Uses of Package
toxTree.tree.rules

Packages that use toxTree.tree.rules

Package	Description
cramer2.rules
eye.rules	The package contains implementations of IDecisionRule rules for SicretRules decision tree.
mic.rules
michaelacceptors.rules
mutant.rules
sicret.rules	The package contains implementations of IDecisionRule rules for SicretRules decision tree.
toxTree.tree.cramer	Class CramerRules is the implementation of Cramer rules [Cramer et al,78].
toxTree.tree.rules	The package contains several generic implementations of IDecisionRule rules
toxtree.plugins.ames.rules
toxtree.plugins.dnabinding.rules
toxtree.plugins.func.rules
toxtree.plugins.kroes.rules
toxtree.plugins.lewis.rules
toxtree.plugins.moa.rules
toxtree.plugins.proteinbinding.rules
toxtree.plugins.skinsensitisation.rules
toxtree.tree.cramer3.rules
toxtree.tree.rules
toxtree.ui	Base classes for ToxTreeApp user interface
toxtree.ui.editors
toxtree.ui.tree.rules
verhaar.rules	The package contains implementations of IDecisionRule rules for VerhaarScheme decision tree.
verhaar.rules.helper

Classes in toxTree.tree.rules used by cramer2.rules

Class and Description
RuleReadilyHydrolised Verifies if a compound is readily hydrolised

Classes in toxTree.tree.rules used by eye.rules

Class and Description
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.

Classes in toxTree.tree.rules used by mic.rules

Class and Description
IAlertCounter
RuleAnySubstructure Verifies if the molecule has at least one substructure of the list
RuleAromatic Verifies if the molecule is aromatic by applying the Hueckel rule
RuleInitAlertCounter
RuleSubstructures An abstract class to implement substructure rules
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
StructureAlert
StructureAlertCDK

Classes in toxTree.tree.rules used by michaelacceptors.rules

Class and Description
IAlertCounter
StructureAlertAmbit

Classes in toxTree.tree.rules used by mutant.rules

Class and Description
IAlertCounter
RuleAromatic Verifies if the molecule is aromatic by applying the Hueckel rule
RuleInitAlertCounter
RuleRings
RuleRingSubstituents A rule to analyze ring substituents
RuleSubstructures An abstract class to implement substructure rules
RuleVerifyAlertsCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
StructureAlert
StructureAlertAmbit
StructureAlertCDK
UserInputRule

Classes in toxTree.tree.rules used by sicret.rules

Class and Description
RuleAllAllowedElements
RuleAllSubstructures Verifies if all of the fragments are a substructure of moleclue
RuleAnySubstructure Verifies if the molecule has at least one substructure of the list
RuleElements Verifies if the molecule consists of only allowed elements
RuleSubstructures An abstract class to implement substructure rules
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.

Classes in toxTree.tree.rules used by toxTree.tree.cramer

Class and Description
RuleAnySubstituents Verifies if the molecule consists of only allowed substituents
RuleAnySubstructure Verifies if the molecule has at least one substructure of the list
RuleAromatic Verifies if the molecule is aromatic by applying the Hueckel rule
RuleCarbohydrate Verifies if the molecule is a carbohydrate
RuleCommonTerpene Verifies if the molecule is a common terpene
RuleElements Verifies if the molecule consists of only allowed elements
RuleHeterocyclic Verifies if the molecule is heterocyclic
RuleManyAromaticRings Verifies if there are many aromatic rings
RuleOnlyAllowedSubstructures Verifies if the structure contains only allowed substructures
RuleOpenChain Verifies if the moleucle is open chain
RuleReadilyHydrolised Verifies if a compound is readily hydrolised
RuleRingAllowedSubstituents A rule to analyze ring substituents
RuleRingOtherThanAllowedSubstituents A rule to analyze ring substituents
RuleRings
RuleRingSubstituents A rule to analyze ring substituents
RuleStructuresList A rule, which returns true if the query is isomorphic to one of the structures read from a preconfigured file of a type SDF, SMI, CSV
RuleSubstructures An abstract class to implement substructure rules

Classes in toxTree.tree.rules used by toxTree.tree.rules

Class and Description
IAlertCounter
ILookupFile
RuleDescriptor An abstract class to allow for descriptor analysis
RuleDescriptorRange Verifies if the descriptor is within a range
RuleElements Verifies if the molecule consists of only allowed elements
RuleInitAlertCounter
RuleRings
RuleRingSubstituents A rule to analyze ring substituents
RuleSubstructures An abstract class to implement substructure rules
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.

Classes in toxTree.tree.rules used by toxtree.plugins.ames.rules

Class and Description
IAlertCounter
RuleInitAlertCounter
RuleVerifyAlertsCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
StructureAlertCDK

Classes in toxTree.tree.rules used by toxtree.plugins.dnabinding.rules

Class and Description
IAlertCounter
RuleInitAlertCounter
RuleVerifyAlertsCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
StructureAlert

Classes in toxTree.tree.rules used by toxtree.plugins.func.rules

Class and Description
IAlertCounter
RuleInitAlertCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
StructureAlert
StructureAlertCDK

Classes in toxTree.tree.rules used by toxtree.plugins.kroes.rules

Class and Description
RuleInitAlertCounter
RuleSubstructures An abstract class to implement substructure rules
RuleVerifyAlertsCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.

Classes in toxTree.tree.rules used by toxtree.plugins.lewis.rules

Class and Description
RuleDescriptor An abstract class to allow for descriptor analysis
RuleDescriptorRange Verifies if the descriptor is within a range

Classes in toxTree.tree.rules used by toxtree.plugins.moa.rules

Class and Description
RuleInitAlertCounter
RuleVerifyAlertsCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.

Classes in toxTree.tree.rules used by toxtree.plugins.proteinbinding.rules

Class and Description
IAlertCounter
RuleInitAlertCounter
RuleVerifyAlertsCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
StructureAlert

Classes in toxTree.tree.rules used by toxtree.plugins.skinsensitisation.rules

Class and Description
IAlertCounter
RuleInitAlertCounter
RuleVerifyAlertsCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
StructureAlert

Classes in toxTree.tree.rules used by toxtree.tree.cramer3.rules

Class and Description
RuleAnySubstituents Verifies if the molecule consists of only allowed substituents
RuleCarbohydrate Verifies if the molecule is a carbohydrate
RuleHeterocyclic Verifies if the molecule is heterocyclic
RuleManyAromaticRings Verifies if there are many aromatic rings

Classes in toxTree.tree.rules used by toxtree.tree.rules

Class and Description
UserInputRule

Classes in toxTree.tree.rules used by toxtree.ui

Class and Description
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.

Classes in toxTree.tree.rules used by toxtree.ui.editors

Class and Description
RuleDescriptorRange Verifies if the descriptor is within a range
RuleManyAromaticRings Verifies if there are many aromatic rings
RuleMolecularMassRange Molecular mass in [RuleDescriptorRange.getMinValue(),RuleDescriptorRange.getMaxValue()] TODO add description
RuleStructuresList A rule, which returns true if the query is isomorphic to one of the structures read from a preconfigured file of a type SDF, SMI, CSV
RuleSubstructures An abstract class to implement substructure rules
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.

Classes in toxTree.tree.rules used by toxtree.ui.tree.rules

Class and Description
RuleStructuresList A rule, which returns true if the query is isomorphic to one of the structures read from a preconfigured file of a type SDF, SMI, CSV
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.

Classes in toxTree.tree.rules used by verhaar.rules

Class and Description
IAlertCounter
RuleDescriptor An abstract class to allow for descriptor analysis
RuleDescriptorRange Verifies if the descriptor is within a range
RuleElements Verifies if the molecule consists of only allowed elements
RuleInitAlertCounter
RuleMolecularMassRange Molecular mass in [RuleDescriptorRange.getMinValue(),RuleDescriptorRange.getMaxValue()] TODO add description
RuleOnlyAllowedSubstructures Verifies if the structure contains only allowed substructures
RuleOpenChain Verifies if the moleucle is open chain
RuleRingAllowedSubstituents A rule to analyze ring substituents
RuleRings
RuleRingSubstituents A rule to analyze ring substituents
RuleSubstructures An abstract class to implement substructure rules
RuleVerifyAlertsCounter
RuleVerifyProperty Verifies if property is >, < or = to a RuleVerifyProperty.getProperty() value.
StructureAlert

Classes in toxTree.tree.rules used by verhaar.rules.helper

Class and Description
IAlertCounter
RuleAnySubstructure Verifies if the molecule has at least one substructure of the list
RuleElements Verifies if the molecule consists of only allowed elements
RuleOnlyAllowedSubstructures Verifies if the structure contains only allowed substructures
RuleSubstructures An abstract class to implement substructure rules