-
- RuleProteinBindingAlerts() - Constructor for class toxtree.plugins.proteinbinding.rules.RuleProteinBindingAlerts
-
- RulePyridineRing - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for pyridines.
- RulePyridineRing() - Constructor for class com.molecularnetworks.start.rules.RulePyridineRing
-
Default constructor
- RuleQ1 - Class in toxtree.tree.cramer3.rules
-
- RuleQ1() - Constructor for class toxtree.tree.cramer3.rules.RuleQ1
-
- RuleQ10 - Class in toxtree.tree.cramer3.rules
-
- RuleQ10() - Constructor for class toxtree.tree.cramer3.rules.RuleQ10
-
- RuleQ11 - Class in toxtree.tree.cramer3.rules
-
- RuleQ11() - Constructor for class toxtree.tree.cramer3.rules.RuleQ11
-
- RuleQ12 - Class in toxtree.tree.cramer3.rules
-
- RuleQ12() - Constructor for class toxtree.tree.cramer3.rules.RuleQ12
-
- RuleQ13 - Class in toxtree.tree.cramer3.rules
-
- RuleQ13() - Constructor for class toxtree.tree.cramer3.rules.RuleQ13
-
- RuleQ14_A - Class in toxtree.tree.cramer3.rules
-
- RuleQ14_A() - Constructor for class toxtree.tree.cramer3.rules.RuleQ14_A
-
- RuleQ14_B - Class in toxtree.tree.cramer3.rules
-
- RuleQ14_B() - Constructor for class toxtree.tree.cramer3.rules.RuleQ14_B
-
- RuleQ15 - Class in toxtree.tree.cramer3.rules
-
- RuleQ15() - Constructor for class toxtree.tree.cramer3.rules.RuleQ15
-
- RuleQ16 - Class in toxtree.tree.cramer3.rules
-
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
- RuleQ16() - Constructor for class toxtree.tree.cramer3.rules.RuleQ16
-
- RuleQ17 - Class in toxtree.tree.cramer3.rules
-
This rule considers ALL possible functional groups, not only the ones listed!
based on toxTree.tree.cramer.Rule3FuncGroups
- RuleQ17() - Constructor for class toxtree.tree.cramer3.rules.RuleQ17
-
- RuleQ18_AI - Class in toxtree.tree.cramer3.rules
-
Very similar to Cramer rule Q18 @{link RuleKetoneAlcoholEtc} with additions
- RuleQ18_AI() - Constructor for class toxtree.tree.cramer3.rules.RuleQ18_AI
-
- RuleQ18_JM - Class in toxtree.tree.cramer3.rules
-
- RuleQ18_JM() - Constructor for class toxtree.tree.cramer3.rules.RuleQ18_JM
-
- RuleQ19 - Class in toxtree.tree.cramer3.rules
-
- RuleQ19() - Constructor for class toxtree.tree.cramer3.rules.RuleQ19
-
- RuleQ2 - Class in toxtree.tree.cramer3.rules
-
- RuleQ2() - Constructor for class toxtree.tree.cramer3.rules.RuleQ2
-
- RuleQ20 - Class in toxtree.tree.cramer3.rules
-
- RuleQ20() - Constructor for class toxtree.tree.cramer3.rules.RuleQ20
-
- RuleQ21 - Class in toxtree.tree.cramer3.rules
-
- RuleQ21() - Constructor for class toxtree.tree.cramer3.rules.RuleQ21
-
- RuleQ22 - Class in toxtree.tree.cramer3.rules
-
- RuleQ22() - Constructor for class toxtree.tree.cramer3.rules.RuleQ22
-
- RuleQ23 - Class in toxtree.tree.cramer3.rules
-
- RuleQ23() - Constructor for class toxtree.tree.cramer3.rules.RuleQ23
-
- RuleQ24 - Class in toxtree.tree.cramer3.rules
-
- RuleQ24() - Constructor for class toxtree.tree.cramer3.rules.RuleQ24
-
- RuleQ25 - Class in toxtree.tree.cramer3.rules
-
- RuleQ25() - Constructor for class toxtree.tree.cramer3.rules.RuleQ25
-
- RuleQ26 - Class in toxtree.tree.cramer3.rules
-
- RuleQ26() - Constructor for class toxtree.tree.cramer3.rules.RuleQ26
-
- RuleQ27 - Class in toxtree.tree.cramer3.rules
-
- RuleQ27() - Constructor for class toxtree.tree.cramer3.rules.RuleQ27
-
- RuleQ28 - Class in toxtree.tree.cramer3.rules
-
- RuleQ28() - Constructor for class toxtree.tree.cramer3.rules.RuleQ28
-
- RuleQ29 - Class in toxtree.tree.cramer3.rules
-
- RuleQ29() - Constructor for class toxtree.tree.cramer3.rules.RuleQ29
-
- RuleQ3 - Class in toxtree.tree.cramer3.rules
-
- RuleQ3() - Constructor for class toxtree.tree.cramer3.rules.RuleQ3
-
- RuleQ4 - Class in toxtree.tree.cramer3.rules
-
- RuleQ4() - Constructor for class toxtree.tree.cramer3.rules.RuleQ4
-
- RuleQ4A - Class in toxtree.tree.cramer3.rules
-
- RuleQ4A() - Constructor for class toxtree.tree.cramer3.rules.RuleQ4A
-
- RuleQ5 - Class in toxtree.tree.cramer3.rules
-
- RuleQ5() - Constructor for class toxtree.tree.cramer3.rules.RuleQ5
-
- RuleQ6 - Class in toxtree.tree.cramer3.rules
-
- RuleQ6() - Constructor for class toxtree.tree.cramer3.rules.RuleQ6
-
- RuleQ7 - Class in toxtree.tree.cramer3.rules
-
- RuleQ7() - Constructor for class toxtree.tree.cramer3.rules.RuleQ7
-
- RuleQ8 - Class in toxtree.tree.cramer3.rules
-
- RuleQ8() - Constructor for class toxtree.tree.cramer3.rules.RuleQ8
-
- RuleQ9_A - Class in toxtree.tree.cramer3.rules
-
- RuleQ9_A() - Constructor for class toxtree.tree.cramer3.rules.RuleQ9_A
-
- RuleQ9_B - Class in toxtree.tree.cramer3.rules
-
- RuleQ9_B() - Constructor for class toxtree.tree.cramer3.rules.RuleQ9_B
-
- RuleQ9_C - Class in toxtree.tree.cramer3.rules
-
- RuleQ9_C() - Constructor for class toxtree.tree.cramer3.rules.RuleQ9_C
-
- RuleQ9_D - Class in toxtree.tree.cramer3.rules
-
- RuleQ9_D() - Constructor for class toxtree.tree.cramer3.rules.RuleQ9_D
-
- RuleQSARModelEditor - Class in toxtree.ui.tree.qsar
-
- RuleQSARModelEditor(LinearDiscriminantRule) - Constructor for class toxtree.ui.tree.qsar.RuleQSARModelEditor
-
- RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts - Class in sicret.rules
-
Rule Quaternary Organic Ammonium And Phosphonium Salts
- RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts() - Constructor for class sicret.rules.RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts
-
- RuleRangeEditor - Class in toxtree.ui.tree.rules
-
- RuleRangeEditor(IRuleRange) - Constructor for class toxtree.ui.tree.rules.RuleRangeEditor
-
- RuleRangeEditor() - Constructor for class toxtree.ui.tree.rules.RuleRangeEditor
-
- RuleReadilyHydrolised - Class in toxTree.tree.rules
-
Verifies if a compound is readily hydrolised
- RuleReadilyHydrolised() - Constructor for class toxTree.tree.rules.RuleReadilyHydrolised
-
- RuleReadilyHydrolysed29 - Class in toxTree.tree.cramer
-
- RuleReadilyHydrolysed29() - Constructor for class toxTree.tree.cramer.RuleReadilyHydrolysed29
-
Constructor
- RuleReadilyHydrolysedMononuclear - Class in toxTree.tree.cramer
-
- RuleReadilyHydrolysedMononuclear() - Constructor for class toxTree.tree.cramer.RuleReadilyHydrolysedMononuclear
-
Constructor
- RuleReadilyHydrolysedPO4 - Class in cramer2.rules
-
cleaves PO4's from compounds, and analyses the remaining fragments
Modified Dec, 2008
- RuleReadilyHydrolysedPO4() - Constructor for class cramer2.rules.RuleReadilyHydrolysedPO4
-
Constructor
- RuleReadilyHydrolysedToCommonterpene - Class in toxTree.tree.cramer
-
- RuleReadilyHydrolysedToCommonterpene() - Constructor for class toxTree.tree.cramer.RuleReadilyHydrolysedToCommonterpene
-
Constructor
- RuleResult - Class in toxTree.tree
-
Stores the result of
IDecisionRule application,
which contains the rule applied, the boolean result and the category assigned (if any).
- RuleResult() - Constructor for class toxTree.tree.RuleResult
-
- RuleResult(IDecisionRule, boolean) - Constructor for class toxTree.tree.RuleResult
-
- RuleResult(IDecisionRule, boolean, IDecisionCategory) - Constructor for class toxTree.tree.RuleResult
-
- ruleResults - Variable in class toxTree.tree.TreeResult
-
- RuleRingAllowedSubstituents - Class in toxTree.tree.rules
-
A rule to analyze ring substituents
- RuleRingAllowedSubstituents() - Constructor for class toxTree.tree.rules.RuleRingAllowedSubstituents
-
- RuleRingComplexSubstituents30 - Class in toxTree.tree.cramer
-
- RuleRingComplexSubstituents30() - Constructor for class toxTree.tree.cramer.RuleRingComplexSubstituents30
-
Constructor
- RuleRingMainStrucSubstituents - Class in verhaar.rules
-
- RuleRingMainStrucSubstituents() - Constructor for class verhaar.rules.RuleRingMainStrucSubstituents
-
- RuleRingOtherThanAllowedSubstituents - Class in toxTree.tree.rules
-
A rule to analyze ring substituents
- RuleRingOtherThanAllowedSubstituents() - Constructor for class toxTree.tree.rules.RuleRingOtherThanAllowedSubstituents
-
- RuleRings - Class in toxTree.tree.rules
-
- RuleRings() - Constructor for class toxTree.tree.rules.RuleRings
-
- RuleRingsSMARTSSubstituents - Class in toxtree.tree.cramer3.rules
-
- RuleRingsSMARTSSubstituents() - Constructor for class toxtree.tree.cramer3.rules.RuleRingsSMARTSSubstituents
-
- RuleRingSubstituents - Class in toxTree.tree.rules
-
A rule to analyze ring substituents
- RuleRingSubstituents() - Constructor for class toxTree.tree.rules.RuleRingSubstituents
-
- RuleRingsWithSubstituents - Class in toxTree.tree.cramer
-
- RuleRingsWithSubstituents() - Constructor for class toxTree.tree.cramer.RuleRingsWithSubstituents
-
Constructor
- RuleRingWithSubstituents - Class in toxTree.tree.cramer
-
- RuleRingWithSubstituents() - Constructor for class toxTree.tree.cramer.RuleRingWithSubstituents
-
Constructor
- rules - Variable in class toxtree.data.DecisionMethodsDataModule
-
- rules - Variable in class toxTree.tree.AbstractTree
-
- rules - Variable in class toxtree.tree.cramer3.TreeSpecification
-
- rules15 - Variable in class verhaar.rules.Rule171
-
- RuleSimplyBranchedAliphaticHydrocarbon - Class in toxTree.tree.cramer
-
Implementation of Cramer rule No.5
Simply branched aliphatic or a common carbohydrate
A descendant of
RuleCarbohydrate
- RuleSimplyBranchedAliphaticHydrocarbon() - Constructor for class toxTree.tree.cramer.RuleSimplyBranchedAliphaticHydrocarbon
-
Constructor
- RuleSkinSensitisationAlerts - Class in toxtree.plugins.skinsensitisation.rules
-
- RuleSkinSensitisationAlerts() - Constructor for class toxtree.plugins.skinsensitisation.rules.RuleSkinSensitisationAlerts
-
- RulesList - Class in toxTree.tree
-
- RulesList() - Constructor for class toxTree.tree.RulesList
-
- RulesList(String[]) - Constructor for class toxTree.tree.RulesList
-
Creates RulesList given the names of
IDecisionRule classes
Example :
RulesList(new String[] {
"toxTree.tree.rules.RuleSubstructure",
"toxTree.tree.rules.RuleAromatic"});
Rules are created from corresponding class names
- rulesListPanel - Variable in class toxtree.ui.wizard.DecisionNodeWizard
-
- RuleSMARTSSubstructureAmbit - Class in toxTree.tree.rules.smarts
-
An IDecisionRule, making use of Ambit SMARTS parser.
- RuleSMARTSSubstructureAmbit() - Constructor for class toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit
-
- RuleSMARTSSubstructureHydrolysis - Class in toxtree.tree.cramer3.rules
-
- RuleSMARTSSubstructureHydrolysis() - Constructor for class toxtree.tree.cramer3.rules.RuleSMARTSSubstructureHydrolysis
-
- RuleSMARTSSubstructureTagged - Class in toxtree.tree.cramer3.rules
-
- RuleSMARTSSubstructureTagged() - Constructor for class toxtree.tree.cramer3.rules.RuleSMARTSSubstructureTagged
-
- RuleSMARTSubstructure - Class in toxTree.tree.rules.smarts
-
For backward compatibility
- RuleSMARTSubstructure() - Constructor for class toxTree.tree.rules.smarts.RuleSMARTSubstructure
-
- RuleSMARTSubstructureCDK - Class in toxTree.tree.rules.smarts
-
An IDecisionRule, making use of CDK SMARTS parser.
- RuleSMARTSubstructureCDK() - Constructor for class toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK
-
- RuleSomeBenzeneDerivatives - Class in toxTree.tree.cramer
-
- RuleSomeBenzeneDerivatives() - Constructor for class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
-
Constructor
- rulesPanel - Variable in class toxtree.ui.tree.TreeEditorPanel
-
- RuleStructuresList - Class in toxTree.tree.rules
-
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
- RuleStructuresList() - Constructor for class toxTree.tree.rules.RuleStructuresList
-
- RuleStructuresList(String) - Constructor for class toxTree.tree.rules.RuleStructuresList
-
- RuleStructuresList(File) - Constructor for class toxTree.tree.rules.RuleStructuresList
-
- RuleStructuresPanel - Class in toxtree.ui.tree.rules
-
- RuleStructuresPanel(RuleStructuresList) - Constructor for class toxtree.ui.tree.rules.RuleStructuresPanel
-
- RuleStructuresPanel() - Constructor for class toxtree.ui.tree.rules.RuleStructuresPanel
-
- RuleSubstructures - Class in toxTree.tree.rules
-
An abstract class to implement substructure rules
- RuleSubstructures() - Constructor for class toxTree.tree.rules.RuleSubstructures
-
- RuleSubstructuresEditAction - Class in toxtree.ui.tree.rules
-
substructure rule
- RuleSubstructuresEditAction(IAtomContainer) - Constructor for class toxtree.ui.tree.rules.RuleSubstructuresEditAction
-
- RuleSubstructuresEditAction(IAtomContainer, String) - Constructor for class toxtree.ui.tree.rules.RuleSubstructuresEditAction
-
- RuleSubstructuresEditAction(IAtomContainer, String, Icon) - Constructor for class toxtree.ui.tree.rules.RuleSubstructuresEditAction
-
- RuleSufficientSulphonateGroups - Class in toxTree.tree.cramer
-
- RuleSufficientSulphonateGroups() - Constructor for class toxTree.tree.cramer.RuleSufficientSulphonateGroups
-
Constructor
- RuleSurfaceTension - Class in sicret.rules
-
SurfaceTension > 62.0.
- RuleSurfaceTension(String, String, String, double) - Constructor for class sicret.rules.RuleSurfaceTension
-
- RuleSurfaceTension() - Constructor for class sicret.rules.RuleSurfaceTension
-
- RuleTerminalIsopropylNonCyclic - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for a non-cyclic chemical with at least two terminal
isopropyl groups.
- RuleTerminalIsopropylNonCyclic() - Constructor for class com.molecularnetworks.start.rules.RuleTerminalIsopropylNonCyclic
-
Default constructor
- RuleTerminalTertButyl - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals with a terminal tert-butyl branch.
- RuleTerminalTertButyl() - Constructor for class com.molecularnetworks.start.rules.RuleTerminalTertButyl
-
Default constructor
- RuleTertiaryAmine - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for tertiary amines.
- RuleTertiaryAmine() - Constructor for class com.molecularnetworks.start.rules.RuleTertiaryAmine
-
Default constructor
- RuleToxicFunctionalGroups - Class in toxTree.tree.cramer
-
- RuleToxicFunctionalGroups() - Constructor for class toxTree.tree.cramer.RuleToxicFunctionalGroups
-
Constructor
- RuleTriAndTetraHalogenatedBenzenes - Class in sicret.rules
-
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)
- RuleTriAndTetraHalogenatedBenzenes() - Constructor for class sicret.rules.RuleTriAndTetraHalogenatedBenzenes
-
- RuleTriazineRing - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals containing triazine ring.
- RuleTriazineRing() - Constructor for class com.molecularnetworks.start.rules.RuleTriazineRing
-
Default constructor
- RuleTrifluoromethyl - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals containing trifluoromethyl group (-CF3).
- RuleTrifluoromethyl() - Constructor for class com.molecularnetworks.start.rules.RuleTrifluoromethyl
-
Default constructor
- RuleTwoHalogensOnUnbranchedNonCyclic - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for unbranched, non-cyclic chemicals with two halogen
substituents.
- RuleTwoHalogensOnUnbranchedNonCyclic() - Constructor for class com.molecularnetworks.start.rules.RuleTwoHalogensOnUnbranchedNonCyclic
-
Default constructor
- RuleTwoOrMoreRings - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals with two or more rings.
- RuleTwoOrMoreRings() - Constructor for class com.molecularnetworks.start.rules.RuleTwoOrMoreRings
-
Default constructor
- RuleTwoTerminalDiaminoGroupsOnNonCyclic - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for chemicals with two terminal diamino groups that are
not attached to a cycle.
- RuleTwoTerminalDiaminoGroupsOnNonCyclic() - Constructor for class com.molecularnetworks.start.rules.RuleTwoTerminalDiaminoGroupsOnNonCyclic
-
Default constructor
- RuleTwoTerminalDoubleBondsOnUnbranched - Class in com.molecularnetworks.start.rules
-
Biodegradation rule for unbranched chemicals with two terminal double-bonded
carbons.
- RuleTwoTerminalDoubleBondsOnUnbranched() - Constructor for class com.molecularnetworks.start.rules.RuleTwoTerminalDoubleBondsOnUnbranched
-
Default constructor
- RuleUnchargedOrganophosphates - Class in cramer2.rules
-
Uncharged Organophosph(othion)ates
Modified Dec, 2008
- RuleUnchargedOrganophosphates() - Constructor for class cramer2.rules.RuleUnchargedOrganophosphates
-
- RuleUrethaneDerivatives - Class in structurefeatures.rules
-
- RuleUrethaneDerivatives() - Constructor for class structurefeatures.rules.RuleUrethaneDerivatives
-
- ruleURL - Static variable in class toxTree.tree.RuleResult
-
- RuleVapourPressure - Class in sicret.rules
-
VapourPressure < 0.0001.
- RuleVapourPressure(String, String, String, double) - Constructor for class sicret.rules.RuleVapourPressure
-
- RuleVapourPressure() - Constructor for class sicret.rules.RuleVapourPressure
-
- RuleVerifyAlertsCounter - Class in toxTree.tree.rules
-
- RuleVerifyAlertsCounter() - Constructor for class toxTree.tree.rules.RuleVerifyAlertsCounter
-
- RuleVerifyClass1Alerts - Class in verhaar.rules
-
- RuleVerifyClass1Alerts() - Constructor for class verhaar.rules.RuleVerifyClass1Alerts
-
- RuleVerifyClass2Alerts - Class in verhaar.rules
-
- RuleVerifyClass2Alerts() - Constructor for class verhaar.rules.RuleVerifyClass2Alerts
-
- RuleVerifyClass3Alerts - Class in verhaar.rules
-
- RuleVerifyClass3Alerts() - Constructor for class verhaar.rules.RuleVerifyClass3Alerts
-
- RuleVerifyIntake - Class in toxtree.plugins.kroes.rules
-
- RuleVerifyIntake() - Constructor for class toxtree.plugins.kroes.rules.RuleVerifyIntake
-
- RuleVerifyProperty - Class in toxTree.tree.rules
-
- RuleVerifyProperty() - Constructor for class toxTree.tree.rules.RuleVerifyProperty
-
- RuleVerifyProperty(String, String, String, double) - Constructor for class toxTree.tree.rules.RuleVerifyProperty
-
- run() - Method in class toxTree.apps.ToxtreeHeadless
-
- runAction() - Method in class toxtree.ui.actions.AboutAction
-
- runAction() - Method in class toxtree.ui.actions.BatchAction
-
- runAction() - Method in class toxtree.ui.actions.ClearResultAction
-
- runAction() - Method in class toxtree.ui.actions.DataModuleAction
-
- runAction() - Method in class toxtree.ui.actions.EditCompoundAction
-
- runAction() - Method in class toxtree.ui.actions.EstimateAction
-
- runAction() - Method in class toxtree.ui.actions.EstimateAllAction
-
- runAction() - Method in class toxtree.ui.actions.ExplainAction
-
- runAction() - Method in class toxtree.ui.actions.InfoAction
-
- runAction() - Method in class toxtree.ui.actions.OpenFileAction
-
- runAction() - Method in class toxtree.ui.actions.QuitAction
-
- runAction() - Method in class toxtree.ui.actions.SaveFileAction
-
- runAction() - Method in class toxtree.ui.molecule.ClearFilteredSubsetsAction
-
- runAction() - Method in class toxtree.ui.molecule.GoToRecordAction
-
- runAction() - Method in class toxtree.ui.molecule.LookupCompoundAction
-
- runAction() - Method in class toxtree.ui.molecule.ShowFilteredFileAction
-
- runAction() - Method in class toxtree.ui.tree.actions.ClearMethodsList
-
- runAction() - Method in class toxtree.ui.tree.actions.EditDecisionMethodAction
-
- runAction() - Method in class toxtree.ui.tree.actions.LiadMethodsListAction
-
- runAction() - Method in class toxtree.ui.tree.actions.LoadTreeAction
-
- runAction() - Method in class toxtree.ui.tree.actions.SaveMethodsListAction
-
- runAction() - Method in class toxtree.ui.tree.actions.SelectNewTreeAction
-
- runAction() - Method in class toxtree.ui.tree.actions.SelectTreeAction
-
- runAction() - Method in class toxtree.ui.tree.actions.TreeOptionsAction
-
- runAction() - Method in class toxtree.ui.tree.actions.ViewTreeAction
-
- s - Static variable in class toxtree.ui.tree.qsar.DescriptorOptions
-
- SA1 - Class in mic.rules
-
- SA1() - Constructor for class mic.rules.SA1
-
- SA10 - Class in mic.rules
-
- SA10() - Constructor for class mic.rules.SA10
-
- SA10_gen - Class in mutant.rules
-
- SA10_gen() - Constructor for class mutant.rules.SA10_gen
-
- SA10_gen - Class in toxtree.plugins.ames.rules
-
- SA10_gen() - Constructor for class toxtree.plugins.ames.rules.SA10_gen
-
- SA11 - Class in mic.rules
-
Aliphatic and aromatic aldehydes.
- SA11() - Constructor for class mic.rules.SA11
-
- SA11_gen - Class in mutant.rules
-
Aliphatic and aromatic aldehydes.
- SA11_gen() - Constructor for class mutant.rules.SA11_gen
-
- SA11_gen - Class in toxtree.plugins.ames.rules
-
Aliphatic and aromatic aldehydes.
- SA11_gen() - Constructor for class toxtree.plugins.ames.rules.SA11_gen
-
- SA12 - Class in mic.rules
-
Quinones
- SA12() - Constructor for class mic.rules.SA12
-
- SA12_gen - Class in mutant.rules
-
Quinones
- SA12_gen() - Constructor for class mutant.rules.SA12_gen
-
- SA12_gen - Class in toxtree.plugins.ames.rules
-
Quinones
- SA12_gen() - Constructor for class toxtree.plugins.ames.rules.SA12_gen
-
- SA13 - Class in mic.rules
-
- SA13() - Constructor for class mic.rules.SA13
-
- SA13_gen - Class in mutant.rules
-
- SA13_gen() - Constructor for class mutant.rules.SA13_gen
-
- SA13_gen - Class in toxtree.plugins.ames.rules
-
- SA13_gen() - Constructor for class toxtree.plugins.ames.rules.SA13_gen
-
- SA14 - Class in mic.rules
-
- SA14() - Constructor for class mic.rules.SA14
-
- SA14_gen - Class in mutant.rules
-
- SA14_gen() - Constructor for class mutant.rules.SA14_gen
-
- SA14_gen - Class in toxtree.plugins.ames.rules
-
- SA14_gen() - Constructor for class toxtree.plugins.ames.rules.SA14_gen
-
- SA15 - Class in mic.rules
-
- SA15() - Constructor for class mic.rules.SA15
-
- SA15_gen - Class in mutant.rules
-
- SA15_gen() - Constructor for class mutant.rules.SA15_gen
-
- SA15_gen - Class in toxtree.plugins.ames.rules
-
- SA15_gen() - Constructor for class toxtree.plugins.ames.rules.SA15_gen
-
- sa15_title - Static variable in class mic.rules.SA15
-
- sa15_title - Static variable in class mutant.rules.SA15_gen
-
- sa15_title - Static variable in class toxtree.plugins.ames.rules.SA15_gen
-
- SA16 - Class in mic.rules
-
- SA16() - Constructor for class mic.rules.SA16
-
- SA16_gen - Class in mutant.rules
-
- SA16_gen() - Constructor for class mutant.rules.SA16_gen
-
- SA16_gen - Class in toxtree.plugins.ames.rules
-
- SA16_gen() - Constructor for class toxtree.plugins.ames.rules.SA16_gen
-
- sa16_smarts - Static variable in class mic.rules.SA16
-
- sa16_smarts - Static variable in class mutant.rules.SA16_gen
-
- sa16_smarts - Static variable in class toxtree.plugins.ames.rules.SA16_gen
-
- sa16_title - Static variable in class mic.rules.SA16
-
- sa16_title - Static variable in class mutant.rules.SA16_gen
-
- sa16_title - Static variable in class toxtree.plugins.ames.rules.SA16_gen
-
- SA17_nogen - Class in mutant.rules
-
- SA17_nogen() - Constructor for class mutant.rules.SA17_nogen
-
- sa17_title - Static variable in class mutant.rules.SA17_nogen
-
- SA18 - Class in mic.rules
-
TODO Reimplement PAH recognition in a more robust way, possibly by
generalized Hueckel rule (Randic)
- SA18() - Constructor for class mic.rules.SA18
-
- SA18_gen - Class in mutant.rules
-
TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic)
- SA18_gen() - Constructor for class mutant.rules.SA18_gen
-
- SA18_gen - Class in toxtree.plugins.ames.rules
-
TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic)
- SA18_gen() - Constructor for class toxtree.plugins.ames.rules.SA18_gen
-
- SA19 - Class in mic.rules
-
If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic
rings, the rule returns true.
- SA19() - Constructor for class mic.rules.SA19
-
- SA19_gen - Class in mutant.rules
-
If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic rings, the rule returns true.
- SA19_gen() - Constructor for class mutant.rules.SA19_gen
-
- SA19_gen - Class in toxtree.plugins.ames.rules
-
If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic rings, the rule returns true.
- SA19_gen() - Constructor for class toxtree.plugins.ames.rules.SA19_gen
-
- SA1_gen - Class in mutant.rules
-
- SA1_gen() - Constructor for class mutant.rules.SA1_gen
-
- SA1_gen - Class in toxtree.plugins.ames.rules
-
- SA1_gen() - Constructor for class toxtree.plugins.ames.rules.SA1_gen
-
- SA2 - Class in mic.rules
-
SA2
- SA2() - Constructor for class mic.rules.SA2
-
Alkyl (C<5) or benzyl ester of sulphonic or phosphonic acid.
- SA20_nogen - Class in mutant.rules
-
- SA20_nogen() - Constructor for class mutant.rules.SA20_nogen
-
- SA20_title - Static variable in class mutant.rules.SA20_nogen
-
- SA21 - Class in mic.rules
-
- SA21() - Constructor for class mic.rules.SA21
-
TODO Please, could you add in this alert also aryl or alkyl substances
with the substructure: -N=N-O-H? Perhaps with the following MSARTS?
[C,c]N[NX2;v3]=O OR [C,c]N=N[OH1]
- SA21_gen - Class in mutant.rules
-
- SA21_gen() - Constructor for class mutant.rules.SA21_gen
-
TODO
Please, could you add in this alert also aryl or alkyl substances with the substructure: -N=N-O-H?
Perhaps with the following MSARTS?
[C,c]N[NX2;v3]=O
OR
[C,c]N=N[OH1]
- SA21_gen - Class in toxtree.plugins.ames.rules
-
- SA21_gen() - Constructor for class toxtree.plugins.ames.rules.SA21_gen
-
TODO
Please, could you add in this alert also aryl or alkyl substances with the substructure: -N=N-O-H?
Perhaps with the following MSARTS?
[C,c]N[NX2;v3]=O
OR
[C,c]N=N[OH1]
- SA21_title - Static variable in class mic.rules.SA21
-
- SA21_title - Static variable in class mutant.rules.SA21_gen
-
- SA21_title - Static variable in class toxtree.plugins.ames.rules.SA21_gen
-
- SA22 - Class in mic.rules
-
- SA22() - Constructor for class mic.rules.SA22
-
- SA22_azide - Static variable in class mic.rules.SA22
-
- SA22_azide - Static variable in class mutant.rules.SA22_gen
-
- SA22_azide - Static variable in class toxtree.plugins.ames.rules.SA22_gen
-
- SA22_azide_smarts - Static variable in class mic.rules.SA22
-
- SA22_azide_smarts - Static variable in class mutant.rules.SA22_gen
-
- SA22_azide_smarts - Static variable in class toxtree.plugins.ames.rules.SA22_gen
-
- SA22_gen - Class in mutant.rules
-
- SA22_gen() - Constructor for class mutant.rules.SA22_gen
-
- SA22_gen - Class in toxtree.plugins.ames.rules
-
- SA22_gen() - Constructor for class toxtree.plugins.ames.rules.SA22_gen
-
- SA22_title - Static variable in class mic.rules.SA22
-
- SA22_title - Static variable in class mutant.rules.SA22_gen
-
- SA22_title - Static variable in class toxtree.plugins.ames.rules.SA22_gen
-
- SA22_triazene - Static variable in class mic.rules.SA22
-
- SA22_triazene - Static variable in class mutant.rules.SA22_gen
-
- SA22_triazene - Static variable in class toxtree.plugins.ames.rules.SA22_gen
-
- SA22_triazene_smarts - Static variable in class mic.rules.SA22
-
- SA22_triazene_smarts - Static variable in class mutant.rules.SA22_gen
-
- SA22_triazene_smarts - Static variable in class toxtree.plugins.ames.rules.SA22_gen
-
- SA23 - Class in mic.rules
-
- SA23() - Constructor for class mic.rules.SA23
-
- SA23_gen - Class in mutant.rules
-
- SA23_gen() - Constructor for class mutant.rules.SA23_gen
-
- SA23_gen - Class in toxtree.plugins.ames.rules
-
- SA23_gen() - Constructor for class toxtree.plugins.ames.rules.SA23_gen
-
- SA23_title - Static variable in class mic.rules.SA23
-
- SA23_title - Static variable in class mutant.rules.SA23_gen
-
- SA23_title - Static variable in class toxtree.plugins.ames.rules.SA23_gen
-
- SA24 - Class in mic.rules
-
- SA24() - Constructor for class mic.rules.SA24
-
- SA24_gen - Class in mutant.rules
-
- SA24_gen() - Constructor for class mutant.rules.SA24_gen
-
- SA24_gen - Class in toxtree.plugins.ames.rules
-
- SA24_gen() - Constructor for class toxtree.plugins.ames.rules.SA24_gen
-
- SA24_title - Static variable in class mic.rules.SA24
-
- SA24_title - Static variable in class mutant.rules.SA24_gen
-
- SA24_title - Static variable in class toxtree.plugins.ames.rules.SA24_gen
-
- SA25 - Class in mic.rules
-
- SA25() - Constructor for class mic.rules.SA25
-
- SA25_gen - Class in mutant.rules
-
- SA25_gen() - Constructor for class mutant.rules.SA25_gen
-
- SA25_gen - Class in toxtree.plugins.ames.rules
-
- SA25_gen() - Constructor for class toxtree.plugins.ames.rules.SA25_gen
-
- SA25_title - Static variable in class mic.rules.SA25
-
- SA25_title - Static variable in class mutant.rules.SA25_gen
-
- SA25_title - Static variable in class toxtree.plugins.ames.rules.SA25_gen
-
- SA26 - Class in mic.rules
-
Aromatic ring N-oxide.
- SA26() - Constructor for class mic.rules.SA26
-
- SA26_gen - Class in mutant.rules
-
Aromatic ring N-oxide.
- SA26_gen() - Constructor for class mutant.rules.SA26_gen
-
- SA26_gen - Class in toxtree.plugins.ames.rules
-
Aromatic ring N-oxide.
- SA26_gen() - Constructor for class toxtree.plugins.ames.rules.SA26_gen
-
- SA26_title - Static variable in class mic.rules.SA26
-
- SA26_title - Static variable in class mutant.rules.SA26_gen
-
- SA26_title - Static variable in class toxtree.plugins.ames.rules.SA26_gen
-
- SA27 - Class in mic.rules
-
Nitro aromatic (and more).
- SA27() - Constructor for class mic.rules.SA27
-
- SA27_gen - Class in mutant.rules
-
Nitro aromatic (and more).
- SA27_gen() - Constructor for class mutant.rules.SA27_gen
-
- SA27_gen - Class in toxtree.plugins.ames.rules
-
Nitro aromatic (and more).
- SA27_gen() - Constructor for class toxtree.plugins.ames.rules.SA27_gen
-
- SA27_title - Static variable in class mic.rules.SA27
-
- SA27_title - Static variable in class mutant.rules.SA27_gen
-
- SA27_title - Static variable in class toxtree.plugins.ames.rules.SA27_gen
-
- SA28 - Class in mic.rules
-
TODO - this is same as mutant.rules.SA28 -to reuse instead of copy
- SA28() - Constructor for class mic.rules.SA28
-
- SA28_gen - Class in mutant.rules
-
[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)]
- SA28_gen() - Constructor for class mutant.rules.SA28_gen
-
- SA28_gen - Class in toxtree.plugins.ames.rules
-
[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)]
- SA28_gen() - Constructor for class toxtree.plugins.ames.rules.SA28_gen
-
- SA28_title - Static variable in class mic.rules.SA28
-
- SA28_title - Static variable in class mutant.rules.SA28_gen
-
- SA28_title - Static variable in class toxtree.plugins.ames.rules.SA28_gen
-
- SA28bis - Class in mic.rules
-
Aromatic mono- and dialkylamine (with exceptions).
- SA28bis() - Constructor for class mic.rules.SA28bis
-
- SA28bis_gen - Class in mutant.rules
-
Aromatic mono- and dialkylamine (with exceptions).
- SA28bis_gen() - Constructor for class mutant.rules.SA28bis_gen
-
- SA28bis_gen - Class in toxtree.plugins.ames.rules
-
Aromatic mono- and dialkylamine (with exceptions).
- SA28bis_gen() - Constructor for class toxtree.plugins.ames.rules.SA28bis_gen
-
- SA28bis_title - Static variable in class mic.rules.SA28bis
-
- SA28bis_title - Static variable in class mutant.rules.SA28bis_gen
-
- SA28bis_title - Static variable in class toxtree.plugins.ames.rules.SA28bis_gen
-
- SA28ter - Class in mic.rules
-
Aromatic N-acyl amine.
- SA28ter() - Constructor for class mic.rules.SA28ter
-
- SA28ter_gen - Class in mutant.rules
-
Aromatic N-acyl amine.
- SA28ter_gen() - Constructor for class mutant.rules.SA28ter_gen
-
- SA28ter_gen - Class in toxtree.plugins.ames.rules
-
Aromatic N-acyl amine.
- SA28ter_gen() - Constructor for class toxtree.plugins.ames.rules.SA28ter_gen
-
- SA28ter_title - Static variable in class mic.rules.SA28ter
-
- SA28ter_title - Static variable in class mutant.rules.SA28ter_gen
-
- SA28ter_title - Static variable in class toxtree.plugins.ames.rules.SA28ter_gen
-
- SA29 - Class in mic.rules
-
- SA29() - Constructor for class mic.rules.SA29
-
- SA29 - Static variable in class mic.rules.SA29
-
- SA29 - Static variable in class mutant.rules.SA29_gen
-
- SA29 - Static variable in class toxtree.plugins.ames.rules.SA29_gen
-
- SA29_gen - Class in mutant.rules
-
- SA29_gen() - Constructor for class mutant.rules.SA29_gen
-
- SA29_gen - Class in toxtree.plugins.ames.rules
-
- SA29_gen() - Constructor for class toxtree.plugins.ames.rules.SA29_gen
-
- SA29_noSO3H - Static variable in class mic.rules.SA29
-
- SA29_noSO3H - Static variable in class mutant.rules.SA29_gen
-
- SA29_noSO3H - Static variable in class toxtree.plugins.ames.rules.SA29_gen
-
- SA29_smarts - Static variable in class mic.rules.SA29
-
- SA29_smarts - Static variable in class mutant.rules.SA29_gen
-
- SA29_smarts - Static variable in class toxtree.plugins.ames.rules.SA29_gen
-
- SA2_gen - Class in mutant.rules
-
SA2_gen
- SA2_gen() - Constructor for class mutant.rules.SA2_gen
-
Alkyl (C<5) or benzyl ester of sulphonic or phosphonic acid.
- SA2_gen - Class in toxtree.plugins.ames.rules
-
SA2_gen
- SA2_gen() - Constructor for class toxtree.plugins.ames.rules.SA2_gen
-
Alkyl (C<5) or benzyl ester of sulphonic or phosphonic acid.
- SA2_phosphonic - Static variable in class mic.rules.SA2
-
- SA2_phosphonic - Static variable in class mutant.rules.SA2_gen
-
- SA2_phosphonic - Static variable in class toxtree.plugins.ames.rules.SA2_gen
-
- SA2_sulphonic - Static variable in class mic.rules.SA2
-
- SA2_sulphonic - Static variable in class mutant.rules.SA2_gen
-
- SA2_sulphonic - Static variable in class toxtree.plugins.ames.rules.SA2_gen
-
- SA3 - Class in mic.rules
-
- SA3() - Constructor for class mic.rules.SA3
-
- SA30 - Class in mic.rules
-
- SA30() - Constructor for class mic.rules.SA30
-
- SA30_gen - Class in mutant.rules
-
- SA30_gen() - Constructor for class mutant.rules.SA30_gen
-
- SA30_gen - Class in toxtree.plugins.ames.rules
-
- SA30_gen() - Constructor for class toxtree.plugins.ames.rules.SA30_gen
-
- SA30_title - Static variable in class mic.rules.SA30
-
- SA30_title - Static variable in class mutant.rules.SA30_gen
-
- SA30_title - Static variable in class toxtree.plugins.ames.rules.SA30_gen
-
- SA31a_nogen - Class in mutant.rules
-
TODO Verify how many level of recursive smarts are supported
TODO verify what's wrong with matching c;R
- SA31a_nogen() - Constructor for class mutant.rules.SA31a_nogen
-
The generated string is:
[c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)]1[c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)][c;$([R1]);!$(c[N+](=O)[O-]);!$(c[N]([#1,C])([#1,C]));!$(cN([OX2H])([#1,C]));!$(cN([#1,C])OC=O);!$(c[NX3v3]([#1,CH3])([#1,CH3]));!$(c[NX3v3]([#1,CH3])([CH2][CH3]));!$(c[NX3v3]([CH2][CH3])([CH2][CH3]));!$(cNC(=O)[#1,CH3]);!$(cN=[N]a);!$(c!@c1ccccc1);!$(c!@*!@c1ccccc1);!$(c!@*!@*!@c1ccccc1)][c]1([Cl,Br,F,I;!$([Cl,Br,I,F]cc[Cl,Br,I,F]);!$([Cl,Br,I,F]ccc[Cl,Br,I,F])])
- SA31a_title - Static variable in class mutant.rules.SA31a_nogen
-
- SA31b_nogen - Class in mutant.rules
-
- SA31b_nogen() - Constructor for class mutant.rules.SA31b_nogen
-
- SA31b_title - Static variable in class mutant.rules.SA31b_nogen
-
- SA31c_nogen - Class in mutant.rules
-
- SA31c_nogen() - Constructor for class mutant.rules.SA31c_nogen
-
- SA31c_title - Static variable in class mutant.rules.SA31c_nogen
-
- SA32 - Class in mic.rules
-
- SA32() - Constructor for class mic.rules.SA32
-
- SA33 - Class in mic.rules
-
- SA33() - Constructor for class mic.rules.SA33
-
- SA34 - Class in mic.rules
-
- SA34() - Constructor for class mic.rules.SA34
-
- SA34 - Static variable in class mic.rules.SA34
-
- SA34_title - Static variable in class mic.rules.SA34
-
- SA35 - Class in mic.rules
-
- SA35() - Constructor for class mic.rules.SA35
-
- SA36 - Class in mic.rules
-
- SA36() - Constructor for class mic.rules.SA36
-
- SA37_gen - Class in mutant.rules
-
- SA37_gen() - Constructor for class mutant.rules.SA37_gen
-
- SA37_gen - Class in toxtree.plugins.ames.rules
-
- SA37_gen() - Constructor for class toxtree.plugins.ames.rules.SA37_gen
-
- SA38_gen - Class in mutant.rules
-
- SA38_gen() - Constructor for class mutant.rules.SA38_gen
-
- SA38_gen - Class in toxtree.plugins.ames.rules
-
- SA38_gen() - Constructor for class toxtree.plugins.ames.rules.SA38_gen
-
- SA39_gen_and_nogen - Class in mutant.rules
-
- SA39_gen_and_nogen() - Constructor for class mutant.rules.SA39_gen_and_nogen
-
- SA39_gen_and_nogen - Class in toxtree.plugins.ames.rules
-
- SA39_gen_and_nogen() - Constructor for class toxtree.plugins.ames.rules.SA39_gen_and_nogen
-
- SA3_gen - Class in mutant.rules
-
- SA3_gen() - Constructor for class mutant.rules.SA3_gen
-
- SA3_gen - Class in toxtree.plugins.ames.rules
-
- SA3_gen() - Constructor for class toxtree.plugins.ames.rules.SA3_gen
-
- SA4 - Class in mic.rules
-
- SA4() - Constructor for class mic.rules.SA4
-
The SMARTS
[CX3]([!Cl;!Br;!F;!I;#1,CX4])(!@[#1,CX4])=[CX3]([Cl,F,Br,I])([#1,CX4])
excludes the possibility to have substituents different from H or CX4.
- SA40_nogen - Class in mutant.rules
-
- SA40_nogen() - Constructor for class mutant.rules.SA40_nogen
-
- SA41_nogen - Class in mutant.rules
-
- SA41_nogen() - Constructor for class mutant.rules.SA41_nogen
-
- SA42_nogen - Class in mutant.rules
-
- SA42_nogen() - Constructor for class mutant.rules.SA42_nogen
-
- SA43_nogen - Class in mutant.rules
-
- SA43_nogen() - Constructor for class mutant.rules.SA43_nogen
-
- SA44_nogen - Class in mutant.rules
-
- SA44_nogen() - Constructor for class mutant.rules.SA44_nogen
-
- SA45_nogen - Class in mutant.rules
-
- SA45_nogen() - Constructor for class mutant.rules.SA45_nogen
-
- SA46_nogen - Class in mutant.rules
-
- SA46_nogen() - Constructor for class mutant.rules.SA46_nogen
-
- SA47_nogen - Class in mutant.rules
-
- SA47_nogen() - Constructor for class mutant.rules.SA47_nogen
-
- SA48_nogen - Class in mutant.rules
-
- SA48_nogen() - Constructor for class mutant.rules.SA48_nogen
-
- SA49_nogen - Class in mutant.rules
-
- SA49_nogen() - Constructor for class mutant.rules.SA49_nogen
-
- SA4_gen - Class in mutant.rules
-
- SA4_gen() - Constructor for class mutant.rules.SA4_gen
-
The SMARTS
[CX3]([!Cl;!Br;!F;!I;#1,CX4])(!@[#1,CX4])=[CX3]([Cl,F,Br,I])([#1,CX4])
excludes the possibility to have substituents different from H or CX4.
- SA4_gen - Class in toxtree.plugins.ames.rules
-
- SA4_gen() - Constructor for class toxtree.plugins.ames.rules.SA4_gen
-
The SMARTS
[CX3]([!Cl;!Br;!F;!I;#1,CX4])(!@[#1,CX4])=[CX3]([Cl,F,Br,I])([#1,CX4])
excludes the possibility to have substituents different from H or CX4.
- SA4_smarts - Static variable in class mic.rules.SA4
-
- SA4_smarts - Static variable in class mutant.rules.SA4_gen
-
- SA4_smarts - Static variable in class toxtree.plugins.ames.rules.SA4_gen
-
- SA4_title - Static variable in class mic.rules.SA4
-
- SA4_title - Static variable in class mutant.rules.SA4_gen
-
- SA4_title - Static variable in class toxtree.plugins.ames.rules.SA4_gen
-
- SA5 - Class in mic.rules
-
- SA5() - Constructor for class mic.rules.SA5
-
- SA50_nogen - Class in mutant.rules
-
- SA50_nogen() - Constructor for class mutant.rules.SA50_nogen
-
- SA51_nogen - Class in mutant.rules
-
- SA51_nogen() - Constructor for class mutant.rules.SA51_nogen
-
- SA52_nogen - Class in mutant.rules
-
- SA52_nogen() - Constructor for class mutant.rules.SA52_nogen
-
- SA53_nogen - Class in mutant.rules
-
- SA53_nogen() - Constructor for class mutant.rules.SA53_nogen
-
- SA54_nogen - Class in mutant.rules
-
- SA54_nogen() - Constructor for class mutant.rules.SA54_nogen
-
- SA55_nogen - Class in mutant.rules
-
- SA55_nogen() - Constructor for class mutant.rules.SA55_nogen
-
- SA56_nogen - Class in mutant.rules
-
- SA56_nogen() - Constructor for class mutant.rules.SA56_nogen
-
- SA57_Ames - Class in toxtree.plugins.ames.rules
-
- SA57_Ames() - Constructor for class toxtree.plugins.ames.rules.SA57_Ames
-
- SA58_Ames - Class in toxtree.plugins.ames.rules
-
- SA58_Ames() - Constructor for class toxtree.plugins.ames.rules.SA58_Ames
-
- SA59_Ames - Class in toxtree.plugins.ames.rules
-
- SA59_Ames() - Constructor for class toxtree.plugins.ames.rules.SA59_Ames
-
- SA5_gen - Class in mutant.rules
-
- SA5_gen() - Constructor for class mutant.rules.SA5_gen
-
- SA5_gen - Class in toxtree.plugins.ames.rules
-
- SA5_gen() - Constructor for class toxtree.plugins.ames.rules.SA5_gen
-
- SA5_smarts - Static variable in class mic.rules.SA5
-
- SA5_smarts - Static variable in class mutant.rules.SA5_gen
-
- SA5_smarts - Static variable in class toxtree.plugins.ames.rules.SA5_gen
-
- SA5_title - Static variable in class mic.rules.SA5
-
- SA5_title - Static variable in class mutant.rules.SA5_gen
-
- SA5_title - Static variable in class toxtree.plugins.ames.rules.SA5_gen
-
- SA6 - Class in mic.rules
-
- SA6() - Constructor for class mic.rules.SA6
-
TODO verify
- SA60_Ames - Class in toxtree.plugins.ames.rules
-
- SA60_Ames() - Constructor for class toxtree.plugins.ames.rules.SA60_Ames
-
- SA61_Ames - Class in toxtree.plugins.ames.rules
-
- SA61_Ames() - Constructor for class toxtree.plugins.ames.rules.SA61_Ames
-
- SA62_Ames - Class in toxtree.plugins.ames.rules
-
- SA62_Ames() - Constructor for class toxtree.plugins.ames.rules.SA62_Ames
-
- SA63_Ames - Class in toxtree.plugins.ames.rules
-
- SA63_Ames() - Constructor for class toxtree.plugins.ames.rules.SA63_Ames
-
- SA64_Ames - Class in toxtree.plugins.ames.rules
-
- SA64_Ames() - Constructor for class toxtree.plugins.ames.rules.SA64_Ames
-
- SA65_Ames - Class in toxtree.plugins.ames.rules
-
- SA65_Ames() - Constructor for class toxtree.plugins.ames.rules.SA65_Ames
-
- SA66_Ames - Class in toxtree.plugins.ames.rules
-
- SA66_Ames() - Constructor for class toxtree.plugins.ames.rules.SA66_Ames
-
- SA67_Ames - Class in toxtree.plugins.ames.rules
-
- SA67_Ames() - Constructor for class toxtree.plugins.ames.rules.SA67_Ames
-
- SA68_Ames - Class in toxtree.plugins.ames.rules
-
- SA68_Ames() - Constructor for class toxtree.plugins.ames.rules.SA68_Ames
-
- SA69_Ames - Class in toxtree.plugins.ames.rules
-
- SA69_Ames() - Constructor for class toxtree.plugins.ames.rules.SA69_Ames
-
- SA6_gen - Class in mutant.rules
-
- SA6_gen() - Constructor for class mutant.rules.SA6_gen
-
TODO verify
- SA6_gen - Class in toxtree.plugins.ames.rules
-
- SA6_gen() - Constructor for class toxtree.plugins.ames.rules.SA6_gen
-
TODO verify
- SA7 - Class in mic.rules
-
- SA7() - Constructor for class mic.rules.SA7
-
- SA7_gen - Class in mutant.rules
-
- SA7_gen() - Constructor for class mutant.rules.SA7_gen
-
- SA7_gen - Class in toxtree.plugins.ames.rules
-
- SA7_gen() - Constructor for class toxtree.plugins.ames.rules.SA7_gen
-
- SA8 - Class in mic.rules
-
- SA8() - Constructor for class mic.rules.SA8
-
- SA8_gen - Class in mutant.rules
-
- SA8_gen() - Constructor for class mutant.rules.SA8_gen
-
- SA8_gen - Class in toxtree.plugins.ames.rules
-
- SA8_gen() - Constructor for class toxtree.plugins.ames.rules.SA8_gen
-
- SA8_title - Static variable in class mic.rules.SA8
-
- SA8_title - Static variable in class mutant.rules.SA8_gen
-
- SA8_title - Static variable in class toxtree.plugins.ames.rules.SA8_gen
-
- SA9 - Class in mic.rules
-
- SA9() - Constructor for class mic.rules.SA9
-
- SA9_gen - Class in mutant.rules
-
- SA9_gen() - Constructor for class mutant.rules.SA9_gen
-
- SA9_gen - Class in toxtree.plugins.ames.rules
-
- SA9_gen() - Constructor for class toxtree.plugins.ames.rules.SA9_gen
-
- salt - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
-
- salt - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
-
- salt1 - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
-
- salt1 - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
-
- salt2 - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
-
- salt2 - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
-
- saltOfCarboxylicAcid(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- saltOfCarboxylicAcid1(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- saltOfCarboxylicAcid2(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- saltOfCarboxylicAcidBreakable(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- saltOfCarboxylicAcidBreakable1(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- saltOfCarboxylicAcidBreakable2(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- saveConfig() - Method in class toxTree.io.batch.BatchProcessing
-
- saveConfig(OutputStream) - Method in class toxTree.io.batch.BatchProcessing
-
- saveConfig() - Method in interface toxTree.io.batch.IBatchProcessing
-
- saveConfig() - Method in class toxTree.io.batch.ToxTreeBatchProcessing
-
- saveConfig(OutputStream) - Method in class toxTree.io.batch.ToxTreeBatchProcessing
-
- saveFile(File) - Method in interface toxTree.core.IMoleculesIterator
-
- saveFile(File) - Method in class toxtree.data.DataContainer
-
- saveFile(File) - Method in class toxTree.data.MoleculesIterator
-
- SaveFileAction - Class in toxtree.ui.actions
-
Saves a file
- SaveFileAction(DataModule) - Constructor for class toxtree.ui.actions.SaveFileAction
-
- SaveFileAction(DataModule, String) - Constructor for class toxtree.ui.actions.SaveFileAction
-
- SaveFileAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.SaveFileAction
-
- SaveMethodsListAction - Class in toxtree.ui.tree.actions
-
- SaveMethodsListAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.tree.actions.SaveMethodsListAction
-
- SaveMethodsListAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.tree.actions.SaveMethodsListAction
-
- SaveMethodsListAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.SaveMethodsListAction
-
- saveRulesXML(IDecisionMethod, OutputStream) - Static method in class toxTree.core.Introspection
-
- saveStateFrequency - Variable in class toxTree.io.batch.BatchProcessing
-
- SaveTreeAction - Class in toxtree.ui.tree.actions
-
- SaveTreeAction(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.SaveTreeAction
-
- SaveTreeAction(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.SaveTreeAction
-
- SaveTreeAction(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.SaveTreeAction
-
- scale - Variable in class toxTree.qsar.LinearPreprocessor
-
- SDF_INDEX - Static variable in class toxTree.io.batch.ChemObjectBatchProcessing
-
- sdg - Variable in class toxTree.query.metabolite.MetabolyteRecycler
-
- sdg - Variable in class toxtree.ui.molecule.MoleculeEditAction
-
- sdg - Variable in class toxtree.ui.molecule.SmilesEntryPanel
-
- searchSite - Variable in class toxtree.plugins.search.rules.Find
-
- SECONDARY_AMINE - Static variable in class toxTree.query.FunctionalGroups
-
- SECONDARY_AMINE_ALIPHATIC - Static variable in class toxTree.query.FunctionalGroups
-
- secondaryAmine(boolean) - Static method in class toxTree.query.FunctionalGroups
-
SMARTS: [C;R0]-;!@[N;R0;H1]-;!@[C;R0]
- select(Hashtable<String, IAtomContainerSet>) - Method in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
-
- select(Hashtable<String, IAtomContainerSet>) - Method in class mutant.descriptors.SubstituentsDescriptor
-
- select(IAtomContainer, IAtomContainer, boolean) - Method in class toxTree.core.SmartElementsList
-
- select(Hashtable<String, IAtomContainerSet>) - Method in class toxtree.plugins.ames.descriptors.AromaticAmineSubstituentsDescriptor
-
- select(Hashtable<String, IAtomContainerSet>) - Method in class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- select(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleElements
-
- select(IAtomContainer, IAtomContainer) - Method in class verhaar.rules.Rule11
-
- selectAll(boolean) - Method in interface toxTree.core.IDecisionCategories
-
- selectAll(boolean) - Method in class toxTree.tree.CategoriesList
-
- SelectAndEditTreeAction - Class in toxtree.ui.tree.actions
-
Selects available tree types, makes a copy if it is read-only and launches a decision tree editor
- SelectAndEditTreeAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.tree.actions.SelectAndEditTreeAction
-
- SelectAndEditTreeAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.tree.actions.SelectAndEditTreeAction
-
- SelectAndEditTreeAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.SelectAndEditTreeAction
-
- SelectCategoryFromListAction - Class in toxtree.ui.tree.actions
-
Shows a list of available categories and adds the selected one to the list of categories.
- SelectCategoryFromListAction(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.SelectCategoryFromListAction
-
- SelectCategoryFromListAction(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.SelectCategoryFromListAction
-
- SelectCategoryFromListAction(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.SelectCategoryFromListAction
-
- selected - Variable in class toxTree.tree.CategoriesList
-
- selected - Variable in class toxTree.tree.DefaultCategory
-
- selectedCell - Variable in class toxtree.ui.tree.TreeLayout
-
- selectedIndex - Variable in class toxTree.data.MoleculesFile
-
- selectedIndex - Variable in class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
-
- selectedIndex - Variable in class toxtree.ui.tree.rules.SMARTSRuleEditor
-
- selectedIndex - Variable in class toxtree.ui.tree.TreeLayout
-
- selectedItem - Variable in class toxtree.ui.molecule.LookupCompoundAction
-
- selectedObject - Variable in class toxtree.ui.wizard.DecisionNodeWizard
-
- selectFile(Component, String[], String[], boolean) - Static method in class toxtree.data.ActionList
-
Invokes OpenFile or SaveFile dialog
- selectFile() - Method in class toxtree.ui.tree.rules.RuleStructuresPanel
-
- selectFilter(Component) - Method in class toxTree.apps.toxForest.ToxForestDataModule
-
- selectFilter(Component) - Method in class toxtree.data.DataContainer
-
- selectFilter(Component) - Method in class toxtree.data.DecisionMethodsDataModule
-
- selectFilter(Component) - Method in class toxtree.data.FilteredMoleculesIterator
-
- selectFromList(Component, String, String, ListTableModel, ActionMap) - Static method in class toxtree.ui.tree.SelectListDialog
-
- selectFromList(Component, String, String, ListTableModel, ActionMap, Dimension) - Static method in class toxtree.ui.tree.SelectListDialog
-
- selectFromList(String, ListPanel[]) - Static method in class toxtree.ui.tree.SelectListDialog
-
Launches a dialog with a several lists arranged in a
JTabbedPane.
- SelectListDialog - Class in toxtree.ui.tree
-
A singleton class, providing several methods to select an object from a
List.
- SelectListDialog() - Constructor for class toxtree.ui.tree.SelectListDialog
-
Singleton class
- selectNewCategory(Component, ClassLoader) - Static method in class toxtree.ui.tree.SelectListDialog
-
- selectNewNode(Component, ClassLoader) - Static method in class toxtree.ui.tree.SelectListDialog
-
- selectNewRule(Component, ClassLoader) - Static method in class toxtree.ui.tree.SelectListDialog
-
- selectNewTree(Component, ClassLoader) - Static method in class toxtree.ui.tree.SelectListDialog
-
- SelectNewTreeAction - Class in toxtree.ui.tree.actions
-
- SelectNewTreeAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.tree.actions.SelectNewTreeAction
-
- SelectNewTreeAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.tree.actions.SelectNewTreeAction
-
- SelectNewTreeAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.SelectNewTreeAction
-
- selectObject(ActionEvent, T) - Method in class toxtree.ui.wizard.RadioBoxPanel
-
- selectRings(IRingSet, IAtomContainer) - Method in class toxTree.tree.cramer.RuleMonocycloalkanoneEtc
-
- SelectTreeAction - Class in toxtree.ui.tree.actions
-
Selects a tree from available decision trees
- SelectTreeAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.tree.actions.SelectTreeAction
-
- SelectTreeAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.tree.actions.SelectTreeAction
-
- SelectTreeAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.SelectTreeAction
-
- set(int, IDecisionCategory) - Method in class toxTree.tree.CategoriesList
-
- set(int, Object) - Method in class toxTree.tree.DecisionMethodsList
-
- set(int, IDecisionRule) - Method in class toxTree.tree.DecisionNodesList
-
- set(int, IDecisionRule) - Method in class toxTree.tree.RulesList
-
- setAcetylenic(boolean) - Method in class toxTree.query.MolFlags
-
- setActiveContainer(ListOfAtomContainers) - Method in class toxtree.data.FilteredMoleculesIterator
-
- setAlicyclic(boolean) - Method in class toxTree.query.MolFlags
-
- setAliphatic(boolean) - Method in class toxTree.query.MolFlags
-
- setAnalysed(boolean) - Method in class toxTree.query.MolFlags
-
- setAnalyzeAromatic(boolean) - Method in class toxTree.tree.rules.RuleRingSubstituents
-
- setAnalyzeHeterocyclic(boolean) - Method in class toxTree.tree.rules.RuleRingSubstituents
-
- setAnalyzeOnlyRingsWithFlagSet(boolean) - Method in class toxTree.tree.rules.RuleRingSubstituents
-
- setAnswer(boolean) - Method in enum toxTree.core.IDecisionInteractive.UserOptions
-
- setAnswer(boolean) - Method in exception toxTree.exceptions.DRuleException
-
- setAnswer(boolean) - Method in class toxtree.ui.tree.rules.RuleExampleEditAction
-
- setAromatic(boolean) - Method in class toxTree.query.MolFlags
-
- setAromaticRings(int) - Method in class toxTree.query.MolFlags
-
- setArrayValue(ArrayResult, int, IAtomContainer, String) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- setArrayValue(ArrayResult, int, IAtomContainer, String) - Method in class toxTree.tree.UserDefinedTree
-
- setAtomContainer(IAtomContainer) - Method in exception toxTree.exceptions.MolAnalyseException
-
- setAtomContainer(IAtomContainer) - Method in class toxtree.ui.molecule.AtomContainerPropertyTableModel
-
- setAtomContainer(IAtomContainer) - Method in class toxtree.ui.molecule.PropertyPanel
-
- setAtomContainer(IAtomContainer, int) - Method in class toxtree.ui.tree.rules.RuleSubstructuresEditAction
-
- setAtomContainers(IAtomContainer[]) - Method in class toxTree.data.MoleculesFile
-
- setBackId(Object) - Method in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
-
- setBatch(String) - Method in class toxTree.apps.ToxtreeOptions
-
- setBatch(IBatchProcessing) - Method in class toxtree.ui.batch.BatchProcessingDialog
-
- setBranch(boolean, IDecisionRule) - Method in class toxTree.tree.DecisionNode
-
Sets the decision rule at the branch No if answer==false or
the decision rule at the branch Yes if answer =true
- setBranch(boolean, IDecisionRule) - Method in class toxTree.tree.MultiLabelDecisionNode
-
- SetBranchAction - Class in toxtree.ui.tree.actions
-
Modify a tree node branch.
- SetBranchAction(IDecisionMethod, boolean) - Constructor for class toxtree.ui.tree.actions.SetBranchAction
-
- SetBranchAction(IDecisionMethod, boolean, String) - Constructor for class toxtree.ui.tree.actions.SetBranchAction
-
- SetBranchAction(IDecisionMethod, boolean, String, Icon) - Constructor for class toxtree.ui.tree.actions.SetBranchAction
-
- setBufferProperties(boolean) - Method in class toxTree.data.MoleculesFile
-
- setCalculated(IMolecularDescriptor, String, boolean) - Method in interface toxTree.core.IDescriptorBased
-
- setCalculated(IMolecularDescriptor, String, boolean) - Method in class toxTree.qsar.AbstractQSARModel
-
- setCalculated(IMolecularDescriptor, String, boolean) - Method in class toxTree.qsar.LinearDiscriminantRule
-
- setCalculated(boolean) - Method in class toxTree.qsar.QSARDescriptor
-
- setCategories(IDecisionCategories) - Method in class toxTree.tree.AbstractTree
-
- setCategories(String[]) - Method in class toxtree.tree.cramer3.TreeSpecification
-
- setCategories(IDecisionCategory[]) - Method in class toxTree.tree.DecisionNode
-
- setCategories(IDecisionCategories) - Method in class toxTree.ui.tree.categories.CategoriesRenderer
-
- setCategories(int) - Method in class toxTree.ui.tree.categories.CategoriesRenderer
-
- setCategories(int, int) - Method in class toxTree.ui.tree.categories.CategoriesRenderer
-
- setCategory(IDecisionCategory) - Method in interface toxTree.core.IDecisionCategoryEditor
-
- setCategory(IDecisionCategory) - Method in interface toxTree.core.IDecisionResult
-
- setCategory(IDecisionCategory) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setCategory(boolean, IDecisionCategory) - Method in class toxTree.tree.DecisionNode
-
/**
Sets the category at the branch No if answer==false or
the category at the branch Yes if answer =true
- setCategory(boolean, IDecisionCategory) - Method in class toxTree.tree.MultiLabelDecisionNode
-
- setCategory(IDecisionCategory) - Method in class toxTree.tree.RuleResult
-
- setCategory(IDecisionCategory) - Method in class toxTree.tree.TreeResult
-
- setCategory(IDecisionCategory) - Method in class toxtree.ui.tree.actions.EditCategoryAction
-
- setCategory(IDecisionCategory) - Method in interface toxtree.ui.tree.actions.ICategoryAction
-
- setCategory(IDecisionCategory) - Method in class toxtree.ui.tree.categories.CategoryPanel
-
- setCategory(IDecisionCategory) - Method in class toxtree.ui.tree.EditTreeActions
-
- setCategory2assign(IDecisionCategory) - Method in exception toxTree.exceptions.DRuleException
-
- setCategoryActions(ActionMap) - Method in class toxtree.ui.tree.EditTreeActions
-
- setCategoryType(ICategory.CategoryType) - Method in class toxTree.tree.DefaultCategory
-
- setChanged() - Method in class toxTree.tree.AbstractTree
-
- setCheckAromaticity(boolean) - Method in class toxTree.tree.rules.LookupFile
-
- setClassName(String) - Method in class toxTree.core.ToxTreePackageEntry
-
- setComparisonMode(int) - Method in class toxTree.tree.rules.RuleElements
-
- setCondition(String) - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- setCondition(String) - Method in class toxtree.ui.tree.rules.RulePropertyEditor
-
- setConfigFile(File) - Method in class toxTree.io.batch.BatchProcessing
-
- setConfigFile(File) - Method in interface toxTree.io.batch.IBatchProcessing
-
- setContainsAllSubstructures(boolean) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- setContainsAllSubstructures(boolean) - Method in interface toxTree.tree.rules.smarts.IRuleSMARTSubstructures
-
- setCreateNewMolecule(boolean) - Method in class toxtree.ui.tree.rules.RuleSubstructuresEditAction
-
- setCurrentDirectory(String) - Static method in class toxtree.data.ActionList
-
- setCurrentNo(int) - Method in interface toxTree.core.IMoleculesIterator
-
- setCurrentNo(int) - Method in class toxTree.data.MoleculesIterator
-
- setCurrentRecord(long) - Method in class toxTree.io.batch.FileState
-
- setData(IDecisionCategories, IDecisionResult) - Method in class toxtree.ui.tree.categories.CategoriesPanel
-
- setDataContainer(DataContainer) - Method in class toxtree.ui.molecule.NavigationPanel
-
- setDataContainer(DataContainer) - Method in class toxtree.ui.molecule.StructureEntryPanel
-
- setDataContainer(DataContainer) - Method in class toxtree.ui.molecule.TopPanel
-
- setDataContainer(DataContainer) - Method in class toxtree.ui.StatusBar
-
- setDataModule(DM) - Method in class toxtree.ui.DataModulePanel
-
- setDecisionMethod(IDecisionMethod) - Method in interface toxTree.core.IDecisionResult
-
- setDecisionMethod(IDecisionMethod) - Method in class toxTree.io.batch.ToxTreeBatchProcessing
-
- setDecisionMethod(IDecisionMethod) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setDecisionMethod(IDecisionMethod) - Method in class toxTree.tree.TreeResult
-
- setDecisionMethod(IDecisionMethod) - Method in class toxtree.ui.batch.BatchProcessingDialog
-
- setDecisionMethod(IDecisionMethod) - Method in class toxtree.ui.tree.DecisionTreeModel
-
- setDecisionMethod(IDecisionMethod) - Method in interface toxtree.ui.tree.ITreeView
-
- setDecisionMethod(IDecisionMethod) - Method in class toxtree.ui.tree.JCustomTreeComponent
-
- setDecisionMethod(IDecisionMethod) - Method in class toxtree.ui.tree.TreeDrawing
-
- setDecisionMethod(IDecisionMethod) - Method in class toxtree.ui.tree.TreeFrame
-
- setDecisionMethod(IDecisionMethod) - Method in class toxtree.ui.tree.TreePanel
-
- setDecisionMethod(IDecisionMethod) - Method in class toxtree.ui.tree.TreePrefuse
-
- setDecisionNode(DecisionNode) - Method in interface toxtree.ui.tree.actions.INodeAction
-
- setDecisionNode(DecisionNode) - Method in class toxtree.ui.tree.actions.SetBranchAction
-
- setDecisionRule(IDecisionRule) - Method in interface toxTree.core.IDecisionMethod
-
- setDecisionRule(IDecisionRule) - Method in class toxTree.tree.AbstractTree
-
- setDecisionRule(IDecisionRule) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setDelimiter(char) - Method in class toxTree.tree.SimpleTreePrinter
-
- setDescriptor(IMolecularDescriptor) - Method in class toxTree.qsar.QSARDescriptor
-
- setDescriptor(IDescriptor) - Method in class toxTree.tree.rules.RuleDescriptor
-
- setDescriptorName(String) - Method in class toxTree.qsar.QSARDescriptor
-
- setDescriptorNames(String[]) - Method in class mutant.descriptors.SubstituentsDescriptor
-
- setDescriptorNames(String[]) - Method in class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- setDescriptorNames(List<String>) - Method in class toxTree.qsar.AbstractQSARModel
-
- setDescriptors(List<IMolecularDescriptor>) - Method in class toxTree.qsar.AbstractQSARModel
-
- setDimension(int) - Method in interface toxTree.qsar.IDescriptorPreprocessor
-
- setDimension(int) - Method in class toxTree.qsar.LinearPreprocessor
-
- setDimension(int) - Method in class toxTree.qsar.MatrixPreprocessor
-
- setDone(boolean) - Method in interface toxTree.core.IMoleculesIterator
-
- setDone(boolean) - Method in class toxTree.data.MoleculesIterator
-
- setEditable(boolean) - Method in class com.molecularnetworks.start.BiodgeradationRules
-
- setEditable(boolean) - Method in class cramer2.CramerRulesWithExtensions
-
- setEditable(boolean) - Method in class eye.EyeIrritationRules
-
- setEditable(boolean) - Method in class mic.MICRules
-
- setEditable(boolean) - Method in class michaelacceptors.MichaelAcceptorRules
-
- setEditable(boolean) - Method in class mutant.BB_CarcMutRules
-
- setEditable(boolean) - Method in class sicret.SicretRules
-
- setEditable(boolean) - Method in interface toxTree.core.IDecisionMethod
-
- setEditable(boolean) - Method in interface toxTree.core.IDecisionRule
-
- setEditable(boolean) - Method in interface toxTree.core.IToxTreeEditor
-
- setEditable(boolean) - Method in class toxtree.plugins.ames.AmesMutagenicityRules
-
- setEditable(boolean) - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
-
- setEditable(boolean) - Method in class toxtree.plugins.func.FuncRules
-
- setEditable(boolean) - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
-
- setEditable(boolean) - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- setEditable(boolean) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- setEditable(boolean) - Method in class toxTree.tree.AbstractRule
-
- setEditable(boolean) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setEditable(boolean) - Method in class toxTree.tree.cramer.CramerRules
-
- setEditable(boolean) - Method in class toxtree.tree.cramer3.RevisedCramerDecisionTree
-
- setEditable(boolean) - Method in class toxTree.tree.DecisionNode
-
- setEditable(boolean) - Method in class toxTree.tree.UserDefinedTree
-
- setEditable(boolean) - Method in class toxtree.ui.tree.DecisionNodePanel
-
- setEditable(boolean) - Method in class toxtree.ui.tree.qsar.QSARModelEditor
-
- setEditable(boolean) - Method in class toxtree.ui.tree.rules.RulePanel
-
- setEditable(boolean) - Method in class toxtree.ui.tree.rules.SubstructureRulePanel
-
- setEditable(boolean) - Method in class toxtree.ui.tree.ToxTreeEditorPanel
-
- setEditable(boolean) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- setEditor(IToxTreeEditor) - Method in class toxtree.ui.wizard.EditorPanel
-
- setEditorFactory() - Method in class toxTree.apps.AbstractApplication
-
- setElements(SmartElementsList) - Method in class toxTree.tree.rules.RuleElements
-
- setEnabled(boolean) - Method in class toxtree.data.DataContainer
-
- setEnabled(boolean) - Method in class toxTree.tree.UserDefinedTree
-
- setError(String) - Method in interface toxTree.core.IProgressStatus
-
- setError(String) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setError(String) - Method in class toxTree.tree.ProgressStatus
-
- setError(String) - Method in class toxTree.tree.TreeResult
-
- setErrorMessage(BatchProcessingException) - Method in class toxtree.ui.batch.BatchProcessingDialog
-
- setEstimated(boolean) - Method in interface toxTree.core.IProgressStatus
-
- setEstimated() - Method in interface toxTree.core.IProgressStatus
-
- setEstimated() - Method in class toxTree.tree.BatchDecisionResultsList
-
- setEstimated(boolean) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setEstimated() - Method in class toxTree.tree.ProgressStatus
-
- setEstimated(boolean) - Method in class toxTree.tree.ProgressStatus
-
- setEstimated() - Method in class toxTree.tree.TreeResult
-
- setEstimated(boolean) - Method in class toxTree.tree.TreeResult
-
- setEstimating() - Method in interface toxTree.core.IProgressStatus
-
- setEstimating() - Method in class toxTree.tree.BatchDecisionResultsList
-
- setEstimating() - Method in class toxTree.tree.ProgressStatus
-
- setEstimating() - Method in class toxTree.tree.TreeResult
-
- setExampleMolecule(IAtomContainer, boolean) - Method in interface toxTree.core.IDecisionRule
-
Sets example molecule for the YES or NO answer of the rule
- setExampleMolecule(IAtomContainer, boolean) - Method in class toxTree.tree.AbstractRule
-
- setExampleMolecule(IAtomContainer, boolean) - Method in class toxTree.tree.DecisionNode
-
- setExamples(boolean, IAtomContainerSet) - Method in class mutant.rules.SMARTSGroup
-
- setExamples(boolean, IAtomContainerSet) - Method in class toxtree.plugins.ames.rules.SMARTSGroup
-
- setExamples(String[]) - Method in class toxTree.tree.AbstractRule
-
- setExpectedTitle(String) - Method in class toxTree.tree.stats.ConfusionMatrix
-
- setExplanation(String) - Method in interface toxTree.core.IDecisionCategory
-
- setExplanation(String) - Method in interface toxTree.core.IDecisionMethod
-
- setExplanation(String) - Method in interface toxTree.core.IDecisionRule
-
Sets rule explanation
- setExplanation(String) - Method in interface toxTree.qsar.IDescriptorPreprocessor
-
- setExplanation(String) - Method in class toxTree.qsar.LinearPreprocessor
-
- setExplanation(String) - Method in class toxTree.qsar.MatrixPreprocessor
-
- setExplanation(String) - Method in class toxTree.tree.AbstractRule
-
- setExplanation(String) - Method in class toxTree.tree.AbstractTree
-
- setExplanation(String) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setExplanation(String) - Method in class toxTree.tree.DecisionNode
-
- setExplanation(String) - Method in class toxTree.tree.DefaultCategory
-
- setExplanation(String) - Method in class toxtree.ui.tree.categories.CategoryPanel
-
- setExplanation(String) - Method in class toxtree.ui.tree.rules.RuleEditor
-
- setExplanation(String) - Method in class toxtree.ui.tree.ToxTreeEditorPanel
-
- setExtension(String) - Method in class toxTree.io.MolFileFilter
-
- setFalseIfRuleNotImplemented(boolean) - Method in class toxTree.tree.AbstractTree
-
- setFile(File) - Method in class toxTree.io.batch.FileState
-
- setFile(File) - Method in interface toxTree.tree.rules.ILookupFile
-
- setFile(File) - Method in class toxTree.tree.rules.InChILookupFile
-
- setFile(File) - Method in class toxTree.tree.rules.LookupFile
-
- setFile(File) - Method in class toxTree.tree.rules.RuleStructuresList
-
- setFilename(String) - Method in exception toxTree.exceptions.ToxTreeIOException
-
- setFilename(String) - Method in class toxTree.io.batch.FileState
-
- setFilename(String) - Method in class toxTree.tree.rules.RuleStructuresList
-
- setFilter(IObjectFilter, boolean) - Method in interface toxTree.core.IFilteredMolecules
-
Sets the active list to be this filtered set.
- setFilter(IObjectFilter, boolean) - Method in class toxtree.data.FilteredMoleculesIterator
-
Sets the current set of molecules.
- setFlag(int, boolean) - Method in class toxTree.data.ListOfAtomContainers
-
- setFlag(int, boolean) - Method in class toxTree.tree.rules.RuleRingSubstituents
-
- setFlags(boolean[]) - Method in class toxTree.data.ListOfAtomContainers
-
- setFrame(Component) - Method in class toxtree.ui.actions.DataModuleAction
-
- setGraph(Graph) - Method in class toxTree.tree.Tree2PrefuseGraph
-
- setHalogens(TreeSet<String>) - Method in class toxTree.core.SmartElementsList
-
- setHalogens(String[]) - Method in class toxTree.core.SmartElementsList
-
- setHalogens(String[]) - Method in class toxTree.tree.rules.RuleElements
-
- setHalogens(TreeSet) - Method in class toxTree.tree.rules.RuleElements
-
- setHashCode(int) - Method in class toxTree.io.batch.FileState
-
- setHeader(Map) - Method in class toxTree.io.PDFWriter
-
- setHeteroaromatic(boolean) - Method in class toxTree.query.MolFlags
-
- setHeterocyclic(boolean) - Method in class toxTree.query.MolFlags
-
- setHeterocyclic3(boolean) - Method in class toxTree.query.MolFlags
-
- setHydrolysisProducts(IAtomContainerSet) - Method in class toxTree.query.MolFlags
-
- setID(int) - Method in interface toxTree.core.IDecisionCategory
-
- setID(String) - Method in interface toxTree.core.IDecisionRule
-
Sets rule identifier
- setID(String) - Method in class toxTree.data.ListOfAtomContainers
-
- setID(String) - Method in class toxTree.tree.AbstractRule
-
- setID(String) - Method in class toxTree.tree.DecisionNode
-
- setID(int) - Method in class toxTree.tree.DefaultCategory
-
- setID(String) - Method in class toxtree.ui.tree.categories.CategoryPanel
-
- setID(String) - Method in class toxtree.ui.tree.rules.RuleEditor
-
- setID(String) - Method in class toxtree.ui.tree.ToxTreeEditorPanel
-
- setId(Object) - Method in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
-
- setIds(ArrayList) - Method in class toxTree.tree.rules.RuleSubstructures
-
- setImageSize(Dimension) - Method in class toxTree.tree.AbstractTree
-
- setImageSize(Dimension) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setInput(File) - Method in class toxTree.apps.ToxtreeOptions
-
- setInRing(boolean) - Method in class toxTree.query.TopologyOrderQueryBond
-
- setInstance(IEditorFactory) - Static method in class toxTree.ui.EditorFactory
-
- setInteractive(boolean) - Method in class com.molecularnetworks.start.BiodgeradationRules
-
- setInteractive(boolean) - Method in class eye.EyeIrritationRules
-
- setInteractive(boolean) - Method in class mutant.rules.QSAR6Applicable
-
- setInteractive(boolean) - Method in class sicret.SicretRules
-
- setInteractive(boolean) - Method in interface toxTree.core.IDecisionInteractive
-
- setInteractive(boolean) - Method in enum toxTree.core.IDecisionInteractive.UserOptions
-
- setInteractive(boolean) - Method in class toxtree.plugins.ames.rules.QSAR6Applicable
-
- setInteractive(boolean) - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- setInteractive(boolean) - Method in class toxTree.tree.rules.UserInputRule
-
- setInteractive(boolean) - Method in class toxTree.tree.UserDefinedTree
-
- setJCPModel() - Method in class toxtree.ui.molecule.MoleculeEditAction
-
- setLastModified(long) - Method in class toxTree.io.batch.FileState
-
- setLength(long) - Method in class toxTree.io.batch.FileState
-
- setList(ArrayList) - Method in class toxTree.tree.DecisionMethodsList
-
- setList(ArrayList<IDecisionRule>) - Method in class toxTree.tree.DecisionNodesList
-
- setList(ArrayList) - Method in class toxTree.tree.RulesList
-
- setList(List) - Method in class toxtree.ui.tree.ListPanel
-
- setList(List<T>) - Method in class toxtree.ui.tree.ListTableModel
-
- setListener(PropertyChangeListener) - Method in class mutant.rules.QSAR6Applicable
-
- setListener(PropertyChangeListener) - Method in interface toxTree.core.IDecisionInteractive
-
- setListener(PropertyChangeListener) - Method in class toxtree.plugins.ames.rules.QSAR6Applicable
-
- setListener(PropertyChangeListener) - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- setListener(PropertyChangeListener) - Method in class toxTree.tree.rules.UserInputRule
-
- setListener(PropertyChangeListener) - Method in class toxTree.tree.UserDefinedTree
-
- setLoader(ClassLoader) - Static method in class toxTree.core.Introspection
-
- setMatrix(double[][]) - Method in class toxTree.qsar.MatrixPreprocessor
-
- setMaxHalogens(int) - Method in class verhaar.rules.Rule21
-
- setMaxNitroGroups(int) - Method in class verhaar.rules.Rule21
-
- setMaxValue(double) - Method in interface toxTree.core.IRuleRange
-
- setMaxValue(double) - Method in class toxTree.tree.rules.RuleDescriptorRange
-
- setMaxValue(double) - Method in class toxTree.tree.rules.RuleManyAromaticRings
-
- setMessage(String) - Method in class toxTree.tree.rules.UserInputRule
-
- setMethod(IDecisionMethod) - Method in interface toxTree.core.IDecisionMethodEditor
-
Each method
IDecisionMethod should provides an editor, which is a class,
implementing this interface.
- setMethod(IDecisionMethod) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- setMethod(IDecisionMethod) - Method in class toxtree.ui.tree.TreeLayout
-
- setMethods(String[]) - Method in interface toxTree.core.IDecisionMethodsList
-
- setMethods(IDecisionMethodsList) - Method in class toxtree.data.DecisionMethodsDataModule
-
- setMethods(String[]) - Method in class toxTree.tree.DecisionMethodsList
-
- setMinValue(double) - Method in interface toxTree.core.IRuleRange
-
- setMinValue(double) - Method in class toxTree.tree.rules.RuleDescriptorRange
-
- setMinValue(double) - Method in class toxTree.tree.rules.RuleManyAromaticRings
-
- setModal(boolean) - Method in class toxtree.ui.molecule.MoleculeEditAction
-
- setMode(int) - Method in class toxTree.tree.rules.RuleElements
-
- setModel(LinearQSARModel) - Method in class toxTree.qsar.LinearDiscriminantRule
-
- setModel(ListTableModel) - Method in class toxtree.ui.tree.ListPanel
-
- setModified(boolean) - Method in interface toxTree.core.IDecisionMethod
-
- setModified(boolean) - Method in class toxTree.tree.AbstractTree
-
- setModified(boolean) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setModule(String) - Method in class toxTree.apps.ToxtreeOptions
-
- setMolecule(IAtomContainer) - Method in interface toxTree.core.IDecisionResult
-
- setMolecule(IAtomContainer) - Method in interface toxTree.core.IMoleculesIterator
-
- setMolecule(IAtomContainer) - Method in class toxtree.data.DataContainer
-
- setMolecule(IAtomContainer) - Method in class toxTree.data.MoleculesIterator
-
- setMolecule(IAtomContainer) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setMolecule(IAtomContainer) - Method in class toxTree.tree.RuleResult
-
- setMolecule(IAtomContainer) - Method in class toxTree.tree.TreeResult
-
- setMolecule(IAtomContainer) - Method in class toxtree.ui.molecule.AbstractMoleculeAction
-
- setMolecule(IAtomContainer) - Method in class toxtree.ui.molecule.MoleculeEditAction
-
- setMolecule(IAtomContainer) - Method in class toxtree.ui.molecule.StructureEntryPanel
-
- setMolecules(List) - Method in interface toxTree.core.IMoleculesIterator
-
- setMolecules(List) - Method in class toxtree.data.FilteredMoleculesIterator
-
- setMolecules(List) - Method in class toxTree.data.MoleculesIterator
-
- setMultilabel(boolean) - Method in interface toxTree.core.IDecisionCategories
-
- setMultilabel(boolean) - Method in class toxTree.tree.CategoriesList
-
- setMultiLabel(boolean) - Method in class toxTree.tree.DecisionNodesFactory
-
- setMultiplier(int, Double) - Method in class toxTree.data.ListOfAtomContainers
-
- setMultiplier(IAtomContainer, Double) - Method in class toxTree.data.ListOfAtomContainers
-
- setMultiplier(IAtomContainer, Double) - Method in class toxTree.data.MoleculesFile
-
- setMultiplier(int, Double) - Method in class toxTree.data.MoleculesFile
-
- setMultipliers(Double[]) - Method in class toxTree.data.ListOfAtomContainers
-
- setMultipliers(Double[]) - Method in class toxTree.data.MoleculesFile
-
- setName(String) - Method in class com.molecularnetworks.start.BiodgeradationRules
-
- setName(String) - Method in class cramer2.CramerRulesWithExtensions
-
- setName(String) - Method in class eye.EyeIrritationRules
-
- setName(String) - Method in class mic.MICRules
-
- setName(String) - Method in class michaelacceptors.MichaelAcceptorRules
-
- setName(String) - Method in class mutant.BB_CarcMutRules
-
- setName(String) - Method in class mutant.rules.SMARTSGroup
-
- setName(String) - Method in class sicret.SicretRules
-
- setName(String) - Method in interface toxTree.core.IDecisionCategory
-
- setName(String) - Method in class toxtree.plugins.ames.AmesMutagenicityRules
-
- setName(String) - Method in class toxtree.plugins.ames.rules.SMARTSGroup
-
- setName(String) - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
-
- setName(String) - Method in class toxtree.plugins.func.FuncRules
-
- setName(String) - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
-
- setName(String) - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- setName(String) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- setName(String) - Method in class toxTree.qsar.AbstractQSARModel
-
- setName(String) - Method in class toxTree.tree.cramer.CramerRules
-
- setName(String) - Method in class toxtree.tree.cramer3.RevisedCramerDecisionTree
-
- setName(String) - Method in class toxTree.tree.DefaultCategory
-
- setNextId(Object) - Method in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
-
- setNoBranch(Observable) - Method in class toxtree.ui.tree.DecisionNodePanel
-
- setNode(int, DecisionNode) - Method in class toxTree.tree.DecisionNodesList
-
- setNode(Observable) - Method in class toxtree.ui.tree.DecisionNodePanel
-
- setNode(DecisionNode) - Method in class toxtree.ui.tree.EditTreeActions
-
- setNode(IDecisionRule) - Method in class toxtree.ui.tree.TreeDrawing
-
- setNode(DecisionNode) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- setNodes(DecisionNode[]) - Method in class toxTree.tree.DecisionNode
-
- setNodesFactory(IDecisionNodesFactory) - Method in class toxTree.tree.UserDefinedTree
-
- setNotification(boolean) - Method in class toxTree.data.ListOfAtomContainers
-
- setNotify(boolean) - Method in interface toxTree.core.IDecisionResult
-
- setNotify(boolean) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setNotify(boolean) - Method in class toxTree.tree.TreeResult
-
- setNoui(boolean) - Method in class toxTree.apps.ToxtreeOptions
-
- setNum(int) - Method in interface toxTree.core.IDecisionRule
-
- setNum(int) - Method in class toxTree.tree.AbstractRule
-
- setNum(int) - Method in class toxTree.tree.DecisionNode
-
- setObject(Object) - Method in class toxTree.qsar.AbstractQSARModel
-
- setObject(T) - Method in class toxtree.ui.tree.qsar.OptionsPanel
-
- setObjectTitle(String) - Method in class toxTree.core.ToxTreePackageEntry
-
- setOffset(long) - Method in class toxTree.io.batch.FileState
-
- setOpenChain(boolean) - Method in class toxTree.query.MolFlags
-
- setOptions(IDecisionInteractive.UserOptions) - Method in class mutant.rules.QSAR6Applicable
-
- setOptions(IDecisionInteractive.UserOptions) - Method in interface toxTree.core.IDecisionInteractive
-
- setOptions(IDecisionInteractive.UserOptions) - Method in class toxtree.plugins.ames.rules.QSAR6Applicable
-
- setOptions(IDecisionInteractive.UserOptions) - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- setOptions(IDecisionInteractive.UserOptions) - Method in class toxTree.tree.rules.UserInputRule
-
- setOptions(IDecisionInteractive.UserOptions) - Method in class toxTree.tree.UserDefinedTree
-
- setOptions(List<T>, int) - Method in class toxtree.ui.wizard.RadioBoxPanel
-
- setOriginalMolecule(IAtomContainer) - Method in class toxTree.tree.TreeResult
-
- setOutput(File) - Method in class toxTree.apps.ToxtreeOptions
-
- setOutputFile(File) - Method in class toxtree.ui.batch.BatchProcessingDialog
-
- setOutputStream(OutputStream) - Method in class toxTree.tree.AbstractTreePrinter
-
- setPackageName(String) - Method in class toxTree.core.ToxTreePackageEntry
-
- setPackageName(String) - Method in class toxtree.ui.actions.AboutAction
-
- setParameterNames(String[]) - Method in class mutant.descriptors.SubstituentsDescriptor
-
- setParameterNames(String[]) - Method in class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- setParameters(IAtomContainer) - Method in class com.molecularnetworks.start.BiodgeradationRules
-
- setParameters(IAtomContainer) - Method in class eye.EyeIrritationRules
-
- setParameters(IAtomContainer) - Method in class mic.MICRules
-
- setParameters(IAtomContainer) - Method in class michaelacceptors.MichaelAcceptorRules
-
- setParameters(IAtomContainer) - Method in class mutant.BB_CarcMutRules
-
- setParameters(Object[]) - Method in class mutant.descriptors.DescriptorIDist
-
- setParameters(Object[]) - Method in class mutant.descriptors.DescriptorMolarRefractivity
-
- setParameters(Object[]) - Method in class mutant.descriptors.DescriptorStructurePresence
-
- setParameters(Object[]) - Method in class mutant.descriptors.SubstituentsDescriptor
-
- setParameters(IAtomContainer) - Method in class sicret.SicretRules
-
- setParameters(IAtomContainer) - Method in interface toxTree.core.IDecisionMethod
-
- setParameters(Object[]) - Method in class toxTree.core.ToxTreeDescriptor
-
- setParameters(IAtomContainer) - Method in class toxtree.plugins.ames.AmesMutagenicityRules
-
- setParameters(Object[]) - Method in class toxtree.plugins.ames.descriptors.DescriptorIDist
-
- setParameters(Object[]) - Method in class toxtree.plugins.ames.descriptors.DescriptorMolarRefractivity
-
- setParameters(Object[]) - Method in class toxtree.plugins.ames.descriptors.DescriptorStructurePresence
-
- setParameters(Object[]) - Method in class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- setParameters(IAtomContainer) - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
-
- setParameters(IAtomContainer) - Method in class toxtree.plugins.func.FuncRules
-
- setParameters(IAtomContainer) - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
-
- setParameters(IAtomContainer) - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- setParameters(IAtomContainer) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- setParameters(IAtomContainer) - Method in class toxTree.tree.AbstractTree
-
Can be used to display some options before applying the rules.
- setParameters(IAtomContainer) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setParameters(IAtomContainer) - Method in class toxTree.tree.UserDefinedTree
-
- setParameters(Object[]) - Method in class toxTree.tree.UserDefinedTree
-
- setParamNames(String[]) - Method in class mutant.descriptors.DescriptorStructurePresence
-
- setParamNames(String[]) - Method in class toxtree.plugins.ames.descriptors.DescriptorStructurePresence
-
- setParentComponent(Component) - Method in class toxtree.ui.molecule.MoleculeEditAction
-
- setParentComponent(ActionMap, Component) - Method in class toxtree.ui.tree.EditTreeActions
-
- setPercentEstimated(int) - Method in interface toxTree.core.IProgressStatus
-
- setPercentEstimated(int) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setPercentEstimated(int) - Method in class toxTree.tree.ProgressStatus
-
- setPercentEstimated(int) - Method in class toxTree.tree.TreeResult
-
- setPosition(int) - Method in class mutant.descriptors.SubstituentPosition
-
- setPosition(int) - Method in class toxtree.plugins.ames.descriptors.SubstituentPosition
-
- setPredictedproperty(String) - Method in class toxTree.qsar.AbstractQSARModel
-
- setPredictedTitle(String) - Method in class toxTree.tree.stats.ConfusionMatrix
-
- setPreprocessor(IDescriptorPreprocessor) - Method in class toxTree.qsar.LinearQSARModel
-
- setPriority(int) - Method in class mutant.categories.MutantCategory
-
- setPriority(int) - Method in interface toxTree.core.IDecisionMethodPrority
-
- setPriority(int) - Method in class toxtree.plugins.ames.categories.AmesMutagenicityCategory
-
- setPriority(int) - Method in class toxTree.tree.AbstractTree
-
- setPriority(int) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setPriority(int) - Method in class toxTree.tree.TreeResult
-
- setProducts(String, IAtomContainerSet) - Method in class toxtree.ui.metabolites.MetabolitesFrame
-
- setProducts(String, IAtomContainerSet) - Method in class toxtree.ui.metabolites.MetabolitesPanel
-
- setProperties(Map) - Method in class toxTree.data.AbstractFilter
-
- setProperties(Map) - Method in interface toxTree.data.IObjectFilter
-
- setProperties(Map<Object, Object>) - Method in class toxTree.data.ListOfAtomContainers
-
- setProperties(Map) - Method in class toxTree.data.ObjectPropertyFilter
-
- setProperty(Object) - Method in interface toxTree.core.IRuleRange
-
- setProperty(Object) - Method in interface toxTree.core.IRuleValue
-
- setProperty(String, Object) - Method in class toxTree.data.AbstractFilter
-
- setProperty(String, Object) - Method in interface toxTree.data.IObjectFilter
-
- setProperty(Object, Object) - Method in class toxTree.data.ListOfAtomContainers
-
- setProperty(int, Object, Object) - Method in class toxTree.data.MoleculesFile
-
- setProperty(String, Object) - Method in class toxTree.data.ObjectPropertyFilter
-
- setProperty(Object) - Method in class toxTree.tree.rules.RuleDescriptorRange
-
- setProperty(Object) - Method in class toxTree.tree.rules.RuleManyAromaticRings
-
- setProperty(Object) - Method in class toxTree.tree.rules.RuleMolecularMassRange
-
- setProperty(double) - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- setPropertyMaxValue(String) - Method in class toxtree.ui.tree.rules.RuleRangeEditor
-
- setPropertyMinValue(String) - Method in class toxtree.ui.tree.rules.RuleRangeEditor
-
- setPropertyName(Object) - Method in class toxTree.data.SortedPropertyList
-
- setPropertyName(String) - Method in exception toxTree.exceptions.DRulePropertyNotAvailable
-
- setPropertyName(String) - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- setPropertyName(String) - Method in class toxtree.ui.tree.rules.RulePropertyEditor
-
- setPropertyName(String) - Method in class toxtree.ui.tree.rules.RuleRangeEditor
-
- setPropertyUnits(String) - Method in class toxTree.tree.rules.RuleVerifyProperty
-
- setPropertyValue(String) - Method in class toxtree.ui.tree.rules.RulePropertyEditor
-
- setQuery(QueryAtomContainers) - Method in class toxTree.tree.rules.RuleSubstructures
-
- setRank(int) - Method in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
-
- setReading() - Method in interface toxTree.core.IMoleculesIterator
-
- setReading() - Method in class toxTree.data.MoleculesIterator
-
- setResidualID(IAtomContainer, IAtomContainerSet) - Static method in class toxTree.query.SimpleReactions
-
- setResidues(IAtomContainerSet) - Method in class toxTree.query.MolFlags
-
- setResiduesIDVisible(boolean) - Method in class com.molecularnetworks.start.BiodgeradationRules
-
- setResiduesIDVisible(boolean) - Method in class cramer2.CramerRulesWithExtensions
-
- setResiduesIDVisible(boolean) - Method in class eye.EyeIrritationRules
-
- setResiduesIDVisible(boolean) - Method in class mic.MICRules
-
- setResiduesIDVisible(boolean) - Method in class michaelacceptors.MichaelAcceptorRules
-
- setResiduesIDVisible(boolean) - Method in class mutant.BB_CarcMutRules
-
- setResiduesIDVisible(boolean) - Method in class sicret.SicretRules
-
- setResiduesIDVisible(boolean) - Method in class toxtree.plugins.ames.AmesMutagenicityRules
-
- setResiduesIDVisible(boolean) - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
-
- setResiduesIDVisible(boolean) - Method in class toxtree.plugins.func.FuncRules
-
- setResiduesIDVisible(boolean) - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
-
- setResiduesIDVisible(boolean) - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- setResiduesIDVisible(boolean) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- setResiduesIDVisible(boolean) - Method in class toxTree.tree.cramer.CramerRules
-
- setResult(IDecisionResult, IAtomContainer) - Method in class toxTree.apps.toxForest.ToxForestData
-
- setResult(IDecisionResult, IAtomContainer) - Method in class toxtree.data.DecisionMethodData
-
- setResult(boolean) - Method in class toxTree.tree.RuleResult
-
- setResult(int) - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
-
- setResultName(String) - Method in class mutant.descriptors.DescriptorStructurePresence
-
- setResultName(String) - Method in class toxtree.plugins.ames.descriptors.DescriptorStructurePresence
-
- setRing(boolean) - Method in class mutant.descriptors.SubstituentPosition
-
- setRing(boolean) - Method in class toxtree.plugins.ames.descriptors.SubstituentPosition
-
- setRingQuery(QueryAtomContainer) - Method in class mutant.descriptors.SubstituentExtractor
-
- setRingQuery(QueryAtomContainer) - Method in class mutant.descriptors.SubstituentsDescriptor
-
- setRingQuery(QueryAtomContainer) - Method in class toxtree.plugins.ames.descriptors.SubstituentExtractor
-
- setRingQuery(QueryAtomContainer) - Method in class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- setRingset(IRingSet) - Method in class toxTree.query.MolFlags
-
- setRule(IDecisionRule) - Method in interface toxTree.core.IDecisionRuleEditor
-
- setRule(IDecisionRule) - Method in class toxTree.tree.DecisionNode
-
Sets rule
- setRule(IDecisionRule) - Method in class toxTree.tree.RuleResult
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.actions.AbstractRuleAction
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.actions.EditRuleAction
-
- setRule(IDecisionRule) - Method in interface toxtree.ui.tree.actions.IRuleAction
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.EditTreeActions
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.rules.RuleEditor
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.rules.RuleMoleculeEditAction
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.rules.RulePanel
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.rules.RuleStructuresPanel
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.rules.SubstructureRulePanel
-
- setRule(IDecisionRule) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- setRuleActions(ActionMap) - Method in class toxtree.ui.tree.EditTreeActions
-
- setRuleResults(ArrayList<RuleResult>) - Method in class toxTree.tree.TreeResult
-
- setRules(IDecisionMethod) - Method in class toxTree.apps.toxForest.ToxForestDataModule
-
- setRules(String[]) - Method in interface toxTree.core.IDecisionRuleList
-
- setRules(IDecisionMethod) - Method in class toxtree.data.DecisionMethodsDataModule
-
- setRules(IDecisionMethod) - Method in class toxtree.data.ToxTreeModule
-
- setRules(String[]) - Method in class toxTree.tree.AbstractTree
-
- setRules(IDecisionRuleList) - Method in class toxTree.tree.AbstractTree
-
- setRules(String[]) - Method in class toxtree.tree.cramer3.TreeSpecification
-
- setRules(String[]) - Method in class toxTree.tree.DecisionNodesList
-
- setRules(String[]) - Method in class toxTree.tree.RulesList
-
Sets RulesList given the names of
IDecisionRule classes
Example :
setRules(new String[] {
"toxTree.tree.rules.RuleSubstructure",
"toxTree.tree.rules.RuleAromatic"});
Rules are created from corresponding class names
- setSaveStateFrequency(int) - Method in class toxTree.io.batch.BatchProcessing
-
BatchProcessing saves its state on each saveStateFrequency records
- setScale(double[]) - Method in class toxTree.qsar.LinearPreprocessor
-
- setSelected(IDecisionCategory) - Method in interface toxTree.core.IDecisionCategories
-
- setSelected(boolean) - Method in interface toxTree.core.IDecisionCategory
-
- setSelected(IDecisionCategory) - Method in class toxTree.tree.CategoriesList
-
- setSelected(boolean) - Method in class toxTree.tree.DefaultCategory
-
- setSelectedIndex(int) - Method in class toxTree.data.MoleculesFile
-
- setSelectedIndex(int) - Method in class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
-
- setSelectedObject(Object, int) - Method in class toxtree.ui.tree.ListPanel
-
- setSelectedObject(Object) - Method in class toxtree.ui.wizard.DecisionNodeWizard
-
- setSetPropertyEditable(boolean) - Method in class toxtree.ui.tree.rules.RuleRangeEditor
-
- setSilent(boolean) - Method in interface toxTree.core.IDecisionResult
-
- setSilent(boolean) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setSilent(boolean) - Method in class toxTree.tree.RuleResult
-
- setSilent(boolean) - Method in class toxTree.tree.TreeResult
-
- setSilentvalue(boolean) - Method in class toxTree.tree.rules.UserInputRule
-
- setSkipRule(boolean) - Method in class mutant.rules.QSAR6Applicable
-
- setSkipRule(boolean) - Method in class toxtree.plugins.ames.rules.QSAR6Applicable
-
- setSMARTS(String) - Method in class mutant.descriptors.DescriptorStructurePresence
-
- setSmarts(String) - Method in class mutant.rules.SMARTSGroup
-
- setSMARTS(String) - Method in class toxtree.plugins.ames.descriptors.DescriptorStructurePresence
-
- setSmarts(String) - Method in class toxtree.plugins.ames.rules.SMARTSGroup
-
- setSmartsPatternFactory(ISmartsPatternFactory) - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
-
- setSmartsPatterns(Hashtable<String, ISmartsPattern<T>>) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- setSmirks(String[][]) - Method in class toxtree.tree.Reactor
-
String[][] smirks = {
{ "Aliphatic hydroxylation", "[C;X4:1][H:2]>>[C:1][O][H:2]" },
{ "Aromatic hydroxylation", "[c:1][H:2]>>[c:1][O][H:2]" }
}
- setStartIndex(int) - Method in class toxtree.ui.wizard.DecisionNodeWizard
-
- setStatus(int) - Method in class toxTree.io.batch.BatchProcessing
-
- setStorage(ArrayList<IDecisionCategory>) - Method in class toxTree.tree.CategoriesList
-
- setSubstituentNumber(String, IAtomContainer, int, SubstituentPosition) - Static method in class mutant.descriptors.SubstituentExtractor
-
- setSubstituentNumber(String, IAtom, SubstituentPosition) - Static method in class mutant.descriptors.SubstituentExtractor
-
- setSubstituentNumber(String, IAtomContainer, int, SubstituentPosition) - Static method in class toxtree.plugins.ames.descriptors.SubstituentExtractor
-
- setSubstituentNumber(String, IAtom, SubstituentPosition) - Static method in class toxtree.plugins.ames.descriptors.SubstituentExtractor
-
- setSubstructure(int, IAtomContainer) - Method in interface toxTree.core.IRuleSubstructures
-
sets substructure at index
- setSubstructure(int, IAtomContainer) - Method in class toxTree.tree.rules.RuleSubstructures
-
- setSubstructure(String, String, boolean) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- setSubstructure(String, String) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- setSubstructure(String, String) - Method in interface toxTree.tree.rules.smarts.IRuleSMARTSubstructures
-
- setTable(Map) - Method in class toxtree.ui.HashtableModel
-
- setTableModel(AtomContainerPropertyTableModel) - Method in class toxtree.ui.molecule.PropertyPanel
-
- setTag(Object) - Method in interface toxTree.data.IPropertyFilter
-
- setTag(Object) - Method in class toxTree.data.ObjectPropertyFilter
-
- setThreshold(String) - Method in interface toxTree.core.IDecisionCategory
-
- setThreshold(double) - Method in class toxTree.qsar.LinearDiscriminantRule
-
- setThreshold(String) - Method in class toxTree.tree.DefaultCategory
-
- setTitle(String) - Method in class sicret.rules.RuleHasOnlyC_H_O
-
- setTitle(String) - Method in class sicret.rules.RuleHasOnlyC_H_O_N_Halogen
-
- setTitle(String) - Method in interface toxTree.core.IDecisionMethod
-
- setTitle(String) - Method in interface toxTree.core.IDecisionRule
-
Sets rule name
- setTitle(String) - Method in class toxtree.plugins.func.rules.FG
-
- setTitle(String) - Method in class toxTree.tree.AbstractRule
-
- setTitle(String) - Method in class toxTree.tree.AbstractTree
-
sets decision tree title (e.g.
- setTitle(String) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setTitle(String) - Method in class toxTree.tree.cramer.RuleHasOtherThanC_H_O_N_S2
-
- setTitle(String) - Method in class toxTree.tree.DecisionNode
-
- setTitle(String) - Method in class toxtree.ui.tree.categories.CategoryPanel
-
- setTitle(String) - Method in class toxtree.ui.tree.rules.RuleEditor
-
- setTitle(String) - Method in class toxtree.ui.tree.ToxTreeEditorPanel
-
- setTransitions(int[][]) - Method in class toxTree.tree.AbstractTree
-
- setTransitions(int[][]) - Method in class toxtree.tree.cramer3.TreeSpecification
-
{if no go to, if yes go to, assign if no, assign if yes}
- setTransitions(IDecisionCategories, int[][]) - Method in class toxTree.tree.DecisionNodesList
-
- setTransitions(int[][]) - Method in class toxTree.tree.UserDefinedTree
-
- setTranslation(double[]) - Method in class toxTree.qsar.LinearPreprocessor
-
- setTree(IDecisionMethod) - Method in class toxtree.ui.tree.actions.AbstractTreeAction
-
- setTree(IDecisionMethod) - Method in interface toxtree.ui.tree.actions.ITreeAction
-
- setTreeActions(ActionMap) - Method in class toxtree.ui.tree.EditTreeActions
-
- setTreeNodeActions(ActionMap) - Method in class toxtree.ui.tree.EditTreeActions
-
- setUseCache(boolean) - Method in class toxTree.tree.rules.LookupFile
-
- setValue(double) - Method in interface toxTree.core.IRuleValue
-
- setValue(Object) - Method in class toxTree.data.ObjectPropertyFilter
-
- setValueAt(Object, int, int) - Method in class toxtree.ui.HashtableModel
-
- setVisited(boolean) - Method in class toxTree.tree.DecisionNode
-
- setVisited(IDecisionRule, boolean) - Method in class toxtree.ui.tree.TreeLayout
-
- setVisualComponent(Component) - Method in class toxtree.ui.wizard.EditorPanel
-
- setWeb(Boolean) - Method in interface toxTree.core.IDecisionMethod
-
- setWeb(Boolean) - Method in interface toxTree.core.IDecisionResult
-
- setWeb(Boolean) - Method in class toxTree.tree.AbstractTree
-
- setWeb(Boolean) - Method in class toxTree.tree.BatchDecisionResultsList
-
- setWeb(boolean) - Method in class toxTree.tree.RuleResult
-
- setWeb(Boolean) - Method in class toxTree.tree.TreeResult
-
- setWeights(double[]) - Method in class toxTree.qsar.LinearQSARModel
-
- setWriter(Writer) - Method in class toxTree.io.PDFWriter
-
- setWriter(OutputStream) - Method in class toxTree.io.PDFWriter
-
- setWriter(Writer) - Method in class toxTree.tree.AbstractTreeWriter
-
- setWriting() - Method in interface toxTree.core.IMoleculesIterator
-
- setWriting() - Method in class toxTree.data.MoleculesIterator
-
- setYesBranch(Observable) - Method in class toxtree.ui.tree.DecisionNodePanel
-
- sg - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
-
- sg - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
-
- ShiffBaseAlerts - Class in toxtree.plugins.dnabinding.categories
-
Shiff base
- ShiffBaseAlerts() - Constructor for class toxtree.plugins.dnabinding.categories.ShiffBaseAlerts
-
- ShiffBaseAlerts - Class in toxtree.plugins.proteinbinding.categories
-
Shiff base
- ShiffBaseAlerts() - Constructor for class toxtree.plugins.proteinbinding.categories.ShiffBaseAlerts
-
- ShiffBaseAlerts - Class in toxtree.plugins.skinsensitisation.categories
-
Shiff base
- ShiffBaseAlerts() - Constructor for class toxtree.plugins.skinsensitisation.categories.ShiffBaseAlerts
-
- ShiffBaseRule - Class in toxtree.plugins.dnabinding.rules
-
Shiff base
- ShiffBaseRule() - Constructor for class toxtree.plugins.dnabinding.rules.ShiffBaseRule
-
- ShiffBaseRule - Class in toxtree.plugins.proteinbinding.rules
-
Shiff base
- ShiffBaseRule() - Constructor for class toxtree.plugins.proteinbinding.rules.ShiffBaseRule
-
- ShiffBaseRule - Class in toxtree.plugins.skinsensitisation.rules
-
Shiff base
- ShiffBaseRule() - Constructor for class toxtree.plugins.skinsensitisation.rules.ShiffBaseRule
-
- shortName - Variable in class toxtree.plugins.dnabinding.rules.DNABindingRule
-
- shortName - Variable in class toxtree.plugins.proteinbinding.rules.ProteinBindingRule
-
- shortName - Variable in class toxtree.plugins.skinsensitisation.rules.SkinSensitisationRule
-
- showCategory(IDecisionCategory) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- showColors - Variable in class toxTree.ui.tree.categories.CategoriesRenderer
-
- ShowFilteredFileAction - Class in toxtree.ui.molecule
-
- ShowFilteredFileAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.molecule.ShowFilteredFileAction
-
- ShowFilteredFileAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.molecule.ShowFilteredFileAction
-
- ShowFilteredFileAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.molecule.ShowFilteredFileAction
-
- showHelp(String) - Method in class toxtree.ui.actions.HelpAction
-
- showHelp() - Method in class toxtree.ui.tree.TreePrefuse
-
- showMessage(String, String) - Method in class toxtree.data.ActionList
-
- showMetabolites() - Method in class toxtree.data.DataModule
-
- showMetabolites(RuleResult) - Method in class toxtree.data.ToxTreeModule
-
- showModalDialog() - Method in class toxtree.ui.wizard.WizardWrapper
-
- showMsg(String, String) - Static method in class toxtree.data.ActionList
-
- showPopup(MouseEvent) - Method in class toxtree.ui.tree.JCustomTreeComponent
-
- showPopupMenu(MouseEvent) - Method in class toxtree.ui.tree.TreeEditorPanel
-
- sicret - package sicret
-
Class
SicretRules is the implementation of BfR rules for estimating skin irritation and corrosion potential.
- sicret.categories - package sicret.categories
-
- sicret.rules - package sicret.rules
-
- SicretRules - Class in sicret
-
Decision tree for estimating skin irritation and corrosion potential.
- SicretRules() - Constructor for class sicret.SicretRules
-
- sidechain_ketone() - Static method in class toxTree.query.FunctionalGroups
-
- silent - Variable in class toxTree.tree.RuleResult
-
- SimpleReactions - Class in toxTree.query
-
Handles hydrolysis and couple of metabolic reactions necessary to implement
Cramer rules Intended to be a general class to perform reactions on arbitrary
molecules ...
- SimpleReactions() - Constructor for class toxTree.query.SimpleReactions
-
- SimpleTreePrinter - Class in toxTree.tree
-
- SimpleTreePrinter() - Constructor for class toxTree.tree.SimpleTreePrinter
-
- SimpleTreePrinter(OutputStream) - Constructor for class toxTree.tree.SimpleTreePrinter
-
- SimpleTreePrinter(Writer) - Constructor for class toxTree.tree.SimpleTreePrinter
-
- singleFusedNonAromaticCarbocyclicRing(IAtomContainer, IRingSet) - Method in class toxTree.tree.cramer.Rule32
-
- singleFusedNonAromaticCarbocyclicRing(IAtomContainer, IRingSet) - Method in class toxTree.tree.cramer.RuleOnlyFuncGroupsQ30
-
- singleFusedRing(IAtomContainer, IRingSet) - Static method in class toxTree.query.FunctionalGroups
-
- SingleOrDoubleQueryBond - Class in toxTree.query
-
TODO add description
- SingleOrDoubleQueryBond(IChemObjectBuilder) - Constructor for class toxTree.query.SingleOrDoubleQueryBond
-
- SingleOrDoubleQueryBond(IQueryAtom, IQueryAtom, IChemObjectBuilder) - Constructor for class toxTree.query.SingleOrDoubleQueryBond
-
- SitesHigherRank - Class in toxtree.plugins.smartcyp.categories
-
- SitesHigherRank() - Constructor for class toxtree.plugins.smartcyp.categories.SitesHigherRank
-
- SitesRank1 - Class in toxtree.plugins.smartcyp.categories
-
- SitesRank1() - Constructor for class toxtree.plugins.smartcyp.categories.SitesRank1
-
- SitesRank2 - Class in toxtree.plugins.smartcyp.categories
-
- SitesRank2() - Constructor for class toxtree.plugins.smartcyp.categories.SitesRank2
-
- SitesRank3 - Class in toxtree.plugins.smartcyp.categories
-
- SitesRank3() - Constructor for class toxtree.plugins.smartcyp.categories.SitesRank3
-
- size() - Method in interface toxTree.core.IDecisionCategories
-
- size() - Method in class toxTree.tree.CategoriesList
-
- size() - Method in class toxTree.tree.DecisionMethodsList
-
- size() - Method in class toxTree.tree.DecisionNodesList
-
- size() - Method in interface toxTree.tree.rules.ILookupFile
-
- size() - Method in class toxTree.tree.rules.InChILookupFile
-
- size() - Method in class toxTree.tree.rules.LookupFile
-
- size() - Method in class toxTree.tree.RulesList
-
- SkinSensitisationAlerts - Enum in toxtree.plugins.skinsensitisation.categories
-
- SkinSensitisationCategory - Class in toxtree.plugins.skinsensitisation.categories
-
- SkinSensitisationCategory(SkinSensitisationAlerts) - Constructor for class toxtree.plugins.skinsensitisation.categories.SkinSensitisationCategory
-
- SkinSensitisationPlugin - Class in toxtree.plugins.skinsensitisation
-
Skin sensitisation
- SkinSensitisationPlugin() - Constructor for class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
-
- SkinSensitisationRule - Class in toxtree.plugins.skinsensitisation.rules
-
Parent class for all skin sens rules
- SkinSensitisationRule(SkinSensitisationAlerts) - Constructor for class toxtree.plugins.skinsensitisation.rules.SkinSensitisationRule
-
- SkinSensitisationTreeResult - Class in toxtree.plugins.skinsensitisation.rules
-
- SkinSensitisationTreeResult() - Constructor for class toxtree.plugins.skinsensitisation.rules.SkinSensitisationTreeResult
-
- SMARTCYPPlugin - Class in toxtree.plugins.smartcyp
-
- SMARTCYPPlugin() - Constructor for class toxtree.plugins.smartcyp.SMARTCYPPlugin
-
- SMARTCYPRuleHigherRank - Class in toxtree.plugins.smartcyp.rules
-
- SMARTCYPRuleHigherRank() - Constructor for class toxtree.plugins.smartcyp.rules.SMARTCYPRuleHigherRank
-
- SMARTCYPRuleRank1 - Class in toxtree.plugins.smartcyp.rules
-
- SMARTCYPRuleRank1() - Constructor for class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
-
- SMARTCYPRuleRank1(int) - Constructor for class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
-
- SMARTCYPRuleRank2 - Class in toxtree.plugins.smartcyp.rules
-
- SMARTCYPRuleRank2() - Constructor for class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank2
-
- SMARTCYPRuleRank3 - Class in toxtree.plugins.smartcyp.rules
-
- SMARTCYPRuleRank3() - Constructor for class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank3
-
- SMARTCypTreeResult - Class in toxtree.plugins.smartcyp
-
- SMARTCypTreeResult() - Constructor for class toxtree.plugins.smartcyp.SMARTCypTreeResult
-
- SmartElementsList - Class in toxTree.core
-
Same as HashSet, but understands "X" as halogen elements.
- SmartElementsList() - Constructor for class toxTree.core.SmartElementsList
-
- smarts - Static variable in class cramer2.rules.RuleBenzeneAnalogues
-
- smarts - Static variable in class cramer2.rules.RuleDivalentSulphur
-
- smarts - Static variable in class eye.rules.Rule33
-
- smarts - Static variable in class mic.rules.SA34
-
- smarts - Variable in class mutant.descriptors.DescriptorIDist
-
- smarts - Variable in class mutant.rules.SMARTSGroup
-
- smarts - Variable in class toxtree.plugins.ames.descriptors.DescriptorIDist
-
- smarts - Variable in class toxtree.plugins.ames.rules.SMARTSGroup
-
- smarts - Variable in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_1
-
- smarts - Variable in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_1_1
-
- smarts - Variable in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_2_1
-
- smarts - Variable in class verhaar.rules.Rule151
-
- smarts - Variable in class verhaar.rules.Rule152
-
- smarts - Variable in class verhaar.rules.Rule153
-
- smarts - Variable in class verhaar.rules.Rule154
-
- smarts - Variable in class verhaar.rules.Rule171
-
- smarts - Variable in class verhaar.rules.Rule24
-
- smarts - Variable in class verhaar.rules.Rule31
-
- smarts - Variable in class verhaar.rules.Rule32
-
- smarts - Variable in class verhaar.rules.Rule33
-
- smarts - Variable in class verhaar.rules.Rule34
-
- smarts - Variable in class verhaar.rules.Rule35
-
- smarts - Variable in class verhaar.rules.Rule36
-
- smarts - Variable in class verhaar.rules.Rule37
-
- smarts - Variable in class verhaar.rules.Rule38
-
- SMARTSGroup - Class in mutant.rules
-
- SMARTSGroup() - Constructor for class mutant.rules.SMARTSGroup
-
- SMARTSGroup - Class in toxtree.plugins.ames.rules
-
- SMARTSGroup() - Constructor for class toxtree.plugins.ames.rules.SMARTSGroup
-
- SMARTSgroups - Class in mutant.rules
-
- SMARTSgroups() - Constructor for class mutant.rules.SMARTSgroups
-
- SMARTSgroups - Class in toxtree.plugins.ames.rules
-
- SMARTSgroups() - Constructor for class toxtree.plugins.ames.rules.SMARTSgroups
-
- SmartsPanelEditor - Class in toxtree.ui.tree.rules
-
- SmartsPanelEditor() - Constructor for class toxtree.ui.tree.rules.SmartsPanelEditor
-
- SmartsPanelEditor(String, String, ISmartsPatternFactory) - Constructor for class toxtree.ui.tree.rules.SmartsPanelEditor
-
- smartsPattern - Variable in class eye.rules.Rule13_AliphaticMonoalcohols
-
- smartsPattern - Variable in class toxtree.ui.tree.rules.SmartsPanelEditor
-
- smartsPatternFactory - Variable in class toxtree.ui.tree.rules.SmartsPanelEditor
-
- smartsPatterns - Variable in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
-
- SMARTSRuleEditor - Class in toxtree.ui.tree.rules
-
- SMARTSRuleEditor(AbstractRuleSmartSubstructure) - Constructor for class toxtree.ui.tree.rules.SMARTSRuleEditor
-
- SMARTSRuleEditor() - Constructor for class toxtree.ui.tree.rules.SMARTSRuleEditor
-
- SMARTSTree - Class in toxTree.tree.demo
-
- SMARTSTree() - Constructor for class toxTree.tree.demo.SMARTSTree
-
- SMI_INDEX - Static variable in class toxTree.io.batch.ChemObjectBatchProcessing
-
- smigen - Variable in class toxTree.data.MoleculesFile
-
- SmilesEntryPanel - Class in toxtree.ui.molecule
-
- SmilesEntryPanel() - Constructor for class toxtree.ui.molecule.SmilesEntryPanel
-
- smilesPanel - Variable in class toxtree.ui.molecule.TopPanel
-
- smirks - Static variable in class toxtree.tree.cramer3.rules.RuleQ18_AI
-
- smp - Variable in class mutant.descriptors.DescriptorIsAniline
-
- smp - Variable in class toxtree.plugins.ames.descriptors.DescriptorIsAniline
-
- smrkMan - Variable in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
-
- smrkMan - Variable in class toxtree.tree.Reactor
-
- SN1Alerts - Class in toxtree.plugins.dnabinding.categories
-
Substrate has structural alerts for Nucleophilic Aromatic Substitution
- SN1Alerts() - Constructor for class toxtree.plugins.dnabinding.categories.SN1Alerts
-
- SN1Rule - Class in toxtree.plugins.dnabinding.rules
-
SNAR
- SN1Rule() - Constructor for class toxtree.plugins.dnabinding.rules.SN1Rule
-
- SN2Alerts - Class in toxtree.plugins.dnabinding.categories
-
second order nucleophilic aliphatic substitution reaction
- SN2Alerts() - Constructor for class toxtree.plugins.dnabinding.categories.SN2Alerts
-
- SN2Alerts - Class in toxtree.plugins.proteinbinding.categories
-
second order nucleophilic aliphatic substitution reaction
- SN2Alerts() - Constructor for class toxtree.plugins.proteinbinding.categories.SN2Alerts
-
- SN2Alerts - Class in toxtree.plugins.skinsensitisation.categories
-
second order nucleophilic aliphatic substitution reaction
- SN2Alerts() - Constructor for class toxtree.plugins.skinsensitisation.categories.SN2Alerts
-
- SN2Rule - Class in toxtree.plugins.dnabinding.rules
-
SN2
- SN2Rule() - Constructor for class toxtree.plugins.dnabinding.rules.SN2Rule
-
- SN2Rule - Class in toxtree.plugins.proteinbinding.rules
-
SN2
- SN2Rule() - Constructor for class toxtree.plugins.proteinbinding.rules.SN2Rule
-
- SN2Rule - Class in toxtree.plugins.skinsensitisation.rules
-
SN2
- SN2Rule() - Constructor for class toxtree.plugins.skinsensitisation.rules.SN2Rule
-
- SNArAlerts - Class in toxtree.plugins.proteinbinding.categories
-
Substrate has structural alerts for Nucleophilic Aromatic Substitution
- SNArAlerts() - Constructor for class toxtree.plugins.proteinbinding.categories.SNArAlerts
-
- SNArAlerts - Class in toxtree.plugins.skinsensitisation.categories
-
Substrate has structural alerts for Nucleophilic Aromatic Substitution
- SNArAlerts() - Constructor for class toxtree.plugins.skinsensitisation.categories.SNArAlerts
-
- SNARRule - Class in toxtree.plugins.proteinbinding.rules
-
SNAR
- SNARRule() - Constructor for class toxtree.plugins.proteinbinding.rules.SNARRule
-
- SNARRule - Class in toxtree.plugins.skinsensitisation.rules
-
SNAR
- SNARRule() - Constructor for class toxtree.plugins.skinsensitisation.rules.SNARRule
-
- sort(boolean) - Method in class toxTree.data.SortedPropertyList
-
- sort() - Method in class toxTree.tree.stats.ConfusionMatrix
-
- sortAtomContainers(Comparator<IAtomContainer>) - Method in class toxTree.data.ListOfAtomContainers
-
- sortAtomContainers(Comparator<IAtomContainer>) - Method in class toxTree.data.MoleculesFile
-
- sortBy(Object, boolean) - Method in class toxTree.data.MoleculesFile
-
- sortedProperties - Variable in class toxTree.data.MoleculesFile
-
- SortedPropertyList - Class in toxTree.data
-
- SortedPropertyList(Object) - Constructor for class toxTree.data.SortedPropertyList
-
- splitPanel - Variable in class toxTree.apps.CompoundMethodApplication
-
- SpringUtilities - Class in toxtree.ui
-
- SpringUtilities() - Constructor for class toxtree.ui.SpringUtilities
-
- sr - Variable in class mutant.rules.RuleAromaticDiazo
-
- sr - Variable in class toxtree.plugins.ames.rules.RuleAromaticDiazo
-
- ssotoken - Variable in class toxtree.lookup.RemoteLookup
-
- start() - Method in class toxTree.io.batch.BatchProcessing
-
- start() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
-
- start() - Method in interface toxTree.io.batch.IBatchProcessing
-
- start() - Method in class toxTree.io.batch.ToxTreeBatchProcessing
-
- startBatch(File) - Method in class toxtree.data.ToxTreeActions
-
- startBatch(File) - Method in class toxtree.ui.actions.BatchAction
-
- startIndex - Variable in class toxtree.ui.wizard.DecisionNodeWizard
-
- stateChanged(IChemObjectChangeEvent) - Method in class toxTree.data.MoleculesFile
-
- status - Variable in class toxTree.data.MoleculesIterator
-
- status - Variable in class toxTree.io.batch.BatchProcessing
-
- status - Variable in class toxTree.tree.BatchDecisionResultsList
-
- status - Variable in class toxTree.tree.TreeResult
-
- status - Variable in class toxtree.ui.tree.rules.SmartsPanelEditor
-
- STATUS_ABORTED - Static variable in class toxTree.io.batch.BatchProcessing
-
- STATUS_FINISHED - Static variable in class toxTree.io.batch.BatchProcessing
-
- STATUS_NOTINITIALIZED - Static variable in class toxTree.io.batch.BatchProcessing
-
- STATUS_NOTSTARTED - Static variable in class toxTree.io.batch.BatchProcessing
-
- STATUS_PAUSED - Static variable in class toxTree.io.batch.BatchProcessing
-
- STATUS_RUNNING - Static variable in class toxTree.io.batch.BatchProcessing
-
- StatusBar - Class in toxtree.ui
-
- StatusBar() - Constructor for class toxtree.ui.StatusBar
-
- statusMsg - Static variable in class toxTree.io.batch.BatchProcessing
-
- stericallyHindered() - Static method in class toxTree.query.FunctionalGroups
-
- storage - Variable in class toxTree.tree.CategoriesList
-
- strucEntryPanel - Variable in class toxTree.apps.CompoundMethodApplication
-
- StructureAlert - Class in toxTree.tree.rules
-
- StructureAlert() - Constructor for class toxTree.tree.rules.StructureAlert
-
- StructureAlertAmbit - Class in toxTree.tree.rules
-
- StructureAlertAmbit() - Constructor for class toxTree.tree.rules.StructureAlertAmbit
-
- StructureAlertCDK - Class in toxTree.tree.rules
-
- StructureAlertCDK() - Constructor for class toxTree.tree.rules.StructureAlertCDK
-
- StructureEntryPanel - Class in toxtree.ui.molecule
-
This is an abstract class to be used as structure entry (by SMILES and other
means)
- StructureEntryPanel() - Constructor for class toxtree.ui.molecule.StructureEntryPanel
-
- structurefeatures.rules - package structurefeatures.rules
-
- structurePanel(Color, Color) - Method in class toxtree.ui.tree.molecule.CompoundPanel
-
- subList(int, int) - Method in class toxTree.tree.CategoriesList
-
- subList(int, int) - Method in class toxTree.tree.DecisionMethodsList
-
- subList(int, int) - Method in class toxTree.tree.DecisionNodesList
-
- subList(int, int) - Method in class toxTree.tree.RulesList
-
- SubstituentExtractor - Class in mutant.descriptors
-
- SubstituentExtractor() - Constructor for class mutant.descriptors.SubstituentExtractor
-
- SubstituentExtractor(QueryAtomContainer) - Constructor for class mutant.descriptors.SubstituentExtractor
-
- SubstituentExtractor - Class in toxtree.plugins.ames.descriptors
-
- SubstituentExtractor() - Constructor for class toxtree.plugins.ames.descriptors.SubstituentExtractor
-
- SubstituentExtractor(QueryAtomContainer) - Constructor for class toxtree.plugins.ames.descriptors.SubstituentExtractor
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class mutant.rules.SA20_nogen
-
Only counts halogens directly connected to the ring and returns true
always.
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxTree.tree.cramer.RuleHeterocyclicComplexSubstituents
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxTree.tree.cramer.RuleOnlyFuncGroupsQ30
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxTree.tree.cramer.RuleRingComplexSubstituents30
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxtree.tree.cramer3.rules.RuleQ11
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxtree.tree.cramer3.rules.RuleQ14_A
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxtree.tree.cramer3.rules.RuleQ14_B
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxtree.tree.cramer3.rules.RuleQ25
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxtree.tree.cramer3.rules.RuleQ26
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxtree.tree.cramer3.rules.RuleRingsSMARTSSubstituents
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxTree.tree.rules.RuleRingAllowedSubstituents
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class toxTree.tree.rules.RuleRingSubstituents
-
returns true if the substituent is allowed and false if it is forbidden
to be implemented by the inheriting class
- substituentIsAllowed(IAtomContainer, int[]) - Method in class verhaar.rules.Rule143
-
- substituentIsAllowed(IAtomContainer, int[]) - Method in class verhaar.rules.Rule21
-
- SubstituentPosition - Class in mutant.descriptors
-
- SubstituentPosition(int, boolean) - Constructor for class mutant.descriptors.SubstituentPosition
-
- SubstituentPosition - Class in toxtree.plugins.ames.descriptors
-
- SubstituentPosition(int, boolean) - Constructor for class toxtree.plugins.ames.descriptors.SubstituentPosition
-
- substituents - Static variable in class mic.rules.SA2
-
- substituents - Static variable in class mutant.rules.SA2_gen
-
- substituents - Static variable in class toxtree.plugins.ames.rules.SA2_gen
-
- SubstituentsDescriptor - Class in mutant.descriptors
-
- SubstituentsDescriptor() - Constructor for class mutant.descriptors.SubstituentsDescriptor
-
- SubstituentsDescriptor(QueryAtomContainer) - Constructor for class mutant.descriptors.SubstituentsDescriptor
-
- SubstituentsDescriptor - Class in toxtree.plugins.ames.descriptors
-
- SubstituentsDescriptor() - Constructor for class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- SubstituentsDescriptor(QueryAtomContainer) - Constructor for class toxtree.plugins.ames.descriptors.SubstituentsDescriptor
-
- substructureEditAction - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
-
- SubstructureFromListAction - Class in toxtree.ui.tree.actions
-
Adds a new substructure from a list of predefined substructures
- SubstructureFromListAction(IDecisionRule) - Constructor for class toxtree.ui.tree.actions.SubstructureFromListAction
-
- SubstructureFromListAction(IDecisionRule, String) - Constructor for class toxtree.ui.tree.actions.SubstructureFromListAction
-
- SubstructureFromListAction(IDecisionRule, String, Icon) - Constructor for class toxtree.ui.tree.actions.SubstructureFromListAction
-
- SubstructureRulePanel - Class in toxtree.ui.tree.rules
-
TODO add description
- SubstructureRulePanel(IRuleSubstructures) - Constructor for class toxtree.ui.tree.rules.SubstructureRulePanel
-
- SubstructuresFromFileAction - Class in toxtree.ui.tree.actions
-
- SubstructuresFromFileAction(IDecisionRule) - Constructor for class toxtree.ui.tree.actions.SubstructuresFromFileAction
-
- SubstructuresFromFileAction(IDecisionRule, String) - Constructor for class toxtree.ui.tree.actions.SubstructuresFromFileAction
-
- SubstructuresFromFileAction(IDecisionRule, String, Icon) - Constructor for class toxtree.ui.tree.actions.SubstructuresFromFileAction
-
- SubstructureTree - Class in toxTree.tree.demo
-
A demo decision tree consisting of a single decision rule , which checks for
the presence of benzene ring.
- SubstructureTree() - Constructor for class toxTree.tree.demo.SubstructureTree
-
- SUFFIX - Static variable in class mutant.rules.MutantTreeResult
-
- SUFFIX - Static variable in class toxtree.plugins.ames.rules.AmesMutagenicityTreeResult
-
- SUFFIX - Static variable in class toxtree.plugins.dnabinding.rules.DNABindingTreeResult
-
- SUFFIX - Static variable in class toxtree.plugins.proteinbinding.rules.ProteinBindingTreeResult
-
- SUFFIX - Static variable in class toxtree.plugins.skinsensitisation.rules.SkinSensitisationTreeResult
-
- SULPHAMATE - Static variable in class toxTree.query.FunctionalGroups
-
- sulphamate(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- sulphate - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
-
- SULPHATE - Static variable in class toxTree.query.FunctionalGroups
-
- sulphate(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- sulphate - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
-
- SULPHATE_OF_AMINE - Static variable in class toxTree.query.FunctionalGroups
-
- sulphateOfAmine(int) - Static method in class toxTree.query.FunctionalGroups
-
- sulphateOfAmineBreakable() - Static method in class toxTree.query.FunctionalGroups
-
- SULPHIDE - Static variable in class toxTree.query.FunctionalGroups
-
- sulphide() - Static method in class toxTree.query.FunctionalGroups
-
- sulphide_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
-
- sulphonate - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
-
- SULPHONATE - Static variable in class toxTree.query.FunctionalGroups
-
- sulphonate(String[]) - Static method in class toxTree.query.FunctionalGroups
-
- sulphonate(String[], boolean) - Static method in class toxTree.query.FunctionalGroups
-
- sulphonate - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
-
- supported_extensions - Static variable in class toxTree.io.MolFileFilter
-
- supported_exts_description - Static variable in class toxTree.io.MolFileFilter
-
- SurfaceTension - Static variable in class sicret.rules.RuleSurfaceTension
-
- SwingEditorFactory - Class in toxtree.ui.editors
-
- SwingEditorFactory() - Constructor for class toxtree.ui.editors.SwingEditorFactory
-