A B C D E F G H I J K L M N O P Q R S T U V W X Y _

A

a_nitroso - Static variable in class mic.rules.SA25
 
a_nitroso - Static variable in class mutant.rules.SA25_gen
 
ab_unsaturated_carbonyl() - Static method in class toxTree.query.FunctionalGroups
 
AB_UNSATURATED_CARBONYLS - Static variable in class mic.rules.SA10
 
AB_UNSATURATED_CARBONYLS - Static variable in class mutant.rules.SA10_gen
 
AB_UNSATURATED_CARBONYLS_SMARTS - Static variable in class mic.rules.SA10
 
AB_UNSATURATED_CARBONYLS_SMARTS - Static variable in class mutant.rules.SA10_gen
 
AboutAction - Class in toxtree.ui.actions
Launches About dialog
AboutAction(DataModule) - Constructor for class toxtree.ui.actions.AboutAction
 
AboutAction(DataModule, String) - Constructor for class toxtree.ui.actions.AboutAction
 
AboutAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.AboutAction
 
AbstractApplication - Class in toxTree.apps
 
AbstractApplication(String) - Constructor for class toxTree.apps.AbstractApplication
 
AbstractFilter - Class in toxTree.data
 
AbstractFilter() - Constructor for class toxTree.data.AbstractFilter
 
AbstractJobProcessingDialog - Class in toxtree.ui.batch
A dialog with start, pause and cancel buttons.
AbstractJobProcessingDialog() - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Dialog) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Dialog, boolean) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Frame) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Frame, boolean) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Dialog, String) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Dialog, String, boolean) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Frame, String) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Frame, String, boolean) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Dialog, String, boolean, GraphicsConfiguration) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractJobProcessingDialog(Frame, String, boolean, GraphicsConfiguration) - Constructor for class toxtree.ui.batch.AbstractJobProcessingDialog
 
AbstractMoleculeAction - Class in toxtree.ui.molecule
An abstract action to perform smth on a molecule
AbstractMoleculeAction(IMolecule) - Constructor for class toxtree.ui.molecule.AbstractMoleculeAction
 
AbstractMoleculeAction(IMolecule, String) - Constructor for class toxtree.ui.molecule.AbstractMoleculeAction
 
AbstractMoleculeAction(IMolecule, String, Icon) - Constructor for class toxtree.ui.molecule.AbstractMoleculeAction
 
AbstractQSARModel - Class in toxTree.qsar
 
AbstractQSARModel() - Constructor for class toxTree.qsar.AbstractQSARModel
 
AbstractQSARModel(List<String>, List<IMolecularDescriptor>, String) - Constructor for class toxTree.qsar.AbstractQSARModel
 
AbstractRule - Class in toxTree.tree
An abstract class implementing IDecisionRule interface.
AbstractRule() - Constructor for class toxTree.tree.AbstractRule
Constructor
AbstractRuleAction - Class in toxtree.ui.tree.actions
An AbstractAction descendant , performing an action on a preset IDecisionRule
AbstractRuleAction(IDecisionRule) - Constructor for class toxtree.ui.tree.actions.AbstractRuleAction
 
AbstractRuleAction(IDecisionRule, String) - Constructor for class toxtree.ui.tree.actions.AbstractRuleAction
 
AbstractRuleAction(IDecisionRule, String, Icon) - Constructor for class toxtree.ui.tree.actions.AbstractRuleAction
 
AbstractRuleHilightHits - Class in toxTree.tree
 
AbstractRuleHilightHits() - Constructor for class toxTree.tree.AbstractRuleHilightHits
 
AbstractRuleSmartSubstructure<T> - Class in toxTree.tree.rules.smarts
 
AbstractRuleSmartSubstructure() - Constructor for class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
AbstractTree - Class in toxTree.tree
An astract class, implementing IDecisionMethod interface.
AbstractTree() - Constructor for class toxTree.tree.AbstractTree
Constructor
AbstractTree(IDecisionCategories) - Constructor for class toxTree.tree.AbstractTree
 
AbstractTree(IDecisionCategories, IDecisionRuleList) - Constructor for class toxTree.tree.AbstractTree
 
AbstractTreeAction - Class in toxtree.ui.tree.actions
An AbstractAction descendant, performing an action on a preset IDecisionMethod
AbstractTreeAction(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.AbstractTreeAction
 
AbstractTreeAction(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.AbstractTreeAction
 
AbstractTreeAction(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.AbstractTreeAction
 
AbstractTreePrinter - Class in toxTree.tree
 
AbstractTreePrinter() - Constructor for class toxTree.tree.AbstractTreePrinter
 
AbstractTreePrinter(OutputStream) - Constructor for class toxTree.tree.AbstractTreePrinter
 
AbstractTreeWriter - Class in toxTree.tree
 
AbstractTreeWriter(Writer) - Constructor for class toxTree.tree.AbstractTreeWriter
 
AbstractTreeWriter(OutputStream) - Constructor for class toxTree.tree.AbstractTreeWriter
 
abunsaturated_aldehyde - Static variable in class mutant.rules.RuleABUnsaturatedAldehyde
 
ac - Variable in class toxtree.ui.molecule.AtomContainerPropertyTableModel
 
accept(IChemObject) - Method in interface toxTree.data.IObjectFilter
 
accept(IChemObject) - Method in class toxTree.data.ObjectPropertyFilter
 
accept(File) - Method in class toxTree.io.MolFileFilter
 
accept(Vector<IAtom>) - Method in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
 
accept(Object) - Method in class toxtree.ui.HashtableModel
 
acceptCategory(IDecisionCategory) - Method in class mutant.rules.MutantTreeResult
 
acceptCategory(IDecisionCategory) - Method in class toxtree.plugins.smartcyp.SMARTCypTreeResult
 
acceptCategory(IDecisionCategory) - Method in class toxTree.tree.TreeResult
 
acceptProperty(Object) - Method in interface toxTree.data.IPropertyFilter
 
acceptProperty(Object) - Method in class toxTree.data.ObjectPropertyFilter
 
acceptRingSet(IRingSet, int, int) - Method in class mic.rules.SA18
 
acceptRingSet(IRingSet, int, int) - Method in class mic.rules.SA19
 
acceptRingSet(IRingSet, int, int) - Method in class mutant.rules.SA18_gen
 
acceptRingSet(IRingSet, int, int) - Method in class mutant.rules.SA19_gen
 
accepts(Class) - Method in class toxTree.io.PDFWriter
 
accepts(Object, Object) - Method in class toxtree.ui.molecule.AtomContainerPropertyTableModel
 
acceptSubstituent(IMolecule) - Method in class eye.rules.Rule38
 
ACETAL - Static variable in class toxTree.query.FunctionalGroups
 
acetal() - Static method in class toxTree.query.FunctionalGroups
 
acetal - Variable in class toxTree.tree.cramer.RuleAcyclicAcetalEsterOfQ30
 
acetal_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
ACETYLENIC - Static variable in class toxTree.query.FunctionalGroups
 
acetylenic - Variable in class toxTree.query.MolFlags
 
aClass - Variable in class toxtree.ui.tree.ListTableModel
 
acrolein() - Static method in class toxTree.query.FunctionalGroups
 
acrylicAcid() - Static method in class toxTree.query.FunctionalGroups
 
ACTION_EDITCATEGORY - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_EDITRULE - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_MODIFYEXPLANATION - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_MODIFYNOBRANCH - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_MODIFYNOCATEGORY - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_MODIFYNODE - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_MODIFYYESBRANCH - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_MODIFYYESCATEGORY - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_NEWCATEGORY - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_NEWRULE - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_VERIFY - Static variable in class toxtree.ui.tree.EditTreeActions
 
ACTION_VERIFYUNUSED - Static variable in class toxtree.ui.tree.EditTreeActions
 
ActionList - Class in toxtree.data
 
ActionList() - Constructor for class toxtree.data.ActionList
 
ActionList(JFrame) - Constructor for class toxtree.data.ActionList
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.actions.AboutAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.actions.ClearResultAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.actions.DataModuleAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.actions.EditCompoundAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.actions.HelpAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.actions.InfoAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.actions.NewMoleculeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.actions.QuitAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.molecule.MoleculeEditAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.molecule.SmilesEntryPanel
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.AddCategoryAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.EditCategoryAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.EditRuleAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.EditTreeExplanation
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.LoadAndEditTreeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.LoadTreeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.NewRuleAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.NewTreeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.SaveTreeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.SelectAndEditTreeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.SelectCategoryFromListAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.SelectNewTreeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.SelectTreeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.SetBranchAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.SubstructureFromListAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.SubstructuresFromFileAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.VerifyUnreachableRulesAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.VerifyUnusedCategories
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.actions.ViewTreeAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.rules.RuleExampleEditAction
 
actionPerformed(ActionEvent) - Method in class toxtree.ui.tree.rules.RuleSubstructuresEditAction
 
actions - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
 
actions - Variable in class toxtree.ui.tree.TreeDrawing
 
activeContainer - Variable in class toxtree.data.FilteredMoleculesIterator
 
activeFilter - Variable in class toxtree.data.FilteredMoleculesIterator
 
acyclic_acetal() - Static method in class toxTree.query.FunctionalGroups
 
AcylTransferAlerts - Class in toxtree.plugins.dnabinding.categories
Acyl transfer
AcylTransferAlerts() - Constructor for class toxtree.plugins.dnabinding.categories.AcylTransferAlerts
 
AcylTransferAlerts - Class in toxtree.plugins.proteinbinding.categories
Acyl transfer
AcylTransferAlerts() - Constructor for class toxtree.plugins.proteinbinding.categories.AcylTransferAlerts
 
AcylTransferAlerts - Class in toxtree.plugins.skinsensitisation.categories
Acyl transfer
AcylTransferAlerts() - Constructor for class toxtree.plugins.skinsensitisation.categories.AcylTransferAlerts
 
AcylTransferRule - Class in toxtree.plugins.dnabinding.rules
Acyl transfer
AcylTransferRule() - Constructor for class toxtree.plugins.dnabinding.rules.AcylTransferRule
 
AcylTransferRule - Class in toxtree.plugins.proteinbinding.rules
Acyl transfer
AcylTransferRule() - Constructor for class toxtree.plugins.proteinbinding.rules.AcylTransferRule
 
AcylTransferRule - Class in toxtree.plugins.skinsensitisation.rules
Acyl transfer
AcylTransferRule() - Constructor for class toxtree.plugins.skinsensitisation.rules.AcylTransferRule
 
add(String) - Method in class toxTree.core.SmartElementsList
 
add(IAtomContainerSet) - Method in class toxTree.data.ListOfAtomContainers
 
add(IAtomContainerSet) - Method in class toxTree.data.MoleculesFile
 
add(int, IDecisionCategory) - Method in class toxTree.tree.CategoriesList
 
add(IDecisionCategory) - Method in class toxTree.tree.CategoriesList
 
add(Object) - Method in class toxTree.tree.DecisionMethodsList
 
add(int, Object) - Method in class toxTree.tree.DecisionMethodsList
 
add(int, IDecisionRule) - Method in class toxTree.tree.DecisionNodesList
 
add(IDecisionRule) - Method in class toxTree.tree.DecisionNodesList
 
add(int, IDecisionRule) - Method in class toxTree.tree.RulesList
not implemented
add(IDecisionRule) - Method in class toxTree.tree.RulesList
Adds an object only if it is a rule IDecisionRule otherwise returns false
addAction(Action, String, String) - Method in class toxtree.data.ActionList
 
addAction(Action, ActionList, String, String) - Method in class toxtree.data.ActionList
 
addActionListener(ActionListener) - Method in class toxtree.ui.HazardPanel
 
addActions(JTaskPane, String, ActionMap) - Method in class toxtree.ui.tree.TreeEditorPanel
 
addAll(Collection) - Method in class toxTree.tree.CategoriesList
 
addAll(int, Collection) - Method in class toxTree.tree.CategoriesList
 
addAll(int, Collection) - Method in class toxTree.tree.DecisionMethodsList
 
addAll(Collection) - Method in class toxTree.tree.DecisionMethodsList
 
addAll(Collection) - Method in class toxTree.tree.DecisionNodesList
 
addAll(int, Collection) - Method in class toxTree.tree.DecisionNodesList
 
addAll(Collection) - Method in class toxTree.tree.RulesList
Adds all objects from the Collection TODO verify if objects are IDecisionRule
addAll(int, Collection) - Method in class toxTree.tree.RulesList
 
addAtomContainer(IAtomContainer) - Method in class toxTree.data.ListOfAtomContainers
 
addAtomContainer(IAtomContainer, double) - Method in class toxTree.data.ListOfAtomContainers
 
addAtomContainer(IAtomContainer) - Method in class toxTree.data.MoleculesFile
 
addAtomContainer(IAtomContainer, double) - Method in class toxTree.data.MoleculesFile
 
addCategory(IDecisionCategory) - Method in interface toxTree.core.IDecisionCategories
 
addCategory(IDecisionCategory) - Method in class toxTree.tree.CategoriesList
 
addCategory(IDecisionCategory) - Method in class toxTree.tree.TreeResult
 
AddCategoryAction - Class in toxtree.ui.tree.actions
A descendant of AbstractAction Used in toxTree.ui Launches a dialog with a list of all available categories IDecisionCategory and adds the selected one to the list
AddCategoryAction(List) - Constructor for class toxtree.ui.tree.actions.AddCategoryAction
 
AddCategoryAction(List, String) - Constructor for class toxtree.ui.tree.actions.AddCategoryAction
 
AddCategoryAction(List, String, Icon) - Constructor for class toxtree.ui.tree.actions.AddCategoryAction
 
addCompoundActions(String, String) - Method in class toxtree.data.ToxTreeActions
 
addDataWidgets(T) - Method in class toxtree.ui.tree.qsar.OptionsPanel
 
addDecisionMethod(IDecisionMethod) - Method in interface toxTree.core.IDecisionMethodsList
 
addDecisionMethod(IDecisionMethod) - Method in class toxTree.tree.DecisionMethodsList
 
addDecisionMethod(IDecisionMethod) - Method in class toxTree.tree.DecisionResultsList
 
addDecisionRule(IDecisionRule) - Method in interface toxTree.core.IDecisionMethod
 
addDecisionRule(IDecisionRule) - Method in class toxTree.tree.AbstractTree
 
addDecisionRule(IDecisionRule) - Method in class toxTree.tree.BatchDecisionResultsList
 
addDirectory(String) - Static method in class toxTree.core.Introspection
 
addEditActions(String, String) - Method in class toxtree.data.ToxTreeActions
 
addElement(String) - Method in class toxTree.tree.rules.RuleElements
 
addEntry(A, B) - Method in class toxTree.tree.stats.ConfusionMatrix
 
adder - Variable in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
 
addFileActions(String, String) - Method in class toxtree.data.ToxTreeActions
 
addFilter(IObjectFilter) - Method in interface toxTree.core.IFilteredMolecules
Adds filtered set of IAtomContainer
addFilter(IObjectFilter) - Method in class toxtree.data.FilteredMoleculesIterator
 
addHazardActions(String, String) - Method in class toxTree.apps.toxForest.ToxForestDataModule
 
addHazardActions(String, String) - Method in class toxtree.data.ToxTreeActions
 
addHeaderWidgets(T) - Method in class toxtree.ui.tree.qsar.OptionsPanel
 
addHelpActions(String, String) - Method in class toxtree.data.ToxTreeActions
 
addList(IAtomContainerSet) - Method in class toxTree.data.SortedPropertyList
 
addListener(IChemObjectListener) - Method in class toxTree.data.ListOfAtomContainers
 
addListSelectionListener(ListSelectionListener) - Method in class toxtree.ui.tree.ListPanel
 
addMolecule(IAtomContainer) - Method in interface toxTree.core.IMoleculesIterator
 
addMolecule() - Method in class toxtree.data.DataContainer
 
addMolecule(IAtomContainer) - Method in class toxtree.data.DataContainer
 
addMolecule(IAtomContainer) - Method in class toxtree.data.FilteredMoleculesIterator
 
addMolecule(IAtomContainer) - Method in class toxTree.data.MoleculesIterator
 
addNode(DecisionNode) - Method in class toxTree.tree.DecisionNodesList
 
addProperty(Object, int) - Method in class toxTree.data.SortedPropertyList
 
addPropertyChangeListener(PropertyChangeListener) - Method in class com.molecularnetworks.start.BiodgeradationRules
 
addPropertyChangeListener(PropertyChangeListener) - Method in class cramer2.CramerRulesWithExtensions
 
addPropertyChangeListener(PropertyChangeListener) - Method in class eye.EyeIrritationRules
 
addPropertyChangeListener(PropertyChangeListener) - Method in class mic.MICRules
 
addPropertyChangeListener(PropertyChangeListener) - Method in class michaelacceptors.MichaelAcceptorRules
 
addPropertyChangeListener(PropertyChangeListener) - Method in class mutant.BB_CarcMutRules
 
addPropertyChangeListener(PropertyChangeListener) - Method in class sicret.SicretRules
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface toxTree.core.IDecisionMethod
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface toxTree.core.IDecisionResult
 
addPropertyChangeListener(PropertyChangeListener) - Method in interface toxTree.core.IDecisionRule
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxTree.data.MoleculesFile
 
addPropertyChangeListener(String, PropertyChangeListener) - Method in class toxTree.data.MoleculesFile
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.func.FuncRules
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.AbstractRule
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.AbstractTree
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.BatchDecisionResultsList
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.cramer.CramerRules
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.DecisionNode
 
addPropertyChangeListener(PropertyChangeListener) - Method in class toxTree.tree.TreeResult
 
addResidue(IAtomContainer) - Method in class toxTree.query.MolFlags
 
addResultPropertyChangeListener(PropertyChangeListener) - Method in class toxtree.data.DecisionMethodsDataModule
 
addRule(IDecisionRule) - Method in interface toxTree.core.IDecisionRuleList
 
addRule(IDecisionRule) - Method in class toxTree.tree.DecisionNodesList
 
addRule(IDecisionRule) - Method in class toxTree.tree.MultiLabelDecisionNodesList
 
addRule(IDecisionRule) - Method in class toxTree.tree.RulesList
adds a rule IDecisionRule
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class cramer2.categories.CramerTreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class mic.rules.MICTreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class michaelacceptors.MATreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class mutant.rules.MutantTreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in interface toxTree.core.IDecisionResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class toxtree.plugins.dnabinding.rules.DNABindingTreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class toxtree.plugins.func.rules.FuncTreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class toxtree.plugins.proteinbinding.rules.ProteinBindingTreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class toxtree.plugins.skinsensitisation.rules.SkinSensitisationTreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class toxTree.tree.BatchDecisionResultsList
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class toxTree.tree.cramer.CramerTreeResult
 
addRuleResult(IDecisionRule, boolean, IAtomContainer) - Method in class toxTree.tree.TreeResult
 
addRulesActions(String, String) - Method in class toxtree.data.ToxTreeActions
 
addRulesPropertyChangeListener(PropertyChangeListener) - Method in class toxtree.data.DecisionMethodsDataModule
 
addSelectRuleListener(PropertyChangeListener) - Method in interface toxtree.ui.tree.ITreeView
 
addSelectRuleListener(PropertyChangeListener) - Method in class toxtree.ui.tree.JCustomTreeComponent
 
addSelectRuleListener(PropertyChangeListener) - Method in class toxtree.ui.tree.TreePrefuse
 
addSubstructure(IAtomContainer) - Method in interface toxTree.core.IRuleSubstructures
Adds a substructure AtomContainer to the rule
addSubstructure(String, String) - Method in class toxtree.plugins.func.rules.FG
 
addSubstructure(IAtomContainer) - Method in class toxTree.tree.rules.RuleSubstructures
The fragment will be added to the list of substructures to be searched for
addSubstructure(String, String, boolean) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
addSubstructure(String, String) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
addSubstructure(String) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
addSubstructure(String) - Method in interface toxTree.tree.rules.smarts.IRuleSMARTSubstructures
 
addSubstructure(String, String) - Method in interface toxTree.tree.rules.smarts.IRuleSMARTSubstructures
 
addTree(IDecisionMethod) - Method in class toxtree.ui.tree.actions.SelectTreeAction
 
addTreeActions(String, String) - Method in class toxTree.apps.toxForest.ToxForestDataModule
 
addTreeModelListener(TreeModelListener) - Method in class toxtree.ui.tree.DecisionTreeModel
 
addURL(URL) - Method in class toxTree.core.ToxTreeClassLoader
 
addWidgets(Color, Color) - Method in class toxTree.apps.toxForest.ToxForestCompoundPanel
 
addWidgets(ActionList) - Method in class toxTree.apps.toxForest.ToxForestDataModulePanel
 
addWidgets() - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
 
addWidgets() - Method in class toxtree.ui.batch.BatchProcessingDialog
 
addWidgets(ActionList) - Method in class toxtree.ui.DataModulePanel
 
addWidgets(ActionList) - Method in class toxtree.ui.HazardPanel
 
addWidgets(IAtomContainerSet) - Method in class toxtree.ui.metabolites.MetabolitesFrame
 
addWidgets() - Method in class toxtree.ui.metabolites.MetabolitesPanel
 
addWidgets(Color, Color) - Method in class toxtree.ui.molecule.NavigationPanel
 
addWidgets(Color, Color) - Method in class toxtree.ui.molecule.PropertyPanel
 
addWidgets() - Method in class toxtree.ui.molecule.TopPanel
 
addWidgets() - Method in class toxtree.ui.StatusBar
 
addWidgets(Object) - Method in class toxtree.ui.tree.categories.CategoryPanel
 
addWidgets(ActionMap) - Method in class toxtree.ui.tree.DecisionNodePanel
 
addWidgets(String, ListTableModel, ActionMap) - Method in class toxtree.ui.tree.ListPanel
 
addWidgets(Color, Color) - Method in class toxtree.ui.tree.molecule.CompoundPanel
 
addWidgets(T) - Method in class toxtree.ui.tree.qsar.OptionsPanel
 
addWidgets() - Method in class toxtree.ui.tree.rules.RulePanel
 
addWidgets(Object) - Method in class toxtree.ui.tree.rules.RulePropertyEditor
 
addWidgets(Object) - Method in class toxtree.ui.tree.rules.RuleRangeEditor
 
addWidgets(Object) - Method in class toxtree.ui.tree.rules.RuleStructuresPanel
 
addWidgets() - Method in class toxtree.ui.tree.rules.SubstructureRulePanel
 
addWidgets(Object) - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
addWidgets(IDecisionMethod, EditTreeActions) - Method in class toxtree.ui.tree.TreeDrawing
 
addWidgets() - Method in class toxtree.ui.tree.TreeEditorPanel
 
addWidgets(IDecisionMethod) - Method in class toxtree.ui.tree.TreeFrame
 
addWidgets(IDecisionMethod) - Method in class toxtree.ui.tree.TreePanel
 
addWidgets(ListPanel[]) - Method in class toxtree.ui.wizard.DecisionNodeWizard
 
ALCOHOL - Static variable in class toxTree.query.FunctionalGroups
 
alcohol(boolean) - Static method in class toxTree.query.FunctionalGroups
 
alcohol_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
alcoholSecondaryAttachedToTerminalVinyl() - Static method in class toxTree.query.FunctionalGroups
 
ALDEHYDE - Static variable in class toxTree.query.FunctionalGroups
 
aldehyde() - Static method in class toxTree.query.FunctionalGroups
RC(=O)H An aldehyde is either a functional group consisting of a terminal carbonyl group, or a compound containing a terminal carbonyl group.
aldehyde_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
alertsCounter - Variable in class mic.rules.SA26
 
alertsCounter - Variable in class mutant.rules.SA20_nogen
 
alertsCounter - Variable in class mutant.rules.SA26_gen
 
ALERTSCounter - Static variable in class toxTree.tree.rules.RuleInitAlertCounter
 
alertsCounter - Variable in class verhaar.rules.helper.RuleAnySubstructureCounter
 
alertsCounter - Variable in class verhaar.rules.helper.RuleElementsCounter
 
alertsCounter - Variable in class verhaar.rules.helper.RuleOnlyAllowedSubstructuresCounter
 
alertsCounter - Variable in class verhaar.rules.Rule03
 
alertsCounter - Variable in class verhaar.rules.Rule141
 
alertsCounter - Variable in class verhaar.rules.Rule143
 
alertsCounter - Variable in class verhaar.rules.Rule21
 
alertsCounter - Variable in class verhaar.rules.Rule34
 
alertsCounter - Variable in class verhaar.rules.RuleIonicGroups
 
alertsCounter - Variable in class verhaar.rules.RuleLogPRange
 
ALERTSMessage - Static variable in class toxTree.tree.rules.RuleInitAlertCounter
 
alertURL - Static variable in class toxTree.tree.RuleResult
 
alicyclic - Variable in class toxTree.query.MolFlags
 
aliphatic - Variable in class toxTree.query.MolFlags
 
AliphaticCHQueryAtom - Class in toxTree.query
Matches if not aromatic and of type set
AliphaticCHQueryAtom() - Constructor for class toxTree.query.AliphaticCHQueryAtom
 
AliphaticCHQueryAtom(IAtom) - Constructor for class toxTree.query.AliphaticCHQueryAtom
 
alkoxy() - Static method in class toxTree.query.FunctionalGroups
 
alkoxyIDs - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
allActionsEnable(boolean) - Method in class toxtree.data.ActionList
 
allBox - Variable in class toxtree.ui.tree.rules.SMARTSRuleEditor
 
allLevels - Variable in class toxtree.ui.tree.TreeLayout
 
ALLOCATED - Static variable in class toxTree.query.FunctionalGroups
The intention is to use this property to mark if an atom/bond was already associated with a functional group.
allowedSubstituents() - Method in class mutant.rules.SA20_nogen
 
allowedSubstituents() - Method in class toxTree.tree.rules.RuleRingSubstituents
 
allyl - Variable in class verhaar.rules.Rule152
 
allylAlcohol() - Static method in class toxTree.query.FunctionalGroups
 
allylAlcoholAcetal() - Static method in class toxTree.query.FunctionalGroups
 
allylAlcoholEsterDerivative() - Static method in class toxTree.query.FunctionalGroups
 
allylAmine() - Static method in class toxTree.query.FunctionalGroups
 
allylMercaptan() - Static method in class toxTree.query.FunctionalGroups
 
allylSulphide() - Static method in class toxTree.query.FunctionalGroups
 
allylThioester() - Static method in class toxTree.query.FunctionalGroups
 
amine_and_SO3H - Static variable in class mic.rules.SA28
 
amine_and_SO3H - Static variable in class mutant.rules.SA28_gen
 
aminePrimary_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
amines - Static variable in class mic.rules.SA28
 
amines - Static variable in class mic.rules.SA28bis
 
amines - Static variable in class mic.rules.SA28ter
 
amines - Static variable in class mutant.rules.SA28_gen
 
amines - Static variable in class mutant.rules.SA28bis_gen
 
amines - Static variable in class mutant.rules.SA28ter_gen
 
amineTertiary_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
aminoSulphate - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
 
aminoSulphate - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
 
analyse(IAtomContainer) - Static method in class toxTree.query.MolAnalyser
 
analysed - Variable in class toxTree.query.MolFlags
 
analyze(IRing) - Method in class mutant.rules.SA20_nogen
Initialize halogen counts to zero and returns true if the ring consists of single bonds only.
analyze(IRing) - Method in class toxTree.tree.rules.RuleRingSubstituents
 
analyzeOnlyRingsWithFlagSet - Variable in class toxTree.tree.rules.RuleRingSubstituents
 
analyzeOnlyRingsWithFlagSet() - Method in class toxTree.tree.rules.RuleRingSubstituents
 
ANHYDRIDE - Static variable in class toxTree.query.FunctionalGroups
 
anhydride() - Static method in class toxTree.query.FunctionalGroups
 
anhydride - Variable in class toxTree.tree.cramer.RuleLactoneOrCyclicDiester
 
Aniline - Static variable in class mutant.descriptors.DescriptorIsAniline
 
ANILINE - Static variable in class verhaar.query.FunctionalGroups
 
aniline() - Static method in class verhaar.query.FunctionalGroups
 
answer - Variable in exception toxTree.exceptions.DRuleException
 
answer - Variable in class toxtree.ui.tree.actions.SetBranchAction
 
answer - Variable in class toxtree.ui.tree.rules.RuleExampleEditAction
 
answerText - Variable in class toxtree.ui.tree.actions.SetBranchAction
 
ApplyRuleOptions - Class in toxtree.tree.rules
 
ApplyRuleOptions() - Constructor for class toxtree.tree.rules.ApplyRuleOptions
 
AqueousSolubility - Static variable in class sicret.rules.RuleAqueousSolubility
 
AromAmine - Static variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
aromatic - Variable in class toxTree.query.MolFlags
 
aromatic_amine - Static variable in class mutant.rules.QSAR6Applicable
 
aromatic_amine - Static variable in class mutant.rules.RuleAromaticAmineNoSulfonicGroup
 
AROMATIC_AMINE - Static variable in class mutant.rules.SMARTSgroups
 
AROMATIC_AMINE - Static variable in class toxTree.query.FunctionalGroups
 
aromatic_diazo - Static variable in class mutant.rules.RuleAromaticDiazo
 
AROMATIC_N_OXIDE - Static variable in class toxTree.query.FunctionalGroups
 
aromaticAmine(String) - Static method in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
AromaticAmineSubstituentsDescriptor - Class in mutant.descriptors
returns "MR","LSTM","B1STM","B5STM" for substituents at postitions 1 to 6 (amine group at 1 position).
AromaticAmineSubstituentsDescriptor() - Constructor for class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
AromaticQueryBond - Class in verhaar.query
A fix until AromaticQueryBond is fixed
AromaticQueryBond() - Constructor for class verhaar.query.AromaticQueryBond
 
AromaticQueryBond(IQueryAtom, IQueryAtom) - Constructor for class verhaar.query.AromaticQueryBond
 
aromaticRings - Variable in class toxTree.query.MolFlags
 
assignedCategories - Variable in class toxTree.tree.TreeResult
 
assignResult(IAtomContainer) - Method in class cramer2.categories.CramerTreeResult
 
assignResult(IAtomContainer) - Method in class mic.rules.MICTreeResult
 
assignResult(IAtomContainer) - Method in class mutant.rules.MutantTreeResult
 
assignResult(IAtomContainer) - Method in interface toxTree.core.IDecisionResult
 
assignResult(IAtomContainer) - Method in class toxtree.plugins.dnabinding.rules.DNABindingTreeResult
 
assignResult(IAtomContainer) - Method in class toxtree.plugins.func.rules.FuncTreeResult
 
assignResult(IAtomContainer) - Method in class toxtree.plugins.proteinbinding.rules.ProteinBindingTreeResult
 
assignResult(IAtomContainer) - Method in class toxtree.plugins.skinsensitisation.rules.SkinSensitisationTreeResult
 
assignResult(IAtomContainer) - Method in class toxtree.plugins.smartcyp.SMARTCypTreeResult
 
assignResult(IAtomContainer) - Method in class toxtree.plugins.verhaar2.rules.Verhaar2TreeResult
 
assignResult(IAtomContainer) - Method in class toxTree.tree.BatchDecisionResultsList
 
assignResult(IAtomContainer) - Method in class toxTree.tree.cramer.CramerTreeResult
 
assignResult(IAtomContainer) - Method in class toxTree.tree.TreeResult
 
assignResult(IAtomContainer) - Method in class verhaar.rules.VerhaarTreeResult
 
associateIonic(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
AssociationQueryBond - Class in toxTree.query
TODO add description
AssociationQueryBond(IAtom, IAtom) - Constructor for class toxTree.query.AssociationQueryBond
 
AssociationQueryBond() - Constructor for class toxTree.query.AssociationQueryBond
 
atom_C - Static variable in class mutant.descriptors.SubstituentExtractor
 
atomContainer - Variable in exception toxTree.exceptions.MolAnalyseException
 
atomContainer - Variable in class toxtree.ui.OptionsPanel
 
AtomContainerPropertyTableModel - Class in toxtree.ui.molecule
Used to display properties of a org.openscience.cdk.interfaces.Molecule obtained by getProperties()
AtomContainerPropertyTableModel() - Constructor for class toxtree.ui.molecule.AtomContainerPropertyTableModel
 
atomContainers() - Method in class toxTree.data.ListOfAtomContainers
 
atomContainers() - Method in class toxTree.data.MoleculesFile
 
authService - Variable in class toxtree.lookup.RemoteLookup
 
AZARIDINE - Static variable in class verhaar.query.FunctionalGroups
 
azaridine() - Static method in class verhaar.query.FunctionalGroups
 

B

backId - Variable in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
batch - Variable in class toxtree.data.DataModule
 
batch(BatchProcessing) - Method in class toxtree.data.DataModule
 
batch(BatchProcessing) - Method in class toxtree.data.ToxTreeModule
 
batch - Variable in exception toxTree.io.batch.BatchProcessingException
 
batch() - Method in class toxtree.ui.batch.BatchProcessingDialog
 
batchAction - Variable in class toxtree.data.ToxTreeActions
 
BatchAction - Class in toxtree.ui.actions
Starts a batch IBatchProcessing
BatchAction(DataModule) - Constructor for class toxtree.ui.actions.BatchAction
 
BatchAction(DataModule, String) - Constructor for class toxtree.ui.actions.BatchAction
 
BatchAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.BatchAction
 
BatchDecisionResultsList - Class in toxTree.tree
Encapsulates DecisionResultsList as IDecisionMethod.
BatchDecisionResultsList() - Constructor for class toxTree.tree.BatchDecisionResultsList
 
BatchFactory - Class in toxTree.io.batch
Provides a static function to create an IBatchProcessing object by a config file.
BatchFactory() - Constructor for class toxTree.io.batch.BatchFactory
 
BatchProcessing - Class in toxTree.io.batch
Accessing & serializing Array: Throwing exception in jre6 while it works in jre5 http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6554519 An abstract class to support Batch processing with several fail safe options
BatchProcessing() - Constructor for class toxTree.io.batch.BatchProcessing
Creates empty BatchProcessing it should be configured prior to use
BatchProcessing(String, String) - Constructor for class toxTree.io.batch.BatchProcessing
Creates BatchProcessing given input and output file names
BatchProcessing(File, File) - Constructor for class toxTree.io.batch.BatchProcessing
Creates BatchProcessing given input and output file names
BatchProcessingDialog - Class in toxtree.ui.batch
UI for batch processing IBatchProcessing
BatchProcessingDialog(IBatchProcessing) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Dialog) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Dialog, boolean) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Frame) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Frame, boolean) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Dialog, String) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Dialog, String, boolean) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Frame, String) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Frame, String, boolean) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Dialog, String, boolean, GraphicsConfiguration) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingDialog(IBatchProcessing, Frame, String, boolean, GraphicsConfiguration) - Constructor for class toxtree.ui.batch.BatchProcessingDialog
 
BatchProcessingException - Exception in toxTree.io.batch
An Exception to be used in IBatchProcessing
BatchProcessingException() - Constructor for exception toxTree.io.batch.BatchProcessingException
 
BatchProcessingException(String) - Constructor for exception toxTree.io.batch.BatchProcessingException
 
BatchProcessingException(String, IBatchProcessing) - Constructor for exception toxTree.io.batch.BatchProcessingException
 
BatchProcessingException(Throwable, IBatchProcessing) - Constructor for exception toxTree.io.batch.BatchProcessingException
 
BatchProcessingException(Throwable) - Constructor for exception toxTree.io.batch.BatchProcessingException
 
BatchProcessingException(String, Throwable) - Constructor for exception toxTree.io.batch.BatchProcessingException
 
BatchProcessingException(String, Throwable, IBatchProcessing) - Constructor for exception toxTree.io.batch.BatchProcessingException
 
BB_CarcMutRules - Class in mutant
 
BB_CarcMutRules() - Constructor for class mutant.BB_CarcMutRules
 
BENZYLALCOHOL - Static variable in class verhaar.query.FunctionalGroups
 
benzylAlcohol() - Static method in class verhaar.query.FunctionalGroups
 
bgColor - Variable in class toxtree.ui.molecule.NavigationPanel
 
bgColor - Variable in class toxtree.ui.tree.DecisionNodePanel
 
bgColor - Variable in class toxtree.ui.tree.ToxTreeEditorPanel
 
BiBr - Static variable in class mutant.descriptors.DescriptorBridgedBiphenyl
 
BiodgeradationRules - Class in com.molecularnetworks.start
Wrapper class that knows the biodegradation rules that are available in the toxBiodegradation plugin.
BiodgeradationRules() - Constructor for class com.molecularnetworks.start.BiodgeradationRules
 
breakBond(IAtomContainer, IAtom, String, int, List<IAtom>) - Static method in class mutant.descriptors.SubstituentExtractor
 
bufferProperties - Variable in class toxTree.data.MoleculesFile
 
build() - Method in class toxTree.qsar.LinearQSARModel
 
bundle - Variable in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
 
buttonPane - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
 

C

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.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.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
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.DecisionNode
 
categories - Variable in class toxtree.ui.tree.categories.CategoriesPanel
 
CategoriesList - Class in toxTree.tree
A list of IDecisionCategory
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
An AbstractTableModel descendant used in CategoriesPanel
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
 
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
 
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
 
CategoryNoGenotoxicAlert - Class in mutant.categories
 
CategoryNoGenotoxicAlert() - Constructor for class mutant.categories.CategoryNoGenotoxicAlert
 
CategoryNonMutagen - Class in mutant.categories
 
CategoryNonMutagen() - Constructor for class mutant.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
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
 
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
These constants are used in Atom.setProperty(CH3,true) fashion in order to mark which atoms/bonds belong to the corresponding group Used by FunctionalGroups.markMaps(IAtomContainer, IAtomContainer, List) method
CH6SubstituentAtBetaCarbon(IAtomContainer) - Method in class mic.rules.SA10
 
CH6SubstituentAtBetaCarbon(IAtomContainer) - Method in class mutant.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() - 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, 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(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
 
cmdArgs - Static variable in class toxTree.apps.AbstractApplication
 
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.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(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#getProperties()
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
 
configureLog4j(boolean) - Static method in class toxTree.logging.TTLogger
 
configureLog4j(String) - Static method in class toxTree.logging.TTLogger
 
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 java.lang.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
 
construct() - Method in class toxtree.ui.GUIWorker
 
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
IDecisionRule.verifyRule(IAtomContainer)
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(IMolecule) - Static method in class toxTree.tree.rules.smarts.Convertor
Converts an org.openscience.cdk.Molecule class into a joelib.molecule.JOEMol class.
convert(IMolecule, 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(IMolecule) - 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
A DefaultCategory descendant, implementation of Cramer class 1 (see CramerRules)
CramerClass1() - Constructor for class toxTree.tree.cramer.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
A DefaultCategory descendant, implementation of Cramer class 2 (see CramerRules)
CramerClass2() - Constructor for class toxTree.tree.cramer.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
A DefaultCategory descendant, implementation of Cramer class 3 (see CramerRules)
CramerClass3() - Constructor for class toxTree.tree.cramer.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
A descendant ot TreeResult, to be used by CramerRules.
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<?>, 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.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
 
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.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
 
createMutagenicityofAromaticAminesModel() - Static method in class mutant.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
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(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
 

D

d - Variable in class toxtree.ui.tree.TreeLayout
 
DataContainer - Class in toxtree.data
 
DataContainer() - Constructor for class toxtree.data.DataContainer
 
DataContainer(File) - Constructor for class toxtree.data.DataContainer
 
dataContainer - Variable in class toxtree.data.DataModule
 
dataContainer - Variable in class toxtree.ui.actions.DataContainerAction
 
dataContainer - Variable in class toxtree.ui.molecule.NavigationPanel
 
dataContainer - Variable in class toxtree.ui.molecule.StructureEntryPanel
 
dataContainer - Variable in class toxtree.ui.tree.molecule.CompoundPanel
 
DataContainerAction - Class in toxtree.ui.actions
 
DataContainerAction(DataContainer) - Constructor for class toxtree.ui.actions.DataContainerAction
 
DataContainerAction(DataContainer, String) - Constructor for class toxtree.ui.actions.DataContainerAction
 
DataContainerAction(DataContainer, String, Icon) - Constructor for class toxtree.ui.actions.DataContainerAction
 
dataModule - Variable in class toxTree.apps.AbstractApplication
 
DataModule - Class in toxtree.data
 
DataModule(File) - Constructor for class toxtree.data.DataModule
 
dataModule - Variable in class toxtree.ui.DataModulePanel
 
DataModuleAction - Class in toxtree.ui.actions
An abstract action to manipulate data in ToxTreeModule
DataModuleAction(DataModule) - Constructor for class toxtree.ui.actions.DataModuleAction
 
DataModuleAction(DataModule, String) - Constructor for class toxtree.ui.actions.DataModuleAction
 
DataModuleAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.DataModuleAction
 
dataModulePanel - Variable in class toxTree.apps.CompoundMethodApplication
 
DataModulePanel<DM extends DataModule> - Class in toxtree.ui
 
DataModulePanel(DM) - Constructor for class toxtree.ui.DataModulePanel
 
DataModulePanel(DM, boolean) - Constructor for class toxtree.ui.DataModulePanel
 
DataModulePanel(DM, LayoutManager) - Constructor for class toxtree.ui.DataModulePanel
 
DataModulePanel(DM, LayoutManager, boolean) - Constructor for class toxtree.ui.DataModulePanel
 
dataProcessing - Variable in class toxtree.ui.StatusBar
 
dateCreated - Variable in class toxTree.io.batch.BatchProcessing
 
dateLastSaved - Variable in class toxTree.io.batch.BatchProcessing
 
DCategoryUnknown - Exception in toxTree.exceptions
TODO Add DCategoryUnassigned description
DCategoryUnknown() - Constructor for exception toxTree.exceptions.DCategoryUnknown
Constructor
DCategoryUnknown(String) - Constructor for exception toxTree.exceptions.DCategoryUnknown
Constructor
DCategoryUnknown(Throwable) - Constructor for exception toxTree.exceptions.DCategoryUnknown
Constructor
DCategoryUnknown(String, Throwable) - Constructor for exception toxTree.exceptions.DCategoryUnknown
Constructor
debug(Object) - Method in class toxTree.logging.TTLogger
Shows DEBUG output for the Object.
debug(Object, Object) - Method in class toxTree.logging.TTLogger
Shows DEBUG output for the given Object's.
debug(Object, int) - Method in class toxTree.logging.TTLogger
Shows DEBUG output for the given Object's.
debug(Object, double) - Method in class toxTree.logging.TTLogger
Shows DEBUG output for the given Object's.
debug(Object, boolean) - Method in class toxTree.logging.TTLogger
Shows DEBUG output for the given Object's.
debug(Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows DEBUG output for the given Object's.
debug(Object, Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows DEBUG output for the given Object's.
debug(Object, Object, Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows DEBUG output for the given Object's.
decisionMethod - Variable in class toxTree.io.batch.ToxTreeBatchProcessing
 
decisionMethod - Variable in class toxTree.tree.TreeResult
 
decisionMethod - Variable in class toxtree.ui.tree.DecisionTreeModel
 
DecisionMethodData - Class in toxtree.data
Contains MoleculesIterator and TTLogger
DecisionMethodData(File) - Constructor for class toxtree.data.DecisionMethodData
 
DecisionMethodException - Exception in toxTree.exceptions
TODO Add DecisionTreeException description
DecisionMethodException() - Constructor for exception toxTree.exceptions.DecisionMethodException
Constructor
DecisionMethodException(String) - Constructor for exception toxTree.exceptions.DecisionMethodException
Constructor
DecisionMethodException(Throwable) - Constructor for exception toxTree.exceptions.DecisionMethodException
Constructor
DecisionMethodException(String, Throwable) - Constructor for exception toxTree.exceptions.DecisionMethodException
Constructor
decisionMethodFile - Variable in class toxTree.io.batch.ToxTreeBatchProcessing
 
DecisionMethodIOException - Exception in toxTree.exceptions
TODO add description
DecisionMethodIOException() - Constructor for exception toxTree.exceptions.DecisionMethodIOException
 
DecisionMethodIOException(String) - Constructor for exception toxTree.exceptions.DecisionMethodIOException
 
DecisionMethodIOException(Throwable) - Constructor for exception toxTree.exceptions.DecisionMethodIOException
 
DecisionMethodIOException(String, Throwable) - Constructor for exception toxTree.exceptions.DecisionMethodIOException
 
DecisionMethodsDataModule - Class in toxtree.data
 
DecisionMethodsDataModule() - Constructor for class toxtree.data.DecisionMethodsDataModule
 
DecisionMethodsDataModule(JFrame, File, DecisionMethodsList) - Constructor for class toxtree.data.DecisionMethodsDataModule
 
DecisionMethodsList - Class in toxTree.tree
A list of IDecisionMethod
DecisionMethodsList() - Constructor for class toxTree.tree.DecisionMethodsList
 
DecisionMethodsTableModel - Class in toxtree.ui.tree
Table model for DecisionResultsList.
DecisionMethodsTableModel(IDecisionMethodsList) - Constructor for class toxtree.ui.tree.DecisionMethodsTableModel
 
DecisionNode - Class in toxTree.tree
A decision node to be used in UserDefinedTree.
DecisionNode() - Constructor for class toxTree.tree.DecisionNode
Constructor
DecisionNode(IDecisionRule) - Constructor for class toxTree.tree.DecisionNode
Constructs a decision node with rule, null next nodes.
DecisionNode(IDecisionRule, DecisionNode, DecisionNode) - Constructor for class toxTree.tree.DecisionNode
Constructs a decision node with rule, nodeNo at branch NO and nodeYes at branch YES.
DecisionNode(IDecisionRule, DecisionNode, DecisionNode, IDecisionCategory, IDecisionCategory) - Constructor for class toxTree.tree.DecisionNode
 
DecisionNodePanel - Class in toxtree.ui.tree
Displays a decision node DecisionNode.
DecisionNodePanel(ActionMap) - Constructor for class toxtree.ui.tree.DecisionNodePanel
 
DecisionNodePanel(boolean, ActionMap) - Constructor for class toxtree.ui.tree.DecisionNodePanel
 
DecisionNodePanel(LayoutManager, ActionMap) - Constructor for class toxtree.ui.tree.DecisionNodePanel
 
DecisionNodePanel(LayoutManager, boolean, ActionMap) - Constructor for class toxtree.ui.tree.DecisionNodePanel
 
DecisionNodesFactory - Class in toxTree.tree
 
DecisionNodesFactory() - Constructor for class toxTree.tree.DecisionNodesFactory
 
DecisionNodesFactory(boolean) - Constructor for class toxTree.tree.DecisionNodesFactory
 
DecisionNodesList - Class in toxTree.tree
A list of DecisionNode, implementing IDecisionRuleList.
DecisionNodesList() - Constructor for class toxTree.tree.DecisionNodesList
 
DecisionNodesList(IDecisionCategories, String[], int[][]) - Constructor for class toxTree.tree.DecisionNodesList
 
DecisionNodesListTableModel - Class in toxtree.ui.tree.rules
table model for DecisionNodesList
DecisionNodesListTableModel(List) - Constructor for class toxtree.ui.tree.rules.DecisionNodesListTableModel
 
DecisionNodeWizard - Class in toxtree.ui.wizard
 
DecisionNodeWizard(IDecisionMethod, ListPanel[]) - Constructor for class toxtree.ui.wizard.DecisionNodeWizard
 
DecisionNodeWizard(Dialog, IDecisionMethod, ListPanel[]) - Constructor for class toxtree.ui.wizard.DecisionNodeWizard
 
DecisionNodeWizard(Frame, IDecisionMethod, ListPanel[]) - Constructor for class toxtree.ui.wizard.DecisionNodeWizard
 
DecisionNodeWizard.RuleOptions - Enum in toxtree.ui.wizard
 
decisionResult - Variable in class toxTree.io.batch.ToxTreeBatchProcessing
 
DecisionResultException - Exception in toxTree.exceptions
TODO Add DecisionResultException description
DecisionResultException() - Constructor for exception toxTree.exceptions.DecisionResultException
Constructor
DecisionResultException(String) - Constructor for exception toxTree.exceptions.DecisionResultException
Constructor
DecisionResultException(Throwable) - Constructor for exception toxTree.exceptions.DecisionResultException
Constructor
DecisionResultException(String, Throwable) - Constructor for exception toxTree.exceptions.DecisionResultException
Constructor
DecisionResultIOException - Exception in toxTree.exceptions
 
DecisionResultIOException() - Constructor for exception toxTree.exceptions.DecisionResultIOException
 
DecisionResultIOException(String) - Constructor for exception toxTree.exceptions.DecisionResultIOException
 
DecisionResultIOException(Throwable) - Constructor for exception toxTree.exceptions.DecisionResultIOException
 
DecisionResultIOException(String, Throwable) - Constructor for exception toxTree.exceptions.DecisionResultIOException
 
DecisionResultsList - Class in toxTree.tree
 
DecisionResultsList() - Constructor for class toxTree.tree.DecisionResultsList
 
DecisionResultUIDException - Exception in toxTree.exceptions
 
DecisionResultUIDException(Serializable) - Constructor for exception toxTree.exceptions.DecisionResultUIDException
 
DecisionResultUIDException(String, Serializable) - Constructor for exception toxTree.exceptions.DecisionResultUIDException
 
DecisionResultUIDException(Throwable, Serializable) - Constructor for exception toxTree.exceptions.DecisionResultUIDException
 
DecisionResultUIDException(String, Throwable, Serializable) - Constructor for exception toxTree.exceptions.DecisionResultUIDException
 
decisionTree - Variable in class toxTree.core.ToxTreeDescriptor
 
DecisionTreeModel - Class in toxtree.ui.tree
A TreeModel
DecisionTreeModel(IDecisionMethod) - Constructor for class toxtree.ui.tree.DecisionTreeModel
 
DecisionTreeModel() - Constructor for class toxtree.ui.tree.DecisionTreeModel
 
DecisionTreeWizard - Class in toxtree.ui.wizard
 
DecisionTreeWizard(IDecisionMethod) - Constructor for class toxtree.ui.wizard.DecisionTreeWizard
 
DecisionTreeWizard(Dialog, IDecisionMethod) - Constructor for class toxtree.ui.wizard.DecisionTreeWizard
 
DecisionTreeWizard(Frame, IDecisionMethod) - Constructor for class toxtree.ui.wizard.DecisionTreeWizard
 
DEFAULT_STACK_LENGTH - Variable in class toxTree.logging.TTLogger
Default number of StackTraceElements to be printed by debug(Exception).
DefaultAlertCounter - Class in toxTree.tree.rules
 
DefaultAlertCounter() - Constructor for class toxTree.tree.rules.DefaultAlertCounter
 
DefaultCategory - Class in toxTree.tree
The default class implementing IDecisionCategory interface
DefaultCategory() - Constructor for class toxTree.tree.DefaultCategory
Constructor
DefaultCategory(String, int) - Constructor for class toxTree.tree.DefaultCategory
Constructor
DefaultClass1 - Class in toxTree.tree.categories
 
DefaultClass1() - Constructor for class toxTree.tree.categories.DefaultClass1
 
DefaultClass1(String, int) - Constructor for class toxTree.tree.categories.DefaultClass1
 
DefaultClass2 - Class in toxTree.tree.categories
 
DefaultClass2() - Constructor for class toxTree.tree.categories.DefaultClass2
 
DefaultClass2(String, int) - Constructor for class toxTree.tree.categories.DefaultClass2
 
defaultLocation - Static variable in class toxTree.core.Introspection
 
deleteAllFilters() - Method in class toxtree.data.FilteredMoleculesIterator
 
deleteConfigOnSuccess - Variable in class toxTree.io.batch.BatchProcessing
 
deleteFilter(IObjectFilter) - Method in interface toxTree.core.IFilteredMolecules
Delete filtered set of IAtomContainer
deleteFilter(IObjectFilter) - Method in class toxtree.data.FilteredMoleculesIterator
 
deleteSmarts() - Method in class toxtree.ui.tree.rules.SMARTSRuleEditor
 
deleteSubstructure(String) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
deleteSubstructure(String) - Method in interface toxTree.tree.rules.smarts.IRuleSMARTSubstructures
 
deleteSubstructureAction - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
 
delimiter - Variable in class toxTree.tree.SimpleTreePrinter
 
deriveAmine(QueryAtomContainer, IMoleculeSet, IMoleculeSet) - Method in class mutant.rules.RuleDerivedAromaticAmines
 
description - Variable in class toxTree.io.MolFileFilter
 
descriptor - Variable in class toxTree.qsar.QSARDescriptor
 
descriptor - Variable in class toxTree.tree.rules.RuleDescriptor
 
DescriptorBridgedBiphenyl - Class in mutant.descriptors
 
DescriptorBridgedBiphenyl() - Constructor for class mutant.descriptors.DescriptorBridgedBiphenyl
 
descriptorClass - Variable in class toxTree.qsar.QSARDescriptor
 
descriptorClass - Variable in class toxTree.tree.rules.RuleDescriptor
 
DescriptorHasNO2Group - Class in mutant.descriptors
 
DescriptorHasNO2Group() - Constructor for class mutant.descriptors.DescriptorHasNO2Group
 
DescriptorIDist - Class in mutant.descriptors
The indicator variable Idist is a structural parameter coding for the presence (Idist = 1, otherwise Idist = 0) of crowded substituents on the positions 3'-, 4'- and 5'- of 4-aminobiphenyl.
DescriptorIDist() - Constructor for class mutant.descriptors.DescriptorIDist
 
DescriptorIsAniline - Class in mutant.descriptors
Returns true if aniline, false otherwise.
DescriptorIsAniline() - Constructor for class mutant.descriptors.DescriptorIsAniline
 
DescriptorMolarRefractivity - Class in mutant.descriptors
This is now a wrapper of Joelib MolarRefractivity, but needs to be rewritten without joelib.
DescriptorMolarRefractivity() - Constructor for class mutant.descriptors.DescriptorMolarRefractivity
 
descriptorName - Variable in class toxTree.qsar.QSARDescriptor
 
descriptorNames - Variable in class mutant.descriptors.SubstituentsDescriptor
 
descriptorNames - Variable in class toxTree.core.ToxTreeDescriptor
 
descriptorNames - Variable in class toxTree.qsar.AbstractQSARModel
 
DescriptorOptions - Class in toxtree.ui.tree.qsar
 
DescriptorOptions() - Constructor for class toxtree.ui.tree.qsar.DescriptorOptions
 
descriptors - Variable in class mutant.rules.MutantTreeResult
 
descriptors - Variable in class toxtree.ui.wizard.DecisionNodeWizard
 
DescriptorStructurePresence<T> - Class in mutant.descriptors
 
DescriptorStructurePresence() - Constructor for class mutant.descriptors.DescriptorStructurePresence
 
DesisionMethodUIDException - Exception in toxTree.exceptions
 
DesisionMethodUIDException(Serializable) - Constructor for exception toxTree.exceptions.DesisionMethodUIDException
 
DesisionMethodUIDException(String, Serializable) - Constructor for exception toxTree.exceptions.DesisionMethodUIDException
 
DesisionMethodUIDException(Throwable, Serializable) - Constructor for exception toxTree.exceptions.DesisionMethodUIDException
 
DesisionMethodUIDException(String, Throwable, Serializable) - Constructor for exception toxTree.exceptions.DesisionMethodUIDException
 
detachGroup(IAtomContainer, QueryAtomContainer) - Static method in class toxTree.query.FunctionalGroups
Identifies the fragment to be detached and breaks the relevant bonds In order to function properly, the group has to be defined with at least one atom marked with setProperty(DONTMARK,dontMark).
detachSubstituent(QueryAtomContainer, IAtomContainer) - Method in class mutant.rules.RuleDerivedAromaticAmines
 
detachSubstituentAtBetaCarbon(IAtomContainer) - Method in class mic.rules.SA10
 
detachSubstituentAtBetaCarbon(IAtomContainer) - Method in class mutant.rules.SA10_gen
 
DIAZO - Static variable in class toxTree.query.FunctionalGroups
 
diAzo() - Static method in class toxTree.query.FunctionalGroups
 
dictionary - Static variable in class toxTree.qsar.LinearDiscriminantRule
 
dim - Variable in class toxtree.ui.tree.qsar.DescriptorOptions
 
dimension - Variable in class toxTree.qsar.LinearPreprocessor
 
dimension - Variable in class toxTree.qsar.MatrixPreprocessor
 
dimmin - Variable in class toxtree.ui.tree.qsar.DescriptorOptions
 
dirty - Variable in class toxTree.tree.stats.ConfusionMatrix
 
display() - Method in class toxtree.ui.tree.molecule.CompoundPanel
 
DMethodNotAssigned - Exception in toxTree.exceptions
TODO Add MethodNotAssigned description
DMethodNotAssigned() - Constructor for exception toxTree.exceptions.DMethodNotAssigned
Constructor
DMethodNotAssigned(String) - Constructor for exception toxTree.exceptions.DMethodNotAssigned
Constructor
DMethodNotAssigned(Throwable) - Constructor for exception toxTree.exceptions.DMethodNotAssigned
Constructor
DMethodNotAssigned(String, Throwable) - Constructor for exception toxTree.exceptions.DMethodNotAssigned
Constructor
DNABindingAlerts - Enum in toxtree.plugins.dnabinding.categories
 
DNABindingCategory - Class in toxtree.plugins.dnabinding.categories
 
DNABindingCategory(DNABindingAlerts) - Constructor for class toxtree.plugins.dnabinding.categories.DNABindingCategory
 
DNABindingPlugin - Class in toxtree.plugins.dnabinding
Protein binding
DNABindingPlugin() - Constructor for class toxtree.plugins.dnabinding.DNABindingPlugin
 
DNABindingRule - Class in toxtree.plugins.dnabinding.rules
Parent class for all skin sens rules
DNABindingRule(DNABindingAlerts) - Constructor for class toxtree.plugins.dnabinding.rules.DNABindingRule
 
DNABindingTreeResult - Class in toxtree.plugins.dnabinding.rules
 
DNABindingTreeResult() - Constructor for class toxtree.plugins.dnabinding.rules.DNABindingTreeResult
 
done() - Method in interface toxTree.core.IProcessRule
 
done() - Method in class toxTree.tree.AbstractTreePrinter
 
done() - Method in class toxTree.tree.AbstractTreeWriter
 
done() - Method in class toxTree.tree.PDFTreePrinter
 
done() - Method in class toxTree.tree.ReportTreePrinter
 
done() - Method in class toxTree.tree.Tree2PrefuseGraph
 
dontAsk - Variable in class toxtree.ui.OptionsPanel
 
DONTMARK - Static variable in class toxTree.query.FunctionalGroups
Use DONTMARK constant when building a query QueryAtom atom; atom.setProperty(DONTMARK,query.getID()); This is used as a flag that the atom belongs not to the group but to the neighboring radicals It is also essential for the FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer) procedure to work, as the bond to break is the one with one atom having the property set, while the other has the property unset
DRuleException - Exception in toxTree.exceptions
 
DRuleException(IDecisionCategory, boolean) - Constructor for exception toxTree.exceptions.DRuleException
 
DRuleException(String, IDecisionCategory, boolean) - Constructor for exception toxTree.exceptions.DRuleException
 
DRuleException(Throwable, IDecisionCategory, boolean) - Constructor for exception toxTree.exceptions.DRuleException
 
DRuleException(String, Throwable, IDecisionCategory, boolean) - Constructor for exception toxTree.exceptions.DRuleException
 
DRuleNotImplemented - Exception in toxTree.exceptions
Thrown when a rule is not implemented.
DRuleNotImplemented() - Constructor for exception toxTree.exceptions.DRuleNotImplemented
Constructor
DRuleNotImplemented(String) - Constructor for exception toxTree.exceptions.DRuleNotImplemented
Constructor
DRuleNotImplemented(Throwable) - Constructor for exception toxTree.exceptions.DRuleNotImplemented
Constructor
DRuleNotImplemented(String, Throwable) - Constructor for exception toxTree.exceptions.DRuleNotImplemented
Constructor
DRulePropertyNotAvailable - Exception in toxTree.exceptions
 
DRulePropertyNotAvailable(String) - Constructor for exception toxTree.exceptions.DRulePropertyNotAvailable
Constructor
DRulePropertyNotAvailable(String, String) - Constructor for exception toxTree.exceptions.DRulePropertyNotAvailable
Constructor
DRulePropertyNotAvailable(String, Throwable) - Constructor for exception toxTree.exceptions.DRulePropertyNotAvailable
Constructor
DRulePropertyNotAvailable(String, String, Throwable) - Constructor for exception toxTree.exceptions.DRulePropertyNotAvailable
Constructor
dumpClasspath() - Method in class toxTree.logging.TTLogger
Outputs the system property for java.class.path.
dumpSystemProperties() - Method in class toxTree.logging.TTLogger
Outputs system properties for the operating system and the java version.

E

EDGES - Static variable in class toxtree.ui.tree.TreePrefuse
 
edit(Component, IDecisionCategory) - Method in interface toxTree.core.IDecisionCategoryEditor
 
edit(Component, IDecisionMethod) - Method in interface toxTree.core.IDecisionMethodEditor
 
edit(Container, IDecisionRule) - Method in interface toxTree.core.IDecisionRuleEditor
 
edit(Component, IDecisionCategory) - Method in class toxtree.ui.tree.categories.CategoryPanel
 
edit(Container, IDecisionRule) - Method in class toxtree.ui.tree.rules.RuleEditor
 
edit(Container, IDecisionRule) - Method in class toxtree.ui.tree.rules.RulePanel
 
edit(Container, IDecisionRule) - Method in class toxtree.ui.tree.rules.SMARTSRuleEditor
 
edit(Container, IDecisionRule) - Method in class toxtree.ui.tree.rules.SubstructureRulePanel
 
edit(Component, IDecisionMethod) - Method in class toxtree.ui.tree.TreeEditorPanel
 
editable - Variable in class toxTree.tree.AbstractRule
 
editable - Variable in class toxTree.tree.UserDefinedTree
 
editable - Variable in class toxtree.ui.tree.rules.RulePanel
 
editable - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
 
editable - Variable in class toxtree.ui.tree.ToxTreeEditorPanel
 
editable - Variable in class toxtree.ui.tree.TreeFrame
 
editAction - Variable in class toxtree.ui.HazardPanel
 
EditCategoryAction - Class in toxtree.ui.tree.actions
Edits a category
EditCategoryAction(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.EditCategoryAction
 
EditCategoryAction(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.EditCategoryAction
 
EditCategoryAction(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.EditCategoryAction
 
editCompoundAction - Variable in class toxtree.data.ToxTreeActions
 
EditCompoundAction - Class in toxtree.ui.actions
Launches JChempaint to edit a compound
EditCompoundAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.actions.EditCompoundAction
 
EditCompoundAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.actions.EditCompoundAction
 
EditCompoundAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.actions.EditCompoundAction
 
EditDecisionMethodAction - Class in toxtree.ui.tree.actions
 
EditDecisionMethodAction(DataModule) - Constructor for class toxtree.ui.tree.actions.EditDecisionMethodAction
 
EditDecisionMethodAction(DataModule, String) - Constructor for class toxtree.ui.tree.actions.EditDecisionMethodAction
 
EditDecisionMethodAction(DataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.EditDecisionMethodAction
 
editMethodAction - Variable in class toxtree.data.ToxTreeActions
 
editMolButton - Variable in class toxtree.ui.tree.rules.RulePanel
 
editMolecule(boolean, JFrame) - Method in class toxtree.data.DataModule
 
editMolecule(boolean, Component) - Method in class toxtree.ui.molecule.MoleculeEditAction
 
editor - Variable in class toxtree.data.DecisionMethodsDataModule
 
EditorFactory - Class in toxTree.ui
 
EditorFactory() - Constructor for class toxTree.ui.EditorFactory
 
editorPanel - Variable in class toxtree.ui.wizard.DecisionNodeWizard
 
EditorPanel - Class in toxtree.ui.wizard
 
EditorPanel() - Constructor for class toxtree.ui.wizard.EditorPanel
 
EditorPanel(IDecisionRuleEditor) - Constructor for class toxtree.ui.wizard.EditorPanel
 
EditRuleAction - Class in toxtree.ui.tree.actions
Launches IDecisionRuleEditor of a preset rule.
EditRuleAction(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.EditRuleAction
 
EditRuleAction(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.EditRuleAction
 
EditRuleAction(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.EditRuleAction
 
editSmarts() - Method in class toxtree.ui.tree.rules.SMARTSRuleEditor
 
editSmarts(String, String) - Method in class toxtree.ui.tree.rules.SMARTSRuleEditor
 
EditTreeActions - Class in toxtree.ui.tree
 
EditTreeActions(IDecisionMethod) - Constructor for class toxtree.ui.tree.EditTreeActions
 
editTreeActions - Variable in class toxtree.ui.tree.TreeEditorPanel
 
EditTreeExplanation - Class in toxtree.ui.tree.actions
modifies tree explanation
EditTreeExplanation(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.EditTreeExplanation
 
EditTreeExplanation(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.EditTreeExplanation
 
EditTreeExplanation(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.EditTreeExplanation
 
elements - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
 
elements - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
 
elements - Variable in class toxTree.tree.rules.RuleElements
 
enable(boolean, String) - Method in class toxtree.data.ActionList
 
enabled - Variable in class toxtree.data.DataContainer
 
enabled - Variable in class toxtree.ui.HashtableModel
 
enableDataControls(boolean) - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
 
enableDataControls(boolean) - Method in class toxtree.ui.batch.BatchProcessingDialog
 
enumerateJars(File) - Static method in class toxTree.core.Introspection
 
EPOXIDE - Static variable in class verhaar.query.FunctionalGroups
 
epoxide() - Static method in class verhaar.query.FunctionalGroups
 
equals(Object) - Method in class toxTree.core.SmartElementsList
 
equals(Object) - Method in class toxTree.data.AbstractFilter
 
equals(Object) - Method in class toxTree.data.MoleculesFile
 
equals(Object) - Method in class toxTree.data.ObjectPropertyFilter
 
equals(Object) - Method in class toxTree.io.batch.BatchProcessing
 
equals(Object) - Method in class toxTree.io.batch.FileState
 
equals(Object) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
equals(Object) - Method in class toxTree.qsar.QSARDescriptor
 
equals(Object) - Method in class toxTree.tree.AbstractRule
 
equals(Object) - Method in class toxTree.tree.AbstractTree
 
equals(Object) - Method in class toxTree.tree.CategoriesList
 
equals(Object) - Method in class toxTree.tree.DecisionNode
 
equals(Object) - Method in class toxTree.tree.DecisionNodesList
 
equals(Object) - Method in class toxTree.tree.DefaultCategory
 
equals(Object) - Method in class toxTree.tree.RuleResult
 
equals(Object) - Method in class toxTree.tree.rules.RuleDescriptor
 
equals(Object) - Method in class toxTree.tree.rules.RuleDescriptorRange
 
equals(Object) - Method in class toxTree.tree.rules.RuleElements
 
equals(Object) - Method in class toxTree.tree.rules.RuleManyAromaticRings
 
equals(Object) - Method in class toxTree.tree.rules.RuleSubstructures
 
equals(Object) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
equals(Object) - Method in class toxTree.tree.RulesList
 
equals(Object) - Method in class toxTree.tree.TreeResult
 
ERR_PRECONDITION_FAILED - Static variable in class toxTree.tree.rules.RuleRingSubstituents
 
ERR_STRUCTURENOTPREPROCESSED - Static variable in class toxTree.tree.AbstractRule
 
errMessage - Variable in class toxTree.tree.ProgressStatus
 
error(Object) - Method in class toxTree.logging.TTLogger
Shows ERROR output for the Object.
error(Object, int) - Method in class toxTree.logging.TTLogger
Shows ERROR output for the given Object's.
error(Object, double) - Method in class toxTree.logging.TTLogger
Shows ERROR output for the given Object's.
error(Object, boolean) - Method in class toxTree.logging.TTLogger
Shows ERROR output for the given Object's.
error(Object, Object) - Method in class toxTree.logging.TTLogger
Shows ERROR output for the given Object's.
error(Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows ERROR output for the given Object's.
error(Object, Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows ERROR output for the given Object's.
error(Object, Object, Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows ERROR output for the given Object's.
ESTER - Static variable in class toxTree.query.FunctionalGroups
 
ester() - Static method in class toxTree.query.FunctionalGroups
 
ester - Variable in class toxTree.tree.cramer.RuleAcyclicAcetalEsterOfQ30
 
ester - Variable in class toxTree.tree.cramer.RuleRingComplexSubstituents30
 
ester_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
esterOfalcoholSecondaryAttachedToTerminalVinyl() - Static method in class toxTree.query.FunctionalGroups
 
estimateAction - Variable in class toxTree.apps.toxForest.ToxForestDataModule
 
estimateAction - Variable in class toxtree.data.ToxTreeActions
 
EstimateAction - Class in toxtree.ui.actions
Applies a decision tree to the current molecule
EstimateAction(DataModule) - Constructor for class toxtree.ui.actions.EstimateAction
 
EstimateAction(DataModule, String) - Constructor for class toxtree.ui.actions.EstimateAction
 
EstimateAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.EstimateAction
 
estimateActions - Variable in class toxtree.data.ToxTreeActions
 
estimateAllAction - Variable in class toxtree.data.ToxTreeActions
 
EstimateAllAction - Class in toxtree.ui.actions
Applies the decision tree on all loaded molecules
EstimateAllAction(DataModule) - Constructor for class toxtree.ui.actions.EstimateAllAction
 
EstimateAllAction(DataModule, String) - Constructor for class toxtree.ui.actions.EstimateAllAction
 
EstimateAllAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.EstimateAllAction
 
estimated - Variable in class toxTree.tree.ProgressStatus
 
ETHER - Static variable in class toxTree.query.FunctionalGroups
 
ether() - Static method in class toxTree.query.FunctionalGroups
 
ethyl() - Static method in class toxTree.query.FunctionalGroups
 
examples - Variable in class mutant.rules.SMARTSGroup
 
examples - Variable in class toxTree.tree.AbstractRule
 
exclusion_rules - Variable in class mic.rules.SA27
 
exclusion_rules - Static variable in class mic.rules.SA28
 
exclusion_rules - Variable in class mutant.rules.SA27_gen
 
exclusion_rules - Static variable in class mutant.rules.SA28_gen
 
exclusion_rules - Static variable in class mutant.rules.SA31a_nogen
 
exclusion_rules_Hal - Static variable in class mutant.rules.SA31a_nogen
 
exit() - Method in class toxTree.apps.AbstractApplication
 
expectedTitle - Variable in class toxTree.tree.stats.ConfusionMatrix
 
explain(boolean) - Method in interface toxTree.core.IDecisionResult
 
explain() - Method in class toxtree.data.DecisionMethodsDataModule
 
explain(boolean) - Method in class toxTree.tree.BatchDecisionResultsList
 
explain(boolean) - Method in class toxTree.tree.RuleResult
 
explain(boolean, int) - Method in class toxTree.tree.RuleResult
 
explain(boolean) - Method in class toxTree.tree.TreeResult
return StringBuffer with textual explanation of the rules executed
explainAction - Variable in class toxtree.data.ToxTreeActions
 
ExplainAction - Class in toxtree.ui.actions
Explains the result of EstimateAction
ExplainAction(DataModule) - Constructor for class toxtree.ui.actions.ExplainAction
 
ExplainAction(DataModule, String) - Constructor for class toxtree.ui.actions.ExplainAction
 
ExplainAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.ExplainAction
 
explainRules(IDecisionResult, boolean) - Method in class com.molecularnetworks.start.BiodgeradationRules
 
explainRules(IDecisionResult, boolean) - Method in class cramer2.CramerRulesWithExtensions
 
explainRules(IDecisionResult, boolean) - Method in class eye.EyeIrritationRules
 
explainRules(IDecisionResult, boolean) - Method in class mic.MICRules
 
explainRules(IDecisionResult, boolean) - Method in class michaelacceptors.MichaelAcceptorRules
 
explainRules(IDecisionResult, boolean) - Method in class mutant.BB_CarcMutRules
 
explainRules(IDecisionResult, boolean) - Method in class sicret.SicretRules
 
explainRules(IDecisionResult, boolean) - Method in interface toxTree.core.IDecisionMethod
 
explainRules(IDecisionResult, boolean) - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
 
explainRules(IDecisionResult, boolean) - Method in class toxtree.plugins.func.FuncRules
 
explainRules(IDecisionResult, boolean) - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
 
explainRules(IDecisionResult, boolean) - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
 
explainRules(IDecisionResult, boolean) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
explainRules(IDecisionResult, boolean) - Method in class toxTree.tree.AbstractTree
 
explainRules(IDecisionResult, boolean) - Method in class toxTree.tree.BatchDecisionResultsList
 
explainRules(IDecisionResult, boolean) - Method in class toxTree.tree.cramer.CramerRules
 
explanation - Variable in class toxTree.qsar.LinearPreprocessor
 
explanation - Variable in class toxTree.qsar.MatrixPreprocessor
 
explanation - Variable in class toxTree.tree.AbstractRule
 
explanation - Variable in class toxTree.tree.AbstractTree
 
explanation - Variable in class toxTree.tree.DefaultCategory
 
explanation - Variable in class toxtree.ui.tree.rules.RulePanel
 
explanation - Variable in class toxtree.ui.tree.ToxTreeEditorPanel
 
explanationPane - Variable in class toxtree.ui.tree.ToxTreeEditorPanel
 
exportRules(OutputStream, String) - Method in class toxtree.ui.tree.actions.SaveTreeAction
 
extension - Variable in class toxTree.io.MolFileFilter
 
extensions - Static variable in class toxTree.io.batch.ChemObjectBatchProcessing
 
extensions_descr - Static variable in class toxTree.io.batch.ChemObjectBatchProcessing
 
extractChains(IAtomContainer, List<List<Integer>>) - Method in class eye.rules.Rule13_AliphaticMonoalcohols
 
extractor - Variable in class mutant.descriptors.SubstituentsDescriptor
 
extractSubstituents(IAtomContainer) - Method in class mutant.descriptors.SubstituentExtractor
Note: Aromaticity flags should already be set before running this method.
eye - package eye
Class SicretRules is the implementation of BfR rules for estimating skin irritation and corrosion potential.
eye.categories - package eye.categories
The package contains implementations of IDecisionCategory categories for EyeIrritationRules decision tree.
eye.rules - package eye.rules
The package contains implementations of IDecisionRule rules for SicretRules decision tree.
EyeIrritationRules - Class in eye
Decision tree for estimating skin irritation and corrosion potential.
EyeIrritationRules() - Constructor for class eye.EyeIrritationRules
 

F

factory - Static variable in class toxTree.ui.EditorFactory
 
falseIfRuleNotImplemented - Variable in class toxTree.tree.AbstractTree
 
fatal(Object) - Method in class toxTree.logging.TTLogger
Shows FATAL output for the Object.
fColor - Variable in class toxtree.ui.molecule.NavigationPanel
 
FG - Class in toxtree.plugins.func.rules
 
FG() - Constructor for class toxtree.plugins.func.rules.FG
 
FG1 - Class in toxtree.plugins.func.rules
 
FG1() - Constructor for class toxtree.plugins.func.rules.FG1
 
FG10 - Class in toxtree.plugins.func.rules
 
FG10() - Constructor for class toxtree.plugins.func.rules.FG10
 
FG11 - Class in toxtree.plugins.func.rules
 
FG11() - Constructor for class toxtree.plugins.func.rules.FG11
 
FG12 - Class in toxtree.plugins.func.rules
 
FG12() - Constructor for class toxtree.plugins.func.rules.FG12
 
FG13 - Class in toxtree.plugins.func.rules
 
FG13() - Constructor for class toxtree.plugins.func.rules.FG13
 
FG14 - Class in toxtree.plugins.func.rules
 
FG14() - Constructor for class toxtree.plugins.func.rules.FG14
 
FG15 - Class in toxtree.plugins.func.rules
 
FG15() - Constructor for class toxtree.plugins.func.rules.FG15
 
FG16 - Class in toxtree.plugins.func.rules
 
FG16() - Constructor for class toxtree.plugins.func.rules.FG16
 
FG17 - Class in toxtree.plugins.func.rules
 
FG17() - Constructor for class toxtree.plugins.func.rules.FG17
 
FG18 - Class in toxtree.plugins.func.rules
 
FG18() - Constructor for class toxtree.plugins.func.rules.FG18
 
FG19 - Class in toxtree.plugins.func.rules
 
FG19() - Constructor for class toxtree.plugins.func.rules.FG19
 
FG2 - Class in toxtree.plugins.func.rules
 
FG2() - Constructor for class toxtree.plugins.func.rules.FG2
 
FG20 - Class in toxtree.plugins.func.rules
 
FG20() - Constructor for class toxtree.plugins.func.rules.FG20
 
FG21 - Class in toxtree.plugins.func.rules
 
FG21() - Constructor for class toxtree.plugins.func.rules.FG21
 
FG22 - Class in toxtree.plugins.func.rules
 
FG22() - Constructor for class toxtree.plugins.func.rules.FG22
 
FG23_1 - Class in toxtree.plugins.func.rules
 
FG23_1() - Constructor for class toxtree.plugins.func.rules.FG23_1
 
FG23_2 - Class in toxtree.plugins.func.rules
 
FG23_2() - Constructor for class toxtree.plugins.func.rules.FG23_2
 
FG23_3 - Class in toxtree.plugins.func.rules
 
FG23_3() - Constructor for class toxtree.plugins.func.rules.FG23_3
 
FG23_4 - Class in toxtree.plugins.func.rules
 
FG23_4() - Constructor for class toxtree.plugins.func.rules.FG23_4
 
FG23_5 - Class in toxtree.plugins.func.rules
 
FG23_5() - Constructor for class toxtree.plugins.func.rules.FG23_5
 
FG23_6 - Class in toxtree.plugins.func.rules
 
FG23_6() - Constructor for class toxtree.plugins.func.rules.FG23_6
 
FG23_7 - Class in toxtree.plugins.func.rules
 
FG23_7() - Constructor for class toxtree.plugins.func.rules.FG23_7
 
FG23_8 - Class in toxtree.plugins.func.rules
 
FG23_8() - Constructor for class toxtree.plugins.func.rules.FG23_8
 
FG23_LS - Class in toxtree.plugins.func.rules
 
FG23_LS() - Constructor for class toxtree.plugins.func.rules.FG23_LS
 
FG24_1 - Class in toxtree.plugins.func.rules
 
FG24_1() - Constructor for class toxtree.plugins.func.rules.FG24_1
 
FG24_2 - Class in toxtree.plugins.func.rules
 
FG24_2() - Constructor for class toxtree.plugins.func.rules.FG24_2
 
FG24_3 - Class in toxtree.plugins.func.rules
 
FG24_3() - Constructor for class toxtree.plugins.func.rules.FG24_3
 
FG24_LS - Class in toxtree.plugins.func.rules
 
FG24_LS() - Constructor for class toxtree.plugins.func.rules.FG24_LS
 
FG25 - Class in toxtree.plugins.func.rules
 
FG25() - Constructor for class toxtree.plugins.func.rules.FG25
 
FG26 - Class in toxtree.plugins.func.rules
 
FG26() - Constructor for class toxtree.plugins.func.rules.FG26
 
FG27 - Class in toxtree.plugins.func.rules
 
FG27() - Constructor for class toxtree.plugins.func.rules.FG27
 
FG28 - Class in toxtree.plugins.func.rules
 
FG28() - Constructor for class toxtree.plugins.func.rules.FG28
 
FG29 - Class in toxtree.plugins.func.rules
 
FG29() - Constructor for class toxtree.plugins.func.rules.FG29
 
FG30 - Class in toxtree.plugins.func.rules
 
FG30() - Constructor for class toxtree.plugins.func.rules.FG30
 
FG31_1 - Class in toxtree.plugins.func.rules
 
FG31_1() - Constructor for class toxtree.plugins.func.rules.FG31_1
 
FG31_2 - Class in toxtree.plugins.func.rules
 
FG31_2() - Constructor for class toxtree.plugins.func.rules.FG31_2
 
FG31_3 - Class in toxtree.plugins.func.rules
 
FG31_3() - Constructor for class toxtree.plugins.func.rules.FG31_3
 
FG31_4 - Class in toxtree.plugins.func.rules
 
FG31_4() - Constructor for class toxtree.plugins.func.rules.FG31_4
 
FG31_5 - Class in toxtree.plugins.func.rules
 
FG31_5() - Constructor for class toxtree.plugins.func.rules.FG31_5
 
FG31_6 - Class in toxtree.plugins.func.rules
 
FG31_6() - Constructor for class toxtree.plugins.func.rules.FG31_6
 
FG31_7 - Class in toxtree.plugins.func.rules
 
FG31_7() - Constructor for class toxtree.plugins.func.rules.FG31_7
 
FG31_8 - Class in toxtree.plugins.func.rules
 
FG31_8() - Constructor for class toxtree.plugins.func.rules.FG31_8
 
FG31_9 - Class in toxtree.plugins.func.rules
 
FG31_9() - Constructor for class toxtree.plugins.func.rules.FG31_9
 
FG31_LS - Class in toxtree.plugins.func.rules
 
FG31_LS() - Constructor for class toxtree.plugins.func.rules.FG31_LS
 
FG32 - Class in toxtree.plugins.func.rules
 
FG32() - Constructor for class toxtree.plugins.func.rules.FG32
 
FG33_1 - Class in toxtree.plugins.func.rules
 
FG33_1() - Constructor for class toxtree.plugins.func.rules.FG33_1
 
FG33_2 - Class in toxtree.plugins.func.rules
 
FG33_2() - Constructor for class toxtree.plugins.func.rules.FG33_2
 
FG33_3 - Class in toxtree.plugins.func.rules
 
FG33_3() - Constructor for class toxtree.plugins.func.rules.FG33_3
 
FG33_4 - Class in toxtree.plugins.func.rules
 
FG33_4() - Constructor for class toxtree.plugins.func.rules.FG33_4
 
FG33_5 - Class in toxtree.plugins.func.rules
 
FG33_5() - Constructor for class toxtree.plugins.func.rules.FG33_5
 
FG33_6 - Class in toxtree.plugins.func.rules
 
FG33_6() - Constructor for class toxtree.plugins.func.rules.FG33_6
 
FG33_7 - Class in toxtree.plugins.func.rules
 
FG33_7() - Constructor for class toxtree.plugins.func.rules.FG33_7
 
FG33_8 - Class in toxtree.plugins.func.rules
 
FG33_8() - Constructor for class toxtree.plugins.func.rules.FG33_8
 
FG33_LS - Class in toxtree.plugins.func.rules
 
FG33_LS() - Constructor for class toxtree.plugins.func.rules.FG33_LS
 
FG34_1 - Class in toxtree.plugins.func.rules
 
FG34_1() - Constructor for class toxtree.plugins.func.rules.FG34_1
 
FG34_2 - Class in toxtree.plugins.func.rules
 
FG34_2() - Constructor for class toxtree.plugins.func.rules.FG34_2
 
FG34_LS - Class in toxtree.plugins.func.rules
 
FG34_LS() - Constructor for class toxtree.plugins.func.rules.FG34_LS
 
FG35_1 - Class in toxtree.plugins.func.rules
 
FG35_1() - Constructor for class toxtree.plugins.func.rules.FG35_1
 
FG35_10 - Class in toxtree.plugins.func.rules
 
FG35_10() - Constructor for class toxtree.plugins.func.rules.FG35_10
 
FG35_11 - Class in toxtree.plugins.func.rules
 
FG35_11() - Constructor for class toxtree.plugins.func.rules.FG35_11
 
FG35_12 - Class in toxtree.plugins.func.rules
 
FG35_12() - Constructor for class toxtree.plugins.func.rules.FG35_12
 
FG35_13 - Class in toxtree.plugins.func.rules
 
FG35_13() - Constructor for class toxtree.plugins.func.rules.FG35_13
 
FG35_2 - Class in toxtree.plugins.func.rules
 
FG35_2() - Constructor for class toxtree.plugins.func.rules.FG35_2
 
FG35_3 - Class in toxtree.plugins.func.rules
 
FG35_3() - Constructor for class toxtree.plugins.func.rules.FG35_3
 
FG35_4 - Class in toxtree.plugins.func.rules
 
FG35_4() - Constructor for class toxtree.plugins.func.rules.FG35_4
 
FG35_5 - Class in toxtree.plugins.func.rules
 
FG35_5() - Constructor for class toxtree.plugins.func.rules.FG35_5
 
FG35_6 - Class in toxtree.plugins.func.rules
 
FG35_6() - Constructor for class toxtree.plugins.func.rules.FG35_6
 
FG35_7 - Class in toxtree.plugins.func.rules
 
FG35_7() - Constructor for class toxtree.plugins.func.rules.FG35_7
 
FG35_8 - Class in toxtree.plugins.func.rules
 
FG35_8() - Constructor for class toxtree.plugins.func.rules.FG35_8
 
FG35_9 - Class in toxtree.plugins.func.rules
 
FG35_9() - Constructor for class toxtree.plugins.func.rules.FG35_9
 
FG35_LS - Class in toxtree.plugins.func.rules
 
FG35_LS() - Constructor for class toxtree.plugins.func.rules.FG35_LS
 
FG36 - Class in toxtree.plugins.func.rules
 
FG36() - Constructor for class toxtree.plugins.func.rules.FG36
 
FG37_1 - Class in toxtree.plugins.func.rules
 
FG37_1() - Constructor for class toxtree.plugins.func.rules.FG37_1
 
FG37_2 - Class in toxtree.plugins.func.rules
 
FG37_2() - Constructor for class toxtree.plugins.func.rules.FG37_2
 
FG37_3 - Class in toxtree.plugins.func.rules
 
FG37_3() - Constructor for class toxtree.plugins.func.rules.FG37_3
 
FG37_4 - Class in toxtree.plugins.func.rules
 
FG37_4() - Constructor for class toxtree.plugins.func.rules.FG37_4
 
FG37_LS - Class in toxtree.plugins.func.rules
 
FG37_LS() - Constructor for class toxtree.plugins.func.rules.FG37_LS
 
FG38 - Class in toxtree.plugins.func.rules
 
FG38() - Constructor for class toxtree.plugins.func.rules.FG38
 
FG39 - Class in toxtree.plugins.func.rules
 
FG39() - Constructor for class toxtree.plugins.func.rules.FG39
 
FG3_1 - Class in toxtree.plugins.func.rules
 
FG3_1() - Constructor for class toxtree.plugins.func.rules.FG3_1
 
FG3_2 - Class in toxtree.plugins.func.rules
 
FG3_2() - Constructor for class toxtree.plugins.func.rules.FG3_2
 
FG3_LS - Class in toxtree.plugins.func.rules
 
FG3_LS() - Constructor for class toxtree.plugins.func.rules.FG3_LS
 
FG4 - Class in toxtree.plugins.func.rules
 
FG4() - Constructor for class toxtree.plugins.func.rules.FG4
 
FG40 - Class in toxtree.plugins.func.rules
 
FG40() - Constructor for class toxtree.plugins.func.rules.FG40
 
FG41_1 - Class in toxtree.plugins.func.rules
 
FG41_1() - Constructor for class toxtree.plugins.func.rules.FG41_1
 
FG41_2 - Class in toxtree.plugins.func.rules
 
FG41_2() - Constructor for class toxtree.plugins.func.rules.FG41_2
 
FG41_3 - Class in toxtree.plugins.func.rules
 
FG41_3() - Constructor for class toxtree.plugins.func.rules.FG41_3
 
FG41_4 - Class in toxtree.plugins.func.rules
 
FG41_4() - Constructor for class toxtree.plugins.func.rules.FG41_4
 
FG41_5 - Class in toxtree.plugins.func.rules
 
FG41_5() - Constructor for class toxtree.plugins.func.rules.FG41_5
 
FG41_LS - Class in toxtree.plugins.func.rules
 
FG41_LS() - Constructor for class toxtree.plugins.func.rules.FG41_LS
 
FG42 - Class in toxtree.plugins.func.rules
 
FG42() - Constructor for class toxtree.plugins.func.rules.FG42
 
FG43 - Class in toxtree.plugins.func.rules
 
FG43() - Constructor for class toxtree.plugins.func.rules.FG43
 
FG44 - Class in toxtree.plugins.func.rules
 
FG44() - Constructor for class toxtree.plugins.func.rules.FG44
 
FG45 - Class in toxtree.plugins.func.rules
 
FG45() - Constructor for class toxtree.plugins.func.rules.FG45
 
FG46_1 - Class in toxtree.plugins.func.rules
 
FG46_1() - Constructor for class toxtree.plugins.func.rules.FG46_1
 
FG46_2 - Class in toxtree.plugins.func.rules
 
FG46_2() - Constructor for class toxtree.plugins.func.rules.FG46_2
 
FG46_LS - Class in toxtree.plugins.func.rules
 
FG46_LS() - Constructor for class toxtree.plugins.func.rules.FG46_LS
 
FG47 - Class in toxtree.plugins.func.rules
 
FG47() - Constructor for class toxtree.plugins.func.rules.FG47
 
FG48_1 - Class in toxtree.plugins.func.rules
 
FG48_1() - Constructor for class toxtree.plugins.func.rules.FG48_1
 
FG48_2 - Class in toxtree.plugins.func.rules
 
FG48_2() - Constructor for class toxtree.plugins.func.rules.FG48_2
 
FG48_LS - Class in toxtree.plugins.func.rules
 
FG48_LS() - Constructor for class toxtree.plugins.func.rules.FG48_LS
 
FG49 - Class in toxtree.plugins.func.rules
 
FG49() - Constructor for class toxtree.plugins.func.rules.FG49
 
FG4_1 - Class in toxtree.plugins.func.rules
 
FG4_1() - Constructor for class toxtree.plugins.func.rules.FG4_1
 
FG4_2 - Class in toxtree.plugins.func.rules
 
FG4_2() - Constructor for class toxtree.plugins.func.rules.FG4_2
 
FG4_LS - Class in toxtree.plugins.func.rules
 
FG4_LS() - Constructor for class toxtree.plugins.func.rules.FG4_LS
 
FG5 - Class in toxtree.plugins.func.rules
 
FG5() - Constructor for class toxtree.plugins.func.rules.FG5
 
FG50_1 - Class in toxtree.plugins.func.rules
 
FG50_1() - Constructor for class toxtree.plugins.func.rules.FG50_1
 
FG50_2 - Class in toxtree.plugins.func.rules
 
FG50_2() - Constructor for class toxtree.plugins.func.rules.FG50_2
 
FG50_3 - Class in toxtree.plugins.func.rules
 
FG50_3() - Constructor for class toxtree.plugins.func.rules.FG50_3
 
FG50_LS - Class in toxtree.plugins.func.rules
 
FG50_LS() - Constructor for class toxtree.plugins.func.rules.FG50_LS
 
FG51_1 - Class in toxtree.plugins.func.rules
 
FG51_1() - Constructor for class toxtree.plugins.func.rules.FG51_1
 
FG51_2 - Class in toxtree.plugins.func.rules
 
FG51_2() - Constructor for class toxtree.plugins.func.rules.FG51_2
 
FG51_3 - Class in toxtree.plugins.func.rules
 
FG51_3() - Constructor for class toxtree.plugins.func.rules.FG51_3
 
FG51_LS - Class in toxtree.plugins.func.rules
 
FG51_LS() - Constructor for class toxtree.plugins.func.rules.FG51_LS
 
FG52_1 - Class in toxtree.plugins.func.rules
 
FG52_1() - Constructor for class toxtree.plugins.func.rules.FG52_1
 
FG52_2 - Class in toxtree.plugins.func.rules
 
FG52_2() - Constructor for class toxtree.plugins.func.rules.FG52_2
 
FG52_3 - Class in toxtree.plugins.func.rules
 
FG52_3() - Constructor for class toxtree.plugins.func.rules.FG52_3
 
FG52_LS - Class in toxtree.plugins.func.rules
 
FG52_LS() - Constructor for class toxtree.plugins.func.rules.FG52_LS
 
FG53_1 - Class in toxtree.plugins.func.rules
 
FG53_1() - Constructor for class toxtree.plugins.func.rules.FG53_1
 
FG53_2 - Class in toxtree.plugins.func.rules
 
FG53_2() - Constructor for class toxtree.plugins.func.rules.FG53_2
 
FG53_3 - Class in toxtree.plugins.func.rules
 
FG53_3() - Constructor for class toxtree.plugins.func.rules.FG53_3
 
FG53_LS - Class in toxtree.plugins.func.rules
 
FG53_LS() - Constructor for class toxtree.plugins.func.rules.FG53_LS
 
FG54 - Class in toxtree.plugins.func.rules
 
FG54() - Constructor for class toxtree.plugins.func.rules.FG54
 
FG55 - Class in toxtree.plugins.func.rules
 
FG55() - Constructor for class toxtree.plugins.func.rules.FG55
 
FG56 - Class in toxtree.plugins.func.rules
 
FG56() - Constructor for class toxtree.plugins.func.rules.FG56
 
FG57 - Class in toxtree.plugins.func.rules
 
FG57() - Constructor for class toxtree.plugins.func.rules.FG57
 
FG58 - Class in toxtree.plugins.func.rules
 
FG58() - Constructor for class toxtree.plugins.func.rules.FG58
 
FG59 - Class in toxtree.plugins.func.rules
 
FG59() - Constructor for class toxtree.plugins.func.rules.FG59
 
FG6 - Class in toxtree.plugins.func.rules
 
FG6() - Constructor for class toxtree.plugins.func.rules.FG6
 
FG60 - Class in toxtree.plugins.func.rules
 
FG60() - Constructor for class toxtree.plugins.func.rules.FG60
 
FG61 - Class in toxtree.plugins.func.rules
 
FG61() - Constructor for class toxtree.plugins.func.rules.FG61
 
FG62 - Class in toxtree.plugins.func.rules
 
FG62() - Constructor for class toxtree.plugins.func.rules.FG62
 
FG63 - Class in toxtree.plugins.func.rules
 
FG63() - Constructor for class toxtree.plugins.func.rules.FG63
 
FG64 - Class in toxtree.plugins.func.rules
 
FG64() - Constructor for class toxtree.plugins.func.rules.FG64
 
FG65 - Class in toxtree.plugins.func.rules
 
FG65() - Constructor for class toxtree.plugins.func.rules.FG65
 
FG66 - Class in toxtree.plugins.func.rules
 
FG66() - Constructor for class toxtree.plugins.func.rules.FG66
 
FG67 - Class in toxtree.plugins.func.rules
 
FG67() - Constructor for class toxtree.plugins.func.rules.FG67
 
FG68 - Class in toxtree.plugins.func.rules
 
FG68() - Constructor for class toxtree.plugins.func.rules.FG68
 
FG69 - Class in toxtree.plugins.func.rules
 
FG69() - Constructor for class toxtree.plugins.func.rules.FG69
 
FG7 - Class in toxtree.plugins.func.rules
 
FG7() - Constructor for class toxtree.plugins.func.rules.FG7
 
FG70 - Class in toxtree.plugins.func.rules
 
FG70() - Constructor for class toxtree.plugins.func.rules.FG70
 
FG71 - Class in toxtree.plugins.func.rules
 
FG71() - Constructor for class toxtree.plugins.func.rules.FG71
 
FG72 - Class in toxtree.plugins.func.rules
 
FG72() - Constructor for class toxtree.plugins.func.rules.FG72
 
FG73 - Class in toxtree.plugins.func.rules
 
FG73() - Constructor for class toxtree.plugins.func.rules.FG73
 
FG74_1 - Class in toxtree.plugins.func.rules
 
FG74_1() - Constructor for class toxtree.plugins.func.rules.FG74_1
 
FG74_2 - Class in toxtree.plugins.func.rules
 
FG74_2() - Constructor for class toxtree.plugins.func.rules.FG74_2
 
FG74_3 - Class in toxtree.plugins.func.rules
 
FG74_3() - Constructor for class toxtree.plugins.func.rules.FG74_3
 
FG74_4 - Class in toxtree.plugins.func.rules
 
FG74_4() - Constructor for class toxtree.plugins.func.rules.FG74_4
 
FG74_5 - Class in toxtree.plugins.func.rules
 
FG74_5() - Constructor for class toxtree.plugins.func.rules.FG74_5
 
FG74_6 - Class in toxtree.plugins.func.rules
 
FG74_6() - Constructor for class toxtree.plugins.func.rules.FG74_6
 
FG74_7 - Class in toxtree.plugins.func.rules
 
FG74_7() - Constructor for class toxtree.plugins.func.rules.FG74_7
 
FG74_LS - Class in toxtree.plugins.func.rules
 
FG74_LS() - Constructor for class toxtree.plugins.func.rules.FG74_LS
 
FG75_1 - Class in toxtree.plugins.func.rules
 
FG75_1() - Constructor for class toxtree.plugins.func.rules.FG75_1
 
FG75_2 - Class in toxtree.plugins.func.rules
 
FG75_2() - Constructor for class toxtree.plugins.func.rules.FG75_2
 
FG75_3 - Class in toxtree.plugins.func.rules
 
FG75_3() - Constructor for class toxtree.plugins.func.rules.FG75_3
 
FG75_4 - Class in toxtree.plugins.func.rules
 
FG75_4() - Constructor for class toxtree.plugins.func.rules.FG75_4
 
FG75_LS - Class in toxtree.plugins.func.rules
 
FG75_LS() - Constructor for class toxtree.plugins.func.rules.FG75_LS
 
FG76 - Class in toxtree.plugins.func.rules
 
FG76() - Constructor for class toxtree.plugins.func.rules.FG76
 
FG77 - Class in toxtree.plugins.func.rules
 
FG77() - Constructor for class toxtree.plugins.func.rules.FG77
 
FG78_1 - Class in toxtree.plugins.func.rules
 
FG78_1() - Constructor for class toxtree.plugins.func.rules.FG78_1
 
FG78_2 - Class in toxtree.plugins.func.rules
 
FG78_2() - Constructor for class toxtree.plugins.func.rules.FG78_2
 
FG78_3 - Class in toxtree.plugins.func.rules
 
FG78_3() - Constructor for class toxtree.plugins.func.rules.FG78_3
 
FG78_4 - Class in toxtree.plugins.func.rules
 
FG78_4() - Constructor for class toxtree.plugins.func.rules.FG78_4
 
FG78_LS - Class in toxtree.plugins.func.rules
 
FG78_LS() - Constructor for class toxtree.plugins.func.rules.FG78_LS
 
FG79_1 - Class in toxtree.plugins.func.rules
 
FG79_1() - Constructor for class toxtree.plugins.func.rules.FG79_1
 
FG79_2 - Class in toxtree.plugins.func.rules
 
FG79_2() - Constructor for class toxtree.plugins.func.rules.FG79_2
 
FG79_3 - Class in toxtree.plugins.func.rules
 
FG79_3() - Constructor for class toxtree.plugins.func.rules.FG79_3
 
FG79_4 - Class in toxtree.plugins.func.rules
 
FG79_4() - Constructor for class toxtree.plugins.func.rules.FG79_4
 
FG79_LS - Class in toxtree.plugins.func.rules
 
FG79_LS() - Constructor for class toxtree.plugins.func.rules.FG79_LS
 
FG8 - Class in toxtree.plugins.func.rules
 
FG8() - Constructor for class toxtree.plugins.func.rules.FG8
 
FG80_1 - Class in toxtree.plugins.func.rules
 
FG80_1() - Constructor for class toxtree.plugins.func.rules.FG80_1
 
FG80_2 - Class in toxtree.plugins.func.rules
 
FG80_2() - Constructor for class toxtree.plugins.func.rules.FG80_2
 
FG80_LS - Class in toxtree.plugins.func.rules
 
FG80_LS() - Constructor for class toxtree.plugins.func.rules.FG80_LS
 
FG81_1 - Class in toxtree.plugins.func.rules
 
FG81_1() - Constructor for class toxtree.plugins.func.rules.FG81_1
 
FG81_2 - Class in toxtree.plugins.func.rules
 
FG81_2() - Constructor for class toxtree.plugins.func.rules.FG81_2
 
FG81_3 - Class in toxtree.plugins.func.rules
 
FG81_3() - Constructor for class toxtree.plugins.func.rules.FG81_3
 
FG81_4 - Class in toxtree.plugins.func.rules
 
FG81_4() - Constructor for class toxtree.plugins.func.rules.FG81_4
 
FG81_LS - Class in toxtree.plugins.func.rules
 
FG81_LS() - Constructor for class toxtree.plugins.func.rules.FG81_LS
 
FG82_1 - Class in toxtree.plugins.func.rules
 
FG82_1() - Constructor for class toxtree.plugins.func.rules.FG82_1
 
FG82_2 - Class in toxtree.plugins.func.rules
 
FG82_2() - Constructor for class toxtree.plugins.func.rules.FG82_2
 
FG82_3 - Class in toxtree.plugins.func.rules
 
FG82_3() - Constructor for class toxtree.plugins.func.rules.FG82_3
 
FG82_4 - Class in toxtree.plugins.func.rules
 
FG82_4() - Constructor for class toxtree.plugins.func.rules.FG82_4
 
FG82_LS - Class in toxtree.plugins.func.rules
 
FG82_LS() - Constructor for class toxtree.plugins.func.rules.FG82_LS
 
FG83_1 - Class in toxtree.plugins.func.rules
 
FG83_1() - Constructor for class toxtree.plugins.func.rules.FG83_1
 
FG83_2 - Class in toxtree.plugins.func.rules
 
FG83_2() - Constructor for class toxtree.plugins.func.rules.FG83_2
 
FG83_3 - Class in toxtree.plugins.func.rules
 
FG83_3() - Constructor for class toxtree.plugins.func.rules.FG83_3
 
FG83_4 - Class in toxtree.plugins.func.rules
 
FG83_4() - Constructor for class toxtree.plugins.func.rules.FG83_4
 
FG83_LS - Class in toxtree.plugins.func.rules
 
FG83_LS() - Constructor for class toxtree.plugins.func.rules.FG83_LS
 
FG84_1 - Class in toxtree.plugins.func.rules
 
FG84_1() - Constructor for class toxtree.plugins.func.rules.FG84_1
 
FG84_2 - Class in toxtree.plugins.func.rules
 
FG84_2() - Constructor for class toxtree.plugins.func.rules.FG84_2
 
FG84_LS - Class in toxtree.plugins.func.rules
 
FG84_LS() - Constructor for class toxtree.plugins.func.rules.FG84_LS
 
FG85 - Class in toxtree.plugins.func.rules
 
FG85() - Constructor for class toxtree.plugins.func.rules.FG85
 
FG86 - Class in toxtree.plugins.func.rules
 
FG86() - Constructor for class toxtree.plugins.func.rules.FG86
 
FG87 - Class in toxtree.plugins.func.rules
 
FG87() - Constructor for class toxtree.plugins.func.rules.FG87
 
FG88 - Class in toxtree.plugins.func.rules
 
FG88() - Constructor for class toxtree.plugins.func.rules.FG88
 
FG89 - Class in toxtree.plugins.func.rules
 
FG89() - Constructor for class toxtree.plugins.func.rules.FG89
 
FG9 - Class in toxtree.plugins.func.rules
 
FG9() - Constructor for class toxtree.plugins.func.rules.FG9
 
FG90 - Class in toxtree.plugins.func.rules
 
FG90() - Constructor for class toxtree.plugins.func.rules.FG90
 
FIELD_ANSWER - Static variable in class toxTree.tree.Tree2PrefuseGraph
 
FIELD_CATEGORY - Static variable in class toxTree.tree.Tree2PrefuseGraph
 
FIELD_EXPLANATION - Static variable in class toxTree.tree.Tree2PrefuseGraph
 
FIELD_ID - Static variable in class toxTree.tree.Tree2PrefuseGraph
 
FIELD_NAME - Static variable in class toxTree.tree.Tree2PrefuseGraph
 
FIELD_NODETYPE - Static variable in class toxTree.tree.Tree2PrefuseGraph
 
FIELD_RULE - Static variable in class toxTree.tree.Tree2PrefuseGraph
 
FIELD_SHORT_NAME - Static variable in class toxTree.tree.Tree2PrefuseGraph
 
file - Variable in class toxTree.io.batch.FileState
 
file - Variable in class toxTree.tree.rules.InChILookupFile
 
file - Variable in class toxTree.tree.rules.LookupFile
 
file4Batch - Variable in class toxTree.apps.ToxTreeApp
 
fileActions - Variable in class toxtree.data.ToxTreeActions
 
fileCache - Variable in class toxTree.tree.rules.LookupFile
 
fileLabel - Variable in class toxtree.ui.molecule.TopPanel
 
fileLabel - Variable in class toxtree.ui.tree.rules.RuleStructuresPanel
 
filename - Variable in class toxTree.data.MoleculesIterator
 
filename - Variable in exception toxTree.exceptions.ToxTreeIOException
 
filename - Variable in class toxTree.io.batch.FileState
 
filename - Variable in class toxTree.tree.rules.RuleStructuresList
 
filePanel - Variable in class toxtree.ui.molecule.TopPanel
 
FileState - Class in toxTree.io.batch
This is to be able to verify if a file has changed since it has been last processed by BatchProcessing
FileState() - Constructor for class toxTree.io.batch.FileState
 
FileState(String) - Constructor for class toxTree.io.batch.FileState
 
FileState(File) - Constructor for class toxTree.io.batch.FileState
 
fileSubstructureAction - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
 
fileToOpen - Variable in class toxTree.apps.CompoundMethodApplication
 
filter(IDecisionResult) - Method in class toxtree.data.DataContainer
 
filter(IObjectFilter) - Method in class toxtree.data.FilteredMoleculesIterator
 
filterAll(IDecisionResult) - Method in class toxtree.data.DecisionMethodData
 
FilteredMoleculesIterator - Class in toxtree.data
 
FilteredMoleculesIterator() - Constructor for class toxtree.data.FilteredMoleculesIterator
 
filteredSets - Variable in class toxtree.data.FilteredMoleculesIterator
 
FilterException - Exception in toxTree.exceptions
 
FilterException() - Constructor for exception toxTree.exceptions.FilterException
 
FilterException(String) - Constructor for exception toxTree.exceptions.FilterException
 
FilterException(Throwable) - Constructor for exception toxTree.exceptions.FilterException
 
FilterException(String, Throwable) - Constructor for exception toxTree.exceptions.FilterException
 
final_and_patch - Variable in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
finalize() - Method in class toxTree.data.MoleculesFile
 
find(IAtomContainer) - Method in interface toxTree.data.IMoleculeLookup
 
find(Object, Object) - Method in interface toxTree.data.IMoleculeLookup
 
find(IAtomContainer) - Method in class toxTree.data.MoleculesFile
TODO introduce isomorphism check to handle nonunique fingerprints
Find - Class in toxtree.plugins.search.rules
Compound lookup
Find() - Constructor for class toxtree.plugins.search.rules.Find
 
find(IAtomContainer) - Method in interface toxTree.tree.rules.ILookupFile
 
find(IAtomContainer) - Method in class toxTree.tree.rules.InChILookupFile
 
find(IAtomContainer) - Method in class toxTree.tree.rules.LookupFile
 
findObject(int, int) - Method in class toxtree.ui.tree.TreeLayout
 
finished() - Method in class toxtree.ui.GUIWorker
 
fireChangeEvent(PropertyChangeEvent) - Method in class toxTree.tree.TreeResult
 
fireNewRoot() - Method in class toxtree.ui.tree.DecisionTreeModel
Call when there is a new root, which may be null, i.e.
firePathLeafStateChanged(TreePath) - Method in class toxtree.ui.tree.DecisionTreeModel
Call when a node has changed its leaf state.
firePropertyChange(String, Object, Object) - Method in class toxTree.data.MoleculesFile
 
firePropertyChange(PropertyChangeEvent) - Method in class toxTree.data.MoleculesFile
 
firePropertyChangeEvent(String, Object, Object) - Method in class toxTree.tree.BatchDecisionResultsList
 
firePropertyChangeEvent(String, int, int) - Method in class toxTree.tree.TreeResult
 
firePropertyChangeEvent(String, boolean, boolean) - Method in class toxTree.tree.TreeResult
 
firePropertyChangeEvent(String, Object, Object) - Method in class toxTree.tree.TreeResult
 
fireStructureChanged() - Method in class toxtree.ui.tree.DecisionTreeModel
Call when everything but the root has changed.
fireTreeStructureChanged(TreePath) - Method in class toxtree.ui.tree.DecisionTreeModel
Call when the tree structure below the path has completely changed.
first() - Method in interface toxTree.core.IMoleculesIterator
 
first() - Method in class toxtree.data.DataContainer
 
first() - Method in class toxTree.data.MoleculesFile
 
first() - Method in class toxTree.data.MoleculesIterator
 
flag_calculated - Variable in class toxTree.qsar.AbstractQSARModel
 
flags - Variable in class toxTree.tree.rules.RuleRingSubstituents
 
focusGained(FocusEvent) - Method in class toxtree.ui.OptionsPanel
 
focusGained(FocusEvent) - Method in class toxtree.ui.tree.rules.RulePanel
 
focusGained(FocusEvent) - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
focusLost(FocusEvent) - Method in class toxtree.ui.OptionsPanel
 
focusLost(FocusEvent) - Method in class toxtree.ui.tree.rules.RulePanel
 
focusLost(FocusEvent) - Method in class toxtree.ui.tree.rules.RulePropertyEditor
 
focusLost(FocusEvent) - Method in class toxtree.ui.tree.rules.RuleRangeEditor
 
focusLost(FocusEvent) - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
folder - Variable in class toxTree.tree.ReportTreePrinter
 
forestFromTree(IDecisionMethod) - Static method in class toxtree.ui.tree.actions.NewRuleAction
Creates forest of trees, each tree consists of a single rule.
FORMAT - Static variable in class toxtree.plugins.smartcyp.SMARTCypTreeResult
 
Found - Class in toxtree.plugins.search.categories
Not found
Found() - Constructor for class toxtree.plugins.search.categories.Found
 
foundIndex - Variable in class toxTree.data.MoleculesFile
 
fp - Variable in class toxTree.data.MoleculesFile
 
fragment - Variable in class mutant.descriptors.DescriptorStructurePresence
 
frame - Variable in class toxtree.data.ActionList
 
frame - Variable in class toxtree.ui.actions.DataModuleAction
 
frame - Static variable in class toxtree.ui.tree.TreeEditorPanel
 
freeCells - Variable in class toxtree.ui.tree.TreeLayout
 
fromXML(Element) - Method in interface toxTree.core.XMLSerializable
 
fromXML(Element) - Method in class toxTree.tree.AbstractRule
 
fromXML(Element) - Method in class toxTree.tree.AbstractTree
 
fromXML(Element) - Method in class toxTree.tree.CategoriesList
 
fromXML(Element) - Method in class toxTree.tree.DecisionMethodsList
 
fromXML(Element) - Method in class toxTree.tree.DecisionNodesList
 
fromXML(Element) - Method in class toxTree.tree.DefaultCategory
 
fromXML(Element) - Method in class toxTree.tree.RulesList
 
fStream - Variable in class toxTree.tree.rules.LookupFile
 
FuncCat1 - Class in toxtree.plugins.func.categories
 
FuncCat1() - Constructor for class toxtree.plugins.func.categories.FuncCat1
 
FuncCat2 - Class in toxtree.plugins.func.categories
 
FuncCat2() - Constructor for class toxtree.plugins.func.categories.FuncCat2
 
FuncRules - Class in toxtree.plugins.func
 
FuncRules() - Constructor for class toxtree.plugins.func.FuncRules
 
FunctionalGroups - Class in toxTree.query
This class provides static methods for various functional groups In addition there are several static methods to manipulate searching
FunctionalGroups() - Constructor for class toxTree.query.FunctionalGroups
 
FunctionalGroups - Class in verhaar.query
A singleton class providing static methods for various functional groups in VerhaarScheme.
FunctionalGroups() - Constructor for class verhaar.query.FunctionalGroups
 
FuncTreeResult - Class in toxtree.plugins.func.rules
 
FuncTreeResult() - Constructor for class toxtree.plugins.func.rules.FuncTreeResult
 

G

g - Variable in class toxTree.tree.SimpleTreePrinter
 
gen - Static variable in class toxTree.query.SimpleReactions
 
generateOutputFileName(File) - Static method in class toxTree.io.batch.BatchFactory
 
get(int) - Method in class toxTree.tree.CategoriesList
 
get(int) - Method in class toxTree.tree.DecisionMethodsList
 
get(int) - Method in class toxTree.tree.DecisionNodesList
 
get(int) - Method in class toxTree.tree.RulesList
 
get() - Method in class toxtree.ui.GUIWorker
 
getActions() - Method in class toxTree.apps.toxForest.ToxForestDataModule
 
getActions() - Method in class toxtree.data.DataModule
 
getActions() - Method in class toxtree.data.DecisionMethodsDataModule
 
getActions() - Method in class toxtree.data.ToxTreeModule
 
getActiveContainer() - Method in class toxtree.data.FilteredMoleculesIterator
 
getAllAssignedMolecules() - Method in class mic.rules.MICTreeResult
 
getAllAssignedMolecules() - Method in class mutant.rules.MutantTreeResult
 
getAllAssignedMolecules() - Method in class toxtree.plugins.func.rules.FuncTreeResult
 
getAllAssignedMolecules() - Method in class toxtree.plugins.smartcyp.SMARTCypTreeResult
 
getAllGroups() - Static method in class toxTree.query.FunctionalGroups
 
getAminoGroupOrder(IAtomContainerSet, String) - Method in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
If more than one amino group is present, the -N with lowest steric hindrance ( 1.
getAminoGroupSubstituents(IAtomContainer, int) - Method in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
getAnswer() - Method in enum toxTree.core.IDecisionInteractive.UserOptions
 
getAnswer() - Method in class toxtree.ui.tree.actions.SetBranchAction
 
getAromaticRings() - Method in class toxTree.query.MolFlags
 
getAssignedCategories() - Method in interface toxTree.core.IDecisionResult
 
getAssignedCategories() - Method in class toxTree.tree.BatchDecisionResultsList
 
getAssignedCategories() - Method in class toxTree.tree.TreeResult
 
getAtomContainer(int) - Method in interface toxTree.core.IMoleculesIterator
 
getAtomContainer(int) - Method in class toxTree.data.ListOfAtomContainers
 
getAtomContainer(int) - Method in class toxTree.data.MoleculesFile
 
getAtomContainer(int) - Method in class toxTree.data.MoleculesIterator
 
getAtomContainer() - Method in exception toxTree.exceptions.MolAnalyseException
 
getAtomContainerCount() - Method in class toxTree.data.ListOfAtomContainers
 
getAtomContainerCount() - Method in class toxTree.data.MoleculesFile
 
getAtomContainers() - Method in class toxTree.data.ListOfAtomContainers
 
getAtomScoresOfRank(IAtomContainer, Integer, MoleculeKU.SMARTCYP_PROPERTY) - Method in class toxtree.plugins.smartcyp.SMARTCypTreeResult
 
getAvailableCategoryTypes(ClassLoader) - Static method in class toxTree.core.Introspection
Returns a list with available categories
getAvailableRuleTypes(ClassLoader) - Static method in class toxTree.core.Introspection
Returns a list with available rule names.
getAvailableTreeTypes(ClassLoader) - Static method in class toxTree.core.Introspection
Returns a list with available decision trees.
getAvailableTypes(ClassLoader, String) - Static method in class toxTree.core.Introspection
This method is the core of ToxTreeApp extension mechanism.
getBackId() - Method in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
getBackPanelDescriptor() - Method in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
getBatch() - Method in class toxtree.ui.batch.BatchProcessingDialog
 
getBondMap(IAtomContainer, IAtomContainer, boolean) - Static method in class toxTree.query.FunctionalGroups
 
getBranch(IDecisionRule, boolean) - Method in interface toxTree.core.IDecisionMethod
 
getBranch(boolean) - Method in interface toxTree.core.IDecisionTransition
 
getBranch(IDecisionRule, boolean) - Method in class toxTree.tree.BatchDecisionResultsList
 
getBranch(boolean) - Method in class toxTree.tree.DecisionNode
returns the decision rule at the branch No if answer==false or the decision rule at the branch Yes if answer =true
getBranch(IDecisionRule, boolean) - Method in class toxTree.tree.UserDefinedTree
 
getBranch(int, boolean) - Method in class toxTree.tree.UserDefinedTree
 
getBuilder() - Method in class toxTree.data.ListOfAtomContainers
 
getCaption() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getCategories() - Method in interface toxTree.core.IDecisionMethod
 
getCategories() - Method in class toxTree.tree.AbstractTree
 
getCategories() - Method in class toxTree.tree.BatchDecisionResultsList
 
getCategories() - Method in class toxTree.tree.DecisionNode
 
getCategory(IDecisionCategory) - Method in interface toxTree.core.IDecisionCategories
 
getCategory() - Method in interface toxTree.core.IDecisionCategoryEditor
 
getCategory(IDecisionRule, boolean) - Method in interface toxTree.core.IDecisionMethod
 
getCategory() - Method in interface toxTree.core.IDecisionResult
 
getCategory(int) - Method in interface toxTree.core.IDecisionResult
 
getCategory(boolean) - Method in interface toxTree.core.IDecisionTransition
 
getCategory(IDecisionRule, boolean) - Method in class toxTree.tree.BatchDecisionResultsList
 
getCategory() - Method in class toxTree.tree.BatchDecisionResultsList
 
getCategory(int) - Method in class toxTree.tree.BatchDecisionResultsList
 
getCategory(IDecisionCategory) - Method in class toxTree.tree.CategoriesList
 
getCategory(boolean) - Method in class toxTree.tree.DecisionNode
returns the decision category at the branch No if answer==false or the category at the branch Yes if answer =true
getCategory() - Method in class toxTree.tree.RuleResult
 
getCategory() - Method in class toxTree.tree.TreeResult
 
getCategory(int) - Method in class toxTree.tree.TreeResult
 
getCategory(IDecisionRule, boolean) - Method in class toxTree.tree.UserDefinedTree
 
getCategory(int, boolean) - Method in class toxTree.tree.UserDefinedTree
 
getCategory() - Method in class toxtree.ui.tree.actions.EditCategoryAction
 
getCategory() - Method in interface toxtree.ui.tree.actions.ICategoryAction
 
getCategory(int) - Method in class toxtree.ui.tree.categories.CategoriesTableModel
 
getCategory() - Method in class toxtree.ui.tree.categories.CategoryPanel
 
getCategory2assign() - Method in exception toxTree.exceptions.DRuleException
 
getCategoryActions() - Method in class toxtree.ui.tree.EditTreeActions
 
getCategoryExplanation() - Method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
 
getCategoryExplanation() - Method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
 
getCategoryExplanation() - Method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
 
getCategoryTitle() - Method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
 
getCategoryTitle() - Method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
 
getCategoryTitle() - Method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
 
getChild(Object, int) - Method in class toxtree.ui.tree.DecisionTreeModel
 
getChildCount(Object) - Method in class toxtree.ui.tree.DecisionTreeModel
 
getClassName() - Method in class toxTree.core.ToxTreePackageEntry
 
getColumnClass(int) - Method in class toxtree.ui.HashtableModel
 
getColumnClass(int) - Method in class toxtree.ui.tree.rules.DecisionNodesListTableModel
 
getColumnCount() - Method in class toxtree.ui.HashtableModel
 
getColumnCount() - Method in class toxtree.ui.molecule.AtomContainerPropertyTableModel
 
getColumnCount() - Method in class toxtree.ui.tree.categories.CategoriesTableModel
 
getColumnCount() - Method in class toxtree.ui.tree.DecisionMethodsTableModel
 
getColumnCount() - Method in class toxtree.ui.tree.ListTableModel
 
getColumnCount() - Method in class toxtree.ui.tree.rules.DecisionNodesListTableModel
 
getColumnCount() - Method in class toxtree.ui.tree.ToxTreePackageEntryModel
 
getColumnName(int) - Method in class toxtree.ui.HashtableModel
 
getColumnName(int) - Method in class toxtree.ui.tree.categories.CategoriesTableModel
 
getColumnName(int) - Method in class toxtree.ui.tree.DecisionMethodsTableModel
 
getColumnName(int) - Method in class toxtree.ui.tree.ListTableModel
 
getColumnName(int) - Method in class toxtree.ui.tree.rules.DecisionNodesListTableModel
 
getCondition() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getCondition() - Method in class toxtree.ui.tree.rules.RulePropertyEditor
 
getConfigFile() - Method in class toxTree.io.batch.BatchProcessing
Where to store batchprocessing configuration itself
getConfiguration() - Static method in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
 
getContainers() - Method in class toxtree.data.FilteredMoleculesIterator
 
getContainers() - Method in class toxTree.data.MoleculesIterator
 
getCurrentDirectory() - Static method in class toxtree.data.ActionList
 
getCurrentNo() - Method in interface toxTree.core.IMoleculesIterator
 
getCurrentNo() - Method in class toxtree.data.DataContainer
 
getCurrentNo() - Method in class toxTree.data.MoleculesIterator
 
getCurrentRecord() - Method in class toxTree.io.batch.FileState
 
getData() - Method in class toxtree.ui.tree.categories.CategoriesTableModel
 
getDataContainer() - Method in class toxtree.data.DataModule
 
getDataContainer() - Method in class toxtree.ui.molecule.NavigationPanel
 
getDataContainer() - Method in class toxtree.ui.molecule.StructureEntryPanel
 
getDataContainer() - Method in class toxtree.ui.molecule.TopPanel
 
getDataModule() - Method in class toxtree.ui.DataModulePanel
 
getDataRows() - Method in class toxtree.ui.tree.qsar.DescriptorOptions
 
getDataRows() - Method in class toxtree.ui.tree.qsar.OptionsPanel
 
getDateCreated() - Method in class toxTree.io.batch.BatchProcessing
 
getDateCreated() - Method in interface toxTree.io.batch.IBatchProcessing
 
getDateLastProcessed() - Method in class toxTree.io.batch.BatchProcessing
 
getDateLastProcessed() - Method in interface toxTree.io.batch.IBatchProcessing
 
getDecisionMethod() - Method in interface toxTree.core.IDecisionResult
 
getDecisionMethod() - Method in class toxTree.io.batch.ToxTreeBatchProcessing
 
getDecisionMethod() - Method in class toxTree.tree.BatchDecisionResultsList
 
getDecisionMethod() - Method in class toxTree.tree.TreeResult
 
getDecisionMethod() - Method in class toxtree.ui.batch.BatchProcessingDialog
 
getDecisionMethod() - Method in interface toxtree.ui.tree.ITreeView
 
getDecisionMethod() - Method in class toxtree.ui.tree.JCustomTreeComponent
 
getDecisionMethod() - Method in class toxtree.ui.tree.TreeDrawing
 
getDecisionMethod() - Method in class toxtree.ui.tree.TreePrefuse
 
getDecisionNode() - Method in interface toxtree.ui.tree.actions.INodeAction
 
getDecisionNode() - Method in class toxtree.ui.tree.actions.SetBranchAction
 
getDefaultDirectories() - Static method in class toxTree.core.Introspection
 
getDelimiter() - Method in class toxTree.tree.SimpleTreePrinter
 
getDescription() - Method in class toxTree.io.MolFileFilter
 
getDescriptor(int) - Method in class toxTree.qsar.AbstractQSARModel
 
getDescriptor() - Method in class toxTree.qsar.QSARDescriptor
 
getDescriptor() - Method in class toxTree.tree.rules.RuleDescriptor
 
getDescriptor(int) - Method in class toxtree.ui.wizard.DecisionNodeWizard
 
getDescriptorName() - Method in class toxTree.qsar.QSARDescriptor
 
getDescriptorNames() - Method in class mutant.descriptors.DescriptorIDist
 
getDescriptorNames() - Method in class mutant.descriptors.DescriptorMolarRefractivity
 
getDescriptorNames() - Method in class mutant.descriptors.DescriptorStructurePresence
 
getDescriptorNames() - Method in class mutant.descriptors.SubstituentsDescriptor
 
getDescriptorNames() - Method in class toxTree.core.ToxTreeDescriptor
 
getDescriptorNames() - Method in class toxTree.qsar.AbstractQSARModel
 
getDescriptorNames() - Method in class toxTree.tree.UserDefinedTree
 
getDescriptorResultType() - Method in class mutant.descriptors.DescriptorIDist
 
getDescriptorResultType() - Method in class mutant.descriptors.DescriptorMolarRefractivity
 
getDescriptorResultType() - Method in class mutant.descriptors.DescriptorStructurePresence
 
getDescriptorResultType() - Method in class mutant.descriptors.SubstituentsDescriptor
 
getDescriptorResultType() - Method in class toxTree.core.ToxTreeDescriptor
 
getDescriptorResultType() - Method in class toxTree.tree.UserDefinedTree
 
getDescriptors() - Method in class toxTree.qsar.AbstractQSARModel
 
getDescriptors(IAtomContainer) - Method in class toxTree.qsar.LinearQSARModel
 
getDimension() - Method in interface toxTree.qsar.IDescriptorPreprocessor
 
getDimension() - Method in class toxTree.qsar.LinearPreprocessor
 
getDimension() - Method in class toxTree.qsar.MatrixPreprocessor
 
getEditCompoundAction() - Method in class toxtree.data.ToxTreeActions
 
getEditor() - Method in interface toxTree.core.IDecisionCategory
 
getEditor() - Method in interface toxTree.core.IDecisionMethod
Each rule provides an editor, which is a class implementing IDecisionMethodEditor.
getEditor() - Method in interface toxTree.core.IDecisionRule
Each rule provides an editor, which is a class implementing IDecisionRuleEditor.
getEditor() - Method in class toxTree.data.AbstractFilter
 
getEditor() - Method in interface toxTree.data.IObjectFilter
 
getEditor() - Method in class toxTree.data.ObjectPropertyFilter
 
getEditor() - Method in class toxTree.qsar.AbstractQSARModel
 
getEditor() - Method in class toxTree.tree.AbstractRule
See IDecisionRule.getEditor()
getEditor() - Method in class toxTree.tree.AbstractTree
 
getEditor() - Method in class toxTree.tree.BatchDecisionResultsList
 
getEditor() - Method in class toxTree.tree.DecisionNode
 
getEditor() - Method in class toxTree.tree.DefaultCategory
 
getElements() - Method in class toxTree.tree.rules.RuleElements
 
getErrMessage() - Method in class toxTree.tree.ProgressStatus
 
getEstimateAction() - Method in class toxTree.apps.toxForest.ToxForestDataModule
 
getEstimateAction() - Method in class toxtree.data.ToxTreeActions
 
getExample(boolean) - Method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
 
getExample(boolean) - Method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
 
getExample(boolean) - Method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
 
getExampleMolecule(boolean) - Method in class eye.rules.RuleAqueousSolubility_10_2
 
getExampleMolecule(boolean) - Method in class eye.rules.RuleMolWeight_12_2
 
getExampleMolecule(boolean) - Method in interface toxTree.core.IDecisionRule
if ruleResult is TRUE, returns the example molecule if the rule is answered YES if ruleResult is FALSE, returns the example molecule if the rule is answered NO
getExampleMolecule(boolean) - Method in class toxTree.tree.AbstractRule
 
getExampleMolecule(boolean) - Method in class toxTree.tree.DecisionNode
 
getExampleMolecule(boolean) - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getExamples(boolean) - Method in class mutant.rules.SMARTSGroup
 
getExamples() - Method in class toxTree.tree.AbstractRule
 
getExpectedTitle() - Method in class toxTree.tree.stats.ConfusionMatrix
 
getExplainAction() - Method in class toxtree.data.ToxTreeActions
 
getExplanation(IAtomContainer) - Method in class mic.rules.MICTreeResult
 
getExplanation(IAtomContainer) - Method in class mutant.rules.MutantTreeResult
 
getExplanation() - Method in interface toxTree.core.IDecisionCategory
 
getExplanation() - Method in interface toxTree.core.IDecisionMethod
 
getExplanation() - Method in interface toxTree.core.IDecisionRule
Rule explanation is an arbitrary text, could be multiline and may contain html tags.
getExplanation() - Method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
 
getExplanation(IAtomContainer) - Method in class toxtree.plugins.dnabinding.rules.DNABindingTreeResult
 
getExplanation(IAtomContainer) - Method in class toxtree.plugins.func.rules.FuncTreeResult
 
getExplanation() - Method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
 
getExplanation(IAtomContainer) - Method in class toxtree.plugins.proteinbinding.rules.ProteinBindingTreeResult
 
getExplanation() - Method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
 
getExplanation(IAtomContainer) - Method in class toxtree.plugins.skinsensitisation.rules.SkinSensitisationTreeResult
 
getExplanation(IAtomContainer) - Method in class toxtree.plugins.smartcyp.SMARTCypTreeResult
 
getExplanation() - Method in interface toxTree.qsar.IDescriptorPreprocessor
 
getExplanation() - Method in class toxTree.qsar.LinearPreprocessor
 
getExplanation() - Method in class toxTree.qsar.MatrixPreprocessor
 
getExplanation() - Method in class toxTree.tree.AbstractRule
 
getExplanation() - Method in class toxTree.tree.AbstractTree
 
getExplanation() - Method in class toxTree.tree.BatchDecisionResultsList
 
getExplanation() - Method in class toxTree.tree.DecisionNode
 
getExplanation() - Method in class toxTree.tree.DefaultCategory
 
getExplanation() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getExplanation() - Method in class toxtree.ui.tree.categories.CategoryPanel
 
getExplanation() - Method in class toxtree.ui.tree.rules.RuleEditor
 
getExplanation() - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
getExtension() - Method in class toxTree.io.MolFileFilter
 
getFile() - Method in class toxTree.io.batch.FileState
 
getFile() - Method in interface toxTree.tree.rules.ILookupFile
 
getFile() - Method in class toxTree.tree.rules.InChILookupFile
 
getFile() - Method in class toxTree.tree.rules.LookupFile
 
getFile() - Method in class toxTree.tree.rules.RuleStructuresList
 
getFileFromResource(String) - Static method in class toxTree.io.Tools
Extract a file from resource and copies it into temporary directory.
getFileFromResourceSilent(String) - Static method in class toxTree.io.Tools
Same as Tools.getFileFromResource(String) but hides the exception
getFilename() - Method in interface toxTree.core.IMoleculesIterator
 
getFileName() - Method in class toxtree.data.DataContainer
 
getFilename() - Method in class toxTree.data.MoleculesIterator
 
getFilename() - Method in exception toxTree.exceptions.ToxTreeIOException
 
getFilename() - Method in class toxTree.io.batch.FileState
 
getFilename() - Method in class toxTree.tree.rules.RuleStructuresList
 
getFilters() - Method in class mutant.rules.MutantTreeResult
 
getFilters() - Method in interface toxTree.core.IDecisionResult
 
getFilters() - Method in class toxtree.plugins.dnabinding.rules.DNABindingTreeResult
 
getFilters() - Method in class toxtree.plugins.proteinbinding.rules.ProteinBindingTreeResult
 
getFilters() - Method in class toxtree.plugins.skinsensitisation.rules.SkinSensitisationTreeResult
 
getFilters() - Method in class toxtree.plugins.smartcyp.SMARTCypTreeResult
 
getFilters() - Method in class toxTree.tree.BatchDecisionResultsList
 
getFilters() - Method in class toxTree.tree.TreeResult
 
getFingerprint(IAtomContainer) - Method in class toxTree.data.MoleculesFile
 
getFlag(int) - Method in class toxTree.data.ListOfAtomContainers
 
getFlags() - Method in class toxTree.data.ListOfAtomContainers
 
getFormat() - Method in class toxTree.io.PDFWriter
 
getFrame() - Method in class toxtree.data.ActionList
 
getFrame() - Method in class toxtree.ui.actions.DataModuleAction
 
getGraph() - Method in class toxTree.tree.Tree2PrefuseGraph
 
getHalogens() - Method in class toxTree.core.SmartElementsList
 
gethalogens() - Method in class toxTree.tree.rules.RuleElements
 
getHalogens() - Method in class verhaar.rules.Rule21
 
getHalogens() - Method in class verhaar.rules.Rule22
 
getHalogens() - Method in class verhaar.rules.Rule23
 
getHalogens() - Method in class verhaar.rules.Rule25
 
getHashCode() - Method in class toxTree.io.batch.FileState
 
getHeaderRows() - Method in class toxtree.ui.tree.qsar.DescriptorOptions
 
getHeaderRows() - Method in class toxtree.ui.tree.qsar.OptionsPanel
 
getHelp(RuleResult) - Method in interface toxTree.core.IMetaboliteGenerator
 
getHelp(RuleResult) - Method in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
 
getHelp(RuleResult) - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
 
getHelp(RuleResult) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
getHelp() - Method in class toxtree.ui.tree.TreePrefuse
 
getHelpAction() - Method in interface toxtree.ui.tree.ITreeView
 
getHelpAction() - Method in class toxtree.ui.tree.JCustomTreeComponent
 
getHelpAction() - Method in class toxtree.ui.tree.TreePrefuse
 
getHideColor(int) - Method in class toxTree.ui.tree.categories.CategoriesRenderer
 
getHydrolysisPO4Reaction(int) - Method in class toxTree.query.SimpleReactions
 
getHydrolysisPO4ReactionCount() - Static method in class toxTree.query.SimpleReactions
 
getHydrolysisProducts() - Method in class toxTree.query.MolFlags
 
getHydrolysisReaction(int) - Method in class toxTree.query.SimpleReactions
 
getHydrolysisReactionCount() - Static method in class toxTree.query.SimpleReactions
 
getIcon() - Method in class toxTree.apps.AbstractApplication
 
getIcon() - Method in class toxTree.apps.CompoundMethodApplication
 
getIcon() - Method in class toxTree.apps.toxForest.ToxForestApp
 
getIcon() - Method in class toxTree.apps.ToxTreeApp
 
getIcon() - Method in class toxtree.ui.tree.TreeEditorPanel
 
getID() - Method in interface toxTree.core.IDecisionCategory
 
getID() - Method in interface toxTree.core.IDecisionRule
Rule identifier is an arbitrary string, preferably short one
getID() - Method in class toxTree.data.ListOfAtomContainers
 
getID() - Method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
 
getID() - Method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
 
getID() - Method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
 
getID() - Method in class toxTree.tree.AbstractRule
 
getID() - Method in class toxTree.tree.DecisionNode
 
getID() - Method in class toxTree.tree.DefaultCategory
 
getID() - Method in class toxtree.ui.tree.categories.CategoryPanel
 
getID() - Method in class toxtree.ui.tree.rules.RuleEditor
 
getID() - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
getId() - Method in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
getIds() - Method in class toxTree.tree.rules.RuleSubstructures
 
getImage(String) - Static method in class toxTree.io.Tools
Loads image
getImage(IAtomContainer) - Method in class toxTree.tree.AbstractTree
 
getImage(IAtomContainer, String, int, int, boolean) - Method in class toxTree.tree.AbstractTree
 
getImage(IAtomContainer, String, int, int, boolean) - Method in class toxTree.tree.BatchDecisionResultsList
 
getImage(IAtomContainer) - Method in class toxTree.tree.BatchDecisionResultsList
 
getImageSize() - Method in class toxTree.tree.AbstractTree
 
getImageSize() - Method in class toxTree.tree.BatchDecisionResultsList
 
getImplementationDetails() - Method in class mic.rules.SA18
 
getImplementationDetails() - Method in class mic.rules.SA19
 
getImplementationDetails() - Method in class mic.rules.SA26
 
getImplementationDetails() - Method in class mutant.rules.RuleDACancerogenicityAromaticAmines
Thus, if calculated w >29.08, then the substance should be carcinogen if calculated w< 29.08, then the substance should be noncarcinogen
getImplementationDetails() - Method in class mutant.rules.RuleDAMutagenicityABUnsaturatedAldehydes
 
getImplementationDetails() - Method in class mutant.rules.RuleDAMutagenicityAromaticAmines
 
getImplementationDetails() - Method in class mutant.rules.SA18_gen
 
getImplementationDetails() - Method in class mutant.rules.SA19_gen
 
getImplementationDetails() - Method in class mutant.rules.SA20_nogen
 
getImplementationDetails() - Method in class sicret.rules.RuleLogP
 
getImplementationDetails() - Method in interface toxTree.core.IImplementationDetails
 
getImplementationDetails() - Method in class toxTree.qsar.LinearDiscriminantRule
 
getImplementationDetails() - Method in class toxTree.tree.rules.DefaultAlertCounter
 
getImplementationDetails() - Method in class toxTree.tree.rules.RuleInitAlertCounter
 
getImplementationDetails() - Method in class toxTree.tree.rules.RuleVerifyAlertsCounter
 
getImplementationDetails() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getImplementationDetails() - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
getImplementationDetails() - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
getImplementationDetails() - Method in class toxTree.tree.rules.StructureAlert
 
getImplementationDetails() - Method in class toxTree.tree.rules.StructureAlertAmbit
 
getImplementationDetails() - Method in class toxTree.tree.rules.StructureAlertCDK
 
getImplementationDetails() - Method in class verhaar.rules.helper.RuleAnySubstructureCounter
 
getImplementationDetails() - Method in class verhaar.rules.helper.RuleElementsCounter
 
getImplementationDetails() - Method in class verhaar.rules.helper.RuleOnlyAllowedSubstructuresCounter
 
getImplementationDetails() - Method in class verhaar.rules.Rule03
 
getImplementationDetails() - Method in class verhaar.rules.Rule141
 
getImplementationDetails() - Method in class verhaar.rules.Rule143
 
getImplementationDetails() - Method in class verhaar.rules.Rule21
 
getImplementationDetails() - Method in class verhaar.rules.RuleIonicGroups
 
getImplementationDetails() - Method in class verhaar.rules.RuleLogPRange
 
getIndexOfChild(Object, Object) - Method in class toxtree.ui.tree.DecisionTreeModel
 
getInputFile() - Method in class toxTree.io.batch.BatchProcessing
 
getInstance() - Static method in class toxTree.ui.EditorFactory
 
getInstance() - Static method in class toxtree.ui.editors.SwingEditorFactory
 
getInteractive() - Method in class com.molecularnetworks.start.BiodgeradationRules
 
getInteractive() - Method in class eye.EyeIrritationRules
 
getInteractive() - Method in class mutant.rules.QSAR6Applicable
 
getInteractive() - Method in class sicret.SicretRules
 
getInteractive() - Method in interface toxTree.core.IDecisionInteractive
 
getInteractive() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getInteractive() - Method in class toxTree.tree.rules.UserInputRule
 
getInteractive() - Method in class toxTree.tree.UserDefinedTree
 
getJComponent() - Method in interface toxtree.ui.tree.ITreeView
 
getJComponent() - Method in class toxtree.ui.tree.JCustomTreeComponent
 
getJComponent() - Method in class toxtree.ui.tree.TreeDrawing
 
getJComponent() - Method in class toxtree.ui.tree.TreePrefuse
 
getKeyFromMap(RMap) - Static method in class toxTree.query.FunctionalGroups
 
getLastModified() - Method in class toxTree.io.batch.FileState
 
getLegend(int, int) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
getLegend(int, int) - Method in class toxTree.tree.AbstractTree
 
getLegend(int, int) - Method in class toxTree.tree.BatchDecisionResultsList
 
getLength() - Method in class toxTree.io.batch.FileState
 
getList() - Method in class toxTree.tree.DecisionMethodsList
 
getList() - Method in class toxTree.tree.DecisionNodesList
 
getList() - Method in class toxTree.tree.RulesList
 
getList() - Method in class toxtree.ui.tree.ListTableModel
 
getListener() - Method in class mutant.rules.QSAR6Applicable
 
getListener() - Method in interface toxTree.core.IDecisionInteractive
 
getListener() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getListener() - Method in class toxTree.tree.rules.UserInputRule
 
getListener() - Method in class toxTree.tree.UserDefinedTree
 
getListenerCount() - Method in class toxTree.data.ListOfAtomContainers
 
getLoader() - Static method in class toxTree.core.Introspection
 
getLogger() - Method in class toxTree.tree.rules.LookupFile
 
getLongestCarbonChainLength(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
getMatchingStructure(IAtomContainer) - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
getMatrix(IAtomContainer) - Static method in class toxTree.core.ConnectionMatrix
Returns the connection matrix representation of this AtomContainer.
getMatrix() - Method in class toxTree.qsar.MatrixPreprocessor
 
getMaxChainLength() - Method in class eye.rules.Rule13_AliphaticMonoalcohols
 
getMaxChainLength() - Method in class eye.rules.Rule30
 
getMaxHalogens() - Method in class verhaar.rules.Rule21
 
getMaxNitroGroups() - Method in class verhaar.rules.Rule21
 
getMaxValue() - Method in interface toxTree.core.IRuleRange
 
getMaxValue() - Method in class toxTree.tree.rules.RuleDescriptorRange
 
getMaxValue() - Method in class toxTree.tree.rules.RuleManyAromaticRings
 
getMessage() - Method in class toxTree.tree.rules.UserInputRule
 
getMetabolicReaction(int) - Method in class toxTree.query.SimpleReactions
 
getMetabolicReactionCount() - Static method in class toxTree.query.SimpleReactions
 
getMethod() - Method in interface toxTree.core.IDecisionMethodEditor
 
getMethod(int) - Method in interface toxTree.core.IDecisionMethodsList
 
getMethod(int) - Method in class toxTree.tree.DecisionMethodsList
 
getMethod(int) - Method in class toxTree.tree.DecisionResultsList
 
getMethod() - Method in class toxtree.ui.tree.TreeEditorPanel
 
getMethod() - Method in class toxtree.ui.tree.TreeLayout
 
getMethods() - Method in class toxtree.data.DecisionMethodsDataModule
 
getMinChainLength() - Method in class eye.rules.Rule13_AliphaticMonoalcohols
 
getMinChainLength() - Method in class eye.rules.Rule30
 
getMinValue() - Method in interface toxTree.core.IRuleRange
 
getMinValue() - Method in class toxTree.tree.rules.RuleDescriptorRange
 
getMinValue() - Method in class toxTree.tree.rules.RuleManyAromaticRings
 
getMode() - Method in class toxTree.tree.rules.RuleElements
 
getModel() - Method in class toxTree.qsar.LinearDiscriminantRule
 
getModel() - Method in class toxtree.ui.tree.ListPanel
 
getMolecule(int) - Method in interface toxTree.core.IDecisionResult
 
getMolecule() - Method in interface toxTree.core.IMoleculesIterator
 
getMolecule() - Method in class toxtree.data.DataContainer
 
getMolecule() - Method in class toxTree.data.MoleculesIterator
 
getMolecule(int) - Method in class toxTree.tree.BatchDecisionResultsList
 
getMolecule() - Method in class toxTree.tree.RuleResult
 
getMolecule(int) - Method in class toxTree.tree.TreeResult
 
getMolecule() - Method in class toxtree.ui.molecule.AbstractMoleculeAction
 
getMolecule() - Method in class toxtree.ui.molecule.StructureEntryPanel
 
getMoleculeForEdit() - Method in interface toxTree.core.IMoleculesIterator
 
getMoleculeForEdit() - Method in class toxTree.data.MoleculesIterator
 
getMoleculeForEdit(IAtomContainer) - Method in class toxtree.ui.molecule.MoleculeEditAction
 
getMolecules() - Method in interface toxTree.core.IMoleculesIterator
 
getMolecules() - Method in class toxTree.data.MoleculesIterator
 
getMoleculesCount() - Method in interface toxTree.core.IMoleculesIterator
 
getMoleculesCount() - Method in class toxtree.data.DataContainer
 
getMoleculesCount() - Method in class toxTree.data.MoleculesIterator
 
getMultiplier(int) - Method in class toxTree.data.ListOfAtomContainers
 
getMultiplier(IAtomContainer) - Method in class toxTree.data.ListOfAtomContainers
 
getMultiplier(int) - Method in class toxTree.data.MoleculesFile
 
getMultiplier(IAtomContainer) - Method in class toxTree.data.MoleculesFile
 
getMultipliers() - Method in class toxTree.data.ListOfAtomContainers
 
getMultipliers() - Method in class toxTree.data.MoleculesFile
 
getName() - Method in class com.molecularnetworks.start.BiodgeradationRules
 
getName() - Method in class cramer2.CramerRulesWithExtensions
 
getName() - Method in class eye.EyeIrritationRules
 
getName() - Method in class mic.MICRules
 
getName() - Method in class michaelacceptors.MichaelAcceptorRules
 
getName() - Method in class mutant.BB_CarcMutRules
 
getName() - Method in class mutant.rules.SMARTSGroup
 
getName() - Method in class sicret.SicretRules
 
getName() - Method in interface toxTree.core.IDecisionCategory
 
getName() - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
 
getName() - Method in class toxtree.plugins.func.FuncRules
 
getName() - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
 
getName() - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
 
getName() - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
getName() - Method in class toxTree.qsar.AbstractQSARModel
 
getName() - Method in class toxTree.tree.cramer.CramerRules
 
getName() - Method in class toxTree.tree.DefaultCategory
 
getNextId() - Method in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
getNextPanelDescriptor() - Method in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
getNoBranch() - Method in class toxtree.ui.tree.DecisionNodePanel
 
getNode(int) - Method in class toxTree.tree.DecisionNodesList
 
getNode() - Method in class toxtree.ui.tree.DecisionNodePanel
 
getNode() - Method in class toxtree.ui.tree.EditTreeActions
 
getNodes() - Method in class toxTree.tree.DecisionNode
 
getNodesFactory() - Method in class toxTree.tree.UserDefinedTree
 
getNotification() - Method in class toxTree.data.ListOfAtomContainers
 
getNum() - Method in interface toxTree.core.IDecisionRule
 
getNum() - Method in class toxTree.tree.AbstractRule
 
getNum() - Method in class toxTree.tree.DecisionNode
 
getNumberOfAromaticAtoms(IRing) - Method in class mic.rules.SA18
 
getNumberOfAromaticAtoms(IRing) - Method in class mutant.rules.SA18_gen
 
getNumberOfClasses() - Method in interface toxTree.core.IDecisionMethod
 
getNumberOfClasses() - Method in class toxTree.tree.AbstractTree
 
getNumberOfClasses() - Method in class toxTree.tree.BatchDecisionResultsList
 
getNumberofDescriptors() - Method in class toxTree.qsar.AbstractQSARModel
 
getNumberOfRules() - Method in interface toxTree.core.IDecisionMethod
 
getNumberOfRules() - Method in class toxTree.tree.AbstractTree
 
getNumberOfRules() - Method in class toxTree.tree.BatchDecisionResultsList
 
getObject() - Method in class toxTree.qsar.AbstractQSARModel
 
getObject() - Method in class toxtree.ui.tree.qsar.OptionsPanel
 
getObjectTitle() - Method in class toxTree.core.ToxTreePackageEntry
 
getObjectToVerify(IAtomContainer) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
getObjectToVerify(IAtomContainer) - Method in class toxTree.tree.rules.smarts.RuleSMARTSSubstructureAmbit
 
getObjectToVerify(IAtomContainer) - Method in class toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK
 
getObjectToVerify(IAtomContainer) - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
getOffset() - Method in class toxTree.io.batch.FileState
 
getOptions() - Method in class mutant.rules.QSAR6Applicable
 
getOptions() - Method in interface toxTree.core.IDecisionInteractive
 
getOptions() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getOptions() - Method in class toxTree.tree.rules.UserInputRule
 
getOptions() - Method in class toxTree.tree.UserDefinedTree
 
getOptions() - Method in class toxtree.ui.wizard.RadioBoxPanel
 
getOriginalIndexOf(int) - Method in class toxTree.data.SortedPropertyList
 
getOriginalIndexOf(Object) - Method in class toxTree.data.SortedPropertyList
 
getOriginalMolecule() - Method in class toxTree.tree.TreeResult
 
getOutputFile() - Method in class toxTree.io.batch.BatchProcessing
 
getOutputStream() - Method in class toxTree.tree.AbstractTreePrinter
 
getOverview() - Method in class toxtree.ui.tree.TreePrefuse
 
getPackageName() - Method in class toxTree.core.ToxTreePackageEntry
 
getPackageName() - Method in class toxtree.ui.actions.AboutAction
 
getParameterNames() - Method in class mutant.descriptors.DescriptorIDist
 
getParameterNames() - Method in class mutant.descriptors.DescriptorMolarRefractivity
 
getParameterNames() - Method in class mutant.descriptors.DescriptorStructurePresence
 
getParameterNames() - Method in class mutant.descriptors.SubstituentsDescriptor
 
getParameterNames() - Method in class toxTree.core.ToxTreeDescriptor
 
getParameterNames() - Method in class toxTree.tree.UserDefinedTree
 
getParameters() - Method in class mutant.descriptors.DescriptorIDist
 
getParameters() - Method in class mutant.descriptors.DescriptorMolarRefractivity
 
getParameters() - Method in class mutant.descriptors.DescriptorStructurePresence
 
getParameters() - Method in class mutant.descriptors.SubstituentsDescriptor
 
getParameters() - Method in class toxTree.core.ToxTreeDescriptor
 
getParameters() - Method in class toxTree.tree.UserDefinedTree
 
getParameterType(String) - Method in class mutant.descriptors.DescriptorIDist
 
getParameterType(String) - Method in class mutant.descriptors.DescriptorMolarRefractivity
 
getParameterType(String) - Method in class mutant.descriptors.DescriptorStructurePresence
 
getParameterType(String) - Method in class mutant.descriptors.SubstituentsDescriptor
 
getParameterType(String) - Method in class toxTree.core.ToxTreeDescriptor
 
getParameterType(String) - Method in class toxTree.tree.UserDefinedTree
 
getParamNames() - Method in class mutant.descriptors.DescriptorStructurePresence
 
getParent(Component) - Method in class toxtree.ui.molecule.MoleculeEditAction
 
getParentComponent() - Method in class toxtree.ui.molecule.MoleculeEditAction
 
getParentFrame() - Method in class toxtree.ui.tree.actions.AbstractRuleAction
 
getParentFrame() - Method in class toxtree.ui.tree.actions.AbstractTreeAction
 
getPeferredSize() - Method in class toxtree.ui.DataModulePanel
 
getPercentEstimated() - Method in class toxTree.tree.ProgressStatus
 
getPopupMenu() - Method in interface toxtree.ui.tree.ITreeView
 
getPopupMenu() - Method in class toxtree.ui.tree.JCustomTreeComponent
 
getPopupMenu() - Method in class toxtree.ui.tree.TreeDrawing
 
getPopupMenu() - Method in class toxtree.ui.tree.TreePrefuse
 
getPosition() - Method in class mutant.descriptors.SubstituentPosition
 
getPredictedproperty() - Method in class toxTree.qsar.AbstractQSARModel
 
getPredictedTitle() - Method in class toxTree.tree.stats.ConfusionMatrix
 
getPreprocessor() - Method in class toxTree.qsar.LinearQSARModel
 
getPriority() - Method in class mutant.categories.MutantCategory
 
getPriority() - Method in interface toxTree.core.IDecisionMethodPrority
 
getPriority() - Method in class toxTree.tree.AbstractTree
 
getPriority() - Method in class toxTree.tree.BatchDecisionResultsList
 
getPriority() - Method in class toxTree.tree.TreeResult
 
getProducts(IAtomContainer, RuleResult) - Method in interface toxTree.core.IMetaboliteGenerator
 
getProducts(IAtomContainer, RuleResult) - Method in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
 
getProducts(IAtomContainer, RuleResult) - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
 
getProducts(IAtomContainer, RuleResult) - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
getProducts() - Method in class toxtree.ui.metabolites.MetabolitesFrame
 
getProducts() - Method in class toxtree.ui.metabolites.MetabolitesPanel
 
getProperties() - Method in class toxTree.data.AbstractFilter
 
getProperties() - Method in interface toxTree.data.IObjectFilter
 
getProperties() - Method in class toxTree.data.ListOfAtomContainers
 
getProperties(int) - Method in class toxTree.data.MoleculesFile
 
getProperty() - Method in interface toxTree.core.IRuleRange
 
getProperty() - Method in interface toxTree.core.IRuleValue
 
getProperty(String) - Method in class toxTree.data.AbstractFilter
 
getProperty(String) - Method in interface toxTree.data.IObjectFilter
 
getProperty(Object) - Method in class toxTree.data.ListOfAtomContainers
 
getProperty(int, Object) - Method in class toxTree.data.MoleculesFile
 
getProperty() - Method in class toxTree.tree.rules.RuleDescriptorRange
 
getProperty() - Method in class toxTree.tree.rules.RuleManyAromaticRings
 
getProperty() - Method in class toxTree.tree.rules.RuleMolecularMassRange
 
getProperty() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getPropertyChangeListeners() - Method in interface toxTree.core.IDecisionResult
 
getPropertyChangeListeners() - Method in class toxTree.tree.BatchDecisionResultsList
 
getPropertyChangeListeners() - Method in class toxTree.tree.TreeResult
 
getPropertyMaxValue() - Method in class toxtree.ui.tree.rules.RuleRangeEditor
 
getPropertyMinValue() - Method in class toxtree.ui.tree.rules.RuleRangeEditor
 
getPropertyName() - Method in class toxTree.data.SortedPropertyList
 
getPropertyName() - Method in exception toxTree.exceptions.DRulePropertyNotAvailable
 
getPropertyName() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getPropertyName() - Method in class toxtree.ui.tree.rules.RulePropertyEditor
 
getPropertyName() - Method in class toxtree.ui.tree.rules.RuleRangeEditor
 
getPropertyUnits() - Method in class toxTree.tree.rules.RuleVerifyProperty
public String inputProperty(IAtomContainer mol) { PropertyEditor p = new PropertyEditor(mol,new OptionsPanel(toString(),mol, this)); if (JOptionPane.showConfirmDialog(null,p,"Rule " + getID() + "." + getCaption(), JOptionPane.OK_CANCEL_OPTION,JOptionPane.PLAIN_MESSAGE) == JOptionPane.OK_OPTION) { setInteractive(!p.isSilent()); return p.getPropertyValue(); } else return null; //return JOptionPane.showInputDialog("Enter " + propertyName + "," + propertyUnits); }
getPropertyValue() - Method in class toxtree.ui.OptionsPanel
 
getPropertyValue() - Method in class toxtree.ui.PropertyEditor
 
getPropertyValue() - Method in class toxtree.ui.tree.rules.RulePropertyEditor
 
getQuery() - Method in class toxTree.tree.rules.RuleSubstructures
 
getQuery() - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
getRank() - Method in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
 
getReader() - Method in class toxTree.data.MoleculesFile
 
getReader(FileState, boolean) - Method in class toxTree.io.batch.ChemObjectBatchProcessing
 
getReadRecordsCount() - Method in class toxTree.io.batch.BatchProcessing
Returns the number of records read from the input file
getReadRecordsCount() - Method in interface toxTree.io.batch.IBatchProcessing
 
getResidues() - Method in class toxTree.query.MolFlags
 
getResult(int) - Method in class toxTree.tree.DecisionResultsList
 
getResult() - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
 
getResultName() - Method in class mutant.descriptors.DescriptorStructurePresence
 
getResultPropertyName() - Method in class toxtree.plugins.verhaar2.rules.Verhaar2TreeResult
 
getResultPropertyName() - Method in class verhaar.rules.VerhaarTreeResult
 
getResultPropertyNames() - Method in class cramer2.categories.CramerTreeResult
 
getResultPropertyNames() - Method in class mic.rules.MICTreeResult
 
getResultPropertyNames() - Method in class mutant.rules.MutantTreeResult
 
getResultPropertyNames() - Method in interface toxTree.core.IDecisionResult
Returns the name of the property that will contain the result
getResultPropertyNames() - Method in class toxtree.plugins.dnabinding.rules.DNABindingTreeResult
 
getResultPropertyNames() - Method in class toxtree.plugins.func.rules.FuncTreeResult
 
getResultPropertyNames() - Method in class toxtree.plugins.proteinbinding.rules.ProteinBindingTreeResult
 
getResultPropertyNames() - Method in class toxtree.plugins.skinsensitisation.rules.SkinSensitisationTreeResult
 
getResultPropertyNames() - Method in class toxtree.plugins.smartcyp.SMARTCypTreeResult
 
getResultPropertyNames() - Method in class toxTree.tree.BatchDecisionResultsList
 
getResultPropertyNames() - Method in class toxTree.tree.cramer.CramerTreeResult
 
getResultPropertyNames() - Method in class toxTree.tree.TreeResult
 
getRingQuery() - Method in class mutant.descriptors.SubstituentExtractor
 
getRingQuery() - Method in class mutant.descriptors.SubstituentsDescriptor
 
getRingset() - Method in class toxTree.query.MolFlags
 
getRoot() - Method in class toxtree.ui.tree.DecisionTreeModel
 
getRowCount() - Method in class toxtree.ui.HashtableModel
 
getRowCount() - Method in class toxtree.ui.molecule.AtomContainerPropertyTableModel
 
getRowCount() - Method in class toxtree.ui.tree.ListTableModel
 
getRule(int) - Method in interface toxTree.core.IDecisionMethod
 
getRule(String) - Method in interface toxTree.core.IDecisionMethod
 
getRule(int) - Method in interface toxTree.core.IDecisionResult
 
getRule() - Method in interface toxTree.core.IDecisionRuleEditor
 
getRule(int) - Method in interface toxTree.core.IDecisionRuleList
 
getRule(int) - Method in class toxTree.tree.AbstractTree
 
getRule(String) - Method in class toxTree.tree.AbstractTree
 
getRule(int) - Method in class toxTree.tree.BatchDecisionResultsList
 
getRule(String) - Method in class toxTree.tree.BatchDecisionResultsList
 
getRule() - Method in class toxTree.tree.DecisionNode
 
getRule(int) - Method in class toxTree.tree.DecisionNodesList
 
getRule() - Method in class toxTree.tree.RuleResult
 
getRule(int) - Method in class toxTree.tree.RulesList
returns a rule IDecisionRule
getRule(int) - Method in class toxTree.tree.TreeResult
 
getRule(int) - Method in class toxTree.tree.UserDefinedTree
 
getRule() - Method in class toxtree.ui.tree.actions.AbstractRuleAction
 
getRule() - Method in class toxtree.ui.tree.actions.EditRuleAction
 
getRule() - Method in interface toxtree.ui.tree.actions.IRuleAction
 
getRule() - Method in class toxtree.ui.tree.rules.RuleEditor
 
getRule() - Method in class toxtree.ui.tree.rules.RuleMoleculeEditAction
 
getRule() - Method in class toxtree.ui.tree.rules.RulePanel
 
getRule() - Method in class toxtree.ui.tree.rules.SubstructureRulePanel
 
getRuleActions() - Method in class toxtree.ui.tree.EditTreeActions
 
getRuleResult(int) - Method in interface toxTree.core.IDecisionResult
 
getRuleResult(int) - Method in class toxTree.tree.BatchDecisionResultsList
 
getRuleResult(int) - Method in class toxTree.tree.TreeResult
 
getRuleResults() - Method in class toxTree.tree.TreeResult
 
getRuleResultsCount() - Method in interface toxTree.core.IDecisionResult
 
getRuleResultsCount() - Method in class toxTree.tree.BatchDecisionResultsList
 
getRuleResultsCount() - Method in class toxTree.tree.TreeResult
 
getRules() - Method in class toxTree.apps.toxForest.ToxForestDataModule
 
getRules() - Method in interface toxTree.core.IDecisionMethod
 
getRules() - Method in class toxtree.data.DecisionMethodsDataModule
 
getRules() - Method in class toxTree.tree.AbstractTree
 
getRules() - Method in class toxTree.tree.BatchDecisionResultsList
 
getSaveStateFrequency() - Method in class toxTree.io.batch.BatchProcessing
BatchProcessing saves its state on each saveStateFrequency records
getScale() - Method in class toxTree.qsar.LinearPreprocessor
 
getSelected() - Method in class toxTree.tree.CategoriesList
 
getSelectedIndex() - Method in class toxTree.data.MoleculesFile
 
getSelectedIndex() - Method in class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
 
getSelectedIndex() - Method in class toxtree.ui.wizard.RadioBoxPanel
 
getSelectedObject() - Method in class toxtree.ui.tree.ListPanel
 
getSelectedObject() - Method in class toxtree.ui.wizard.DecisionNodeWizard
 
getSelectedRules() - Method in class toxtree.data.DecisionMethodsDataModule
 
getSelector() - Method in class eye.rules.Rule13_AliphaticMonoalcohols
 
getSelector() - Method in class eye.rules.Rule38
 
getSelector() - Method in class mutant.rules.SA20_nogen
 
getSelector() - Method in interface toxTree.core.IDecisionRule
 
getSelector() - Method in class toxtree.plugins.dnabinding.rules.VerifyAlertsDNABinding
 
getSelector() - Method in class toxtree.plugins.kroes.rules.KroesRule8
 
getSelector() - Method in class toxtree.plugins.proteinbinding.rules.VerifyAlertsProteinBinding
 
getSelector() - Method in class toxtree.plugins.skinsensitisation.rules.VerifyAlertsSkinSensitisation
 
getSelector() - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
 
getSelector() - Method in class toxTree.qsar.LinearDiscriminantRule
 
getSelector() - Method in class toxTree.tree.AbstractRule
 
getSelector() - Method in class toxTree.tree.AbstractRuleHilightHits
 
getSelector() - Method in class toxTree.tree.cramer.Rule3MemberedHeterocycle
 
getSelector() - Method in class toxTree.tree.cramer.RuleLactonesFusedOrUnsaturated
 
getSelector() - Method in class toxTree.tree.DecisionNode
 
getSelector() - Method in class toxTree.tree.rules.RuleAnySubstituents
 
getSelector() - Method in class toxTree.tree.rules.RuleDescriptor
 
getSelector() - Method in class toxTree.tree.rules.RuleElements
 
getSelector() - Method in class toxTree.tree.rules.RuleHeterocyclic
 
getSelector() - Method in class toxTree.tree.rules.RuleManyAromaticRings
 
getSelector() - Method in class toxTree.tree.rules.RuleOpenChain
 
getSelector() - Method in class toxTree.tree.rules.RuleStructuresList
 
getSelector() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
getSelector() - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
getSetOfAtomContainers() - Method in class toxTree.data.MoleculesIterator
 
getShortName() - Method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
 
getShortName() - Method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
 
getShortName() - Method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
 
getShowColor(int) - Method in class toxTree.ui.tree.categories.CategoriesRenderer
 
getSMARTS() - Method in class mutant.descriptors.DescriptorStructurePresence
 
getSmarts() - Method in class mutant.rules.SMARTSGroup
 
getSMARTS() - Method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
 
getSMARTS() - Method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
 
getSMARTS() - Method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
 
getSmarts() - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
getSMARTS() - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
 
getSmartsPatternFactory() - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
 
getSmartsPatterns() - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
getSpecification() - Method in class com.molecularnetworks.start.BiodgeradationRules
 
getSpecification() - Method in class cramer2.CramerRulesWithExtensions
 
getSpecification() - Method in class eye.EyeIrritationRules
 
getSpecification() - Method in class mic.MICRules
 
getSpecification() - Method in class michaelacceptors.MichaelAcceptorRules
 
getSpecification() - Method in class mutant.BB_CarcMutRules
 
getSpecification() - Method in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
getSpecification() - Method in class mutant.descriptors.DescriptorBridgedBiphenyl
 
getSpecification() - Method in class mutant.descriptors.DescriptorHasNO2Group
 
getSpecification() - Method in class mutant.descriptors.DescriptorIDist
 
getSpecification() - Method in class mutant.descriptors.DescriptorIsAniline
 
getSpecification() - Method in class mutant.descriptors.DescriptorMolarRefractivity
 
getSpecification() - Method in class mutant.descriptors.DescriptorStructurePresence
 
getSpecification() - Method in class mutant.descriptors.SubstituentsDescriptor
 
getSpecification() - Method in class sicret.SicretRules
 
getSpecification() - Method in class toxTree.core.ToxTreeDescriptor
 
getSpecification() - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
 
getSpecification() - Method in class toxtree.plugins.func.FuncRules
 
getSpecification() - Method in class toxtree.plugins.kroes.Kroes1Tree
 
getSpecification() - Method in class toxtree.plugins.lewis.LewisTree
 
getSpecification() - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
 
getSpecification() - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
 
getSpecification() - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
getSpecification() - Method in class toxtree.plugins.verhaar2.VerhaarScheme2
 
getSpecification() - Method in class toxTree.tree.cramer.CramerRules
 
getSpecification() - Method in class toxTree.tree.UserDefinedTree
 
getSpecification() - Method in class verhaar.VerhaarScheme
 
getStatus() - Method in class toxTree.apps.toxForest.ToxForestData
 
getStatus() - Method in interface toxTree.core.IMoleculesIterator
 
getStatus() - Method in class toxtree.data.DataContainer
 
getStatus() - Method in class toxTree.data.MoleculesIterator
 
getStatus() - Method in class toxTree.io.batch.BatchProcessing
 
getStorage() - Method in class toxTree.tree.CategoriesList
 
getSubstituentNumber(String, IAtomContainer, int) - Static method in class mutant.descriptors.SubstituentExtractor
 
getSubstituentNumber(String, IAtom) - Static method in class mutant.descriptors.SubstituentExtractor
 
getSubstructure(int) - Method in interface toxTree.core.IRuleSubstructures
Returns a substructure AtomContainer at a given rules
getSubstructure(int) - Method in class toxTree.tree.rules.RuleSubstructures
 
getSubstructure(String) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
getSubstructure(String) - Method in interface toxTree.tree.rules.smarts.IRuleSMARTSubstructures
 
getSubstructures() - Method in interface toxTree.core.IRuleSubstructures
Returns a list ArrayList of AtomContainer defined for the rule
getSubstructures() - Method in class toxTree.tree.rules.RuleSubstructures
 
getSubstructuresCount() - Method in interface toxTree.core.IRuleSubstructures
 
getSubstructuresCount() - Method in class toxTree.tree.rules.RuleSubstructures
 
getSuffix(String) - Static method in class toxTree.io.MolFileFilter
 
getSuffix(File) - Static method in class toxTree.io.MolFileFilter
 
getSupportedDataFeatures() - Method in class toxTree.io.PDFWriter
 
getTable() - Method in class toxtree.ui.HashtableModel
 
getTableModel() - Method in class toxtree.ui.molecule.PropertyPanel
 
getTag() - Method in interface toxTree.data.IPropertyFilter
 
getTag() - Method in class toxTree.data.ObjectPropertyFilter
 
getTempDir() - Method in class toxTree.io.batch.BatchProcessing
 
getThreshold() - Method in interface toxTree.core.IDecisionCategory
 
getThreshold() - Method in class toxTree.qsar.LinearDiscriminantRule
 
getThreshold() - Method in class toxTree.tree.DefaultCategory
 
getTitle() - Method in class sicret.rules.RuleHasOnlyC_H_O
 
getTitle() - Method in class sicret.rules.RuleHasOnlyC_H_O_N_Halogen
 
getTitle() - Method in class toxTree.apps.CompoundMethodApplication
 
getTitle() - Method in class toxTree.apps.toxForest.ToxForestApp
 
getTitle() - Method in class toxTree.apps.ToxTreeApp
 
getTitle() - Method in interface toxTree.core.IDecisionMethod
 
getTitle() - Method in interface toxTree.core.IDecisionRule
Rule name is an arbitrary string, preferably one line, reflecting the essence of the rule
(e.g.
getTitle() - Method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
 
getTitle() - Method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
 
getTitle() - Method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
 
getTitle() - Method in class toxTree.tree.AbstractRule
 
getTitle() - Method in class toxTree.tree.AbstractTree
returns the decision tree title (e.g.
getTitle() - Method in class toxTree.tree.BatchDecisionResultsList
 
getTitle() - Method in class toxTree.tree.cramer.RuleHasOtherThanC_H_O_N_S2
 
getTitle() - Method in class toxTree.tree.DecisionNode
 
getTitle() - Method in class toxTree.tree.rules.RuleElements
 
getTitle() - Method in class toxtree.ui.tree.categories.CategoryPanel
 
getTitle() - Method in class toxtree.ui.tree.rules.RuleEditor
 
getTitle() - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
 
getTitle() - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
getTooltip(int) - Method in class toxtree.ui.tree.DecisionMethodsTableModel
 
getToolTipLocation(MouseEvent) - Method in class toxtree.ui.tree.JCustomTreeComponent
 
getToolTipText(MouseEvent) - Method in class toxtree.ui.tree.JCustomTreeComponent
 
getTopRule() - Method in interface toxTree.core.IDecisionMethod
 
getTopRule() - Method in class toxTree.tree.AbstractTree
 
getTopRule() - Method in class toxTree.tree.BatchDecisionResultsList
 
getToxTreeRoot() - Static method in class toxTree.core.Introspection
 
getTranslation() - Method in class toxTree.qsar.LinearPreprocessor
 
getTree() - Method in class toxtree.ui.tree.actions.AbstractTreeAction
 
getTree() - Method in interface toxtree.ui.tree.actions.ITreeAction
 
getTreeActions() - Method in class toxtree.ui.tree.EditTreeActions
 
getTreeNodeActions() - Method in class toxtree.ui.tree.EditTreeActions
 
getTreeResult() - Method in class toxtree.data.DecisionMethodsDataModule
 
getUniqueAtomMaps(List) - Method in class mutant.descriptors.SubstituentExtractor
 
getUniqueBondMap(IAtomContainer, IAtomContainer, boolean) - Static method in class toxTree.query.FunctionalGroups
 
getUniqueMatchingAtoms() - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
getValue() - Method in interface toxTree.core.IRuleValue
 
getValue() - Method in class toxTree.data.ObjectPropertyFilter
 
getValue() - Method in class toxtree.ui.GUIWorker
 
getValueAt(int, int) - Method in class toxtree.ui.HashtableModel
 
getValueAt(int, int) - Method in class toxtree.ui.molecule.AtomContainerPropertyTableModel
 
getValueAt(int, int) - Method in class toxtree.ui.tree.categories.CategoriesTableModel
 
getValueAt(int, int) - Method in class toxtree.ui.tree.DecisionMethodsTableModel
 
getValueAt(int, int) - Method in class toxtree.ui.tree.ListPanel
 
getValueAt(int, int) - Method in class toxtree.ui.tree.ListTableModel
 
getValueAt(int, int) - Method in class toxtree.ui.tree.QueryAtomContainersModel
 
getValueAt(int, int) - Method in class toxtree.ui.tree.rules.DecisionNodesListTableModel
 
getValueAt(int, int) - Method in class toxtree.ui.tree.ToxTreePackageEntryModel
 
getValuesPerField(Object, int) - Method in class toxTree.data.MoleculesFile
 
getViewMethodAction() - Method in class toxtree.data.ToxTreeActions
 
getVisualCompoment() - Method in interface toxTree.core.IDecisionRuleEditor
 
getVisualCompoment() - Method in interface toxTree.core.IToxTreeEditor
 
getVisualCompoment() - Method in class toxtree.ui.tree.qsar.QSARModelEditor
 
getVisualCompoment() - Method in class toxtree.ui.tree.rules.RulePanel
 
getVisualCompoment() - Method in class toxtree.ui.tree.rules.SubstructureRulePanel
 
getVisualCompoment() - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
getVisualCompoment() - Method in class toxtree.ui.tree.TreeEditorPanel
 
getVisualComponent() - Method in class toxtree.ui.wizard.EditorPanel
 
getWeights() - Method in class toxTree.qsar.LinearQSARModel
 
getWriter() - Method in class toxTree.tree.AbstractTreeWriter
 
getWrittenRecordsCount() - Method in class toxTree.io.batch.BatchProcessing
Returns the number of records written to the output file
getWrittenRecordsCount() - Method in interface toxTree.io.batch.IBatchProcessing
 
getYesBranch() - Method in class toxtree.ui.tree.DecisionNodePanel
 
gotoRecord(int) - Method in class toxtree.data.DataContainer
 
gotoRecord(String) - Method in class toxtree.data.DecisionMethodsDataModule
 
GoToRecordAction - Class in toxtree.ui.molecule
 
GoToRecordAction(DataModule) - Constructor for class toxtree.ui.molecule.GoToRecordAction
 
GoToRecordAction(DataModule, String) - Constructor for class toxtree.ui.molecule.GoToRecordAction
 
GoToRecordAction(DataModule, String, Icon) - Constructor for class toxtree.ui.molecule.GoToRecordAction
 
graph - Variable in class toxTree.tree.Tree2PrefuseGraph
 
GRAPH - Static variable in class toxtree.ui.tree.TreePrefuse
 
graph - Variable in class toxtree.ui.tree.TreePrefuse
 
group1() - Static method in class mutant.rules.RuleDerivedAromaticAmines
 
group2() - Static method in class mutant.rules.RuleDerivedAromaticAmines
 
groups - Variable in class mutant.rules.RuleDerivedAromaticAmines
 
GUIWorker - Class in toxtree.ui
An abstract class to run a job in a thread.
GUIWorker() - Constructor for class toxtree.ui.GUIWorker
 

H

H - Static variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
h - Static variable in class toxTree.query.FunctionalGroups
 
halogen - Static variable in class toxTree.core.SmartElementsList
 
HALOGEN - Static variable in class verhaar.query.FunctionalGroups
 
halogen() - Static method in class verhaar.query.FunctionalGroups
 
halogen(String[]) - Static method in class verhaar.query.FunctionalGroups
 
HALOGEN_ALPHA_FROM_UNSATURATION - Static variable in class verhaar.query.FunctionalGroups
 
HALOGEN_BETA_FROM_UNSATURATION - Static variable in class verhaar.query.FunctionalGroups
 
halogenAtAlphaFromUnsaturation(String[]) - Static method in class verhaar.query.FunctionalGroups
Halogen at alpha position from unsaturation.
halogenAtBetaFromUnsaturation(String[]) - Static method in class verhaar.query.FunctionalGroups
Halogen at beta position from unsaturation.
halogenIDs - Variable in class verhaar.rules.Rule21
 
halogens - Variable in class toxTree.core.SmartElementsList
 
halogens - Static variable in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
 
halogens - Static variable in class verhaar.rules.Rule141
 
halogens - Static variable in class verhaar.rules.Rule142
 
halogens - Variable in class verhaar.rules.Rule143
 
halogens - Variable in class verhaar.rules.Rule21
 
halogensCount - Variable in class verhaar.rules.Rule21
 
handleproduct(IAtomContainer) - Method in class toxTree.query.metabolite.MetabolyteRecycler
 
hasAllSubstructure(IAtomContainer, ArrayList, boolean) - Static method in class toxTree.query.FunctionalGroups
 
hasAnySubstructure(IAtomContainer, ArrayList) - Static method in class toxTree.query.FunctionalGroups
 
hasAnySubstructure(IAtomContainer, ArrayList, IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
hasGroup(IAtomContainer, IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
hasGroup(IAtomContainer, IAtomContainer, IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
hasGroup(IAtomContainer, IAtomContainer, boolean) - Static method in class toxTree.query.FunctionalGroups
 
hasGroup(IAtomContainer, IAtomContainer, boolean, IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
hasGroupMarked(IAtomContainer, String) - Static method in class toxTree.query.FunctionalGroups
 
hasGroupMarked(IAtomContainer, String, IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
hashCode() - Method in class toxTree.data.AbstractFilter
 
hashCode - Variable in class toxTree.io.batch.FileState
 
hashCode() - Method in class toxTree.tree.DecisionNodesList
 
hashCode() - Method in class toxTree.tree.RulesList
 
HashtableModel - Class in toxtree.ui
AbstractTableModel for Hashtable.
HashtableModel(Hashtable) - Constructor for class toxtree.ui.HashtableModel
 
HashtableModel(Hashtable, boolean) - Constructor for class toxtree.ui.HashtableModel
 
hasManyDifferentFunctionalGroups(IAtomContainer, int) - Static method in class toxTree.query.FunctionalGroups
 
hasMarkedOnlyTheseGroups(IAtomContainer, Collection) - Static method in class toxTree.query.FunctionalGroups
Has to be preprocessed with getBondMap or getUniqueBondMap and markMaps
hasMarkedOnlyTheseGroups(IAtomContainer, Collection, IAtomContainer, IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
hasMarkedOnlyTheseGroups(IAtomContainer, QueryAtomContainers) - Static method in class toxTree.query.FunctionalGroups
 
hasNext() - Method in class toxTree.data.MoleculesFile
 
hasNext() - Method in class toxTree.data.MoleculesIterator
 
hasNextRecord() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
 
hasNextRecord() - Method in interface toxTree.io.batch.IBatchProcessing
 
hasOnlySpecifiedElements(SmartElementsList) - Method in class toxTree.core.SmartElementsList
 
hasOnlySpecifiedElements() - Method in class toxTree.tree.rules.RuleElements
 
hasOnlyTheseGroups(IAtomContainer, QueryAtomContainers, Collection, boolean) - Static method in class toxTree.query.FunctionalGroups
 
hasOnlyTheseGroups(IAtomContainer, QueryAtomContainers, Collection, boolean, IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
hasPrevious() - Method in class toxTree.data.MoleculesFile
 
hasRank(int) - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleHigherRank
 
hasRank(int) - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
 
hasRingsToProcess(IAtomContainer) - Method in class toxTree.tree.cramer.RuleCyclopropaneEtc
 
hasRingsToProcess(IAtomContainer) - Method in class toxTree.tree.cramer.RuleMonocarbocyclic
 
hasRingsToProcess(IAtomContainer) - Method in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
hasRingsToProcess(IAtomContainer) - Method in class toxTree.tree.rules.RuleRings
 
hasRingsToProcess(IAtomContainer) - Method in class verhaar.rules.Rule142
 
hasRingsToProcess(IAtomContainer) - Method in class verhaar.rules.Rule143
 
hasRingsToProcess(IAtomContainer) - Method in class verhaar.rules.Rule144
 
hasSMARTSPattern(JOEMol) - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
hasSpecifiedElements(SmartElementsList) - Method in class toxTree.core.SmartElementsList
 
hasSubstituents(IAtomContainer, IRingSet) - Static method in class toxTree.query.FunctionalGroups
 
hasUnreachableRules() - Method in interface toxTree.core.IDecisionMethod
 
hasUnreachableRules() - Method in class toxTree.tree.BatchDecisionResultsList
 
hasUnreachableRules() - Method in class toxTree.tree.UserDefinedTree
 
hasUnusedCategories() - Method in interface toxTree.core.IDecisionMethod
 
hasUnusedCategories() - Method in class toxTree.tree.BatchDecisionResultsList
 
hasUnusedCategories() - Method in class toxTree.tree.UserDefinedTree
 
HazardPanel - Class in toxtree.ui
The panel at the right of ToxTreeApp main screen.
HazardPanel(ToxTreeModule) - Constructor for class toxtree.ui.HazardPanel
 
hClAmine - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
 
hClAmine - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
 
header - Variable in class toxtree.ui.tree.DecisionMethodsTableModel
 
help - Variable in class toxtree.ui.metabolites.MetabolitesPanel
 
HelpAction - Class in toxtree.ui.actions
Help
HelpAction() - Constructor for class toxtree.ui.actions.HelpAction
 
HelpAction(String) - Constructor for class toxtree.ui.actions.HelpAction
 
HelpAction(String, Icon) - Constructor for class toxtree.ui.actions.HelpAction
 
helpActions - Variable in class toxtree.data.ToxTreeActions
 
HETEROAROMATIC - Static variable in class toxTree.query.MolAnalyser
 
heteroaromatic - Variable in class toxTree.query.MolFlags
 
HETEROCYCLIC - Static variable in class toxTree.query.MolAnalyser
 
heterocyclic - Variable in class toxTree.query.MolFlags
 
HETEROCYCLIC3 - Static variable in class toxTree.query.MolAnalyser
 
heterocyclic3 - Variable in class toxTree.query.MolFlags
 
hideColors - Variable in class toxTree.ui.tree.categories.CategoriesRenderer
 
hideResiduesID(boolean) - Method in interface toxTree.core.IDecisionRule
 
hideResiduesID(boolean) - Method in class toxTree.tree.AbstractRule
 
hideResiduesID(boolean) - Method in class toxTree.tree.DecisionNode
 
hilightAlert(IDecisionRule) - Method in interface toxTree.core.IDecisionResult
 
hilightAlert(RuleResult) - Method in interface toxTree.core.IDecisionResult
 
hilightAlert(IDecisionRule) - Method in class toxTree.tree.BatchDecisionResultsList
 
hilightAlert(RuleResult) - Method in class toxTree.tree.BatchDecisionResultsList
 
hilightAlert(RuleResult) - Method in class toxTree.tree.TreeResult
 
hilightAlert(IDecisionRule) - Method in class toxTree.tree.TreeResult
 
hint() - Method in class toxTree.qsar.LinearDiscriminantRule
 
HYDRAZINE - Static variable in class mic.rules.SA13
 
HYDRAZINE - Static variable in class mutant.rules.SA13_gen
 
HYDRAZINE_SMARTS - Static variable in class mic.rules.SA13
 
HYDRAZINE_SMARTS - Static variable in class mutant.rules.SA13_gen
 
HYDROCARBON - Static variable in class toxTree.query.FunctionalGroups
 
hydrocarbon() - Static method in class toxTree.query.FunctionalGroups
 
HYDROCHLORIDE_OF_AMINE - Static variable in class toxTree.query.FunctionalGroups
 
hydrochlorideOfAmine(int) - Static method in class toxTree.query.FunctionalGroups
 
hydrochlorideOfAmine3() - Static method in class toxTree.query.FunctionalGroups
 
hydrochlorideOfAmineBreakable() - Static method in class toxTree.query.FunctionalGroups
 
hydrogen - Static variable in class toxTree.core.SmartElementsList
 
hydrolize - Static variable in class toxTree.query.SimpleReactions
 
hydrolize(IAtomContainer, QueryAtomContainer, List, IChemObjectBuilder) - Static method in class toxTree.query.SimpleReactions
 
hydrolizePO4 - Static variable in class toxTree.query.SimpleReactions
 
hydrolizesPO4(IAtomContainer) - Method in class toxTree.query.SimpleReactions
 
hydrolizesPO4(IAtomContainer, IChemObjectBuilder) - Method in class toxTree.query.SimpleReactions
 
hydrolysis - Static variable in class toxTree.query.SimpleReactions
 
hydrolysisPO4 - Static variable in class toxTree.query.SimpleReactions
 
hydrolysisProducts - Variable in class toxTree.query.MolFlags
 
HYDROXY - Static variable in class toxTree.query.FunctionalGroups
 
HYDROXY1 - Static variable in class toxTree.query.FunctionalGroups
 
hydroxy1() - Static method in class toxTree.query.FunctionalGroups
 
hydroxy_ring() - Static method in class toxTree.query.FunctionalGroups
 
HYDROXYESTERSUBSTITED - Static variable in class toxTree.query.FunctionalGroups
 
hydroxyEsterSubstituted() - Static method in class toxTree.query.FunctionalGroups
 
hydroxyIDs - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
hydroxyl - Static variable in class mutant.rules.SA31a_nogen
Overlaps are accepted, except with the following alerts: NA_27, NA_28s (NA_28, NA_28bis, NA_28ter) and NA_29.

I

IAlertCounter - Interface in toxTree.tree.rules
 
IBatchProcessing - Interface in toxTree.io.batch
Interface for batch processing
ICategoryAction - Interface in toxtree.ui.tree.actions
 
id - Variable in class toxTree.data.ListOfAtomContainers
 
id - Variable in class toxTree.tree.AbstractRule
 
id - Variable in class toxTree.tree.DefaultCategory
 
id - Variable in class toxtree.ui.molecule.TopPanel
 
id - Variable in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
IDecisionCategories - Interface in toxTree.core
A list of IDecisionCategory instances
IDecisionCategory - Interface in toxTree.core
An interface definition to represent a chemical category The application of a decision tree IDecisionMethod results in assigning a category to the query chemical.
IDecisionCategoryEditor - Interface in toxTree.core
 
IDecisionInteractive - Interface in toxTree.core
An interface for rules, requiring user interaction (e.g.
IDecisionInteractive.UserOptions - Enum in toxTree.core
 
IDecisionMethod - Interface in toxTree.core
An interface to represent a decision tree.
IDecisionMethodEditor - Interface in toxTree.core
 
IDecisionMethodPrority - Interface in toxTree.core
 
IDecisionMethodsList - Interface in toxTree.core
A list of IDecisionMethod instances
IDecisionNodesFactory - Interface in toxTree.tree
 
IDecisionResult - Interface in toxTree.core
An interface definition to represent the result of applying a IDecisionMethod.
IDecisionRule - Interface in toxTree.core
An interface definition to represent a rule, that will be used in a IDecisionMethod.
IDecisionRuleEditor - Interface in toxTree.core
Each rule IDecisionRule should provides an editor, which is a class, implementing this interface.
IDecisionRuleList - Interface in toxTree.core
A list of IDecisionRule
IDecisionTransition - Interface in toxTree.core
An interface representing a transition between decision rules IDecisionRule in a decision tree IDecisionMethod.
IDescriptorBased - Interface in toxTree.core
 
IDescriptorPreprocessor - Interface in toxTree.qsar
 
idField - Variable in class toxtree.ui.tree.rules.RulePanel
 
idField - Variable in class toxtree.ui.tree.ToxTreeEditorPanel
 
ids - Variable in class toxTree.tree.rules.RuleSubstructures
 
idsAcyclic - Variable in class toxTree.tree.rules.RuleCarbohydrate
 
idsCyclic - Variable in class toxTree.tree.rules.RuleCarbohydrate
 
IEditorFactory - Interface in toxTree.ui
 
IFilteredMolecules - Interface in toxTree.core
 
IImplementationDetails - Interface in toxTree.core
 
ILookupFile - Interface in toxTree.tree.rules
 
imageSize - Variable in class toxTree.tree.AbstractTree
 
imageSize - Variable in class toxTree.tree.BatchDecisionResultsList
 
imageTools - Variable in class toxTree.io.PDFWriter
 
imageTools - Variable in class toxTree.tree.AbstractTreePrinter
 
IMetaboliteGenerator - Interface in toxTree.core
 
IMoleculeLookup - Interface in toxTree.data
 
IMoleculesIterator - Interface in toxTree.core
 
implementInterface(ClassLoader, File, String) - Static method in class toxTree.core.Introspection
Finds classes implementing an interface in all .jar files in a user defined directory.
implementsInterface(String, String) - Static method in class toxTree.core.Introspection
Verifies if a class implements an interface
implementsInterface(Class, String) - Static method in class toxTree.core.Introspection
Verifies if a class implements an interface
InChILookupFile - Class in toxTree.tree.rules
In-memory InChI lookup.
InChILookupFile(File) - Constructor for class toxTree.tree.rules.InChILookupFile
 
inchiProcessor - Variable in class toxTree.tree.rules.InChILookupFile
 
inchis - Variable in class toxTree.tree.rules.InChILookupFile
 
incrementCounter(IAtomContainer) - Method in class mic.rules.SA18
 
incrementCounter(IAtomContainer) - Method in class mic.rules.SA26
 
incrementCounter(IAtomContainer) - Method in class mutant.rules.SA18_gen
 
incrementCounter(IAtomContainer) - Method in class mutant.rules.SA20_nogen
 
incrementCounter(IAtomContainer) - Method in class toxTree.tree.rules.DefaultAlertCounter
 
incrementCounter(IAtomContainer) - Method in interface toxTree.tree.rules.IAlertCounter
 
incrementCounter(IAtomContainer) - Method in class toxTree.tree.rules.StructureAlert
 
incrementCounter(IAtomContainer) - Method in class toxTree.tree.rules.StructureAlertAmbit
 
incrementCounter(IAtomContainer) - Method in class toxTree.tree.rules.StructureAlertCDK
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.helper.RuleAnySubstructureCounter
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.helper.RuleElementsCounter
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.helper.RuleOnlyAllowedSubstructuresCounter
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.Rule03
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.Rule141
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.Rule143
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.Rule21
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.RuleIonicGroups
 
incrementCounter(IAtomContainer) - Method in class verhaar.rules.RuleLogPRange
 
index - Variable in class toxtree.ui.tree.rules.RuleSubstructuresEditAction
 
index_alcohol - Variable in class toxTree.tree.rules.RuleCarbohydrate
 
index_aldehyde - Variable in class toxTree.tree.rules.RuleCarbohydrate
 
index_alkoxy - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
index_biphenyl - Static variable in class mutant.rules.SA31a_nogen
 
index_diazo - Static variable in class mutant.rules.SA31a_nogen
 
index_diphenyl1 - Static variable in class mutant.rules.SA31a_nogen
 
index_diphenyl2 - Static variable in class mutant.rules.SA31a_nogen
 
index_ester - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
index_ether - Variable in class toxTree.tree.rules.RuleCarbohydrate
 
index_hydrocarbon - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
index_hydroxy - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
index_hydroxy1 - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
index_hydroxyl_amine - Static variable in class mutant.rules.SA31a_nogen
 
index_hydroxyl_amineester - Static variable in class mutant.rules.SA31a_nogen
 
index_ketone - Variable in class toxTree.tree.rules.RuleCarbohydrate
 
index_lactone - Variable in class toxTree.tree.cramer.RuleLactoneOrCyclicDiester
 
index_monodialkylamine1 - Static variable in class mutant.rules.SA31a_nogen
 
index_monodialkylamine2 - Static variable in class mutant.rules.SA31a_nogen
 
index_monodialkylamine3 - Static variable in class mutant.rules.SA31a_nogen
 
index_nacymamine - Static variable in class mutant.rules.SA31a_nogen
 
index_nitro_aromatic - Static variable in class mutant.rules.SA31a_nogen
 
index_ortho_carboxylicacid - Static variable in class mic.rules.SA28
 
index_ortho_carboxylicacid - Static variable in class mutant.rules.SA28_gen
 
index_ortho_disubstitution - Static variable in class mic.rules.SA28
 
index_ortho_disubstitution - Static variable in class mutant.rules.SA28_gen
 
index_polyoxyethylene - Variable in class toxTree.tree.cramer.RuleOnlyFuncGroupsQ30
 
index_primary_aromatic_amine - Static variable in class mutant.rules.SA31a_nogen
 
index_singlering - Static variable in class mutant.rules.SA31a_nogen
 
index_so3h_1 - Static variable in class mic.rules.SA28
 
index_so3h_1 - Static variable in class mutant.rules.SA28_gen
 
index_so3h_2 - Static variable in class mic.rules.SA28
 
index_so3h_2 - Static variable in class mutant.rules.SA28_gen
 
index_so3h_3 - Static variable in class mic.rules.SA28
 
index_so3h_3 - Static variable in class mutant.rules.SA28_gen
 
index_so3h_4 - Static variable in class mic.rules.SA28
 
index_so3h_4 - Static variable in class mutant.rules.SA28_gen
 
indexOf(Object, Object) - Method in class toxTree.data.MoleculesFile
 
indexOf(Object) - Method in class toxTree.data.SortedPropertyList
 
indexOf(Object) - Method in class toxTree.tree.CategoriesList
 
indexOf(Object) - Method in class toxTree.tree.DecisionMethodsList
 
indexOf(Object) - Method in class toxTree.tree.DecisionNodesList
 
indexOf(Object) - Method in class toxTree.tree.RulesList
 
info(Object) - Method in class toxTree.logging.TTLogger
Shows INFO output for the Object.
info(Object, int) - Method in class toxTree.logging.TTLogger
Shows INFO output for the given Object's.
info(Object, double) - Method in class toxTree.logging.TTLogger
Shows INFO output for the given Object's.
info(Object, boolean) - Method in class toxTree.logging.TTLogger
Shows INFO output for the given Object's.
info(Object, Object) - Method in class toxTree.logging.TTLogger
Shows INFO output for the given Object's.
info(Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows INFO output for the given Object's.
info(Object, Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows INFO output for the given Object's.
info(Object, Object, Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows INFO output for the given Object's.
InfoAction - Class in toxtree.ui.actions
Provides inforation about files, etc.
InfoAction(ToxTreeModule) - Constructor for class toxtree.ui.actions.InfoAction
 
InfoAction(ToxTreeModule, String) - Constructor for class toxtree.ui.actions.InfoAction
 
InfoAction(ToxTreeModule, String, Icon) - Constructor for class toxtree.ui.actions.InfoAction
 
init(IDecisionMethod) - Method in interface toxTree.core.IProcessRule
 
init() - Method in class toxtree.lookup.RemoteLookup
 
init() - Method in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
 
init() - Method in class toxTree.tree.cramer.RuleCommonComponentOfFood
 
init(IDecisionMethod) - Method in class toxTree.tree.PDFTreePrinter
 
init(IDecisionMethod) - Method in class toxTree.tree.ReportTreePrinter
 
init(IDecisionMethod) - Method in class toxTree.tree.SimpleTreePrinter
 
init(IDecisionMethod) - Method in class toxTree.tree.Tree2PrefuseGraph
 
initGroups() - Method in class toxtree.ui.tree.actions.SubstructureFromListAction
 
initLookAndFeel() - Static method in class toxTree.apps.AbstractApplication
 
initRules() - Method in class toxTree.tree.AbstractTree
public AbstractTree( IDecisionCategories classes, String[] customRules, int[][] customTransitions) throws DecisionMethodException { this(categories,customRules,customTransitions); } public AbstractTree( String[] customRules, int[][] customTransitions) throws DecisionMethodException { this(); setRules(customRules); setTransitions(customTransitions); setChanged(); notifyObservers(); }
initRules() - Method in class toxTree.tree.UserDefinedTree
 
initSingleSMARTS(Hashtable<String, ISmartsPattern<T>>, String, String) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
INodeAction - Interface in toxtree.ui.tree.actions
Interface
inputFile - Variable in class toxTree.io.batch.BatchProcessing
 
inputProperty(IAtomContainer) - Method in class sicret.rules.RuleLogP
 
inputProperty(IAtomContainer) - Method in class sicret.rules.RuleMolWeight
 
inputProperty(IAtomContainer) - Method in class toxTree.tree.rules.RuleVerifyProperty
 
inRing - Variable in class toxTree.query.TopologyAnyAtom
 
inRing - Variable in class toxTree.query.TopologyAnyBond
 
inRing - Variable in class toxTree.query.TopologyOrderQueryBond
 
inRing - Variable in class toxTree.query.TopologySymbolQueryAtom
 
interactive - Variable in class eye.EyeIrritationRules
 
interactive - Variable in class sicret.SicretRules
 
interrupt() - Method in class toxtree.ui.GUIWorker
 
Introspection - Class in toxTree.core
A singleton class with static method to provide some sort of introspection :) Used in decision tree editor to provide a list of available decision trees, available rules, available categories.
Introspection() - Constructor for class toxTree.core.Introspection
 
IntrospectionException - Exception in toxTree.exceptions
To care for all failures that can happen in Introspection
IntrospectionException() - Constructor for exception toxTree.exceptions.IntrospectionException
 
IntrospectionException(String) - Constructor for exception toxTree.exceptions.IntrospectionException
 
IntrospectionException(Throwable) - Constructor for exception toxTree.exceptions.IntrospectionException
 
IntrospectionException(String, Throwable) - Constructor for exception toxTree.exceptions.IntrospectionException
 
introspectionPanel - Variable in class toxtree.ui.wizard.DecisionNodeWizard
 
IObjectFilter - Interface in toxTree.data
 
IONICGROUP - Static variable in class verhaar.query.FunctionalGroups
 
ionicGroup() - Static method in class verhaar.query.FunctionalGroups
 
IProcessRule - Interface in toxTree.core
 
IProgressStatus - Interface in toxTree.core
 
IPropertyFilter - Interface in toxTree.data
 
IRuleAction - Interface in toxtree.ui.tree.actions
 
IRuleRange - Interface in toxTree.core
 
IRuleSMARTSubstructures - Interface in toxTree.tree.rules.smarts
 
IRuleSubstructures - Interface in toxTree.core
An interface to support substructure rules
IRuleValue - Interface in toxTree.core
 
isAcetylenic(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
isAcetylenic() - Method in class toxTree.query.MolFlags
 
isAlicyclic() - Method in class toxTree.query.MolFlags
 
isAliphatic() - Method in class toxTree.query.MolFlags
 
isAllyl(IAtomContainer) - Method in class verhaar.rules.Rule152
 
isAnalysed() - Method in class toxTree.query.MolFlags
 
isAnswer() - Method in exception toxTree.exceptions.DRuleException
 
isAnswer() - Method in class toxtree.ui.tree.rules.RuleExampleEditAction
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mic.rules.SA2
Simple prescreening
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mic.rules.SA25
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mic.rules.SA27
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mic.rules.SA28
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mic.rules.SA28bis
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mic.rules.SA28ter
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.QSAR6Applicable
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.RuleAromaticAmineNoSulfonicGroup
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.SA25_gen
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.SA27_gen
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.SA28_gen
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.SA28bis_gen
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.SA28ter_gen
 
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.SA2_gen
Simple prescreening
isAPossibleHit(IAtomContainer, IAtomContainer) - Method in class mutant.rules.SA31a_nogen
 
isAPossibleHit(IAtomContainer, T) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
Returns true always.
isAromatic() - Method in class toxTree.query.MolFlags
 
isAromaticRing(int, int) - Method in class mic.rules.SA18
 
isAromaticRing(int, int) - Method in class mic.rules.SA19
 
isAromaticRing(int, int) - Method in class mutant.rules.SA18_gen
 
isAromaticRing(int, int) - Method in class mutant.rules.SA19_gen
 
isBuffered(int, Object) - Method in class toxTree.data.MoleculesFile
 
isBufferProperties() - Method in class toxTree.data.MoleculesFile
 
isCalculated(String) - Method in interface toxTree.core.IDescriptorBased
 
isCalculated(String) - Method in class toxTree.qsar.AbstractQSARModel
 
isCalculated(String) - Method in class toxTree.qsar.LinearDiscriminantRule
 
isCalculated() - Method in class toxTree.qsar.QSARDescriptor
 
isCancelled() - Method in class toxTree.io.batch.BatchProcessing
 
isCancelled() - Method in interface toxTree.io.batch.IBatchProcessing
 
isCellEditable(int, int) - Method in class toxtree.ui.HashtableModel
 
isCellEditable(int, int) - Method in class toxtree.ui.tree.categories.CategoriesTableModel
 
isCheckAromaticity() - Method in class toxTree.tree.rules.LookupFile
 
isCommonTerpene(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
isCommonTerpene(IAtomContainer, IRingSet) - Static method in class toxTree.query.FunctionalGroups
 
isCreateNewMolecule() - Method in class toxtree.ui.tree.rules.RuleSubstructuresEditAction
 
isCyclicDiester(IAtomContainer, IRingSet) - Static method in class toxTree.query.FunctionalGroups
 
isDebugEnabled() - Method in class toxTree.logging.TTLogger
Use this method for computational demanding debug info.
isEditable() - Method in interface toxTree.core.IDecisionMethod
 
isEditable() - Method in interface toxTree.core.IDecisionRule
 
isEditable() - Method in interface toxTree.core.IToxTreeEditor
 
isEditable() - Method in class toxTree.tree.AbstractRule
 
isEditable() - Method in class toxTree.tree.BatchDecisionResultsList
 
isEditable() - Method in class toxTree.tree.DecisionNode
 
isEditable() - Method in class toxTree.tree.UserDefinedTree
 
isEditable() - Method in class toxtree.ui.tree.DecisionNodePanel
 
isEditable() - Method in class toxtree.ui.tree.qsar.QSARModelEditor
 
isEditable() - Method in class toxtree.ui.tree.rules.RulePanel
 
isEditable() - Method in class toxtree.ui.tree.rules.SubstructureRulePanel
 
isEditable() - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
isEditable() - Method in class toxtree.ui.tree.TreeEditorPanel
 
isEmpty() - Method in class toxTree.tree.CategoriesList
 
isEmpty() - Method in class toxTree.tree.DecisionMethodsList
 
isEmpty() - Method in class toxTree.tree.DecisionNodesList
 
isEmpty() - Method in class toxTree.tree.RulesList
 
isEnabled() - Method in class toxtree.data.DataContainer
 
isEnabled() - Method in interface toxTree.tree.rules.ILookupFile
 
isEnabled() - Method in class toxTree.tree.rules.InChILookupFile
 
isEnabled() - Method in class toxTree.tree.rules.LookupFile
 
isError() - Method in interface toxTree.core.IProgressStatus
 
isError() - Method in class toxTree.tree.BatchDecisionResultsList
 
isError() - Method in class toxTree.tree.ProgressStatus
 
isError() - Method in class toxTree.tree.TreeResult
 
isEstimated() - Method in interface toxTree.core.IProgressStatus
 
isEstimated() - Method in class toxTree.tree.BatchDecisionResultsList
 
isEstimated() - Method in class toxTree.tree.ProgressStatus
 
isEstimated() - Method in class toxTree.tree.TreeResult
 
isEstimating() - Method in interface toxTree.core.IProgressStatus
 
isEstimating() - Method in class toxTree.tree.BatchDecisionResultsList
 
isEstimating() - Method in class toxTree.tree.ProgressStatus
 
isEstimating() - Method in class toxTree.tree.TreeResult
 
isFalseIfRuleNotImplemented() - Method in class toxTree.tree.AbstractTree
 
isHeteroaromatic() - Method in class toxTree.query.MolFlags
 
isHeterocyclic(IRing) - Method in class mic.rules.SA18
 
isHeterocyclic(IRing) - Method in class mutant.rules.SA18_gen
 
isHeterocyclic() - Method in class toxTree.query.MolFlags
 
isHeterocyclic3() - Method in class toxTree.query.MolFlags
 
isImplemented() - Method in class com.molecularnetworks.start.rules.RuleTwoOrMoreRings
Overrides the default behaviour.
isImplemented() - Method in class eye.rules.Rule13_AliphaticMonoalcohols
 
isImplemented() - Method in class mic.rules.SA18
 
isImplemented() - Method in class mutant.rules.SA18_gen
 
isImplemented() - Method in class mutant.rules.SA20_nogen
 
isImplemented() - Method in class sicret.rules.RuleAcidAnhydrides
 
isImplemented() - Method in class sicret.rules.RuleAcrylicAcids
 
isImplemented() - Method in class sicret.rules.RuleAcrylicAndMethacrylicEsters
 
isImplemented() - Method in class sicret.rules.RuleAromaticAmines
 
isImplemented() - Method in class sicret.rules.RuleC10_C20AliphaticAlcohols
 
isImplemented() - Method in class sicret.rules.RuleCarbamoylHalide
 
isImplemented() - Method in class sicret.rules.RuleCatecholsResorcinolsHydroquinones
 
isImplemented() - Method in class sicret.rules.RuleDi_Tri_Nitrobenzenes
 
isImplemented() - Method in class sicret.rules.RuleHalonitrobenzene
 
isImplemented() - Method in class sicret.rules.RuleHasOnlyC_H_O
 
isImplemented() - Method in class sicret.rules.RuleHasOnlyC_H_O_N_Halogen
 
isImplemented() - Method in class sicret.rules.RuleLactonesFusedOrUnsaturated
 
isImplemented() - Method in class sicret.rules.RuleOandPQuinones
 
isImplemented() - Method in class sicret.rules.RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts
 
isImplemented() - Method in class sicret.rules.RuleTriAndTetraHalogenatedBenzenes
 
isImplemented() - Method in interface toxTree.core.IDecisionRule
 
isImplemented() - Method in class toxtree.plugins.dnabinding.rules.RuleDNABindingAlerts
 
isImplemented() - Method in class toxtree.plugins.dnabinding.rules.VerifyAlertsDNABinding
 
isImplemented() - Method in class toxtree.plugins.kroes.rules.KroesRule8
 
isImplemented() - Method in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
 
isImplemented() - Method in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_1
 
isImplemented() - Method in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_1_1
 
isImplemented() - Method in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_2_1
 
isImplemented() - Method in class toxtree.plugins.proteinbinding.rules.RuleProteinBindingAlerts
 
isImplemented() - Method in class toxtree.plugins.proteinbinding.rules.VerifyAlertsProteinBinding
 
isImplemented() - Method in class toxtree.plugins.skinsensitisation.rules.RuleSkinSensitisationAlerts
 
isImplemented() - Method in class toxtree.plugins.skinsensitisation.rules.VerifyAlertsSkinSensitisation
 
isImplemented() - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
 
isImplemented() - Method in class toxTree.qsar.LinearDiscriminantRule
 
isImplemented() - Method in class toxTree.tree.AbstractRule
 
isImplemented() - Method in class toxTree.tree.cramer.Rule32
 
isImplemented() - Method in class toxTree.tree.cramer.Rule3FuncGroups
 
isImplemented() - Method in class toxTree.tree.cramer.Rule3MemberedHeterocycle
 
isImplemented() - Method in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
isImplemented() - Method in class toxTree.tree.cramer.RuleCyclopropaneEtc
 
isImplemented() - Method in class toxTree.tree.cramer.RuleHasOtherThanC_H_O_N_S2
 
isImplemented() - Method in class toxTree.tree.cramer.RuleHeteroaromatic
 
isImplemented() - Method in class toxTree.tree.cramer.RuleHeterocyclicComplexSubstituents
 
isImplemented() - Method in class toxTree.tree.cramer.RuleKetoneAlcoholEtc
 
isImplemented() - Method in class toxTree.tree.cramer.RuleLactoneOrCyclicDiester
 
isImplemented() - Method in class toxTree.tree.cramer.RuleMonocarbocyclic
 
isImplemented() - Method in class toxTree.tree.cramer.RuleOnlyFuncGroupsQ30
 
isImplemented() - Method in class toxTree.tree.cramer.RuleSimplyBranchedAliphaticHydrocarbon
 
isImplemented() - Method in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
isImplemented() - Method in class toxTree.tree.cramer.RuleSufficientSulphonateGroups
 
isImplemented() - Method in class toxTree.tree.cramer.RuleToxicFunctionalGroups
 
isImplemented() - Method in class toxTree.tree.DecisionNode
 
isImplemented() - Method in class toxTree.tree.rules.RuleAnySubstituents
 
isImplemented() - Method in class toxTree.tree.rules.RuleAnySubstructure
 
isImplemented() - Method in class toxTree.tree.rules.RuleAromatic
 
isImplemented() - Method in class toxTree.tree.rules.RuleCarbohydrate
 
isImplemented() - Method in class toxTree.tree.rules.RuleCommonTerpene
 
isImplemented() - Method in class toxTree.tree.rules.RuleDescriptor
 
isImplemented() - Method in class toxTree.tree.rules.RuleElements
 
isImplemented() - Method in class toxTree.tree.rules.RuleHeterocyclic
 
isImplemented() - Method in class toxTree.tree.rules.RuleInitAlertCounter
 
isImplemented() - Method in class toxTree.tree.rules.RuleManyAromaticRings
 
isImplemented() - Method in class toxTree.tree.rules.RuleMolecularMassRange
 
isImplemented() - Method in class toxTree.tree.rules.RuleOnlyAllowedSubstructures
 
isImplemented() - Method in class toxTree.tree.rules.RuleOpenChain
 
isImplemented() - Method in class toxTree.tree.rules.RuleReadilyHydrolised
 
isImplemented() - Method in class toxTree.tree.rules.RuleRingAllowedSubstituents
 
isImplemented() - Method in class toxTree.tree.rules.RuleRingOtherThanAllowedSubstituents
 
isImplemented() - Method in class toxTree.tree.rules.RuleStructuresList
 
isImplemented() - Method in class toxTree.tree.rules.RuleSubstructures
 
isImplemented() - Method in class toxTree.tree.rules.RuleVerifyAlertsCounter
 
isImplemented() - Method in class toxTree.tree.rules.RuleVerifyProperty
 
isImplemented() - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
isImplemented() - Method in class toxTree.tree.rules.UserInputRule
 
isImplemented() - Method in class verhaar.rules.Rule141
 
isImplemented() - Method in class verhaar.rules.Rule142
 
isImplemented() - Method in class verhaar.rules.Rule143
 
isImplemented() - Method in class verhaar.rules.Rule144
 
isImplemented() - Method in class verhaar.rules.Rule151
 
isImplemented() - Method in class verhaar.rules.Rule152
 
isImplemented() - Method in class verhaar.rules.Rule153
 
isImplemented() - Method in class verhaar.rules.Rule161
 
isImplemented() - Method in class verhaar.rules.Rule21
 
isImplemented() - Method in class verhaar.rules.Rule24
 
isImplemented() - Method in class verhaar.rules.Rule31
 
isImplemented() - Method in class verhaar.rules.Rule32
 
isImplemented() - Method in class verhaar.rules.Rule33
 
isImplemented() - Method in class verhaar.rules.Rule36
 
isImplemented() - Method in class verhaar.rules.Rule37
 
isImplemented() - Method in class verhaar.rules.Rule38
 
isImplemented() - Method in class verhaar.rules.Rule4
 
isImplemented() - Method in class verhaar.rules.RuleIonicGroups
 
isInChI(String) - Method in class toxtree.ui.molecule.SmilesEntryPanel
 
isInRing() - Method in class toxTree.query.TopologyOrderQueryBond
 
isInteractive() - Method in enum toxTree.core.IDecisionInteractive.UserOptions
 
isLeaf(Object) - Method in class toxtree.ui.tree.DecisionTreeModel
 
isModal() - Method in class toxtree.ui.molecule.MoleculeEditAction
 
isModified() - Method in interface toxTree.core.IDecisionMethod
 
isModified() - Method in class toxTree.tree.AbstractTree
 
isModified() - Method in class toxTree.tree.BatchDecisionResultsList
 
isMultilabel() - Method in interface toxTree.core.IDecisionCategories
 
isMultilabel() - Method in class toxTree.tree.CategoriesList
 
isMultiLabel() - Method in class toxTree.tree.DecisionNodesFactory
 
isNotify() - Method in class toxTree.tree.BatchDecisionResultsList
 
isNotify() - Method in class toxTree.tree.TreeResult
 
isOpenChain() - Method in class toxTree.query.MolFlags
 
ISOPRENE - Static variable in class toxTree.query.FunctionalGroups
 
isopreneUnit() - Static method in class toxTree.query.FunctionalGroups
 
isOverlapped(IAtomContainer, IAtomContainer, List) - Static method in class toxTree.query.FunctionalGroups
 
isPaused() - Method in class toxTree.io.batch.BatchProcessing
 
isPaused() - Method in interface toxTree.io.batch.IBatchProcessing
 
isProcessing() - Method in class toxtree.data.DataContainer
 
isReadilyHydrolised(IAtomContainer) - Method in class toxTree.query.SimpleReactions
 
isReadilyHydrolised(IAtomContainer, IChemObjectBuilder) - Method in class toxTree.query.SimpleReactions
Checks if 6 predefined hydrolysis reactions can be applied to Molecule mol
isReadilyHydrolisedSimpleEster(IAtomContainer) - Method in class toxTree.query.SimpleReactions
Checks if simple ester hydrolysis can be applied to Molecule mol
isReadilyHydrolisedSimpleEster(IAtomContainer, IChemObjectBuilder) - Method in class toxTree.query.SimpleReactions
 
isReading() - Method in interface toxTree.core.IMoleculesIterator
 
isReading() - Method in class toxTree.data.MoleculesIterator
 
isResidueIDHidden() - Method in interface toxTree.core.IDecisionRule
 
isResidueIDHidden() - Method in class toxTree.tree.AbstractRule
 
isResidueIDHidden() - Method in class toxTree.tree.DecisionNode
 
isResiduesIDVisible() - Method in class com.molecularnetworks.start.BiodgeradationRules
 
isResiduesIDVisible() - Method in class cramer2.CramerRulesWithExtensions
 
isResiduesIDVisible() - Method in class eye.EyeIrritationRules
 
isResiduesIDVisible() - Method in class mic.MICRules
 
isResiduesIDVisible() - Method in class michaelacceptors.MichaelAcceptorRules
 
isResiduesIDVisible() - Method in class mutant.BB_CarcMutRules
 
isResiduesIDVisible() - Method in class sicret.SicretRules
 
isResiduesIDVisible() - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
 
isResiduesIDVisible() - Method in class toxtree.plugins.func.FuncRules
 
isResiduesIDVisible() - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
 
isResiduesIDVisible() - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
 
isResiduesIDVisible() - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
isResiduesIDVisible() - Method in class toxTree.tree.cramer.CramerRules
 
isResult() - Method in class toxTree.tree.RuleResult
 
isRing() - Method in class mutant.descriptors.SubstituentPosition
 
isRunning() - Method in class toxTree.io.batch.BatchProcessing
 
isRunning() - Method in interface toxTree.io.batch.IBatchProcessing
 
isSelected() - Method in interface toxTree.core.IDecisionCategory
 
isSelected() - Method in class toxTree.tree.DefaultCategory
 
isSelected(int) - Method in class toxtree.ui.tree.categories.CategoriesTableModel
 
isSetPropertyEditable() - Method in class toxtree.ui.tree.rules.RuleRangeEditor
 
isSilent() - Method in class toxTree.tree.RuleResult
 
isSilent() - Method in class toxtree.ui.OptionsPanel
 
isSilent() - Method in class toxtree.ui.PropertyEditor
 
isSilentvalue() - Method in class toxTree.tree.rules.UserInputRule
 
isSkipRule() - Method in class mutant.rules.QSAR6Applicable
 
isStatus(int) - Method in class toxTree.io.batch.BatchProcessing
 
isSubstance(IAtomContainer, IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
isUseCache() - Method in class toxTree.tree.rules.LookupFile
 
isValidSMARTS(String) - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
If not valid throws exception
isVisited() - Method in class toxTree.tree.DecisionNode
 
isVisited(IDecisionRule) - Method in class toxtree.ui.tree.TreeLayout
 
isWeb() - Method in interface toxTree.core.IDecisionMethod
 
isWeb() - Method in class toxTree.tree.AbstractTree
 
isWeb() - Method in class toxTree.tree.BatchDecisionResultsList
 
isWeb() - Method in class toxTree.tree.RuleResult
 
isWriting() - Method in interface toxTree.core.IMoleculesIterator
 
isWriting() - Method in class toxTree.data.MoleculesIterator
 
itemStateChanged(ItemEvent) - Method in class toxtree.ui.molecule.SmilesEntryPanel
 
itemStateChanged(ItemEvent) - Method in class toxtree.ui.OptionsPanel
 
iterateSubstituents(IAtomContainerSet, String, ISubstituentAction<Double>, double[]) - Method in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
iterator() - Method in class toxTree.tree.CategoriesList
 
iterator() - Method in class toxTree.tree.DecisionMethodsList
 
iterator() - Method in class toxTree.tree.DecisionNodesList
 
iterator() - Method in class toxTree.tree.RulesList
 
IToxTreeEditor - Interface in toxTree.core
Parent interface for all editors in ToxTree.
ITreeAction - Interface in toxtree.ui.tree.actions
 
ITreeView - Interface in toxtree.ui.tree
 

J

jcpDialog - Variable in class toxtree.data.DataModule
 
jcpDialog - Variable in class toxtree.ui.molecule.MoleculeEditAction
 
jcpModel - Variable in class toxtree.data.DataModule
 
jcpModel - Variable in class toxtree.ui.molecule.MoleculeEditAction
 
JCustomTreeComponent - Class in toxtree.ui.tree
Encapsulates TreeLayout in a JComponent.
JCustomTreeComponent(IDecisionMethod, ActionMap) - Constructor for class toxtree.ui.tree.JCustomTreeComponent
 
jobFinished(Exception) - Method in class toxtree.ui.batch.BatchProcessingDialog
 
joeSmartsPatern - Variable in class toxTree.tree.rules.smarts.SmartsPattern
 

K

ketalAttachedToTerminalVinyl() - Static method in class toxTree.query.FunctionalGroups
 
KETONE - Static variable in class toxTree.query.FunctionalGroups
 
ketone() - Static method in class toxTree.query.FunctionalGroups
 
KETONE_A_B_UNSATURATED - Static variable in class verhaar.query.FunctionalGroups
 
ketone_a_b_unsaturated() - Static method in class verhaar.query.FunctionalGroups
 
ketone_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
ketone_ring() - Static method in class toxTree.query.FunctionalGroups
 
KETONE_SIDECHAIN - Static variable in class toxTree.query.FunctionalGroups
 
ketoneAttachedToTerminalVinyl() - Static method in class toxTree.query.FunctionalGroups
 
keys - Variable in class toxtree.ui.HashtableModel
 
Kroes1Tree - Class in toxtree.plugins.kroes
 
Kroes1Tree() - Constructor for class toxtree.plugins.kroes.Kroes1Tree
 
KroesRule10 - Class in toxtree.plugins.kroes.rules
 
KroesRule10() - Constructor for class toxtree.plugins.kroes.rules.KroesRule10
 
KroesRule11 - Class in toxtree.plugins.kroes.rules
 
KroesRule11() - Constructor for class toxtree.plugins.kroes.rules.KroesRule11
 
KroesRule12 - Class in toxtree.plugins.kroes.rules
Does estimated intake exceed 1800 µg/day ?
KroesRule12() - Constructor for class toxtree.plugins.kroes.rules.KroesRule12
 
KroesRule2 - Class in toxtree.plugins.kroes.rules
Are there structural alerts that raise concern for potential genotoxicity?
KroesRule2() - Constructor for class toxtree.plugins.kroes.rules.KroesRule2
 
KroesRule3 - Class in toxtree.plugins.kroes.rules
Is the chemical an aflatoxin-like, azoxy-, or N-nitroso compound
KroesRule3() - Constructor for class toxtree.plugins.kroes.rules.KroesRule3
 
KroesRule4 - Class in toxtree.plugins.kroes.rules
Does estimated intake exceed TTC of 0.15 µg/day ?
KroesRule4() - Constructor for class toxtree.plugins.kroes.rules.KroesRule4
 
KroesRule5 - Class in toxtree.plugins.kroes.rules
Does estimated intake exceed TTC of 1.5 mcg/day ?
KroesRule5() - Constructor for class toxtree.plugins.kroes.rules.KroesRule5
 
KroesRule6 - Class in toxtree.plugins.kroes.rules
Is the compound an organophosphate?
KroesRule6() - Constructor for class toxtree.plugins.kroes.rules.KroesRule6
 
KroesRule7 - Class in toxtree.plugins.kroes.rules
Does estimated intake exceed TTC of 18µg/day ?
KroesRule7() - Constructor for class toxtree.plugins.kroes.rules.KroesRule7
 
KroesRule8 - Class in toxtree.plugins.kroes.rules
Is the compound in Cramer structural class III?
KroesRule8() - Constructor for class toxtree.plugins.kroes.rules.KroesRule8
 
KroesRule9 - Class in toxtree.plugins.kroes.rules
 
KroesRule9() - Constructor for class toxtree.plugins.kroes.rules.KroesRule9
 

L

label - Variable in class toxtree.ui.StatusBar
 
labels - Variable in class toxtree.ui.molecule.SmilesEntryPanel
 
labels - Variable in class toxtree.ui.tree.qsar.OptionsPanel
 
labelsDescriptor - Variable in class toxtree.ui.tree.qsar.OptionsPanel
 
LACTONE - Static variable in class toxTree.query.FunctionalGroups
 
lactone(boolean) - Static method in class toxTree.query.FunctionalGroups
 
lactoneBreakable() - Static method in class toxTree.query.FunctionalGroups
 
lactoneBreakable - Static variable in class toxTree.tree.cramer.RuleLactonesFusedOrUnsaturated
 
lactoneUnsaturated - Variable in class sicret.rules.RuleLactonesFusedOrUnsaturated
 
lactoneUnsaturated - Static variable in class toxTree.tree.cramer.RuleLactonesFusedOrUnsaturated
 
last() - Method in interface toxTree.core.IMoleculesIterator
 
last() - Method in class toxtree.data.DataContainer
 
last() - Method in class toxTree.data.MoleculesFile
 
last() - Method in class toxTree.data.MoleculesIterator
 
lastIndexOf(Object) - Method in class toxTree.data.SortedPropertyList
 
lastIndexOf(Object) - Method in class toxTree.tree.CategoriesList
 
lastIndexOf(Object) - Method in class toxTree.tree.DecisionMethodsList
 
lastIndexOf(Object) - Method in class toxTree.tree.DecisionNodesList
 
lastIndexOf(Object) - Method in class toxTree.tree.RulesList
 
lastModified - Variable in class toxTree.io.batch.FileState
 
launchEditor(IDecisionMethod) - Method in class toxtree.ui.tree.actions.EditDecisionMethodAction
 
launchErrorDialog(Exception) - Method in class toxtree.ui.tree.rules.SMARTSRuleEditor
 
length - Variable in class toxTree.io.batch.FileState
 
LewisTree - Class in toxtree.plugins.lewis
derived by Weka from table2.
LewisTree() - Constructor for class toxtree.plugins.lewis.LewisTree
 
LiadMethodsListAction - Class in toxtree.ui.tree.actions
 
LiadMethodsListAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.tree.actions.LiadMethodsListAction
 
LiadMethodsListAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.tree.actions.LiadMethodsListAction
 
LiadMethodsListAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.LiadMethodsListAction
 
LinearDiscriminantRule - Class in toxTree.qsar
Uses LinearQSARModel and returns true if LinearQSARModel.predict(IAtomContainer) is >= LinearDiscriminantRule.getThreshold() and false otherwise.
LinearDiscriminantRule(LinearQSARModel, double) - Constructor for class toxTree.qsar.LinearDiscriminantRule
 
LinearDiscriminantRule() - Constructor for class toxTree.qsar.LinearDiscriminantRule
 
LinearPreprocessor - Class in toxTree.qsar
 
LinearPreprocessor(double[], double[]) - Constructor for class toxTree.qsar.LinearPreprocessor
 
LinearQSARModel - Class in toxTree.qsar
 
LinearQSARModel() - Constructor for class toxTree.qsar.LinearQSARModel
 
LinearQSARModel(List<String>, List<IMolecularDescriptor>, String, double[]) - Constructor for class toxTree.qsar.LinearQSARModel
 
LipidSolubility - Static variable in class sicret.rules.RuleLipidSolubility
 
list - Variable in class toxTree.tree.DecisionMethodsList
 
list - Variable in class toxTree.tree.DecisionNodesList
 
list - Variable in class toxTree.tree.RulesList
 
list - Variable in class toxtree.ui.tree.ListTableModel
 
listBaseTypes(Class, String) - Static method in class toxTree.core.Introspection
this is just a test for the concept of introspection
listener - Variable in class mutant.rules.QSAR6Applicable
 
listener - Variable in class toxtree.data.ToxTreeModule
 
listener - Variable in class toxTree.tree.rules.RuleVerifyProperty
 
listener - Variable in class toxTree.tree.rules.UserInputRule
 
listener - Variable in class toxTree.tree.UserDefinedTree
 
listeners - Variable in class toxtree.ui.tree.DecisionTreeModel
 
listIterator() - Method in class toxTree.tree.CategoriesList
 
listIterator(int) - Method in class toxTree.tree.CategoriesList
 
listIterator() - Method in class toxTree.tree.DecisionMethodsList
 
listIterator(int) - Method in class toxTree.tree.DecisionMethodsList
 
listIterator() - Method in class toxTree.tree.DecisionNodesList
 
listIterator(int) - Method in class toxTree.tree.DecisionNodesList
 
listIterator() - Method in class toxTree.tree.RulesList
 
listIterator(int) - Method in class toxTree.tree.RulesList
 
ListOfAtomContainers - Class in toxTree.data
An attempt to implement org.openscience.cdk.interfaces.SetOfAtomContainers interface as a List
ListOfAtomContainers() - Constructor for class toxTree.data.ListOfAtomContainers
 
ListOfAtomContainers(int) - Constructor for class toxTree.data.ListOfAtomContainers
 
ListOfAtomContainers(Collection) - Constructor for class toxTree.data.ListOfAtomContainers
 
ListPanel - Class in toxtree.ui.tree
A JPanel, displaying a table based on ListTableModel.
ListPanel(String, ListTableModel, ActionMap) - Constructor for class toxtree.ui.tree.ListPanel
 
ListPanel(String, ListTableModel, boolean, ActionMap) - Constructor for class toxtree.ui.tree.ListPanel
 
ListPanel(String, ListTableModel, LayoutManager, ActionMap) - Constructor for class toxtree.ui.tree.ListPanel
 
ListPanel(String, ListTableModel, LayoutManager, boolean, ActionMap) - Constructor for class toxtree.ui.tree.ListPanel
 
listPanel - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
 
ListPanelDescriptor - Class in toxtree.ui.wizard
 
ListPanelDescriptor(Object, Object, Object, ListPanel, ImageIcon) - Constructor for class toxtree.ui.wizard.ListPanelDescriptor
 
listSubstructureAction - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
 
ListTableModel - Class in toxtree.ui.tree
TODO add description
ListTableModel(List) - Constructor for class toxtree.ui.tree.ListTableModel
 
loadAllFromPlugins() - Method in class toxTree.tree.DecisionMethodsList
 
LoadAndEditTreeAction - Class in toxtree.ui.tree.actions
Loads a decision tree from a file and launches a decision tree editor
LoadAndEditTreeAction(DataModule) - Constructor for class toxtree.ui.tree.actions.LoadAndEditTreeAction
 
LoadAndEditTreeAction(DataModule, String) - Constructor for class toxtree.ui.tree.actions.LoadAndEditTreeAction
 
LoadAndEditTreeAction(DataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.LoadAndEditTreeAction
 
loadConfig() - Method in class toxTree.io.batch.BatchProcessing
 
loadConfig() - Method in interface toxTree.io.batch.IBatchProcessing
 
loadCreateObject(String) - Static method in class toxTree.core.Introspection
 
loadedFromFile() - Method in class toxtree.data.DataContainer
 
loader - Static variable in class toxTree.core.Introspection
 
loadForest(InputStream) - Static method in class toxTree.core.Introspection
 
loadForestXML(InputStream) - Static method in class toxTree.core.Introspection
 
loadFromFile() - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
 
loadFromPlugins(String) - Method in class toxTree.tree.DecisionMethodsList
 
loadHydrolysisReaction(int) - Method in class toxTree.query.SimpleReactions
 
loadMetabolicReaction(int) - Method in class toxTree.query.SimpleReactions
 
loadPreconfiguredReaction(String) - Method in class toxTree.query.SimpleReactions
 
loadRules(InputStream, String) - Static method in class toxTree.core.Introspection
Loads a decision tree from an InputStream Uses Java serialization mechanism
loadRulesXML(InputStream, String) - Static method in class toxTree.core.Introspection
 
LoadTreeAction - Class in toxtree.ui.tree.actions
 
LoadTreeAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.tree.actions.LoadTreeAction
 
LoadTreeAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.tree.actions.LoadTreeAction
 
LoadTreeAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.LoadTreeAction
 
log(Level, String) - Method in class toxTree.tree.AbstractRule
 
log(Level, String, Object) - Method in class toxTree.tree.AbstractRule
 
log(Level, String, Object[]) - Method in class toxTree.tree.AbstractRule
 
logger - Static variable in class mutant.descriptors.DescriptorStructurePresence
 
logger - Static variable in class mutant.descriptors.SubstituentExtractor
 
logger - Static variable in class mutant.descriptors.SubstituentsDescriptor
 
logger - Static variable in class toxTree.apps.AbstractApplication
 
logger - Static variable in class toxTree.core.Introspection
 
logger - Static variable in class toxtree.data.DataContainer
 
logger - Static variable in class toxtree.data.DataModule
 
logger - Variable in class toxTree.data.ListOfAtomContainers
 
logger - Variable in class toxTree.data.MoleculesFile
 
logger - Static variable in class toxTree.data.MoleculesIterator
 
logger - Static variable in class toxTree.io.batch.BatchFactory
 
logger - Static variable in class toxTree.io.batch.BatchProcessing
 
logger - Static variable in class toxTree.qsar.AbstractQSARModel
 
logger - Static variable in class toxTree.query.FunctionalGroups
 
logger - Static variable in class toxTree.query.MolAnalyser
 
logger - Static variable in class toxTree.query.MolFlags
 
logger - Static variable in class toxTree.query.SimpleReactions
 
logger - Static variable in class toxTree.tree.AbstractRule
 
logger - Static variable in class toxTree.tree.AbstractTree
 
logger - Variable in class toxTree.tree.rules.LookupFile
 
logger - Static variable in class toxTree.tree.TreeResult
 
logger - Static variable in class toxtree.ui.tree.TreeEditorPanel
 
logger - Static variable in class verhaar.query.QueryUnsaturatedBond
 
login() - Method in class toxtree.lookup.RemoteLookup
 
login(String, String) - Method in class toxtree.lookup.RemoteLookup
 
LogKow - Static variable in class sicret.rules.RuleLogP
 
logout() - Method in class toxtree.lookup.RemoteLookup
 
LONGCHAIN_SUBSTITUENT - Static variable in class toxTree.tree.rules.RuleRingSubstituents
 
lookup - Variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
lookup(String, Object) - Method in class toxtree.data.DataContainer
 
lookup(String, Object, boolean) - Method in class toxtree.data.DataContainer
 
lookup(String, Object) - Method in class toxtree.data.DecisionMethodsDataModule
 
lookup(String) - Method in class toxtree.lookup.RemoteLookup
 
lookup(IAtomContainer) - Method in class toxTree.tree.rules.LookupFile
 
LookupCompoundAction - Class in toxtree.ui.molecule
 
LookupCompoundAction(DataModule) - Constructor for class toxtree.ui.molecule.LookupCompoundAction
 
LookupCompoundAction(DataModule, String) - Constructor for class toxtree.ui.molecule.LookupCompoundAction
 
LookupCompoundAction(DataModule, String, Icon) - Constructor for class toxtree.ui.molecule.LookupCompoundAction
 
LookupFile - Class in toxTree.tree.rules
 
LookupFile(String) - Constructor for class toxTree.tree.rules.LookupFile
 
LookupFile(File) - Constructor for class toxTree.tree.rules.LookupFile
 
lookupFile - Variable in class toxTree.tree.rules.RuleStructuresList
 
lookupService - Static variable in class toxtree.lookup.RemoteLookup
 

M

main(String[]) - Static method in class toxTree.apps.AbstractApplication
 
main(String[]) - Static method in class toxTree.apps.toxForest.ToxForestApp
 
main(String[]) - Static method in class toxTree.apps.ToxTreeApp
Command line options:
java -jar toxTree.jar -f input_file_for_normal_open
java -jar toxTree.jar -b input_file_for_batch_processing
mainFrame - Variable in class toxTree.apps.AbstractApplication
 
mainPanel - Variable in class toxTree.apps.CompoundMethodApplication
 
mainPanel - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
 
mainStructure - Variable in class verhaar.rules.RuleRingMainStrucSubstituents
 
makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class toxtree.ui.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeGrid(Container, int, int, int, int, int, int) - Static method in class toxtree.ui.SpringUtilities
Aligns the first rows * cols components of parent in a grid.
makeMolecule(boolean) - Static method in class toxTree.tree.AbstractRule
This is to ensure each derived class will provide an example of a molecule which resolves to the yes and no rule outcome
makeNitroPhenol() - Static method in class verhaar.query.FunctionalGroups
 
mapHydrocarbon(IMolecule) - Static method in class toxTree.query.FunctionalGroups
 
mapToString(IAtomContainer, String) - Static method in class toxTree.query.FunctionalGroups
 
mapToString(IAtomContainer, Collection) - Static method in class toxTree.query.FunctionalGroups
 
mapToString(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
mark(IAtomContainer, ArrayList) - Static method in class toxTree.query.FunctionalGroups
 
markAtomsInRing(String, List, IAtomContainer, QueryAtomContainer) - Static method in class mutant.descriptors.SubstituentExtractor
 
markAtomsInRing(IAtomContainer, QueryAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
markCHn(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
markMaps(IAtomContainer, IAtomContainer, List) - Static method in class toxTree.query.FunctionalGroups
 
markOneMap(IAtomContainer, IAtomContainer, List, int) - Static method in class toxTree.query.FunctionalGroups
 
marks - Static variable in class toxTree.query.CHQueryAtom
 
markUniqueBondMap(IMolecule, ArrayList, boolean) - Static method in class toxTree.query.FunctionalGroups
 
match() - Method in class toxTree.io.batch.FileState
 
match(File) - Method in class toxTree.io.batch.FileState
 
matches(IBond) - Method in class toxtree.plugins.kroes.rules.MyOrderQueryBond
 
matches(IAtom) - Method in class toxTree.query.AliphaticCHQueryAtom
 
matches(IBond) - Method in class toxTree.query.AssociationQueryBond
 
matches(IAtom) - Method in class toxTree.query.CHQueryAtom
 
matches(IAtom) - Method in class toxTree.query.ReallyAnyAtom
 
matches(Bond) - Method in class toxTree.query.SingleOrDoubleQueryBond
 
matches(Atom) - Method in class toxTree.query.TopologyAnyAtom
 
matches(IBond) - Method in class toxTree.query.TopologyAnyBond
 
matches(IBond) - Method in class toxTree.query.TopologyOrderQueryBond
 
matches(IAtom) - Method in class toxTree.query.TopologySymbolQueryAtom
 
matches(IBond) - Method in class verhaar.query.AromaticQueryBond
 
matches(IBond) - Method in class verhaar.query.OrderQueryBondAromatic
 
matches(IBond) - Method in class verhaar.query.QueryAssociationBond
 
matches(IBond) - Method in class verhaar.query.QueryUnsaturatedBond
 
MATreeResult - Class in michaelacceptors
 
MATreeResult() - Constructor for class michaelacceptors.MATreeResult
 
matrix - Variable in class toxTree.qsar.MatrixPreprocessor
 
MatrixPreprocessor - Class in toxTree.qsar
 
MatrixPreprocessor(double[][]) - Constructor for class toxTree.qsar.MatrixPreprocessor
 
maxHalogens - Variable in class verhaar.rules.Rule21
 
maxLevel - Variable in class toxtree.ui.tree.TreeLayout
 
maxNitroGroups - Variable in class verhaar.rules.Rule21
 
maxValue - Variable in class toxTree.tree.rules.RuleDescriptorRange
 
maxValue - Variable in class toxTree.tree.rules.RuleManyAromaticRings
 
Me - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
 
Me - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
 
Me1 - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
 
Me1 - Static variable in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
 
me_essential - Static variable in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
 
me_nonessential - Static variable in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
 
MeltingPoint - Static variable in class sicret.rules.RuleMeltingPoint
 
MERCAPTAN - Static variable in class toxTree.query.FunctionalGroups
 
mercaptan() - Static method in class toxTree.query.FunctionalGroups
 
mercaptan_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
message - Variable in class toxTree.tree.rules.UserInputRule
 
metabolic - Static variable in class toxTree.query.SimpleReactions
 
metabolicReactions - Static variable in class toxTree.tree.cramer.RuleSufficientSulphonateGroups
 
MetaboliteGenerator - Class in toxtree.plugins.smartcyp.rules
 
MetaboliteGenerator() - Constructor for class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
 
MetabolitesFrame - Class in toxtree.ui.metabolites
 
MetabolitesFrame() - Constructor for class toxtree.ui.metabolites.MetabolitesFrame
 
metabolitesPanel - Variable in class toxtree.ui.metabolites.MetabolitesFrame
 
MetabolitesPanel - Class in toxtree.ui.metabolites
 
MetabolitesPanel() - Constructor for class toxtree.ui.metabolites.MetabolitesPanel
 
metabolize - Static variable in class toxTree.query.SimpleReactions
 
MetabolyteRecycler - Class in toxTree.query.metabolite
 
MetabolyteRecycler() - Constructor for class toxTree.query.metabolite.MetabolyteRecycler
 
metals - Static variable in class toxTree.tree.cramer.RuleMonocycloalkanoneEtc
 
metals - Static variable in class toxTree.tree.cramer.RuleSufficientSulphonateGroups
 
methacrolein() - Static method in class toxTree.query.FunctionalGroups
 
methacroleinAcetal() - Static method in class toxTree.query.FunctionalGroups
 
methacrylicAcid() - Static method in class toxTree.query.FunctionalGroups
 
method - Variable in class toxtree.ui.tree.TreeEditorPanel
 
method - Variable in class toxtree.ui.tree.TreeLayout
 
methods - Variable in class toxtree.data.DecisionMethodsDataModule
 
METHOXY - Static variable in class toxTree.query.FunctionalGroups
 
methoxy() - Static method in class toxTree.query.FunctionalGroups
Query for methoxy group.
methoxy_ring() - Static method in class toxTree.query.FunctionalGroups
 
methyl() - Static method in class toxTree.query.FunctionalGroups
Query for Methyl group.
METHYLETHER - Static variable in class toxTree.query.FunctionalGroups
 
methylether() - Static method in class toxTree.query.FunctionalGroups
 
mic - package mic
 
mic.categories - package mic.categories
 
mic.rules - package mic.rules
 
MichaelAcceptorRule - Class in toxtree.plugins.dnabinding.rules
Michael acceptors
MichaelAcceptorRule() - Constructor for class toxtree.plugins.dnabinding.rules.MichaelAcceptorRule
 
MichaelAcceptorRule - Class in toxtree.plugins.proteinbinding.rules
Michael acceptors
MichaelAcceptorRule() - Constructor for class toxtree.plugins.proteinbinding.rules.MichaelAcceptorRule
 
MichaelAcceptorRule - Class in toxtree.plugins.skinsensitisation.rules
Michael acceptors
MichaelAcceptorRule() - Constructor for class toxtree.plugins.skinsensitisation.rules.MichaelAcceptorRule
 
MichaelAcceptorRules - Class in michaelacceptors
 
MichaelAcceptorRules() - Constructor for class michaelacceptors.MichaelAcceptorRules
 
michaelacceptors - package michaelacceptors
 
MichaelAcceptors - Class in toxtree.plugins.dnabinding.categories
Michael Acceptors
MichaelAcceptors() - Constructor for class toxtree.plugins.dnabinding.categories.MichaelAcceptors
 
MichaelAcceptors - Class in toxtree.plugins.proteinbinding.categories
Michael Acceptors
MichaelAcceptors() - Constructor for class toxtree.plugins.proteinbinding.categories.MichaelAcceptors
 
MichaelAcceptors - Class in toxtree.plugins.skinsensitisation.categories
Michael Acceptors
MichaelAcceptors() - Constructor for class toxtree.plugins.skinsensitisation.categories.MichaelAcceptors
 
michaelacceptors.categories - package michaelacceptors.categories
 
michaelacceptors.rules - package michaelacceptors.rules
 
micronucleusClass1 - Class in mic.categories
 
micronucleusClass1() - Constructor for class mic.categories.micronucleusClass1
 
micronucleusClass2 - Class in mic.categories
 
micronucleusClass2() - Constructor for class mic.categories.micronucleusClass2
 
MICRules - Class in mic
 
MICRules() - Constructor for class mic.MICRules
 
MICTreeResult - Class in mic.rules
 
MICTreeResult() - Constructor for class mic.rules.MICTreeResult
 
minValue - Variable in class toxTree.tree.rules.RuleDescriptorRange
 
minValue - Variable in class toxTree.tree.rules.RuleManyAromaticRings
 
MOARules - Class in toxtree.plugins.moa
 
MOARules() - Constructor for class toxtree.plugins.moa.MOARules
 
modal - Variable in class toxtree.ui.molecule.MoleculeEditAction
 
mode - Variable in class toxtree.plugins.search.rules.Find
 
mode - Variable in class toxTree.tree.rules.RuleElements
 
modeAllSpecifiedElements - Static variable in class toxTree.tree.rules.RuleElements
 
modeAnySpecifiedElements - Static variable in class toxTree.tree.rules.RuleElements
 
model - Variable in class toxtree.data.ToxTreeActions
 
model - Variable in class toxTree.qsar.LinearDiscriminantRule
 
model - Variable in class toxtree.ui.tree.ListPanel
 
modelProcessing - Variable in class toxtree.ui.StatusBar
 
modeOnlySpecifiedElements - Static variable in class toxTree.tree.rules.RuleElements
 
modified - Variable in class toxtree.data.DataContainer
 
modified - Variable in class toxTree.tree.AbstractTree
 
module - Variable in class toxtree.ui.actions.DataModuleAction
 
MolAnalyseException - Exception in toxTree.exceptions
TODO add description
MolAnalyseException() - Constructor for exception toxTree.exceptions.MolAnalyseException
 
MolAnalyseException(String) - Constructor for exception toxTree.exceptions.MolAnalyseException
 
MolAnalyseException(String, IAtomContainer) - Constructor for exception toxTree.exceptions.MolAnalyseException
 
MolAnalyseException(Throwable) - Constructor for exception toxTree.exceptions.MolAnalyseException
 
MolAnalyseException(Throwable, IAtomContainer) - Constructor for exception toxTree.exceptions.MolAnalyseException
 
MolAnalyseException(String, Throwable) - Constructor for exception toxTree.exceptions.MolAnalyseException
 
MolAnalyseException(String, Throwable, IAtomContainer) - Constructor for exception toxTree.exceptions.MolAnalyseException
 
MolAnalyser - Class in toxTree.query
 
MolAnalyser() - Constructor for class toxTree.query.MolAnalyser
 
molecule - Variable in class toxTree.tree.RuleResult
 
molecule - Variable in class toxtree.ui.molecule.AbstractMoleculeAction
 
MoleculeEditAction - Class in toxtree.ui.molecule
Launches JChemPaint structure diagram editor for a preset molecule
MoleculeEditAction(IMolecule) - Constructor for class toxtree.ui.molecule.MoleculeEditAction
 
MoleculeEditAction(IMolecule, String) - Constructor for class toxtree.ui.molecule.MoleculeEditAction
 
MoleculeEditAction(IMolecule, String, Icon) - Constructor for class toxtree.ui.molecule.MoleculeEditAction
 
moleculeEditAction - Variable in class toxtree.ui.tree.rules.RulePanel
 
moleculeEditAction - Variable in class toxtree.ui.tree.rules.SmartsPanelEditor
 
molecules - Variable in class toxtree.ui.molecule.MoleculeEditAction
 
MoleculesFile - Class in toxTree.data
 
MoleculesFile(String, IChemObjectBuilder, IReaderListener) - Constructor for class toxTree.data.MoleculesFile
 
MoleculesFile(File, IChemObjectBuilder) - Constructor for class toxTree.data.MoleculesFile
 
MoleculesFile(File, IChemObjectBuilder, IReaderListener) - Constructor for class toxTree.data.MoleculesFile
 
MoleculesIterator - Class in toxTree.data
Contains molecules loaded from a file, entered by SMILES SmilesEntryPanel entered by structure diagram editor toxTree.ui.molecule.JChemPaintDialog
MoleculesIterator() - Constructor for class toxTree.data.MoleculesIterator
 
MolFileFilter - Class in toxTree.io
 
MolFileFilter() - Constructor for class toxTree.io.MolFileFilter
 
MolFileFilter(String, String) - Constructor for class toxTree.io.MolFileFilter
 
MolFlags - Class in toxTree.query
 
MolFlags() - Constructor for class toxTree.query.MolFlags
 
MOLFLAGS - Static variable in class toxTree.query.MolFlags
 
MolWeight - Static variable in class sicret.rules.RuleMolWeight
 
MR - Static variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
mr - Variable in class mutant.descriptors.DescriptorMolarRefractivity
 
MSG16 - Static variable in class eye.rules.Rule16
 
MSG17 - Static variable in class eye.rules.Rule17
 
MSG31 - Static variable in class eye.rules.Rule31
 
MSG32 - Static variable in class eye.rules.Rule32
 
MSG33 - Static variable in class eye.rules.Rule33
 
MSG34 - Static variable in class eye.rules.Rule34
 
MSG35 - Static variable in class eye.rules.Rule35
 
MSG36 - Static variable in class eye.rules.Rule36
 
MSG37 - Static variable in class eye.rules.Rule37
 
MSG38 - Static variable in class eye.rules.Rule38
 
MSG39 - Static variable in class eye.rules.Rule39
 
MSG_15 - Static variable in class eye.rules.Rule15
 
MSG_18H - Static variable in class sicret.rules.RuleAcidAnhydrides
 
MSG_18H - Static variable in class sicret.rules.RuleAcrylicAcids
 
MSG_18H - Static variable in class sicret.rules.RuleC10_C20AliphaticAlcohols
 
MSG_18H - Static variable in class sicret.rules.RuleCarbamoylHalide
 
MSG_18H - Static variable in class sicret.rules.RuleDi_Tri_Nitrobenzenes
 
MSG_18H - Static variable in class sicret.rules.RuleHalonitrobenzene
 
MSG_18H - Static variable in class sicret.rules.RuleOandPQuinones
 
MSG_18H - Static variable in class toxTree.tree.cramer.RuleKetoneAlcoholEtc
 
MSG_ALIPHATIC - Static variable in class toxTree.tree.cramer.RuleSimplyBranchedAliphaticHydrocarbon
 
MSG_ALKOXYPARACH - Static variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
MSG_BENZENESUBSTITUENT - Static variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
MSG_CANTCREATEFILE - Static variable in class toxTree.io.batch.BatchProcessing
 
MSG_COMMONCARBOHYDRATE - Static variable in class toxTree.tree.rules.RuleCarbohydrate
 
MSG_EMPTYFILE - Static variable in interface toxTree.core.IMoleculesIterator
 
MSG_ERRORCOUNTING - Static variable in class toxTree.io.batch.BatchProcessing
 
MSG_ERRORONOPEN - Static variable in interface toxTree.core.IMoleculesIterator
 
MSG_ERRORONSAVE - Static variable in interface toxTree.core.IMoleculesIterator
 
MSG_ERRORSAVE - Static variable in class toxTree.io.batch.BatchProcessing
 
MSG_FILEDONOTEXISTS - Static variable in class toxTree.io.batch.BatchProcessing
 
MSG_HASGROUP - Static variable in class toxTree.query.FunctionalGroups
Messages
MSG_HASGROUP - Static variable in class toxTree.tree.rules.RuleSubstructures
 
MSG_MANYGROUPSOFAKIND - Static variable in class toxTree.tree.rules.RuleCarbohydrate
 
MSG_MOLECULEIS - Static variable in class toxTree.query.FunctionalGroups
 
MSG_NO - Static variable in class toxTree.tree.AbstractRule
 
MSG_NOTACOMMONCARBOHYDRATE - Static variable in class toxTree.tree.rules.RuleCarbohydrate
 
MSG_OPEN - Static variable in class toxTree.io.batch.BatchProcessing
 
MSG_OPENSUCCESS - Static variable in interface toxTree.core.IMoleculesIterator
 
MSG_SAVESUCCESS - Static variable in interface toxTree.core.IMoleculesIterator
 
MSG_SIMPLYBRANCHED - Static variable in class toxTree.tree.cramer.RuleSimplyBranchedAliphaticHydrocarbon
 
MSG_UNSUPPORTEDFORMAT - Static variable in interface toxTree.core.IMoleculesIterator
 
MSG_UNSUPPORTEDFORMAT - Static variable in class toxTree.io.batch.BatchProcessing
 
MSG_YES - Static variable in class toxTree.tree.AbstractRule
 
multilabel - Variable in class toxTree.tree.CategoriesList
 
multiLabel - Variable in class toxTree.tree.DecisionNodesFactory
 
MultiLabelDecisionNode - Class in toxTree.tree
 
MultiLabelDecisionNode() - Constructor for class toxTree.tree.MultiLabelDecisionNode
Constructor
MultiLabelDecisionNode(IDecisionRule) - Constructor for class toxTree.tree.MultiLabelDecisionNode
Constructs a decision node with rule, null next nodes.
MultiLabelDecisionNodesList - Class in toxTree.tree
 
MultiLabelDecisionNodesList() - Constructor for class toxTree.tree.MultiLabelDecisionNodesList
 
MultiLabelDecisionNodesList(IDecisionCategories, String[], int[][]) - Constructor for class toxTree.tree.MultiLabelDecisionNodesList
 
mutant - package mutant
 
mutant.categories - package mutant.categories
 
mutant.descriptors - package mutant.descriptors
 
mutant.rules - package mutant.rules
 
MutantCategory - Class in mutant.categories
 
MutantCategory(String, int, int) - Constructor for class mutant.categories.MutantCategory
 
MutantCategory(String, int) - Constructor for class mutant.categories.MutantCategory
 
MutantTreeResult - Class in mutant.rules
 
MutantTreeResult() - Constructor for class mutant.rules.MutantTreeResult
 
MyAssociationBond - Class in toxTree.query
Modified 2005-9-23 Modified 2012-2-25
MyAssociationBond() - Constructor for class toxTree.query.MyAssociationBond
 
MyAssociationBond(IAtom, IAtom) - Constructor for class toxTree.query.MyAssociationBond
 
MyOrderQueryBond - Class in toxtree.plugins.kroes.rules
 
MyOrderQueryBond() - Constructor for class toxtree.plugins.kroes.rules.MyOrderQueryBond
 
MyOrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class toxtree.plugins.kroes.rules.MyOrderQueryBond
 

N

N - Static variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
n - Static variable in class verhaar.query.FunctionalGroups
 
NA - Static variable in class toxTree.data.MoleculesFile
 
name - Variable in class mutant.rules.SMARTSGroup
 
name - Variable in class toxTree.qsar.AbstractQSARModel
 
name - Variable in class toxTree.tree.AbstractTree
 
name - Variable in class toxTree.tree.DefaultCategory
 
nameField - Variable in class toxtree.ui.tree.rules.RulePanel
 
nameField - Variable in class toxtree.ui.tree.ToxTreeEditorPanel
 
names - Variable in class mutant.descriptors.DescriptorIDist
 
names - Static variable in class mutant.descriptors.DescriptorMolarRefractivity
 
names - Variable in class toxtree.ui.molecule.AtomContainerPropertyTableModel
 
NavigationPanel - Class in toxtree.ui.molecule
 
NavigationPanel(DataContainer, Color, Color) - Constructor for class toxtree.ui.molecule.NavigationPanel
 
NavigationPanel(DataContainer, boolean, Color, Color) - Constructor for class toxtree.ui.molecule.NavigationPanel
 
NavigationPanel(DataContainer, LayoutManager, Color, Color) - Constructor for class toxtree.ui.molecule.NavigationPanel
 
NavigationPanel(DataContainer, LayoutManager, boolean, Color, Color) - Constructor for class toxtree.ui.molecule.NavigationPanel
 
navPanel - Variable in class toxtree.ui.tree.molecule.CompoundPanel
 
navStat - Variable in class toxtree.ui.molecule.NavigationPanel
 
needsPreprocessing(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
NegligibleRisk - Class in toxtree.plugins.kroes.categories
 
NegligibleRisk() - Constructor for class toxtree.plugins.kroes.categories.NegligibleRisk
 
NegligibleRisk(String, int) - Constructor for class toxtree.plugins.kroes.categories.NegligibleRisk
 
newMolecule() - Method in class toxtree.data.DataContainer
 
newMolecule(IAtomContainer) - Method in class toxtree.data.DataContainer
 
NewMoleculeAction - Class in toxtree.ui.actions
Creates new empty molecule
NewMoleculeAction(DataContainer) - Constructor for class toxtree.ui.actions.NewMoleculeAction
 
NewMoleculeAction(DataContainer, String) - Constructor for class toxtree.ui.actions.NewMoleculeAction
 
NewMoleculeAction(DataContainer, String, Icon) - Constructor for class toxtree.ui.actions.NewMoleculeAction
 
NewRuleAction - Class in toxtree.ui.tree.actions
Shows a list of available rules and adds the selected one to the list of rules.
NewRuleAction(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.NewRuleAction
 
NewRuleAction(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.NewRuleAction
 
NewRuleAction(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.NewRuleAction
 
newSubstructureAction - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
 
NewTreeAction - Class in toxtree.ui.tree.actions
Creates new UserDefinedTree and launches toxTree.ui.tree.EditTreeFrame
NewTreeAction(DecisionMethodsDataModule) - Constructor for class toxtree.ui.tree.actions.NewTreeAction
 
NewTreeAction(DecisionMethodsDataModule, String) - Constructor for class toxtree.ui.tree.actions.NewTreeAction
 
NewTreeAction(DecisionMethodsDataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.NewTreeAction
 
next() - Method in class toxtree.data.DataContainer
 
next() - Method in class toxTree.data.MoleculesFile
 
next() - Method in class toxTree.data.MoleculesIterator
 
nextId - Variable in class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
nextIndex() - Method in class toxTree.data.MoleculesFile
 
nf - Static variable in class toxTree.tree.rules.RuleVerifyProperty
 
nf - Static variable in class toxtree.ui.molecule.AtomContainerPropertyTableModel
 
nitro - Variable in class mic.rules.SA27
 
nitro - Variable in class mutant.rules.SA27_gen
 
NITRO - Static variable in class toxTree.query.FunctionalGroups
 
nitro1double() - Static method in class toxTree.query.FunctionalGroups
SMARTS: [N+](=O)([O-])([!#1])
nitro2double() - Static method in class toxTree.query.FunctionalGroups
SMARTS: N(=O)(=O)([!#1])
NITRO_CHARGED - Static variable in class mutant.rules.SMARTSgroups
 
NITRO_UNCHARGED - Static variable in class mutant.rules.SMARTSgroups
 
nitroGroupsCount - Variable in class verhaar.rules.Rule21
 
nitroIDs - Variable in class verhaar.rules.Rule21
 
NNITROSO - Static variable in class toxTree.query.FunctionalGroups
 
Nnitroso() - Static method in class toxTree.query.FunctionalGroups
SMARTS: O=NN([!#1])([!#1])
no - Variable in class toxtree.data.ActionList
 
no - Variable in class toxTree.tree.AbstractRule
 
NO2 - Static variable in class mutant.descriptors.DescriptorHasNO2Group
 
NoAlerts - Class in toxtree.plugins.dnabinding.categories
No alerts
NoAlerts() - Constructor for class toxtree.plugins.dnabinding.categories.NoAlerts
 
NoAlerts - Class in toxtree.plugins.proteinbinding.categories
No alerts
NoAlerts() - Constructor for class toxtree.plugins.proteinbinding.categories.NoAlerts
 
NoAlerts - Class in toxtree.plugins.skinsensitisation.categories
No alerts
NoAlerts() - Constructor for class toxtree.plugins.skinsensitisation.categories.NoAlerts
 
noBranch - Variable in class toxtree.ui.tree.DecisionNodePanel
 
node - Variable in class toxtree.ui.tree.actions.SetBranchAction
 
node - Variable in class toxtree.ui.tree.DecisionNodePanel
 
node - Variable in class toxtree.ui.tree.EditTreeActions
 
nodePanel - Variable in class toxtree.ui.tree.TreeDrawing
 
nodePanel - Variable in class toxtree.ui.tree.TreeEditorPanel
 
nodePanel - Variable in class toxtree.ui.wizard.DecisionNodeWizard
 
nodes - Variable in class toxTree.tree.DecisionNode
 
NODES - Static variable in class toxtree.ui.tree.TreePrefuse
 
nodesFactory - Variable in class toxTree.tree.UserDefinedTree
 
noExample - Variable in class toxtree.ui.tree.rules.RulePanel
 
NoSites - Class in toxtree.plugins.smartcyp.categories
 
NoSites() - Constructor for class toxtree.plugins.smartcyp.categories.NoSites
 
NotASafetyConcern - Class in toxtree.plugins.kroes.categories
Substance would not be expected to be a safety concern
NotASafetyConcern() - Constructor for class toxtree.plugins.kroes.categories.NotASafetyConcern
 
NotASafetyConcern(String, int) - Constructor for class toxtree.plugins.kroes.categories.NotASafetyConcern
 
NotFound - Class in toxtree.plugins.search.categories
Not found
NotFound() - Constructor for class toxtree.plugins.search.categories.NotFound
 
notify - Variable in class toxTree.tree.TreeResult
 
notifyChanged() - Method in class toxTree.data.ListOfAtomContainers
 
notifyChanged(IChemObjectChangeEvent) - Method in class toxTree.data.ListOfAtomContainers
 
noxide_aromatic() - Static method in class toxTree.query.FunctionalGroups
 

O

object - Variable in class toxTree.qsar.AbstractQSARModel
 
object - Variable in class toxtree.ui.tree.qsar.OptionsPanel
 
objectAt(int, int) - Method in class toxtree.ui.tree.JCustomTreeComponent
 
ObjectPropertyFilter - Class in toxTree.data
 
ObjectPropertyFilter() - Constructor for class toxTree.data.ObjectPropertyFilter
 
ObjectPropertyFilter(Object, Object) - Constructor for class toxTree.data.ObjectPropertyFilter
 
objectTitle - Variable in class toxTree.core.ToxTreePackageEntry
 
offset - Variable in class toxTree.io.batch.FileState
 
offset - Variable in class toxtree.ui.tree.TreeLayout
 
okAction() - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
 
okAction() - Method in class toxtree.ui.batch.BatchProcessingDialog
 
okButton - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
 
okPressed - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
 
oldVerifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleHasOtherThanC_H_O_N_S2
 
openChain - Variable in class toxTree.query.MolFlags
 
openFile(File) - Method in interface toxTree.core.IMoleculesIterator
 
openFile(File) - Method in class toxtree.data.DataContainer
 
openFile(File) - Method in class toxTree.data.MoleculesIterator
 
OpenFileAction - Class in toxtree.ui.actions
Loads a file inti DataModule.getDataContainer()
OpenFileAction(DataModule) - Constructor for class toxtree.ui.actions.OpenFileAction
 
OpenFileAction(DataModule, String) - Constructor for class toxtree.ui.actions.OpenFileAction
 
OpenFileAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.OpenFileAction
 
openInputFile() - Method in class toxTree.io.batch.BatchProcessing
 
openInputFile() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
Opens the input file as set by constructor and creates IteratingChemObjectReader
openInputFile() - Method in interface toxTree.io.batch.IBatchProcessing
 
openURL(String) - Static method in class toxTree.io.Tools
 
options - Variable in class mutant.rules.QSAR6Applicable
 
options - Variable in class toxTree.tree.rules.RuleVerifyProperty
 
options - Variable in class toxTree.tree.rules.UserInputRule
 
options - Variable in class toxTree.tree.UserDefinedTree
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleAqueousSolubility
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleAqueousSolubility_10_2
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleAqueousSolubility_10_5
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleAqueousSolubility_11_7
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleAqueousSolubility_8_3
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleAqueousSolubility_8_4
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleAqueousSolubility_9_3
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleLipidSolubility_10_4
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleLipidSolubility_9_1
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleMelting_Point_11_3
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleMeltingPoint_11_2
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleMeltingPoint_12_3
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleMeltingPoint_8_1
 
optionsPanel(IAtomContainer) - Method in class eye.rules.RuleMolWeight_9_2
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule12
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule14
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule15
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule18
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule20
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule21
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule22
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule23
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule25
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule26
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule27
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule4
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.Rule8
 
optionsPanel(IAtomContainer) - Method in class sicret.rules.RuleMolWeight
 
optionsPanel(IAtomContainer) - Method in class toxTree.tree.AbstractTree
 
optionsPanel(UserInputRule, String, String) - Method in class toxtree.tree.rules.ApplyRuleOptions
 
optionsPanel(IDecisionMethod, IAtomContainer) - Method in class toxTree.ui.EditorFactory
 
optionsPanel(IDecisionMethod, IAtomContainer) - Method in class toxtree.ui.editors.SwingEditorFactory
 
optionsPanel(IDecisionMethod, IAtomContainer) - Method in interface toxTree.ui.IEditorFactory
 
OptionsPanel - Class in toxtree.ui
 
OptionsPanel(String, IAtomContainer, RuleVerifyProperty) - Constructor for class toxtree.ui.OptionsPanel
 
optionsPanel - Variable in class toxtree.ui.PropertyEditor
 
OptionsPanel<T> - Class in toxtree.ui.tree.qsar
 
OptionsPanel() - Constructor for class toxtree.ui.tree.qsar.OptionsPanel
 
OptionsPanel(T) - Constructor for class toxtree.ui.tree.qsar.OptionsPanel
 
OrderQueryBondAromatic - Class in verhaar.query
 
OrderQueryBondAromatic(boolean) - Constructor for class verhaar.query.OrderQueryBondAromatic
 
OrderQueryBondAromatic(IQueryAtom, IQueryAtom, IBond.Order, boolean) - Constructor for class verhaar.query.OrderQueryBondAromatic
 
originalMolecule - Variable in class toxTree.tree.TreeResult
 
outputFile - Variable in class toxTree.io.batch.BatchProcessing
 
outputStream - Variable in class toxTree.tree.AbstractTreePrinter
 

P

p_tag - Static variable in class toxTree.data.ObjectPropertyFilter
 
p_value - Static variable in class toxTree.data.ObjectPropertyFilter
 
packageName - Variable in class toxTree.core.ToxTreePackageEntry
 
packageName - Variable in class toxtree.ui.actions.AboutAction
 
pageAll - Static variable in class toxtree.ui.wizard.DecisionNodeWizard
 
pageCategoryOptions - Static variable in class toxtree.ui.wizard.DecisionNodeWizard
 
pageDetails - Static variable in class toxtree.ui.wizard.DecisionNodeWizard
 
pageIntrospection - Static variable in class toxtree.ui.wizard.DecisionNodeWizard
 
pageOptions - Static variable in class toxtree.ui.wizard.DecisionNodeWizard
 
pagePanel - Static variable in class toxtree.ui.wizard.DecisionNodeWizard
 
pageRuleOptions - Static variable in class toxtree.ui.wizard.DecisionNodeWizard
 
pages - Static variable in class toxtree.ui.wizard.DecisionNodeWizard
 
paint(Graphics) - Method in class toxtree.ui.tree.TreeLayout
 
paintComponent(Graphics) - Method in class toxtree.ui.tree.JCustomTreeComponent
 
panel2D - Variable in class toxtree.ui.tree.rules.RulePanel
 
panel2D - Variable in class toxtree.ui.tree.rules.SmartsPanelEditor
 
panel2D - Variable in class toxtree.ui.tree.rules.SubstructureRulePanel
 
panel2DBorder - Variable in class toxtree.ui.tree.rules.RulePanel
 
parameters - Variable in class toxTree.core.ToxTreeDescriptor
 
parameters - Variable in class toxTree.data.AbstractFilter
 
paramNames - Variable in class mutant.descriptors.DescriptorStructurePresence
 
paramNames - Variable in class mutant.descriptors.SubstituentsDescriptor
 
paramNames - Variable in class toxTree.core.ToxTreeDescriptor
 
params - Variable in class toxTree.tree.rules.RuleLipinski5
 
params - Variable in class verhaar.rules.RuleLogPRange
 
PARENT - Static variable in class toxTree.query.MolFlags
 
parentComponent - Variable in class toxtree.ui.molecule.MoleculeEditAction
 
PARENTKEY - Static variable in class toxtree.ui.tree.actions.AbstractTreeAction
 
parseCmdArgs(String[]) - Method in class toxTree.apps.CompoundMethodApplication
 
parseCmdArgs(String[]) - Method in class toxTree.apps.toxForest.ToxForestApp
 
parseCmdArgs(String[]) - Method in class toxTree.apps.ToxTreeApp
 
pattern - Variable in class toxtree.ui.tree.rules.SmartsPanelEditor
 
patternName - Variable in class toxtree.ui.tree.rules.SmartsPanelEditor
 
pause() - Method in class toxTree.io.batch.BatchProcessing
 
pause() - Method in interface toxTree.io.batch.IBatchProcessing
 
pauseAction() - Method in class toxtree.ui.batch.AbstractJobProcessingDialog
 
pauseAction() - Method in class toxtree.ui.batch.BatchProcessingDialog
 
pauseButton - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
 
pausePressed - Variable in class toxtree.ui.batch.AbstractJobProcessingDialog
 
PB29 - Class in mic.rules
 
PB29() - Constructor for class mic.rules.PB29
 
PB30 - Class in mic.rules
 
PB30() - Constructor for class mic.rules.PB30
 
pdfDoc - Variable in class toxTree.io.PDFWriter
 
pdfDoc - Variable in class toxTree.tree.PDFTreePrinter
 
PDFTreePrinter - Class in toxTree.tree
 
PDFTreePrinter(OutputStream) - Constructor for class toxTree.tree.PDFTreePrinter
 
PDFWriter - Class in toxTree.io
Exporting set of structures as PDF file.
PDFWriter(OutputStream) - Constructor for class toxTree.io.PDFWriter
 
pdfWriter - Variable in class toxTree.io.PDFWriter
 
pdfWriter - Variable in class toxTree.tree.PDFTreePrinter
 
percent - Variable in class toxTree.tree.ProgressStatus
 
PEROXIDE - Static variable in class verhaar.query.FunctionalGroups
 
peroxide() - Static method in class verhaar.query.FunctionalGroups
 
PHENOL - Static variable in class verhaar.query.FunctionalGroups
 
phenol() - Static method in class verhaar.query.FunctionalGroups
 
phenolIDs - Variable in class verhaar.rules.Rule21
 
phosphate - Static variable in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
 
PHOSPHATE - Static variable in class toxTree.query.FunctionalGroups
 
phosphate(String[]) - Static method in class toxTree.query.FunctionalGroups
 
picturePanel - Variable in class toxtree.ui.tree.molecule.CompoundPanel
 
places - Variable in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
placeWidgets() - Method in class toxtree.ui.tree.qsar.OptionsPanel
 
policyService - Variable in class toxtree.lookup.RemoteLookup
 
POLYOXYETHYLENE - Static variable in class toxTree.query.FunctionalGroups
 
polyoxyethylene(int) - Static method in class toxTree.query.FunctionalGroups
 
popup - Variable in class toxtree.ui.molecule.SmilesEntryPanel
 
popup - Variable in class toxtree.ui.tree.JCustomTreeComponent
 
position - Variable in class mutant.descriptors.SubstituentPosition
 
predict(IAtomContainer) - Method in class toxTree.qsar.AbstractQSARModel
 
predict() - Method in class toxTree.qsar.LinearQSARModel
 
predict(IAtomContainer) - Method in class toxTree.qsar.LinearQSARModel
 
predictedproperty - Variable in class toxTree.qsar.AbstractQSARModel
 
predictedTitle - Variable in class toxTree.tree.stats.ConfusionMatrix
 
prefix - Static variable in class toxTree.tree.RuleResult
 
prepare(IAtomContainer) - Method in class toxTree.query.metabolite.MetabolyteRecycler
 
prepareActions() - Method in class toxtree.ui.tree.actions.SelectAndEditTreeAction
 
prepareProperty(Object) - Method in class toxTree.data.MoleculesFile
 
preprocess(IChemObject) - Method in class toxTree.data.AbstractFilter
 
preprocess(IChemObject) - Method in interface toxTree.data.IObjectFilter
 
preProcess(IAtomContainer) - Static method in class toxTree.query.FunctionalGroups
 
preprocessor - Variable in class toxTree.qsar.LinearQSARModel
 
prescreenPhosphonic - Variable in class mic.rules.SA2
 
prescreenPhosphonic - Variable in class mutant.rules.SA2_gen
 
prescreenSulphonic - Variable in class mic.rules.SA2
 
prescreenSulphonic - Variable in class mutant.rules.SA2_gen
 
prev() - Method in interface toxTree.core.IMoleculesIterator
 
prev() - Method in class toxtree.data.DataContainer
 
prev() - Method in class toxTree.data.MoleculesIterator
 
previous() - Method in class toxTree.data.MoleculesFile
 
previousIndex() - Method in class toxTree.data.MoleculesFile
 
PRIMARY_AMINE - Static variable in class toxTree.query.FunctionalGroups
 
primaryAmine(boolean) - Static method in class toxTree.query.FunctionalGroups
 
print(IAtomContainer) - Method in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
 
printBuilders(IAtomContainer) - Static method in class toxTree.query.MolAnalyser
 
printMatrix() - Method in class toxTree.tree.stats.ConfusionMatrix
 
printResults(String) - Method in class toxTree.tree.AbstractTree
 
printSizes(Component) - Static method in class toxtree.ui.SpringUtilities
A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.
printToStream(OutputStream) - Method in class toxTree.tree.AbstractTree
 
priority - Variable in class mutant.categories.MutantCategory
 
priority - Variable in class toxTree.tree.AbstractTree
 
process(IDecisionMethod, IDecisionRule) - Method in interface toxTree.core.IProcessRule
 
process(double[]) - Method in interface toxTree.qsar.IDescriptorPreprocessor
 
process(double[]) - Method in class toxTree.qsar.LinearPreprocessor
 
process(double[]) - Method in class toxTree.qsar.MatrixPreprocessor
 
process(IAtomContainer, IReaction) - Static method in class toxTree.query.SimpleReactions
 
process(IAtomContainer, IReaction, IChemObjectBuilder) - Static method in class toxTree.query.SimpleReactions
 
process(IDecisionMethod, IDecisionRule) - Method in class toxTree.tree.PDFTreePrinter
 
process(IDecisionMethod, IDecisionRule) - Method in class toxTree.tree.ReportTreePrinter
 
process(IDecisionMethod, IDecisionRule) - Method in class toxTree.tree.SimpleTreePrinter
 
process(IDecisionMethod, IDecisionRule) - Method in class toxTree.tree.Tree2PrefuseGraph
 
processingFile - Variable in class toxtree.data.DataContainer
 
processNaNDescriptors(String) - Method in class toxTree.qsar.LinearQSARModel
 
processRecord() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
 
processRecord() - Method in interface toxTree.io.batch.IBatchProcessing
 
processRecord() - Method in class toxTree.io.batch.ToxTreeBatchProcessing
 
processSelectedObject(Object) - Method in class toxtree.ui.wizard.DecisionNodeWizard
 
processStream(String, String, InputStream) - Method in class toxtree.lookup.RemoteLookup
 
processStream(String, String, InputStream) - Method in class toxTree.query.remote.RemoteCompoundLookup
 
processUnavailableDescriptors(String) - Method in class toxTree.qsar.LinearQSARModel
 
products - Variable in class toxtree.ui.metabolites.MetabolitesPanel
 
profile - Variable in class toxtree.plugins.search.rules.Find
 
progressBar - Variable in class toxtree.ui.StatusBar
 
ProgressStatus - Class in toxTree.tree
 
ProgressStatus() - Constructor for class toxTree.tree.ProgressStatus
 
ProgressStatus.STATUS - Enum in toxTree.tree
 
properties - Variable in class toxTree.data.ListOfAtomContainers
 
propertiesPanel - Variable in class toxtree.ui.tree.molecule.CompoundPanel
 
propertiesPanel(Color, Color) - Method in class toxtree.ui.tree.molecule.CompoundPanel
 
propertyChange(PropertyChangeEvent) - Method in class toxTree.query.metabolite.MetabolyteRecycler
 
propertyChange(PropertyChangeEvent) - Method in class toxtree.tree.rules.ApplyRuleOptions
 
propertyChange(PropertyChangeEvent) - Method in class toxtree.ui.PropertyInput
 
propertyChange(PropertyChangeEvent) - Method in class toxtree.ui.StatusBar
 
propertyChange(PropertyChangeEvent) - Method in class toxtree.ui.tree.molecule.CompoundPanel
 
propertyChange(PropertyChangeEvent) - Method in class toxtree.ui.tree.TreeDrawing
 
propertyChangeSupport - Variable in class toxTree.data.MoleculesFile
 
propertyChangeSupport - Variable in class toxtree.ui.tree.TreePrefuse
 
PropertyEditor - Class in toxtree.ui
 
PropertyEditor(IAtomContainer, JComponent) - Constructor for class toxtree.ui.PropertyEditor
 
propertyExamples - Variable in class toxTree.tree.rules.RuleVerifyProperty
 
propertyField - Variable in class toxtree.ui.OptionsPanel
 
propertyFingerprint - Static variable in class toxTree.data.MoleculesFile
 
PropertyInput - Class in toxtree.ui
 
PropertyInput() - Constructor for class toxtree.ui.PropertyInput
 
propertyMaxValueField - Variable in class toxtree.ui.tree.rules.RuleRangeEditor
 
propertyMinValueField - Variable in class toxtree.ui.tree.rules.RuleRangeEditor
 
propertyName - Variable in class toxTree.data.SortedPropertyList
 
propertyName - Variable in exception toxTree.exceptions.DRulePropertyNotAvailable
 
propertyName - Variable in class toxTree.tree.rules.RuleVerifyProperty
 
propertyNameField - Variable in class toxtree.ui.tree.rules.RulePropertyEditor
 
propertyNameField - Variable in class toxtree.ui.tree.rules.RuleRangeEditor
 
PropertyPanel - Class in toxtree.ui.molecule
 
PropertyPanel() - Constructor for class toxtree.ui.molecule.PropertyPanel
 
PropertyPanel(Color, Color) - Constructor for class toxtree.ui.molecule.PropertyPanel
 
propertyStaticValue - Variable in class toxTree.tree.rules.RuleVerifyProperty
 
propertyUnits - Variable in class toxTree.tree.rules.RuleVerifyProperty
 
propertyValueField - Variable in class toxtree.ui.tree.rules.RulePropertyEditor
 
ProteinBindingAlerts - Enum in toxtree.plugins.proteinbinding.categories
 
ProteinBindingCategory - Class in toxtree.plugins.proteinbinding.categories
 
ProteinBindingCategory(ProteinBindingAlerts) - Constructor for class toxtree.plugins.proteinbinding.categories.ProteinBindingCategory
 
ProteinBindingPlugin - Class in toxtree.plugins.proteinbinding
Protein binding
ProteinBindingPlugin() - Constructor for class toxtree.plugins.proteinbinding.ProteinBindingPlugin
 
ProteinBindingRule - Class in toxtree.plugins.proteinbinding.rules
Parent class for all skin sens rules
ProteinBindingRule(ProteinBindingAlerts) - Constructor for class toxtree.plugins.proteinbinding.rules.ProteinBindingRule
 
ProteinBindingTreeResult - Class in toxtree.plugins.proteinbinding.rules
 
ProteinBindingTreeResult() - Constructor for class toxtree.plugins.proteinbinding.rules.ProteinBindingTreeResult
 
pssupport - Variable in class toxTree.tree.BatchDecisionResultsList
 
PYRIDINE - Static variable in class verhaar.query.FunctionalGroups
 
pyridine() - Static method in class verhaar.query.FunctionalGroups
 
pyridine_character() - Static method in class verhaar.query.FunctionalGroups
 

Q

qsar - Variable in class mutant.rules.MutantTreeResult
 
QSAR6Applicable - Class in mutant.rules
 
QSAR6Applicable() - Constructor for class mutant.rules.QSAR6Applicable
 
QSARApplicable - Class in mutant.categories
 
QSARApplicable() - Constructor for class mutant.categories.QSARApplicable
 
QSARApplicable(int) - Constructor for class mutant.categories.QSARApplicable
 
QSARApplicable(String, int) - Constructor for class mutant.categories.QSARApplicable
 
QSARDescriptor - Class in toxTree.qsar
Encapsulating descriptor name (in a model) and descriptor calculation
QSARDescriptor(String, IMolecularDescriptor) - Constructor for class toxTree.qsar.QSARDescriptor
 
QSARModelEditor - Class in toxtree.ui.tree.qsar
 
QSARModelEditor(AbstractQSARModel) - Constructor for class toxtree.ui.tree.qsar.QSARModelEditor
 
quarternaryNitrogenException() - Static method in class toxTree.query.FunctionalGroups
 
QUATERNARY_NITROGEN - Static variable in class toxTree.query.FunctionalGroups
 
QUATERNARY_NITROGEN_EXCEPTION - Static variable in class toxTree.query.FunctionalGroups
 
quaternaryNitrogen1(boolean) - Static method in class toxTree.query.FunctionalGroups
 
quaternaryNitrogen2(boolean) - Static method in class toxTree.query.FunctionalGroups
 
query - Variable in class mic.rules.SA10
 
query - Variable in class mutant.rules.SA10_gen
 
query - Variable in class toxTree.tree.rules.RuleSubstructures
 
QueryAssociationBond - Class in verhaar.query
Used to query for ionic (association ) bond.
QueryAssociationBond() - Constructor for class verhaar.query.QueryAssociationBond
 
QueryAssociationBond(Atom, Atom) - Constructor for class verhaar.query.QueryAssociationBond
 
QueryAssociationBond(Atom, Atom, IBond.Order) - Constructor for class verhaar.query.QueryAssociationBond
 
QueryAssociationBond(Atom, Atom, IBond.Order, IBond.Stereo) - Constructor for class verhaar.query.QueryAssociationBond
 
QueryAtomContainers - Class in toxTree.query
TODO add description
QueryAtomContainers(int) - Constructor for class toxTree.query.QueryAtomContainers
 
QueryAtomContainers() - Constructor for class toxTree.query.QueryAtomContainers
 
QueryAtomContainers(Collection) - Constructor for class toxTree.query.QueryAtomContainers
 
QueryAtomContainersModel - Class in toxtree.ui.tree
Table model for QueryAtomContainers.
QueryAtomContainersModel(List, IDecisionRule) - Constructor for class toxtree.ui.tree.QueryAtomContainersModel
 
QueryAtomContainersModel(QueryAtomContainers, IDecisionRule) - Constructor for class toxtree.ui.tree.QueryAtomContainersModel
 
QueryUnsaturatedBond - Class in verhaar.query
Verifies if a bond is unsaturated (double, triple, aromatic)
QueryUnsaturatedBond() - Constructor for class verhaar.query.QueryUnsaturatedBond
 
QueryUnsaturatedBond(IAtom, IAtom) - Constructor for class verhaar.query.QueryUnsaturatedBond
 
QueryUnsaturatedBond(IAtom, IAtom, IBond.Order) - Constructor for class verhaar.query.QueryUnsaturatedBond
 
QueryUnsaturatedBond(IAtom, IAtom, IBond.Order, IBond.Stereo) - Constructor for class verhaar.query.QueryUnsaturatedBond
 
quick_and_dirty_viacml(IAtomContainer) - Method in class toxTree.query.metabolite.MetabolyteRecycler
 
quick_and_dirty_viainchi(String) - Method in class toxTree.query.metabolite.MetabolyteRecycler
 
quick_and_dirty_viamol(IAtomContainer) - Method in class toxTree.query.metabolite.MetabolyteRecycler
 
QUINONES - Static variable in class mic.rules.SA12
 
QUINONES - Static variable in class mutant.rules.SA12_gen
 
Quinones_Title - Static variable in class mic.rules.SA12
 
Quinones_Title - Static variable in class mutant.rules.SA12_gen
 
QuitAction - Class in toxtree.ui.actions
Quit ToxTreeApp
QuitAction(DataModule) - Constructor for class toxtree.ui.actions.QuitAction
 
QuitAction(DataModule, String) - Constructor for class toxtree.ui.actions.QuitAction
 
QuitAction(DataModule, String, Icon) - Constructor for class toxtree.ui.actions.QuitAction
 

R

R - Static variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
RadioBoxPanel - Class in toxtree.ui.wizard
 
RadioBoxPanel() - Constructor for class toxtree.ui.wizard.RadioBoxPanel
 
RadioBoxPanel(String, List<?>, 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
 
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
 
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() - 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
 
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.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.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.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.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
 
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
 
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
 
reverse_numbers - Variable in class mutant.descriptors.AromaticAmineSubstituentsDescriptor
 
ring - Variable in class mutant.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
 
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
Rule 32 of the Cramer scheme (see CramerRules)
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
Rule 21 of the Cramer scheme (see CramerRules)
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
 
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
Rule 31 of the Cramer scheme (see CramerRules)
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
 
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
 
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
 
RuleAlertsForMIC - Class in mic.rules
 
RuleAlertsForMIC() - Constructor for class mic.rules.RuleAlertsForMIC
 
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 - Class in toxtree.plugins.moa.rules
 
RuleAlertsNarcosis1_1_2() - Constructor for class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_2
 
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
Rule 20 of the Cramer scheme (see CramerRules)
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
Aqueous solubility [g/l] < 2.0E-5 Expects property to be read from IMolecule.getProperty(RuleAqueousSolubility.AqueousSolubility).
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
 
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
 
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
Constructor
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
Rule 22 of the Cramer scheme (see CramerRules)
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
Rule 25 of the Cramer scheme (see CramerRules)
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
 
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
 
RuleDeleteSubstructureAction - Class in toxtree.ui.tree.rules
 
RuleDeleteSubstructureAction(IMolecule) - Constructor for class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
 
RuleDeleteSubstructureAction(IMolecule, String) - Constructor for class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
 
RuleDeleteSubstructureAction(IMolecule, String, Icon) - Constructor for class toxtree.ui.tree.rules.RuleDeleteSubstructureAction
 
RuleDerivedAromaticAmines - Class in mutant.rules
 
RuleDerivedAromaticAmines() - Constructor for class mutant.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
Constructor
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
Rule 4 of the Cramer scheme (see CramerRules)
RuleHasOnlySaltSulphonateSulphate() - Constructor for class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
 
RuleHasOtherThanC_H_O_N_S2 - Class in toxTree.tree.cramer
Rule 3 of the Cramer scheme (see CramerRules)
RuleHasOtherThanC_H_O_N_S2() - Constructor for class toxTree.tree.cramer.RuleHasOtherThanC_H_O_N_S2
Constructor
RuleHeteroaromatic - Class in toxTree.tree.cramer
Rule 12 of the Cramer scheme (see CramerRules)
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
Rule 11 of the Cramer scheme (see CramerRules)
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
Uses QueryAssociationBond ro verify if the query compound has an ionic bond.
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
Rule 7 of the Cramer scheme (see CramerRules)
RuleIsHeterocyclic() - Constructor for class toxTree.tree.cramer.RuleIsHeterocyclic
Constructor
RuleIsOpenChain - Class in toxTree.tree.cramer
Rule 19 of the Cramer scheme (see CramerRules)
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
Rule 18 of the Cramer scheme (see CramerRules)
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
 
RuleLactoneOrCyclicDiester - Class in toxTree.tree.cramer
Rule 8 of the Cramer scheme (see CramerRules)
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
Rule 9 of the Cramer scheme (see CramerRules)
RuleLactonesFusedOrUnsaturated() - Constructor for class toxTree.tree.cramer.RuleLactonesFusedOrUnsaturated
Constructor
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
Rule 14 of the Cramer scheme (see CramerRules)
RuleManyAromaticRings14() - Constructor for class toxTree.tree.cramer.RuleManyAromaticRings14
Constructor
RuleManyAromaticRings28 - Class in toxTree.tree.cramer
Rule 28 of the Cramer scheme (see CramerRules)
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
Molecular mass in [RuleDescriptorRange.getMinValue(),RuleDescriptorRange.getMaxValue()] TODO add description
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(IMolecule) - Constructor for class toxtree.ui.tree.rules.RuleMoleculeEditAction
 
RuleMoleculeEditAction(IMolecule, String) - Constructor for class toxtree.ui.tree.rules.RuleMoleculeEditAction
 
RuleMoleculeEditAction(IMolecule, 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
Rule 24 of the Cramer scheme (see CramerRules)
RuleMonocarbocyclic() - Constructor for class toxTree.tree.cramer.RuleMonocarbocyclic
Constructor
RuleMonocycloalkanoneEtc - Class in toxTree.tree.cramer
Rule 26 of the Cramer scheme (see CramerRules)
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
Rule 1 of the Cramer scheme (see CramerRules)
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
Rule 32 of the Cramer scheme (see CramerRules)
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
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
Rule 29 of the Cramer scheme (see CramerRules)
RuleReadilyHydrolysed29() - Constructor for class toxTree.tree.cramer.RuleReadilyHydrolysed29
Constructor
RuleReadilyHydrolysedMononuclear - Class in toxTree.tree.cramer
Rule 15 of the Cramer scheme (see CramerRules)
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
Rule 17 of the Cramer scheme (see CramerRules)
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
Rule 30 of the Cramer scheme (see CramerRules)
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
 
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
Rule 27 of the Cramer scheme (see CramerRules)
RuleRingsWithSubstituents() - Constructor for class toxTree.tree.cramer.RuleRingsWithSubstituents
Constructor
RuleRingWithSubstituents - Class in toxTree.tree.cramer
Rule 13 of the Cramer scheme (see CramerRules)
RuleRingWithSubstituents() - Constructor for class toxTree.tree.cramer.RuleRingWithSubstituents
Constructor
rules - Variable in class toxtree.data.DecisionMethodsDataModule
 
rules - Variable in class toxTree.tree.AbstractTree
 
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
List of IDecisionRule
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
 
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
Rule 6 of the Cramer scheme (see CramerRules)
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(IMolecule) - Constructor for class toxtree.ui.tree.rules.RuleSubstructuresEditAction
 
RuleSubstructuresEditAction(IMolecule, String) - Constructor for class toxtree.ui.tree.rules.RuleSubstructuresEditAction
 
RuleSubstructuresEditAction(IMolecule, String, Icon) - Constructor for class toxtree.ui.tree.rules.RuleSubstructuresEditAction
 
RuleSufficientSulphonateGroups - Class in toxTree.tree.cramer
Rule 33 of the Cramer scheme (see CramerRules)
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
Rule 2 of the Cramer scheme (see CramerRules)
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
Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
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.ui.actions.AboutAction
 
run() - Method in class toxtree.ui.actions.BatchAction
 
run() - Method in class toxtree.ui.actions.ClearResultAction
 
run() - Method in class toxtree.ui.actions.DataModuleAction
 
run() - Method in class toxtree.ui.actions.EditCompoundAction
 
run() - Method in class toxtree.ui.actions.EstimateAction
 
run() - Method in class toxtree.ui.actions.EstimateAllAction
 
run() - Method in class toxtree.ui.actions.ExplainAction
 
run() - Method in class toxtree.ui.actions.InfoAction
 
run() - Method in class toxtree.ui.actions.OpenFileAction
 
run() - Method in class toxtree.ui.actions.QuitAction
 
run() - Method in class toxtree.ui.actions.SaveFileAction
 
run() - Method in class toxtree.ui.molecule.ClearFilteredSubsetsAction
 
run() - Method in class toxtree.ui.molecule.GoToRecordAction
 
run() - Method in class toxtree.ui.molecule.LookupCompoundAction
 
run() - Method in class toxtree.ui.molecule.ShowFilteredFileAction
 
run() - Method in class toxtree.ui.tree.actions.ClearMethodsList
 
run() - Method in class toxtree.ui.tree.actions.EditDecisionMethodAction
 
run() - Method in class toxtree.ui.tree.actions.LiadMethodsListAction
 
run() - Method in class toxtree.ui.tree.actions.LoadTreeAction
 
run() - Method in class toxtree.ui.tree.actions.SaveMethodsListAction
 
run() - Method in class toxtree.ui.tree.actions.SelectNewTreeAction
 
run() - Method in class toxtree.ui.tree.actions.SelectTreeAction
 
run() - Method in class toxtree.ui.tree.actions.TreeOptionsAction
 
run() - Method in class toxtree.ui.tree.actions.ViewTreeAction
 

S

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
 
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
 
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
 
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
 
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
 
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_title - Static variable in class mic.rules.SA15
 
sa15_title - Static variable in class mutant.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_smarts - Static variable in class mic.rules.SA16
 
sa16_smarts - Static variable in class mutant.rules.SA16_gen
 
sa16_title - Static variable in class mic.rules.SA16
 
sa16_title - Static variable in class mutant.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
 
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
 
SA1_gen - Class in mutant.rules
 
SA1_gen() - Constructor for class mutant.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_title - Static variable in class mic.rules.SA21
 
SA21_title - Static variable in class mutant.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_smarts - Static variable in class mic.rules.SA22
 
SA22_azide_smarts - Static variable in class mutant.rules.SA22_gen
 
SA22_gen - Class in mutant.rules
 
SA22_gen() - Constructor for class mutant.rules.SA22_gen
 
SA22_title - Static variable in class mic.rules.SA22
 
SA22_title - Static variable in class mutant.rules.SA22_gen
 
SA22_triazene - Static variable in class mic.rules.SA22
 
SA22_triazene - Static variable in class mutant.rules.SA22_gen
 
SA22_triazene_smarts - Static variable in class mic.rules.SA22
 
SA22_triazene_smarts - Static variable in class mutant.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_title - Static variable in class mic.rules.SA23
 
SA23_title - Static variable in class mutant.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_title - Static variable in class mic.rules.SA24
 
SA24_title - Static variable in class mutant.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_title - Static variable in class mic.rules.SA25
 
SA25_title - Static variable in class mutant.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_title - Static variable in class mic.rules.SA26
 
SA26_title - Static variable in class mutant.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_title - Static variable in class mic.rules.SA27
 
SA27_title - Static variable in class mutant.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_title - Static variable in class mic.rules.SA28
 
SA28_title - Static variable in class mutant.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_title - Static variable in class mic.rules.SA28bis
 
SA28bis_title - Static variable in class mutant.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_title - Static variable in class mic.rules.SA28ter
 
SA28ter_title - Static variable in class mutant.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_gen - Class in mutant.rules
 
SA29_gen() - Constructor for class mutant.rules.SA29_gen
 
SA29_noSO3H - Static variable in class mic.rules.SA29
 
SA29_noSO3H - Static variable in class mutant.rules.SA29_gen
 
SA29_smarts - Static variable in class mic.rules.SA29
 
SA29_smarts - Static variable in class mutant.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_phosphonic - Static variable in class mic.rules.SA2
 
SA2_phosphonic - Static variable in class mutant.rules.SA2_gen
 
SA2_sulphonic - Static variable in class mic.rules.SA2
 
SA2_sulphonic - Static variable in class mutant.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_title - Static variable in class mic.rules.SA30
 
SA30_title - Static variable in class mutant.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
 
SA38_gen - Class in mutant.rules
 
SA38_gen() - Constructor for class mutant.rules.SA38_gen
 
SA39_gen_and_nogen - Class in mutant.rules
 
SA39_gen_and_nogen() - Constructor for class mutant.rules.SA39_gen_and_nogen
 
SA3_gen - Class in mutant.rules
 
SA3_gen() - Constructor for class mutant.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_smarts - Static variable in class mic.rules.SA4
 
SA4_smarts - Static variable in class mutant.rules.SA4_gen
 
SA4_title - Static variable in class mic.rules.SA4
 
SA4_title - Static variable in class mutant.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
 
SA5_gen - Class in mutant.rules
 
SA5_gen() - Constructor for class mutant.rules.SA5_gen
 
SA5_smarts - Static variable in class mic.rules.SA5
 
SA5_smarts - Static variable in class mutant.rules.SA5_gen
 
SA5_title - Static variable in class mic.rules.SA5
 
SA5_title - Static variable in class mutant.rules.SA5_gen
 
SA6 - Class in mic.rules
 
SA6() - Constructor for class mic.rules.SA6
TODO verify
SA6_gen - Class in mutant.rules
 
SA6_gen() - Constructor for class mutant.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
 
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_title - Static variable in class mic.rules.SA8
 
SA8_title - Static variable in class mutant.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
 
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
Saves a IDecisionMethod to a file Uses serialization mechanism.
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(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
Provides a list of names of the classes implementing IDecisionCategory If the user selects an object, the tree is created and returned
Uses Introspection.getAvailableCategoryTypes(ClassLoader)
selectNewNode(Component, ClassLoader) - Static method in class toxtree.ui.tree.SelectListDialog
Provides a list of names of the classes implementing IDecisionRule If the user selects an object, a DecisionNode containing the rule is created and returned
Uses Introspection.getAvailableRuleTypes(ClassLoader)
selectNewRule(Component, ClassLoader) - Static method in class toxtree.ui.tree.SelectListDialog
Provides a list of names of the classes implementing IDecisionRule If the user selects an object, the rule is created and returned
Uses Introspection.getAvailableRuleTypes(ClassLoader)
selectNewTree(Component, ClassLoader) - Static method in class toxtree.ui.tree.SelectListDialog
Provides a list of names of the classes implementing IDecisionMethod If the user selects a name, the tree is created and returned
Uses Introspection.getAvailableTreeTypes(ClassLoader)
SelectNewTreeAction - Class in toxtree.ui.tree.actions
Uses SelectListDialog.selectNewTree(Component, ClassLoader) to present a list of classes that implement IDecisionMethod .
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, Object) - 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(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(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
 
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(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.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.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
 
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(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
 
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(HashSet<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(HashSet) - 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
 
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.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) - 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.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
 
setLogger(TTLogger) - Method in class toxTree.tree.rules.LookupFile
 
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
 
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(IMolecule) - Method in class toxtree.ui.molecule.AbstractMoleculeAction
 
setMolecule(IMolecule) - 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.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.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
 
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.tree.rules.RuleVerifyProperty
 
setOptions(IDecisionInteractive.UserOptions) - Method in class toxTree.tree.rules.UserInputRule
 
setOptions(IDecisionInteractive.UserOptions) - Method in class toxTree.tree.UserDefinedTree
 
setOptions(List<?>, int) - Method in class toxtree.ui.wizard.RadioBoxPanel
 
setOriginalMolecule(IAtomContainer) - Method in class toxTree.tree.TreeResult
 
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
 
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.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
 
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
 
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.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.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
 
setRing(boolean) - Method in class mutant.descriptors.SubstituentPosition
 
setRingQuery(QueryAtomContainer) - Method in class mutant.descriptors.SubstituentExtractor
 
setRingQuery(QueryAtomContainer) - Method in class mutant.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.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
 
setSMARTS(String) - Method in class mutant.descriptors.DescriptorStructurePresence
 
setSmarts(String) - Method in class mutant.rules.SMARTSGroup
 
setSmarts(String) - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
setSmartsPatternFactory(ISmartsPatternFactory) - Method in class toxtree.ui.tree.rules.SmartsPanelEditor
 
setSmartsPatterns(Hashtable<String, ISmartsPattern<T>>) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
setStackLength(int) - Method in class toxTree.logging.TTLogger
Sets the number of StackTraceElements to be printed in DEBUG mode when calling debug(Throwable).
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
 
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(Hashtable) - 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(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
The package contains implementations of IDecisionCategory categories for SicretRules decision tree.
sicret.rules - package sicret.rules
The package contains implementations of IDecisionRule rules for SicretRules decision tree.
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() - Constructor for class toxTree.query.SingleOrDoubleQueryBond
 
SingleOrDoubleQueryBond(IQueryAtom, IQueryAtom) - 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 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.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
 
SMARTSgroups - Class in mutant.rules
 
SMARTSgroups() - Constructor for class mutant.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 - Class in toxTree.tree.rules.smarts
Encapsulates Joelib SMARTS parser.
SmartsPattern() - Constructor for class toxTree.tree.rules.smarts.SmartsPattern
 
SmartsPattern(String) - Constructor for class toxTree.tree.rules.smarts.SmartsPattern
 
SmartsPattern(String, boolean) - Constructor for class toxTree.tree.rules.smarts.SmartsPattern
 
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
Editor for RuleSMARTSubstructure.
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
A JPanel to enter a SMILES.
SmilesEntryPanel() - Constructor for class toxtree.ui.molecule.SmilesEntryPanel
 
smilesPanel - Variable in class toxtree.ui.molecule.TopPanel
 
smp - Variable in class mutant.descriptors.DescriptorIsAniline
 
smrkMan - Variable in class toxtree.plugins.smartcyp.rules.MetaboliteGenerator
 
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
 
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
 
start() - Method in class toxtree.ui.GUIWorker
 
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
The statusbar of ToxTreeApp
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
 
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.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
 
substituents - Static variable in class mic.rules.SA2
 
substituents - Static variable in class mutant.rules.SA2_gen
 
SubstituentsDescriptor - Class in mutant.descriptors
 
SubstituentsDescriptor() - Constructor for class mutant.descriptors.SubstituentsDescriptor
 
SubstituentsDescriptor(QueryAtomContainer) - Constructor for class mutant.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.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
This is FunctionalGroups.sulphateOfAmine(int) with the ionic bonnd between [N+] and [O-] marked with FunctionalGroups.DONTMARK so it can be broken by FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer) method
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
 

T

table - Variable in class toxTree.io.PDFWriter
 
table - Variable in class toxtree.ui.HashtableModel
 
table - Variable in class toxtree.ui.tree.ListPanel
 
table - Variable in class toxtree.ui.tree.rules.SMARTSRuleEditor
 
tableModel - Variable in class toxtree.ui.molecule.PropertyPanel
 
tableModel - Variable in class toxtree.ui.tree.rules.SMARTSRuleEditor
 
taskPane - Variable in class toxtree.ui.tree.TreeEditorPanel
 
TERTIARY_AMINE - Static variable in class toxTree.query.FunctionalGroups
 
tertiaryAmine() - Static method in class toxTree.query.FunctionalGroups
 
testMolecule - Variable in class toxtree.ui.tree.rules.SmartsPanelEditor
 
testRulesWithSelector() - Method in class toxTree.tree.AbstractTree
 
text - Variable in class toxtree.ui.tree.qsar.OptionsPanel
 
textDescriptor - Variable in class toxtree.ui.tree.qsar.OptionsPanel
 
THIOESTER - Static variable in class toxTree.query.FunctionalGroups
 
thioester() - Static method in class toxTree.query.FunctionalGroups
 
thioester_id - Static variable in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
threshold - Variable in class toxTree.qsar.LinearDiscriminantRule
 
threshold - Variable in class toxTree.tree.DefaultCategory
 
title - Static variable in class toxtree.plugins.moa.categories.CategoryAcetylcholinesteraseInhibitors
 
title - Static variable in class toxtree.plugins.moa.categories.CategoryCentralNervousSystemSeizureAgents
 
title - Static variable in class toxtree.plugins.moa.categories.CategoryElectrophileProelectrophileReactivity
 
title - Static variable in class toxtree.plugins.moa.categories.CategoryOxidativePhosphorylationUncouplers
 
title - Static variable in class toxtree.plugins.moa.categories.CategoryUnknown
 
title - Variable in class toxTree.tree.AbstractRule
 
tmpDir - Variable in class toxTree.io.batch.BatchProcessing
 
toArray() - Method in class toxTree.tree.CategoriesList
 
toArray(T[]) - Method in class toxTree.tree.CategoriesList
 
toArray() - Method in class toxTree.tree.DecisionMethodsList
 
toArray(Object[]) - Method in class toxTree.tree.DecisionMethodsList
 
toArray() - Method in class toxTree.tree.DecisionNodesList
 
toArray(Object[]) - Method in class toxTree.tree.DecisionNodesList
 
toArray() - Method in class toxTree.tree.RulesList
 
toArray(Object[]) - Method in class toxTree.tree.RulesList
 
Tools - Class in toxTree.io
 
Tools() - Constructor for class toxTree.io.Tools
 
tooltips - Variable in class toxtree.ui.tree.DecisionMethodsTableModel
 
TopologyAnyAtom - Class in toxTree.query
TODO add description
TopologyAnyAtom(boolean) - Constructor for class toxTree.query.TopologyAnyAtom
 
TopologyAnyBond - Class in toxTree.query
TODO add description
TopologyAnyBond(boolean) - Constructor for class toxTree.query.TopologyAnyBond
 
TopologyAnyBond(IAtom, IAtom, boolean) - Constructor for class toxTree.query.TopologyAnyBond
 
TopologyAnyBond(IAtom, IAtom, IBond.Order, boolean) - Constructor for class toxTree.query.TopologyAnyBond
 
TopologyAnyBond(IAtom, IAtom, IBond.Order, IBond.Stereo, boolean) - Constructor for class toxTree.query.TopologyAnyBond
 
TopologyOrderQueryBond - Class in toxTree.query
The same as OrderQueryBond with additional condition to be acyclic or cyclic.
TopologyOrderQueryBond() - Constructor for class toxTree.query.TopologyOrderQueryBond
 
TopologyOrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order) - Constructor for class toxTree.query.TopologyOrderQueryBond
 
TopologyOrderQueryBond(IQueryAtom, IQueryAtom, IBond.Order, boolean) - Constructor for class toxTree.query.TopologyOrderQueryBond
 
TopologySymbolQueryAtom - Class in toxTree.query
TODO add description
TopologySymbolQueryAtom(boolean) - Constructor for class toxTree.query.TopologySymbolQueryAtom
 
TopologySymbolQueryAtom(IAtom) - Constructor for class toxTree.query.TopologySymbolQueryAtom
 
TopologySymbolQueryAtom(IAtom, boolean) - Constructor for class toxTree.query.TopologySymbolQueryAtom
 
TopPanel - Class in toxtree.ui.molecule
The top panel of ToxTreeApp
TopPanel() - Constructor for class toxtree.ui.molecule.TopPanel
 
TopPanel(boolean) - Constructor for class toxtree.ui.molecule.TopPanel
 
TopPanel(LayoutManager) - Constructor for class toxtree.ui.molecule.TopPanel
 
TopPanel(LayoutManager, boolean) - Constructor for class toxtree.ui.molecule.TopPanel
 
toShallowXML(Document) - Method in interface toxTree.core.XMLSerializable
 
toShallowXML(Document) - Method in class toxTree.tree.AbstractRule
 
toShallowXML(Document) - Method in class toxTree.tree.AbstractTree
 
toShallowXML(Document) - Method in class toxTree.tree.CategoriesList
 
toShallowXML(Document) - Method in class toxTree.tree.DecisionMethodsList
 
toShallowXML(Document) - Method in class toxTree.tree.DecisionNodesList
 
toShallowXML(Document) - Method in class toxTree.tree.DefaultCategory
 
toShallowXML(Document) - Method in class toxTree.tree.RulesList
 
toString() - Method in class com.molecularnetworks.start.BiodgeradationRules
 
toString() - Method in class cramer2.CramerRulesWithExtensions
 
toString() - Method in class eye.EyeIrritationRules
 
toString() - Method in class mic.MICRules
 
toString() - Method in class michaelacceptors.MichaelAcceptorRules
 
toString() - Method in class mutant.BB_CarcMutRules
 
toString() - Method in class mutant.descriptors.DescriptorStructurePresence
 
toString() - Method in class mutant.descriptors.SubstituentPosition
 
toString() - Method in class mutant.descriptors.SubstituentsDescriptor
 
toString() - Method in class sicret.SicretRules
 
toString() - Method in interface toxTree.core.IDecisionResult
 
toString() - Method in interface toxTree.core.IDecisionRule
 
toString() - Method in class toxTree.core.ToxTreeClassLoader
 
toString() - Method in class toxTree.core.ToxTreePackageEntry
 
toString() - Method in class toxTree.data.CategoryFilter
 
toString() - Method in class toxtree.data.DataContainer
 
toString() - Method in class toxtree.data.FilteredMoleculesIterator
 
toString() - Method in class toxTree.data.MoleculesFile
 
toString() - Method in class toxTree.data.MoleculesIterator
 
toString() - Method in class toxTree.data.ObjectPropertyFilter
 
toString() - Method in class toxTree.data.SortedPropertyList
 
toString() - Method in class toxTree.io.batch.BatchProcessing
 
toString() - Method in class toxTree.io.batch.FileState
 
toString() - Method in class toxtree.plugins.dnabinding.DNABindingPlugin
 
toString() - Method in class toxtree.plugins.func.FuncRules
 
toString() - Method in class toxtree.plugins.proteinbinding.ProteinBindingPlugin
 
toString() - Method in class toxtree.plugins.skinsensitisation.SkinSensitisationPlugin
 
toString() - Method in class toxtree.plugins.smartcyp.SMARTCYPPlugin
 
toString() - Method in class toxTree.qsar.AbstractQSARModel
 
toString() - Method in class toxTree.qsar.LinearPreprocessor
 
toString() - Method in class toxTree.qsar.LinearQSARModel
 
toString() - Method in class toxTree.query.MolFlags
 
toString() - Method in class toxTree.query.ReallyAnyAtom
 
toString() - Method in class toxTree.tree.AbstractRule
 
toString() - Method in class toxTree.tree.AbstractTree
 
toString() - Method in class toxTree.tree.BatchDecisionResultsList
 
toString() - Method in class toxTree.tree.CategoriesList
 
toString() - Method in class toxTree.tree.cramer.CramerRules
 
toString(boolean) - Method in class toxTree.tree.DecisionNode
Returns string representation of the decision node if (verbose) returns getId() + "." + getName() else returns "Q"+getId();
toString() - Method in class toxTree.tree.DecisionNode
 
toString() - Method in class toxTree.tree.DecisionNodesList
 
toString() - Method in class toxTree.tree.DefaultCategory
 
toString() - Method in class toxTree.tree.ProgressStatus
 
toString() - Method in class toxTree.tree.RuleResult
 
toString() - Method in class toxTree.tree.rules.InChILookupFile
 
toString() - Method in class toxTree.tree.RulesList
 
toString() - Method in class toxTree.tree.stats.ConfusionMatrix
 
toString() - Method in class toxTree.tree.TreeResult
toString
toString() - Method in class toxTree.tree.UserDefinedTree
 
toString() - Method in class toxtree.ui.tree.ListPanel
 
toxData - Variable in class toxtree.ui.StatusBar
 
toxForest_ext - Static variable in class toxTree.io.MolFileFilter
 
toxForest_ext_descr - Static variable in class toxTree.io.MolFileFilter
 
ToxForestActions - Class in toxTree.apps.toxForest
Toxforest actions.
ToxForestActions() - Constructor for class toxTree.apps.toxForest.ToxForestActions
 
ToxForestActions(JFrame) - Constructor for class toxTree.apps.toxForest.ToxForestActions
 
ToxForestApp - Class in toxTree.apps.toxForest
Toxforest application - multiple decision trees.
ToxForestApp() - Constructor for class toxTree.apps.toxForest.ToxForestApp
 
ToxForestCompoundPanel - Class in toxTree.apps.toxForest
Top panel of ToxForestApp (structures browser).
ToxForestCompoundPanel(DataContainer, Color, Color) - Constructor for class toxTree.apps.toxForest.ToxForestCompoundPanel
 
ToxForestData - Class in toxTree.apps.toxForest
Main data container of ToxForestApp.
ToxForestData(File) - Constructor for class toxTree.apps.toxForest.ToxForestData
 
ToxForestDataModule - Class in toxTree.apps.toxForest
Main data class of ToxForestApp.
ToxForestDataModule() - Constructor for class toxTree.apps.toxForest.ToxForestDataModule
 
ToxForestDataModule(JFrame, File, DecisionMethodsList) - Constructor for class toxTree.apps.toxForest.ToxForestDataModule
 
ToxForestDataModulePanel - Class in toxTree.apps.toxForest
Bottom panel of ToxForestApp (decision trees table).
ToxForestDataModulePanel(ToxForestDataModule) - Constructor for class toxTree.apps.toxForest.ToxForestDataModulePanel
 
ToxForestDataModulePanel(ToxForestDataModule, boolean) - Constructor for class toxTree.apps.toxForest.ToxForestDataModulePanel
 
ToxForestDataModulePanel(ToxForestDataModule, LayoutManager) - Constructor for class toxTree.apps.toxForest.ToxForestDataModulePanel
 
ToxForestDataModulePanel(ToxForestDataModule, LayoutManager, boolean) - Constructor for class toxTree.apps.toxForest.ToxForestDataModulePanel
 
toXML(Document) - Method in interface toxTree.core.XMLSerializable
 
toXML(Document) - Method in class toxTree.tree.AbstractRule
 
toXML(Document) - Method in class toxTree.tree.AbstractTree
 
toXML(Document) - Method in class toxTree.tree.CategoriesList
 
toXML(Document) - Method in class toxTree.tree.DecisionMethodsList
 
toXML(Document) - Method in class toxTree.tree.DecisionNodesList
 
toXML(Document) - Method in class toxTree.tree.DefaultCategory
 
toXML(Document) - Method in class toxTree.tree.RulesList
 
toxTree.apps - package toxTree.apps
 
toxTree.apps.toxForest - package toxTree.apps.toxForest
 
toxTree.core - package toxTree.core
This packages contains only interface definitions, defining essential classes in toxTree application.
toxTree.data - package toxTree.data
Classes that hold the data used in ToxTreeApp
toxtree.data - package toxtree.data
 
toxTree.exceptions - package toxTree.exceptions
Exceptions defined for toxTree classes
toxTree.io - package toxTree.io
Input output support.
toxTree.io.batch - package toxTree.io.batch
Batch processing facility.
toxTree.logging - package toxTree.logging
Logging facility.
toxtree.lookup - package toxtree.lookup
 
toxtree.plugins.dnabinding - package toxtree.plugins.dnabinding
 
toxtree.plugins.dnabinding.categories - package toxtree.plugins.dnabinding.categories
 
toxtree.plugins.dnabinding.rules - package toxtree.plugins.dnabinding.rules
 
toxtree.plugins.func - package toxtree.plugins.func
 
toxtree.plugins.func.categories - package toxtree.plugins.func.categories
 
toxtree.plugins.func.rules - package toxtree.plugins.func.rules
 
toxtree.plugins.kroes - package toxtree.plugins.kroes
 
toxtree.plugins.kroes.categories - package toxtree.plugins.kroes.categories
 
toxtree.plugins.kroes.rules - package toxtree.plugins.kroes.rules
 
toxtree.plugins.lewis - package toxtree.plugins.lewis
 
toxtree.plugins.lewis.categories - package toxtree.plugins.lewis.categories
 
toxtree.plugins.lewis.rules - package toxtree.plugins.lewis.rules
 
toxtree.plugins.moa - package toxtree.plugins.moa
 
toxtree.plugins.moa.categories - package toxtree.plugins.moa.categories
 
toxtree.plugins.moa.rules - package toxtree.plugins.moa.rules
 
toxtree.plugins.proteinbinding - package toxtree.plugins.proteinbinding
 
toxtree.plugins.proteinbinding.categories - package toxtree.plugins.proteinbinding.categories
 
toxtree.plugins.proteinbinding.rules - package toxtree.plugins.proteinbinding.rules
 
toxtree.plugins.search - package toxtree.plugins.search
 
toxtree.plugins.search.categories - package toxtree.plugins.search.categories
 
toxtree.plugins.search.rules - package toxtree.plugins.search.rules
 
toxtree.plugins.skinsensitisation - package toxtree.plugins.skinsensitisation
 
toxtree.plugins.skinsensitisation.categories - package toxtree.plugins.skinsensitisation.categories
 
toxtree.plugins.skinsensitisation.rules - package toxtree.plugins.skinsensitisation.rules
 
toxtree.plugins.smartcyp - package toxtree.plugins.smartcyp
 
toxtree.plugins.smartcyp.categories - package toxtree.plugins.smartcyp.categories
 
toxtree.plugins.smartcyp.rules - package toxtree.plugins.smartcyp.rules
 
toxtree.plugins.verhaar2 - package toxtree.plugins.verhaar2
Class toxtree.plugins.verhaar2.VerhaarScheme is the implementation of modified Verhaar structural scheme, according to recommendation from
toxtree.plugins.verhaar2.rules - package toxtree.plugins.verhaar2.rules
The package contains implementations of IDecisionRule rules for VerhaarScheme decision tree.
toxTree.qsar - package toxTree.qsar
 
toxTree.query - package toxTree.query
Various classes
toxTree.query.metabolite - package toxTree.query.metabolite
 
toxTree.query.remote - package toxTree.query.remote
 
toxTree.tree - package toxTree.tree
This packages contains abstract and default classes implementing the interfaces defined in toxTree.core package.
toxTree.tree.categories - package toxTree.tree.categories
The package contains default implementations of IDecisionCategory categories.
toxTree.tree.cramer - package toxTree.tree.cramer
Class CramerRules is the implementation of Cramer rules [Cramer et al,78].
toxTree.tree.demo - package toxTree.tree.demo
Two simple demo decision trees.
toxTree.tree.rules - package toxTree.tree.rules
The package contains several generic implementations of IDecisionRule rules
toxtree.tree.rules - package toxtree.tree.rules
 
toxTree.tree.rules.smarts - package toxTree.tree.rules.smarts
SMARTS support.
toxTree.tree.stats - package toxTree.tree.stats
 
toxTree.ui - package toxTree.ui
 
toxtree.ui - package toxtree.ui
Base classes for ToxTreeApp user interface
toxtree.ui.actions - package toxtree.ui.actions
Actions (derived from AbstractAction used in ToxTreeApp main menu.
toxtree.ui.batch - package toxtree.ui.batch
User interface for toxTree.io.batch
toxtree.ui.editors - package toxtree.ui.editors
 
toxtree.ui.metabolites - package toxtree.ui.metabolites
 
toxtree.ui.molecule - package toxtree.ui.molecule
UI classes for viewing and editing a molecule
toxtree.ui.tree - package toxtree.ui.tree
User interface for viewing and editing a decision tree IDecisionMethod
toxtree.ui.tree.actions - package toxtree.ui.tree.actions
Actions (derived from AbstractAction for the decision tree user interface toxTree.ui.tree
toxTree.ui.tree.categories - package toxTree.ui.tree.categories
 
toxtree.ui.tree.categories - package toxtree.ui.tree.categories
User interface for viewing and editing categories IDecisionCategory in a decision tree IDecisionMethod
toxtree.ui.tree.molecule - package toxtree.ui.tree.molecule
 
toxtree.ui.tree.qsar - package toxtree.ui.tree.qsar
 
toxtree.ui.tree.rules - package toxtree.ui.tree.rules
 
toxtree.ui.wizard - package toxtree.ui.wizard
Wizard support.
toxTree_ext - Static variable in class toxTree.io.MolFileFilter
 
toxTree_ext_descr - Static variable in class toxTree.io.MolFileFilter
 
toxTree_ext_descr_save - Static variable in class toxTree.io.MolFileFilter
 
toxTree_ext_save - Static variable in class toxTree.io.MolFileFilter
 
TOXTREE_HOME - Static variable in class toxTree.core.Introspection
 
ToxTreeActions - Class in toxtree.data
Actions used in ToxTreeApp
ToxTreeActions(JFrame, ToxTreeModule) - Constructor for class toxtree.data.ToxTreeActions
 
ToxTreeApp - Class in toxTree.apps
ToxTreeApp is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach.
ToxTreeApp() - Constructor for class toxTree.apps.ToxTreeApp
 
ToxTreeBatchProcessing - Class in toxTree.io.batch
A ChemObjectBatchProcessing descendant , where processing is performed by IDecisionMethod
ToxTreeBatchProcessing() - Constructor for class toxTree.io.batch.ToxTreeBatchProcessing
 
ToxTreeBatchProcessing(String, String) - Constructor for class toxTree.io.batch.ToxTreeBatchProcessing
 
ToxTreeBatchProcessing(File, File) - Constructor for class toxTree.io.batch.ToxTreeBatchProcessing
 
ToxTreeClassLoader - Class in toxTree.core
 
ToxTreeClassLoader(URL[]) - Constructor for class toxTree.core.ToxTreeClassLoader
 
ToxTreeClassLoader(URL[], ClassLoader) - Constructor for class toxTree.core.ToxTreeClassLoader
 
ToxTreeClassLoader(URL[], ClassLoader, URLStreamHandlerFactory) - Constructor for class toxTree.core.ToxTreeClassLoader
 
ToxTreeDescriptor - Class in toxTree.core
 
ToxTreeDescriptor() - Constructor for class toxTree.core.ToxTreeDescriptor
 
ToxTreeEditorPanel - Class in toxtree.ui.tree
Absatract class, implementing IToxTreeEditor.
ToxTreeEditorPanel(Object) - Constructor for class toxtree.ui.tree.ToxTreeEditorPanel
 
ToxTreeEditorPanel() - Constructor for class toxtree.ui.tree.ToxTreeEditorPanel
 
ToxTreeIOException - Exception in toxTree.exceptions
TODO add description
ToxTreeIOException() - Constructor for exception toxTree.exceptions.ToxTreeIOException
 
ToxTreeIOException(Throwable) - Constructor for exception toxTree.exceptions.ToxTreeIOException
 
ToxTreeIOException(String, String) - Constructor for exception toxTree.exceptions.ToxTreeIOException
 
ToxTreeIOException(Throwable, String) - Constructor for exception toxTree.exceptions.ToxTreeIOException
 
ToxTreeIOException(String, Throwable, String) - Constructor for exception toxTree.exceptions.ToxTreeIOException
 
ToxTreeModule - Class in toxtree.data
Contains data essential for ToxTreeApp application the current method IDecisionMethod the result IDecisionResult the list of available methods IDecisionMethodsList the data DecisionMethodData the tree data DecisionMethodData the batch processing object ToxTreeBatchProcessing Also contains some UI frames : a Frame to view a decision tree TreeFrame a Frame to edit a decision tree toxTree.ui.tree.EditTreeFrame a dialog with structure diagram editor JChemPaintDialog and a org.openscience.cdk.applications.jchempaint.JChemPaintModel
ToxTreeModule(JFrame, File, DecisionMethodsList) - Constructor for class toxtree.data.ToxTreeModule
 
ToxTreeObjectInputStream - Class in toxTree.core
Loading non-default serialized classes is tricky ...
ToxTreeObjectInputStream() - Constructor for class toxTree.core.ToxTreeObjectInputStream
 
ToxTreeObjectInputStream(InputStream) - Constructor for class toxTree.core.ToxTreeObjectInputStream
 
ToxTreePackageEntries - Class in toxTree.core
a List of ToxTreePackageEntry
ToxTreePackageEntries() - Constructor for class toxTree.core.ToxTreePackageEntries
 
ToxTreePackageEntries(int) - Constructor for class toxTree.core.ToxTreePackageEntries
 
ToxTreePackageEntries(Collection) - Constructor for class toxTree.core.ToxTreePackageEntries
 
ToxTreePackageEntry - Class in toxTree.core
A class, containing information about className, its package and a toString() output
ToxTreePackageEntry(String, String, String) - Constructor for class toxTree.core.ToxTreePackageEntry
 
ToxTreePackageEntryModel - Class in toxtree.ui.tree
Table model for displaying ToxTreePackageEntries.
ToxTreePackageEntryModel(ToxTreePackageEntries) - Constructor for class toxtree.ui.tree.ToxTreePackageEntryModel
 
ToxTreeWizardPanelDescriptor - Class in toxtree.ui.wizard
 
ToxTreeWizardPanelDescriptor(Object, Object, Object, JComponent, ImageIcon) - Constructor for class toxtree.ui.wizard.ToxTreeWizardPanelDescriptor
 
transferMolecule(IAtomContainer) - Method in class toxtree.ui.metabolites.MetabolitesPanel
 
translation - Variable in class toxTree.qsar.LinearPreprocessor
 
tree - Variable in class toxtree.ui.tree.actions.AbstractTreeAction
 
tree - Variable in class toxtree.ui.tree.EditTreeActions
 
tree - Variable in class toxtree.ui.tree.TreePanel
 
tree - Variable in class toxtree.ui.tree.TreePrefuse
 
tree - Variable in class toxtree.ui.wizard.DecisionTreeWizard
 
tree2cells(Object, int) - Method in class toxtree.ui.tree.TreeLayout
 
Tree2PrefuseGraph - Class in toxTree.tree
 
Tree2PrefuseGraph(Graph) - Constructor for class toxTree.tree.Tree2PrefuseGraph
 
treeActions - Variable in class toxtree.ui.tree.actions.SelectAndEditTreeAction
 
treeActions - Variable in class toxtree.ui.tree.EditTreeActions
 
treeComponent - Variable in class toxtree.ui.tree.TreeDrawing
 
treeComponent - Variable in class toxtree.ui.tree.TreeEditorPanel
 
TreeDrawing - Class in toxtree.ui.tree
Displays a clickable decision tree.
TreeDrawing(IDecisionMethod, EditTreeActions) - Constructor for class toxtree.ui.tree.TreeDrawing
 
TreeEditorPanel - Class in toxtree.ui.tree
The default IDecisionMethodEditor for AbstractTree descendants.
TreeEditorPanel() - Constructor for class toxtree.ui.tree.TreeEditorPanel
 
TreeEditorPanel(IDecisionMethod) - Constructor for class toxtree.ui.tree.TreeEditorPanel
 
TreeFrame - Class in toxtree.ui.tree
A frame to visualise a decision tree IDecisionMethod by TreeDrawing.
TreeFrame(IDecisionMethod) - Constructor for class toxtree.ui.tree.TreeFrame
 
TreeFrame() - Constructor for class toxtree.ui.tree.TreeFrame
 
TreeFrame(GraphicsConfiguration) - Constructor for class toxtree.ui.tree.TreeFrame
 
TreeFrame(String) - Constructor for class toxtree.ui.tree.TreeFrame
 
TreeFrame(String, GraphicsConfiguration) - Constructor for class toxtree.ui.tree.TreeFrame
 
treeFromRule(IDecisionRule) - Static method in class toxtree.ui.tree.actions.NewRuleAction
 
treeLayout - Variable in class toxtree.ui.tree.JCustomTreeComponent
 
TreeLayout - Class in toxtree.ui.tree
Bottom-up layout of a binary decision tree IDecisionMethod.
TreeLayout(IDecisionMethod) - Constructor for class toxtree.ui.tree.TreeLayout
 
TreeLayout() - Constructor for class toxtree.ui.tree.TreeLayout
 
treeModel - Variable in class toxtree.ui.tree.TreePanel
 
treeNodeActions - Variable in class toxtree.ui.tree.EditTreeActions
 
TreeOptions - Class in toxtree.ui.tree
 
TreeOptions(IDecisionMethod, IAtomContainer) - Constructor for class toxtree.ui.tree.TreeOptions
 
TreeOptionsAction - Class in toxtree.ui.tree.actions
 
TreeOptionsAction(DataModule) - Constructor for class toxtree.ui.tree.actions.TreeOptionsAction
 
TreeOptionsAction(DataModule, String) - Constructor for class toxtree.ui.tree.actions.TreeOptionsAction
 
TreeOptionsAction(DataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.TreeOptionsAction
 
treePanel - Variable in class toxtree.ui.tree.TreeFrame
 
TreePanel - Class in toxtree.ui.tree
Displays decision tree by standart JTree component.
TreePanel(IDecisionMethod) - Constructor for class toxtree.ui.tree.TreePanel
 
TreePrefuse - Class in toxtree.ui.tree
 
TreePrefuse(IDecisionMethod, EditTreeActions) - Constructor for class toxtree.ui.tree.TreePrefuse
 
TreePrefuse(IDecisionMethod, EditTreeActions, boolean) - Constructor for class toxtree.ui.tree.TreePrefuse
 
treeResult - Variable in class toxtree.data.DecisionMethodsDataModule
 
TreeResult - Class in toxTree.tree
A default class implementing IDecisionResult
TreeResult() - Constructor for class toxTree.tree.TreeResult
Constructor
treeRoot - Variable in class toxTree.tree.AbstractTree
 
TRIAZENO - Static variable in class toxTree.query.FunctionalGroups
 
triAzeno() - Static method in class toxTree.query.FunctionalGroups
SMARTS: [#6][#7]=[#7][#7;H2]
TTLogger - Class in toxTree.logging
Logging facility
TTLogger() - Constructor for class toxTree.logging.TTLogger
 
TTLogger(Object) - Constructor for class toxTree.logging.TTLogger
Constructs a LoggingTool which produces log lines indicating them to be for the Class of the Object.
TTLogger(Class) - Constructor for class toxTree.logging.TTLogger
 
TXT_INDEX - Static variable in class toxTree.io.batch.ChemObjectBatchProcessing
 

U

update(Observable, Object) - Method in class toxTree.apps.toxForest.ToxForestDataModule
 
update(Observable, Object) - Method in class toxTree.apps.toxForest.ToxForestDataModulePanel
 
update(Observable, Object) - Method in class toxtree.data.DecisionMethodsDataModule
 
update(IObjectFilter) - Method in class toxtree.data.FilteredMoleculesIterator
 
update(Observable, Object) - Method in class toxtree.data.ToxTreeModule
 
update(Observable, Object) - Method in class toxTree.tree.AbstractTree
 
update(Observable, Object) - Method in class toxTree.tree.BatchDecisionResultsList
 
update(Observable, Object) - Method in class toxTree.tree.CategoriesList
 
update(Observable, Object) - Method in class toxTree.tree.DecisionNode
 
update(Observable, Object) - Method in class toxTree.tree.DecisionNodesList
 
update(Observable, Object) - Method in class toxTree.tree.DecisionResultsList
 
update(Observable, Object) - Method in class toxtree.ui.batch.BatchProcessingDialog
 
update(Observable, Object) - Method in class toxtree.ui.HazardPanel
 
update(Observable, Object) - Method in class toxtree.ui.molecule.NavigationPanel
 
update(Observable, Object) - Method in class toxtree.ui.molecule.TopPanel
 
update(Observable, Object) - Method in class toxtree.ui.StatusBar
 
update(Observable, Object) - Method in class toxtree.ui.tree.categories.CategoriesPanel
 
update(Observable, Object) - Method in class toxtree.ui.tree.categories.CategoriesTableModel
 
update(Observable, Object) - Method in class toxtree.ui.tree.DecisionNodePanel
 
update(Observable, Object) - Method in class toxtree.ui.tree.JCustomTreeComponent
 
update(Observable, Object) - Method in class toxtree.ui.tree.ListTableModel
 
update(Observable, Object) - Method in class toxtree.ui.tree.molecule.CompoundPanel
 
update(Observable, Object) - Method in class toxtree.ui.tree.QueryAtomContainersModel
 
update(Observable, Object) - Method in class toxtree.ui.tree.rules.RulePanel
 
update(Observable, Object) - Method in class toxtree.ui.tree.rules.RulePropertyEditor
 
update(Observable, Object) - Method in class toxtree.ui.tree.rules.RuleRangeEditor
 
update(Observable, Object) - Method in class toxtree.ui.tree.ToxTreeEditorPanel
 
update(Observable, Object) - Method in class toxtree.ui.tree.TreeLayout
 
update(Observable, Object) - Method in class toxtree.ui.tree.TreePanel
 
updatedProperties - Variable in class toxTree.data.MoleculesFile
 
updateExampleView() - Method in class toxtree.ui.tree.rules.RulePanel
 
updateMethod() - Method in class toxtree.ui.tree.TreeLayout
 
updateMolecule(IMolecule) - Method in class toxtree.ui.molecule.MoleculeEditAction
 
updateMolecule(IMolecule) - Method in class toxtree.ui.tree.rules.RuleExampleEditAction
 
updateMolecule(IMolecule) - Method in class toxtree.ui.tree.rules.RuleSubstructuresEditAction
 
updateNode(IDecisionMethod, DecisionNode) - Static method in class toxtree.ui.tree.actions.NewRuleAction
 
updateStatus(ProgressStatus) - Method in class toxtree.ui.StatusBar
 
useCache - Variable in class toxTree.tree.rules.LookupFile
 
useDatabase - Variable in class toxtree.data.DataModule
 
useIterativeReader(InputStream) - Method in class toxTree.data.MoleculesIterator
 
useMOEvPrimitive(boolean) - Method in class toxTree.tree.rules.smarts.SmartsPattern
 
user - Variable in class toxtree.lookup.RemoteLookup
 
UserDefinedTree - Class in toxTree.tree
A default decision tree class, implementing IDecisionMethod interface.
UserDefinedTree(IDecisionNodesFactory) - Constructor for class toxTree.tree.UserDefinedTree
 
UserDefinedTree() - Constructor for class toxTree.tree.UserDefinedTree
 
UserDefinedTree(IDecisionCategories, IDecisionRuleList) - Constructor for class toxTree.tree.UserDefinedTree
 
UserDefinedTree(IDecisionCategories, String[], int[][], IDecisionNodesFactory) - Constructor for class toxTree.tree.UserDefinedTree
 
UserInputABUnsaturatedAldehyde - Class in mutant.rules
 
UserInputABUnsaturatedAldehyde() - Constructor for class mutant.rules.UserInputABUnsaturatedAldehyde
 
UserInputAromaticAmine - Class in mutant.rules
 
UserInputAromaticAmine() - Constructor for class mutant.rules.UserInputAromaticAmine
 
UserInputRule - Class in toxTree.tree.rules
 
UserInputRule() - Constructor for class toxTree.tree.rules.UserInputRule
 
UserInputRule(String) - Constructor for class toxTree.tree.rules.UserInputRule
 

V

valueChanged(ListSelectionEvent) - Method in class toxtree.ui.tree.ListPanel
 
valueChanged(TreeSelectionEvent) - Method in class toxtree.ui.tree.TreePanel
 
valueChanged(ListSelectionEvent) - Method in class toxtree.ui.wizard.DecisionNodeWizard
 
valueForPathChanged(TreePath, Object) - Method in class toxtree.ui.tree.DecisionTreeModel
 
valueOf(String) - Static method in enum toxTree.core.IDecisionInteractive.UserOptions
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum toxTree.tree.ProgressStatus.STATUS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum toxtree.ui.wizard.DecisionNodeWizard.RuleOptions
Returns the enum constant of this type with the specified name.
values() - Static method in enum toxTree.core.IDecisionInteractive.UserOptions
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum toxtree.plugins.dnabinding.categories.DNABindingAlerts
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum toxtree.plugins.proteinbinding.categories.ProteinBindingAlerts
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum toxtree.plugins.skinsensitisation.categories.SkinSensitisationAlerts
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum toxTree.tree.ProgressStatus.STATUS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum toxtree.ui.wizard.DecisionNodeWizard.RuleOptions
Returns an array containing the constants of this enum type, in the order they are declared.
VapourPressure - Static variable in class sicret.rules.RuleVapourPressure
 
verhaar - package verhaar
Class VerhaarScheme is the implementation of Verhaar structural scheme for estimating toxicity mode of action.
verhaar.categories - package verhaar.categories
The package contains implementations of IDecisionCategory categories for VerhaarScheme decision tree.
verhaar.query - package verhaar.query
 
verhaar.rules - package verhaar.rules
The package contains implementations of IDecisionRule rules for VerhaarScheme decision tree.
verhaar.rules.helper - package verhaar.rules.helper
 
Verhaar2TreeResult - Class in toxtree.plugins.verhaar2.rules
 
Verhaar2TreeResult() - Constructor for class toxtree.plugins.verhaar2.rules.Verhaar2TreeResult
 
VerhaarScheme - Class in verhaar
An implementaton of Verhaar scheme for predicting toxicity mode of action.
VerhaarScheme() - Constructor for class verhaar.VerhaarScheme
 
VerhaarScheme(boolean) - Constructor for class verhaar.VerhaarScheme
 
VerhaarScheme2 - Class in toxtree.plugins.verhaar2
An implementaton of Verhaar scheme for predicting toxicity mode of action.
VerhaarScheme2() - Constructor for class toxtree.plugins.verhaar2.VerhaarScheme2
 
VerhaarScheme2(boolean) - Constructor for class toxtree.plugins.verhaar2.VerhaarScheme2
 
VerhaarTreeResult - Class in verhaar.rules
 
VerhaarTreeResult() - Constructor for class verhaar.rules.VerhaarTreeResult
 
verify() - Method in class toxTree.qsar.AbstractQSARModel
 
verify() - Method in class toxTree.qsar.LinearQSARModel
 
VerifyAlertsAche - Class in toxtree.plugins.moa.rules
 
VerifyAlertsAche() - Constructor for class toxtree.plugins.moa.rules.VerifyAlertsAche
 
VerifyAlertsCNS - Class in toxtree.plugins.moa.rules
 
VerifyAlertsCNS() - Constructor for class toxtree.plugins.moa.rules.VerifyAlertsCNS
 
VerifyAlertsDNABinding - Class in toxtree.plugins.dnabinding.rules
 
VerifyAlertsDNABinding() - Constructor for class toxtree.plugins.dnabinding.rules.VerifyAlertsDNABinding
 
VerifyAlertsGenotoxic - Class in mutant.rules
 
VerifyAlertsGenotoxic() - Constructor for class mutant.rules.VerifyAlertsGenotoxic
 
VerifyAlertsNarcosis1 - Class in toxtree.plugins.moa.rules
 
VerifyAlertsNarcosis1() - Constructor for class toxtree.plugins.moa.rules.VerifyAlertsNarcosis1
 
VerifyAlertsNarcosis2 - Class in toxtree.plugins.moa.rules
 
VerifyAlertsNarcosis2() - Constructor for class toxtree.plugins.moa.rules.VerifyAlertsNarcosis2
 
VerifyAlertsNarcosis3 - Class in toxtree.plugins.moa.rules
 
VerifyAlertsNarcosis3() - Constructor for class toxtree.plugins.moa.rules.VerifyAlertsNarcosis3
 
VerifyAlertsNongenotoxic - Class in mutant.rules
 
VerifyAlertsNongenotoxic() - Constructor for class mutant.rules.VerifyAlertsNongenotoxic
 
VerifyAlertsProteinBinding - Class in toxtree.plugins.proteinbinding.rules
 
VerifyAlertsProteinBinding() - Constructor for class toxtree.plugins.proteinbinding.rules.VerifyAlertsProteinBinding
 
VerifyAlertsReactive - Class in toxtree.plugins.moa.rules
 
VerifyAlertsReactive() - Constructor for class toxtree.plugins.moa.rules.VerifyAlertsReactive
 
VerifyAlertsSkinSensitisation - Class in toxtree.plugins.skinsensitisation.rules
 
VerifyAlertsSkinSensitisation() - Constructor for class toxtree.plugins.skinsensitisation.rules.VerifyAlertsSkinSensitisation
 
VerifyAlertsUncouplers - Class in toxtree.plugins.moa.rules
 
VerifyAlertsUncouplers() - Constructor for class toxtree.plugins.moa.rules.VerifyAlertsUncouplers
 
verifyResidues(IAtomContainerSet, IDecisionResult, IDecisionRule) - Method in class toxTree.tree.AbstractTree
 
verifyRule(IAtomContainer) - Method in class com.molecularnetworks.start.rules.RuleMoreThanTwoHydroxyOnAromaticRing
Overrides the default IDecisionRule behaviour.
verifyRule(IAtomContainer) - Method in class com.molecularnetworks.start.rules.RuleOneHalogenOnUnbranched
Overrides the default IDecisionRule behaviour.
verifyRule(IAtomContainer) - Method in class com.molecularnetworks.start.rules.RuleTerminalIsopropylNonCyclic
Overrides the default IDecisionRule behaviour.
verifyRule(IAtomContainer) - Method in class com.molecularnetworks.start.rules.RuleTwoHalogensOnUnbranchedNonCyclic
Overrides the default IDecisionRule behaviour.
verifyRule(IAtomContainer) - Method in class com.molecularnetworks.start.rules.RuleTwoOrMoreRings
Overrides the default IDecisionRule behaviour.
verifyRule(IAtomContainer) - Method in class com.molecularnetworks.start.rules.RuleTwoTerminalDiaminoGroupsOnNonCyclic
Overrides the default IDecisionRule behaviour.
verifyRule(IAtomContainer) - Method in class com.molecularnetworks.start.rules.RuleTwoTerminalDoubleBondsOnUnbranched
Overrides the default IDecisionRule behaviour.
verifyRule(IAtomContainer, IAtomContainer) - Method in class cramer2.rules.RuleHasOnlySaltSulphonateSulphate
Calls the inherited RuleOnlyAllowedSubstructures.verifyRule(IAtomContainer) Removes sulphonate and sulphate groups if any by FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer) and sets molflag property of a molecule to mf.setResidue(residue); This makes subsequent rules to work with the residue rather than with the original molecule If a rule needs the original structure instead, it can get it by getProperty(MolFlags.PARENT) See for example Q24 and Q33 TODO treat hydrochloride of amine as free amine
verifyRule(IAtomContainer) - Method in class cramer2.rules.RuleReadilyHydrolysedPO4
 
verifyRule(IAtomContainer) - Method in class eye.rules.Rule13_AliphaticMonoalcohols
 
verifyRule(IAtomContainer) - Method in class eye.rules.Rule38
 
verifyRule(IAtomContainer) - Method in class mic.rules.SA10
 
verifyRule(IAtomContainer) - Method in class mic.rules.SA18
Find essential rings through SSSRFinder.findEssentialRings.
verifyRule(IAtomContainer) - Method in class mic.rules.SA26
 
verifyRule(IAtomContainer) - Method in class mutant.rules.QSAR6Applicable
 
verifyRule(IAtomContainer) - Method in class mutant.rules.RuleAromaticAmineNoSulfonicGroup
 
verifyRule(IAtomContainer) - Method in class mutant.rules.RuleAromaticDiazo
 
verifyRule(IAtomContainer) - Method in class mutant.rules.RuleDerivedAromaticAmines
 
verifyRule(IAtomContainer) - Method in class mutant.rules.SA10_gen
 
verifyRule(IAtomContainer) - Method in class mutant.rules.SA18_gen
Find essential rings through SSSRFinder.findEssentialRings.
verifyRule(IAtomContainer, IAtomContainer) - Method in class mutant.rules.SA20_nogen
 
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleAcidAnhydrides
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleAcrylicAcids
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleAcrylicAndMethacrylicEsters
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleAromaticAmines
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleC10_C20AliphaticAlcohols
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleCarbamoylHalide
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleCatecholsResorcinolsHydroquinones
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleDi_Tri_Nitrobenzenes
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleHalonitrobenzene
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleHasOnlyC_H_O
 
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleLactonesFusedOrUnsaturated
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleOandPQuinones
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class sicret.rules.RuleTriAndTetraHalogenatedBenzenes
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in interface toxTree.core.IDecisionRule
This is the core of a IDecisionRule behaviour.
verifyRule(IAtomContainer) - Method in class toxtree.plugins.kroes.rules.KroesRule8
 
verifyRule(IAtomContainer) - Method in class toxtree.plugins.kroes.rules.RuleKroesFig1Q1
 
verifyRule(IAtomContainer) - Method in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_1
 
verifyRule(IAtomContainer) - Method in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_1_1
 
verifyRule(IAtomContainer) - Method in class toxtree.plugins.moa.rules.RuleAlertsNarcosis1_1_2_1
 
verifyRule(IAtomContainer) - Method in class toxtree.plugins.search.rules.Find
 
verifyRule(IAtomContainer) - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
returns true if at least one atom has a score assigned
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxtree.plugins.smartcyp.rules.SMARTCYPRuleRank1
 
verifyRule(IAtomContainer) - Method in class toxTree.qsar.LinearDiscriminantRule
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.AbstractRuleHilightHits
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.Rule32
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.Rule3FuncGroups
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.Rule3FuncGroups
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.Rule3MemberedHeterocycle
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleAcyclicAcetalEsterOfQ30
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleAcyclicAcetalEsterOfQ30
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleAliphaticWithSomeFuncGroups
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
Calls the inherited RuleOnlyAllowedSubstructures.verifyRule(IAtomContainer) Removes sulphonate and sulphate groups if any by FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer) and sets molflag property of a molecule to mf.setResidue(residue); This makes subsequent rules to work with the residue rather than with the original molecule If a rule needs the original structure instead, it can get it by getProperty(MolFlags.PARENT) See for example Q24 and Q33 TODO treat hydrochloride of amine as free amine
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleHasOnlySaltSulphonateSulphate
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleHasOtherThanC_H_O_N_S2
Verifies the rule.
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleHasOtherThanC_H_O_N_S2
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleHeteroaromatic
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleHeterocyclicComplexSubstituents
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleKetoneAlcoholEtc
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleLactoneOrCyclicDiester
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleLactonesFusedOrUnsaturated
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleMonocarbocyclic
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleMonocarbocyclic
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleMonocycloalkanoneEtc
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleMonocycloalkanoneEtc
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleOnlyFuncGroupsQ30
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleOnlyFuncGroupsQ30
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleReadilyHydrolysedMononuclear
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleReadilyHydrolysedToCommonterpene
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleRingComplexSubstituents30
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleRingComplexSubstituents30
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleSimplyBranchedAliphaticHydrocarbon
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleSomeBenzeneDerivatives
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleSufficientSulphonateGroups
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.cramer.RuleToxicFunctionalGroups
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.cramer.RuleToxicFunctionalGroups
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.DecisionNode
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleAllSubstructures
returns true if all of the fragments are a substructure of mol IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleAnySubstituents
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleAnySubstructure
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleAnySubstructure
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleAromatic
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleCarbohydrate
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleCarbohydrate
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleCommonTerpene
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleCommonTerpene
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleDescriptor
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleDescriptorRange
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleElements
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleElements
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleHeterocyclic
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleInitAlertCounter
Assings value returned by RuleVerifyProperty.getProperty() to molecule property with name given by RuleVerifyProperty.getPropertyName().
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleLipinski5
Returns true if all Lipinski Rule of Five are true
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleManyAromaticRings
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleOnlyAllowedSubstructures
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleOnlyAllowedSubstructures
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleOpenChain
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleReadilyHydrolised
Returns true if the compound is readily hydrolised Sets MolFlags hydrolysis products (to be used further )
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleReadilyHydrolised
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleRingAllowedSubstituents
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleRingAllowedSubstituents
returns true if only allowed substituents are found
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleRingOtherThanAllowedSubstituents
return true if other than listed substructures are found in a ring substituent
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleRingOtherThanAllowedSubstituents
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleRingSubstituents
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleRingSubstituents
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleStructuresList
IDecisionRule.verifyRule(IAtomContainer)
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleStructuresList
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.RuleSubstructures
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleVerifyAlertsCounter
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.RuleVerifyProperty
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.smarts.RuleSMARTSubstructureCDK
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.StructureAlert
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.StructureAlertAmbit
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.StructureAlertCDK
 
verifyRule(IAtomContainer) - Method in class toxTree.tree.rules.UserInputRule
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.helper.RuleAnySubstructureCounter
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.helper.RuleElementsCounter
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.helper.RuleOnlyAllowedSubstructuresCounter
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule03
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule11
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule141
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule142
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule143
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule151
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule152
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class verhaar.rules.Rule152
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule153
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule154
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule161
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class verhaar.rules.Rule161
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class verhaar.rules.Rule171
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule21
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class verhaar.rules.Rule21
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule23
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class verhaar.rules.Rule23
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.Rule24
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class verhaar.rules.Rule24
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.RuleIonicGroups
 
verifyRule(IAtomContainer, IAtomContainer) - Method in class verhaar.rules.RuleIonicGroups
 
verifyRule(IAtomContainer) - Method in class verhaar.rules.RuleLogPRange
 
verifyRules(IAtomContainer, IDecisionResult) - Method in interface toxTree.core.IDecisionMethod
 
verifyRules(IAtomContainer, IDecisionResult) - Method in class toxTree.tree.AbstractTree
IDecisionRule.verifyRule(IAtomContainer)
verifyRules(IAtomContainer, IDecisionResult, IDecisionRule) - Method in class toxTree.tree.AbstractTree
abstract method, to be implemented in the child class
verifyRules(IAtomContainer, IDecisionResult) - Method in class toxTree.tree.BatchDecisionResultsList
 
verifyRules(IAtomContainer, IDecisionResult, IDecisionRule) - Method in class toxTree.tree.UserDefinedTree
 
VerifyUnreachableRulesAction - Class in toxtree.ui.tree.actions
Verifies if there are unreachable rules; If found, ask user to delete them.
VerifyUnreachableRulesAction(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.VerifyUnreachableRulesAction
 
VerifyUnreachableRulesAction(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.VerifyUnreachableRulesAction
 
VerifyUnreachableRulesAction(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.VerifyUnreachableRulesAction
 
VerifyUnusedCategories - Class in toxtree.ui.tree.actions
 
VerifyUnusedCategories(IDecisionMethod) - Constructor for class toxtree.ui.tree.actions.VerifyUnusedCategories
 
VerifyUnusedCategories(IDecisionMethod, String) - Constructor for class toxtree.ui.tree.actions.VerifyUnusedCategories
 
VerifyUnusedCategories(IDecisionMethod, String, Icon) - Constructor for class toxtree.ui.tree.actions.VerifyUnusedCategories
 
vicinalDiKetone() - Static method in class toxTree.query.FunctionalGroups
 
viewCategory(IDecisionCategory) - Method in class toxTree.apps.toxForest.ToxForestDataModulePanel
 
viewMethod(IDecisionMethod, boolean) - Method in class toxtree.data.DataModule
 
viewMethod(IDecisionMethod, boolean) - Method in class toxtree.data.DecisionMethodsDataModule
 
viewMethod(int, boolean) - Method in class toxtree.data.DecisionMethodsDataModule
 
viewMethod(boolean) - Method in class toxtree.data.ToxTreeModule
 
viewMethodAction - Variable in class toxtree.data.ToxTreeActions
 
ViewTreeAction - Class in toxtree.ui.tree.actions
Views a IDecisionMethod
ViewTreeAction(DataModule) - Constructor for class toxtree.ui.tree.actions.ViewTreeAction
 
ViewTreeAction(DataModule, String) - Constructor for class toxtree.ui.tree.actions.ViewTreeAction
 
ViewTreeAction(DataModule, String, Icon) - Constructor for class toxtree.ui.tree.actions.ViewTreeAction
 
viewVerboseResult(IDecisionResult) - Method in class toxTree.apps.toxForest.ToxForestDataModulePanel
 
visitCategories(DecisionNode, IDecisionCategories) - Method in class toxTree.tree.UserDefinedTree
 
visited - Variable in class toxTree.tree.DecisionNode
 
visited - Variable in class toxtree.ui.tree.TreeLayout
 
visitRules(DecisionNode) - Method in class toxTree.tree.UserDefinedTree
 

W

walkRules(IDecisionRule, IProcessRule) - Method in interface toxTree.core.IDecisionMethod
 
walkRules(IDecisionRule, IProcessRule) - Method in class toxTree.tree.AbstractTree
 
walkRules(IDecisionRule, ArrayList<Integer>, IProcessRule) - Method in class toxTree.tree.AbstractTree
 
walkRules(IDecisionRule, IProcessRule) - Method in class toxTree.tree.BatchDecisionResultsList
 
walkRules(IDecisionMethod) - Method in class toxTree.tree.Tree2PrefuseGraph
 
walkRules(IDecisionMethod, IDecisionRule, ArrayList<Integer>) - Method in class toxTree.tree.Tree2PrefuseGraph
 
warn(Object) - Method in class toxTree.logging.TTLogger
Shows WARN output for the Object.
warn(Object, int) - Method in class toxTree.logging.TTLogger
Shows WARN output for the given Object's.
warn(Object, boolean) - Method in class toxTree.logging.TTLogger
Shows WARN output for the given Object's.
warn(Object, double) - Method in class toxTree.logging.TTLogger
Shows WARN output for the given Object's.
warn(Object, Object) - Method in class toxTree.logging.TTLogger
Shows WARN output for the given Object's.
warn(Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows WARN output for the given Object's.
warn(Object, Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows WARN output for the given Object's.
warn(Object, Object, Object, Object, Object) - Method in class toxTree.logging.TTLogger
Shows WARN output for the given Object's.
web - Variable in class toxTree.tree.AbstractTree
 
web - Variable in class toxTree.tree.RuleResult
 
web - Variable in class toxTree.tree.TreeResult
 
weights - Variable in class toxTree.qsar.LinearQSARModel
 
WizardWrapper - Class in toxtree.ui.wizard
 
WizardWrapper() - Constructor for class toxtree.ui.wizard.WizardWrapper
 
WizardWrapper(Dialog) - Constructor for class toxtree.ui.wizard.WizardWrapper
 
WizardWrapper(Frame) - Constructor for class toxtree.ui.wizard.WizardWrapper
 
write(IChemObject) - Method in class toxTree.io.PDFWriter
 
writeHeader() - Method in class toxTree.io.PDFWriter
 
writeMolecule(IMolecule) - Method in class toxTree.io.PDFWriter
 
writeMolecule(IDecisionRule, boolean, OutputStream) - Method in class toxTree.tree.AbstractTreePrinter
 
writeMolecule(IDecisionRule, boolean) - Method in class toxTree.tree.ReportTreePrinter
 
writer - Variable in class toxTree.io.batch.ChemObjectBatchProcessing
 
writer - Variable in class toxTree.tree.AbstractTreeWriter
 
writeRecord() - Method in class toxTree.io.batch.ChemObjectBatchProcessing
 
writeRecord() - Method in interface toxTree.io.batch.IBatchProcessing
 
writeRecord() - Method in class toxTree.io.batch.ToxTreeBatchProcessing
 
writeSetOfMolecules(IMoleculeSet) - Method in class toxTree.io.PDFWriter
 
wwwAlertFormat - Static variable in class toxTree.tree.RuleResult
 

X

x - Variable in class verhaar.rules.Rule141
 
x - Variable in class verhaar.rules.Rule143
 
XMLDecisionMethodException - Exception in toxTree.exceptions
Thrown when processing XMLSerializable.
XMLDecisionMethodException() - Constructor for exception toxTree.exceptions.XMLDecisionMethodException
 
XMLDecisionMethodException(String) - Constructor for exception toxTree.exceptions.XMLDecisionMethodException
 
XMLDecisionMethodException(Throwable) - Constructor for exception toxTree.exceptions.XMLDecisionMethodException
 
XMLDecisionMethodException(String, Throwable) - Constructor for exception toxTree.exceptions.XMLDecisionMethodException
 
XMLSerializable - Interface in toxTree.core
 
xmltag_CATEGORIES - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_CATEGORY - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_CATEGORYTHRESHOLD - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_CLASS - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_EXPLANATION - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_ID - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_METHOD - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_METHODPARAMETER - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_METHODS - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_NAME - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_RULE - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_RULEEXAMPLE - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_RULES - Static variable in interface toxTree.core.XMLSerializable
 
xmltag_TREEROOT - Static variable in interface toxTree.core.XMLSerializable
 

Y

yes - Static variable in class mutant.descriptors.SubstituentExtractor
 
yesBranch - Variable in class toxtree.ui.tree.DecisionNodePanel
 
yesExample - Variable in class toxtree.ui.tree.rules.RulePanel
 

_

_aClearResults - Static variable in class toxtree.ui.actions.ClearResultAction
 
_aEditCompound - Static variable in class toxtree.ui.actions.EditCompoundAction
 
_aEditMethod - Static variable in class toxTree.apps.toxForest.ToxForestActions
 
_aEditMethod - Static variable in class toxtree.data.ToxTreeActions
 
_aEditMethod - Static variable in class toxtree.ui.tree.actions.LoadAndEditTreeAction
 
_aEditMethod - Static variable in class toxtree.ui.tree.actions.SelectAndEditTreeAction
 
_aEstimate - Static variable in class toxtree.ui.actions.EstimateAction
 
_aEstimateAll - Static variable in class toxtree.ui.actions.EstimateAllAction
 
_aExplain - Static variable in class toxtree.ui.actions.ExplainAction
 
_aNewMethod - Static variable in class toxtree.ui.tree.actions.NewTreeAction
 
_aSelectMethod - Static variable in class toxtree.ui.tree.actions.SelectTreeAction
 
_aSkipNotImplemented - Static variable in class toxTree.apps.toxForest.ToxForestActions
 
_aSkipNotImplemented - Static variable in class toxtree.data.ToxTreeActions
 
_aViewMethod - Static variable in class toxtree.ui.tree.actions.ViewTreeAction
 
_CHILDREN - Static variable in class toxtree.data.ActionList
 
_CompoundAction - Static variable in class toxTree.apps.toxForest.ToxForestActions
 
_CompoundAction - Static variable in class toxtree.data.ToxTreeActions
 
_EditAction - Static variable in class toxTree.apps.toxForest.ToxForestActions
 
_EditAction - Static variable in class toxtree.data.ToxTreeActions
 
_eError - Static variable in class toxTree.tree.ProgressStatus
 
_eMethodNotAssigned - Static variable in class toxTree.tree.ProgressStatus
 
_eResultIsEstimating - Static variable in class toxTree.tree.ProgressStatus
 
_eResultNotEstimated - Static variable in class toxTree.tree.ProgressStatus
 
_eUnknownState - Static variable in class toxTree.tree.ProgressStatus
 
_FileAction - Static variable in class toxTree.apps.toxForest.ToxForestActions
 
_FileAction - Static variable in class toxtree.data.ToxTreeActions
 
_HazardAction - Static variable in class toxTree.apps.toxForest.ToxForestActions
 
_HazardAction - Static variable in class toxtree.data.ToxTreeActions
 
_MESSAGE - Static variable in exception toxTree.exceptions.DRuleNotImplemented
 
_mismatchMessage - Static variable in exception toxTree.exceptions.DecisionResultUIDException
 
_mismatchMessage - Static variable in exception toxTree.exceptions.DesisionMethodUIDException
 
_MNEMONICID - Static variable in class toxtree.data.ActionList
 
_pClassID - Static variable in class toxTree.tree.ProgressStatus
 
_pDecisionMethod - Static variable in class toxTree.tree.ProgressStatus
 
_pRuleResult - Static variable in class toxTree.tree.ProgressStatus
 
_TYPEID - Static variable in class toxtree.data.ActionList
 

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