Uses of Class
toxTree.exceptions.DecisionMethodException

Packages that use DecisionMethodException

Package	Description
com.molecularnetworks.start
com.molecularnetworks.start.rules
cramer2	Class CramerRules is the implementation of Cramer rules [Cramer et al,78].
cramer2.rules
eye	Class SicretRules is the implementation of BfR rules for estimating skin irritation and corrosion potential.
eye.rules	The package contains implementations of IDecisionRule rules for SicretRules decision tree.
mic
mic.rules
michaelacceptors
mutant
mutant.rules
sicret	Class SicretRules is the implementation of BfR rules for estimating skin irritation and corrosion potential.
sicret.rules	The package contains implementations of IDecisionRule rules for SicretRules decision tree.
toxTree.core	This packages contains only interface definitions, defining essential classes in toxTree application.
toxtree.data
toxTree.data	Classes that hold the data used in ToxTreeApp
toxTree.exceptions	Exceptions defined for toxTree classes
toxtree.plugins.ames
toxtree.plugins.ames.rules
toxtree.plugins.dnabinding
toxtree.plugins.func
toxtree.plugins.kroes.rules
toxtree.plugins.moa
toxtree.plugins.moa.rules
toxtree.plugins.proteinbinding
toxtree.plugins.search.rules
toxtree.plugins.skinsensitisation
toxtree.plugins.smartcyp
toxtree.plugins.smartcyp.rules
toxtree.plugins.verhaar2	Class toxtree.plugins.verhaar2.VerhaarScheme is the implementation of modified Verhaar structural scheme, according to recommendation from
toxTree.qsar
toxTree.tree	This packages contains abstract and default classes implementing the interfaces defined in toxTree.core package.
toxTree.tree.cramer	Class CramerRules is the implementation of Cramer rules [Cramer et al,78].
toxtree.tree.cramer3
toxtree.tree.cramer3.rules
toxTree.tree.demo	Two simple demo decision trees.
toxTree.tree.rules	The package contains several generic implementations of IDecisionRule rules
toxTree.tree.rules.smarts	SMARTS support.
toxtree.ui.tree	User interface for viewing and editing a decision tree IDecisionMethod
toxtree.ui.tree.actions	Actions (derived from AbstractAction for the decision tree user interface toxTree.ui.tree
verhaar	Class VerhaarScheme is the implementation of Verhaar structural scheme for estimating toxicity mode of action.
verhaar.rules	The package contains implementations of IDecisionRule rules for VerhaarScheme decision tree.
verhaar.rules.helper

Uses of DecisionMethodException in com.molecularnetworks.start

Methods in com.molecularnetworks.start that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	BiodgeradationRules.explainRules(IDecisionResult result, boolean verbose)

Constructors in com.molecularnetworks.start that throw DecisionMethodException

Constructor and Description
BiodgeradationRules()

Uses of DecisionMethodException in com.molecularnetworks.start.rules

Methods in com.molecularnetworks.start.rules that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	RuleMoreThanTwoHydroxyOnAromaticRing.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Overrides the default IDecisionRule behaviour.
boolean	RuleTerminalIsopropylNonCyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Overrides the default IDecisionRule behaviour.
boolean	RuleTwoHalogensOnUnbranchedNonCyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Overrides the default IDecisionRule behaviour.
boolean	RuleOneHalogenOnUnbranched.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Overrides the default IDecisionRule behaviour.
boolean	RuleTwoTerminalDoubleBondsOnUnbranched.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Overrides the default IDecisionRule behaviour.
boolean	RuleTwoTerminalDiaminoGroupsOnNonCyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Overrides the default IDecisionRule behaviour.
boolean	RuleTwoOrMoreRings.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Overrides the default IDecisionRule behaviour.

Uses of DecisionMethodException in cramer2

Methods in cramer2 that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	CramerRulesWithExtensions.explainRules(IDecisionResult result, boolean verbose)

Constructors in cramer2 that throw DecisionMethodException

Constructor and Description
CramerRulesWithExtensions()

Uses of DecisionMethodException in cramer2.rules

Methods in cramer2.rules that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	RuleReadilyHydrolysedPO4.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleHasOnlySaltSulphonateSulphate.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected) 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

Uses of DecisionMethodException in eye

Methods in eye that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	EyeIrritationRules.explainRules(IDecisionResult result, boolean verbose)

Constructors in eye that throw DecisionMethodException

Constructor and Description
EyeIrritationRules()

Uses of DecisionMethodException in eye.rules

Methods in eye.rules that throw DecisionMethodException

Modifier and Type	Method and Description
protected boolean	Rule38.acceptSubstituent(org.openscience.cdk.interfaces.IAtomContainer m)
protected int	Rule13_AliphaticMonoalcohols.countChain(org.openscience.cdk.interfaces.IAtomContainer m)
protected org.openscience.cdk.interfaces.IAtomContainerSet	Rule13_AliphaticMonoalcohols.extractChains(org.openscience.cdk.interfaces.IAtomContainer mol, List<List<Integer>> matchedAtoms)
org.openscience.cdk.interfaces.IAtomContainer	RuleAqueousSolubility_10_2.getExampleMolecule(boolean ruleResult)
org.openscience.cdk.interfaces.IAtomContainer	RuleMolWeight_12_2.getExampleMolecule(boolean ruleResult)
boolean	Rule13_AliphaticMonoalcohols.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule38.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)

Uses of DecisionMethodException in mic

Methods in mic that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	MICRules.explainRules(IDecisionResult result, boolean verbose)

Constructors in mic that throw DecisionMethodException

Constructor and Description
MICRules()

Uses of DecisionMethodException in mic.rules

Methods in mic.rules that throw DecisionMethodException

Modifier and Type	Method and Description
protected boolean	SA28.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA28ter.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA28bis.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA25.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA2.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject) Simple prescreening
protected boolean	SA27.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
boolean	SA18.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Find essential rings through SSSRFinder.findEssentialRings.
boolean	SA26.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	SA10.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)

Uses of DecisionMethodException in michaelacceptors

Methods in michaelacceptors that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	MichaelAcceptorRules.explainRules(IDecisionResult result, boolean verbose)

Constructors in michaelacceptors that throw DecisionMethodException

Constructor and Description
MichaelAcceptorRules()

Uses of DecisionMethodException in mutant

Methods in mutant that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	BB_CarcMutRules.explainRules(IDecisionResult result, boolean verbose)

Constructors in mutant that throw DecisionMethodException

Constructor and Description
BB_CarcMutRules()

Uses of DecisionMethodException in mutant.rules

Methods in mutant.rules that throw DecisionMethodException

Modifier and Type	Method and Description
protected boolean	RuleAromaticAmineNoSulfonicGroup.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA28bis_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA31a_nogen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA2_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject) Simple prescreening
protected boolean	SA28_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA28ter_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA27_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	QSAR6Applicable.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA25_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
boolean	SA20_nogen.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place) Only counts halogens directly connected to the ring and returns true always.
boolean	RuleAromaticAmineNoSulfonicGroup.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAromaticDiazo.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	SA18_gen.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Find essential rings through SSSRFinder.findEssentialRings.
boolean	SA10_gen.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleDerivedAromaticAmines.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	QSAR6Applicable.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	SA20_nogen.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Uses of DecisionMethodException in sicret

Methods in sicret that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	SicretRules.explainRules(IDecisionResult result, boolean verbose)

Constructors in sicret that throw DecisionMethodException

Constructor and Description
SicretRules()

Uses of DecisionMethodException in sicret.rules

Methods in sicret.rules that throw DecisionMethodException

Modifier and Type	Method and Description
String	RuleLogP.inputProperty(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAcidAnhydrides.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleAcrylicAndMethacrylicEsters.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleOandPQuinones.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleDi_Tri_Nitrobenzenes.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleCarbamoylHalide.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleAromaticAmines.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleTriAndTetraHalogenatedBenzenes.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleLactonesFusedOrUnsaturated.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleAcrylicAcids.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleHasOnlyC_H_O.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleHalonitrobenzene.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleCatecholsResorcinolsHydroquinones.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleC10_C20AliphaticAlcohols.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)

Uses of DecisionMethodException in toxTree.core

Methods in toxTree.core that throw DecisionMethodException

Modifier and Type	Method and Description
void	IDecisionMethod.addDecisionRule(IDecisionRule rule)
boolean	IDecisionMethod.classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
IDecisionMethod	IDecisionMethodEditor.edit(Component owner, IDecisionMethod method)
StringBuffer	IDecisionMethod.explainRules(IDecisionResult result, boolean verbose)
org.openscience.cdk.interfaces.IAtomContainer	IDecisionRule.getExampleMolecule(boolean ruleResult) 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
void	IDecisionMethod.setDecisionRule(IDecisionRule rule)
void	IDecisionRuleList.setRules(String[] customRules)
boolean	IDecisionRule.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) This is the core of a IDecisionRule behaviour.
boolean	IDecisionMethod.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
void	IDecisionMethod.walkRules(IDecisionRule rule, IProcessRule processor)

Uses of DecisionMethodException in toxtree.data

Methods in toxtree.data that throw DecisionMethodException

Modifier and Type	Method and Description
void	DecisionMethodsDataModule.viewMethod(IDecisionMethod method, boolean editable)
abstract void	DataModule.viewMethod(IDecisionMethod method, boolean editable)
void	DecisionMethodsDataModule.viewMethod(int methodIndex, boolean editable)

Uses of DecisionMethodException in toxTree.data

Methods in toxTree.data that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	IMoleculeLookup.find(org.openscience.cdk.interfaces.IAtomContainer mol)
int	IMoleculeLookup.find(Object property, Object value)

Uses of DecisionMethodException in toxTree.exceptions

Subclasses of DecisionMethodException in toxTree.exceptions

Modifier and Type	Class and Description
class	DecisionMethodIOException TODO add description
class	DesisionMethodUIDException
class	DRuleException
class	DRuleNotImplemented Thrown when a rule is not implemented.
class	DRulePropertyNotAvailable
class	XMLDecisionMethodException Thrown when processing XMLSerializable.

Uses of DecisionMethodException in toxtree.plugins.ames

Methods in toxtree.plugins.ames that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	AmesMutagenicityRules.explainRules(IDecisionResult result, boolean verbose)

Constructors in toxtree.plugins.ames that throw DecisionMethodException

Constructor and Description
AmesMutagenicityRules()

Uses of DecisionMethodException in toxtree.plugins.ames.rules

Methods in toxtree.plugins.ames.rules that throw DecisionMethodException

Modifier and Type	Method and Description
protected boolean	SA25_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA27_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	RuleAromaticAmineNoSulfonicGroup.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	QSAR6Applicable.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA28bis_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA28_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
protected boolean	SA2_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject) Simple prescreening
protected boolean	SA28ter_gen.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
boolean	RuleAromaticAmineNoSulfonicGroup.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	QSAR6Applicable.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAromaticDiazo.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	SA10_gen.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	SA18_gen.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Find essential rings through SSSRFinder.findEssentialRings.
boolean	RuleDerivedAromaticAmines.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)

Uses of DecisionMethodException in toxtree.plugins.dnabinding

Methods in toxtree.plugins.dnabinding that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	DNABindingPlugin.explainRules(IDecisionResult result, boolean verbose)

Constructors in toxtree.plugins.dnabinding that throw DecisionMethodException

Constructor and Description
DNABindingPlugin()

Uses of DecisionMethodException in toxtree.plugins.func

Methods in toxtree.plugins.func that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	FuncRules.explainRules(IDecisionResult result, boolean verbose)

Constructors in toxtree.plugins.func that throw DecisionMethodException

Constructor and Description
FuncRules()

Uses of DecisionMethodException in toxtree.plugins.kroes.rules

Methods in toxtree.plugins.kroes.rules that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	KroesRule8.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleKroesFig1Q1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)

Uses of DecisionMethodException in toxtree.plugins.moa

Constructors in toxtree.plugins.moa that throw DecisionMethodException

Constructor and Description
MOARules()

Uses of DecisionMethodException in toxtree.plugins.moa.rules

Methods in toxtree.plugins.moa.rules that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	RuleAlertsNarcosis1_1_2_1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAlertsNarcosis1_1_1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAlertsNarcosis1_1_1_1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)

Uses of DecisionMethodException in toxtree.plugins.proteinbinding

Methods in toxtree.plugins.proteinbinding that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	ProteinBindingPlugin.explainRules(IDecisionResult result, boolean verbose)

Constructors in toxtree.plugins.proteinbinding that throw DecisionMethodException

Constructor and Description
ProteinBindingPlugin()

Uses of DecisionMethodException in toxtree.plugins.search.rules

Methods in toxtree.plugins.search.rules that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	Find.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)

Uses of DecisionMethodException in toxtree.plugins.skinsensitisation

Methods in toxtree.plugins.skinsensitisation that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	SkinSensitisationPlugin.explainRules(IDecisionResult result, boolean verbose)

Constructors in toxtree.plugins.skinsensitisation that throw DecisionMethodException

Constructor and Description
SkinSensitisationPlugin()

Uses of DecisionMethodException in toxtree.plugins.smartcyp

Methods in toxtree.plugins.smartcyp that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	SMARTCYPPlugin.explainRules(IDecisionResult result, boolean verbose)

Constructors in toxtree.plugins.smartcyp that throw DecisionMethodException

Constructor and Description
SMARTCYPPlugin()

Uses of DecisionMethodException in toxtree.plugins.smartcyp.rules

Methods in toxtree.plugins.smartcyp.rules that throw DecisionMethodException

Modifier and Type	Method and Description
dk.smartcyp.core.MoleculeKU	SMARTCYPRuleRank1.calculate(org.openscience.cdk.interfaces.IAtomContainer iAtomContainerTmp)
boolean	SMARTCYPRuleRank1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) returns true if at least one atom has a score assigned
boolean	SMARTCYPRuleRank1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Uses of DecisionMethodException in toxtree.plugins.verhaar2

Constructors in toxtree.plugins.verhaar2 that throw DecisionMethodException

Constructor and Description
VerhaarScheme2()
VerhaarScheme2(boolean reversed)

Uses of DecisionMethodException in toxTree.qsar

Methods in toxTree.qsar that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	LinearDiscriminantRule.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)

Uses of DecisionMethodException in toxTree.tree

Methods in toxTree.tree that throw DecisionMethodException

Modifier and Type	Method and Description
void	AbstractTree.addDecisionRule(IDecisionRule rule)
void	BatchDecisionResultsList.addDecisionRule(IDecisionRule rule)
boolean	AbstractTree.classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
boolean	BatchDecisionResultsList.classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
DecisionNodesList	DecisionNodesFactory.createNodesList(IDecisionCategories classes, String[] customRules, int[][] customTransitions)
DecisionNodesList	IDecisionNodesFactory.createNodesList(IDecisionCategories classes, String[] customRules, int[][] customTransitions)
static IDecisionRule	AbstractRule.createRule(String className)
StringBuffer	AbstractTree.explainRules(IDecisionResult result, boolean verbose)
StringBuffer	BatchDecisionResultsList.explainRules(IDecisionResult result, boolean verbose)
org.openscience.cdk.interfaces.IAtomContainer	DecisionNode.getExampleMolecule(boolean ruleResult)
org.openscience.cdk.interfaces.IAtomContainer	AbstractRule.getExampleMolecule(boolean ruleResult)
static org.openscience.cdk.interfaces.IAtomContainer	AbstractRule.makeMolecule(boolean yes) This is to ensure each derived class will provide an example of a molecule which resolves to the yes and no rule outcome
void	AbstractTree.setDecisionRule(IDecisionRule rule)
void	BatchDecisionResultsList.setDecisionRule(IDecisionRule rule)
void	RulesList.setRules(String[] customRules) 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
protected void	AbstractTree.setRules(String[] customRules)
protected boolean	AbstractTree.verifyResidues(org.openscience.cdk.interfaces.IAtomContainerSet mols, IDecisionResult result, IDecisionRule rule)
boolean	DecisionNode.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
abstract boolean	AbstractRuleHilightHits.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	AbstractTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result) IDecisionRule.verifyRule(IAtomContainer)
boolean	BatchDecisionResultsList.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
protected abstract boolean	AbstractTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result, IDecisionRule rule) abstract method, to be implemented in the child class
protected boolean	UserDefinedTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result, IDecisionRule topRule)
prefuse.data.Node	Tree2PrefuseGraph.walkRules(IDecisionMethod tree)
protected prefuse.data.Node	Tree2PrefuseGraph.walkRules(IDecisionMethod tree, IDecisionRule rule, ArrayList<Integer> visited)
protected void	AbstractTree.walkRules(IDecisionRule rule, ArrayList<Integer> visited, IProcessRule processor)
void	AbstractTree.walkRules(IDecisionRule rule, IProcessRule processor)
void	BatchDecisionResultsList.walkRules(IDecisionRule rule, IProcessRule processor)

Constructors in toxTree.tree that throw DecisionMethodException

Constructor and Description
RulesList(String[] customRules) 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
UserDefinedTree(IDecisionCategories classes, String[] customRules, int[][] customTransitions, IDecisionNodesFactory nodesFactory)

Uses of DecisionMethodException in toxTree.tree.cramer

Methods in toxTree.tree.cramer that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	CramerRules.explainRules(IDecisionResult result, boolean verbose)
protected org.openscience.cdk.interfaces.IRingSet	RuleMonocarbocyclic.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IRingSet	RuleSomeBenzeneDerivatives.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IRingSet	RuleCyclopropaneEtc.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleHasOtherThanC_H_O_N_S2.oldVerifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleOnlyFuncGroupsQ30.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleRingComplexSubstituents30.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleHeterocyclicComplexSubstituents.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleSomeBenzeneDerivatives.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleLactonesFusedOrUnsaturated.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	Rule32.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule3FuncGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleSufficientSulphonateGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer molecule) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleMonocycloalkanoneEtc.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleOnlyFuncGroupsQ30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule3MemberedHeterocycle.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleLactoneOrCyclicDiester.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleRingComplexSubstituents30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleToxicFunctionalGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleHasOtherThanC_H_O_N_S2.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Verifies the rule.
boolean	RuleSimplyBranchedAliphaticHydrocarbon.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleMonocarbocyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleHasOnlySaltSulphonateSulphate.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) 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
boolean	RuleReadilyHydrolysedMononuclear.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAliphaticWithSomeFuncGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleSomeBenzeneDerivatives.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleReadilyHydrolysedToCommonterpene.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleHeteroaromatic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleKetoneAlcoholEtc.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleAcyclicAcetalEsterOfQ30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule3FuncGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleMonocycloalkanoneEtc.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selector)
boolean	RuleOnlyFuncGroupsQ30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleRingComplexSubstituents30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleToxicFunctionalGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleHasOtherThanC_H_O_N_S2.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleHeterocyclicComplexSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleMonocarbocyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleHasOnlySaltSulphonateSulphate.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleAliphaticWithSomeFuncGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleAcyclicAcetalEsterOfQ30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Constructors in toxTree.tree.cramer that throw DecisionMethodException

Constructor and Description
CramerRules()

Uses of DecisionMethodException in toxtree.tree.cramer3

Methods in toxtree.tree.cramer3 that throw DecisionMethodException

Modifier and Type	Method and Description
StringBuffer	RevisedCramerDecisionTree.explainRules(IDecisionResult result, boolean verbose)

Constructors in toxtree.tree.cramer3 that throw DecisionMethodException

Constructor and Description
RevisedCramerDecisionTree()
RevisedCramerDecisionTree(TreeSpecification spec)
TreeSpecification()

Uses of DecisionMethodException in toxtree.tree.cramer3.rules

Methods in toxtree.tree.cramer3.rules that throw DecisionMethodException

Modifier and Type	Method and Description
protected boolean	RuleQ9_C.extraTest(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
protected boolean	RuleSMARTSSubstructureHydrolysis.extraTest(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected) Allows to apply non-SMART based tests
protected boolean	RuleQ9_D.extraTest(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
protected boolean	RuleLactone.isFused(org.openscience.cdk.interfaces.IAtomContainer mol, String tag_ring, org.openscience.cdk.interfaces.IRingSet rings) if we have fused rings, the tag_ring will appear in more than one ring
boolean	RuleRingsSMARTSSubstituents.processRings(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ14_B.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleQ14_A.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleQ26.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleQ11.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleQ25.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
abstract boolean	RuleRingsSMARTSSubstituents.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
Map<String,Integer>	RuleSMARTSSubstructureTagged.tagAtoms(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected, Map<String,ambit2.smarts.query.ISmartsPattern<org.openscience.cdk.interfaces.IAtomContainer>> smartsPatterns)
protected org.openscience.cdk.interfaces.IRingSet	RuleLactone.tagRings(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ22.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ17.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ2.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ21.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ16.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ5.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ28.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleSMARTSSubstructureHydrolysis.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ6.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleQ14_B.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ15.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ18_JM.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ3.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ20.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ14_A.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ21.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleLactone.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ16.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ26.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ11.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ4.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ28.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleSMARTSSubstructureHydrolysis.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ25.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ29.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ6.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleQ4A.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer arg1)
protected boolean	RuleQ6.verifyTerpene(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected, int c, int h)

Uses of DecisionMethodException in toxTree.tree.demo

Constructors in toxTree.tree.demo that throw DecisionMethodException

Constructor and Description
SMARTSTree()
SubstructureTree()

Uses of DecisionMethodException in toxTree.tree.rules

Methods in toxTree.tree.rules that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	LookupFile.find(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	ILookupFile.find(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	InChILookupFile.find(org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainer	RuleVerifyProperty.getExampleMolecule(boolean ruleResult)
protected org.openscience.cdk.interfaces.IRingSet	RuleRings.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
String	RuleVerifyProperty.inputProperty(org.openscience.cdk.interfaces.IAtomContainer mol)
org.openscience.cdk.interfaces.IAtomContainer	LookupFile.lookup(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleRingAllowedSubstituents.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
abstract boolean	RuleRingSubstituents.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place) returns true if the substituent is allowed and false if it is forbidden to be implemented by the inheriting class
boolean	StructureAlertAmbit.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleStructuresList.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleCommonTerpene.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleVerifyProperty.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleElements.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAnySubstructure.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleRingAllowedSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAnySubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleManyAromaticRings.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	StructureAlert.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	StructureAlertCDK.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleReadilyHydrolised.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Returns true if the compound is readily hydrolised Sets MolFlags hydrolysis products (to be used further )
boolean	RuleAllSubstructures.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) returns true if all of the fragments are a substructure of mol IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleVerifyAlertsCounter.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleRingSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleHeterocyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleOpenChain.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleOnlyAllowedSubstructures.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleLipinski5.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Returns true if all Lipinski Rule of Five are true
boolean	RuleAromatic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleCarbohydrate.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	RuleRingOtherThanAllowedSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleInitAlertCounter.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) Assings value returned by RuleVerifyProperty.getProperty() to molecule property with name given by RuleVerifyProperty.getPropertyName().
boolean	RuleDescriptorRange.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	UserInputRule.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleStructuresList.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleCommonTerpene.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleElements.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleAnySubstructure.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleRingAllowedSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected) returns true if only allowed substituents are found
boolean	RuleReadilyHydrolised.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleRingSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleSubstructures.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleOnlyAllowedSubstructures.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleCarbohydrate.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleRingOtherThanAllowedSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleDescriptor.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Uses of DecisionMethodException in toxTree.tree.rules.smarts

Methods in toxTree.tree.rules.smarts that throw DecisionMethodException

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IRingSet	RuleSMARTSSubstructureAmbit.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
protected boolean	AbstractRuleSmartSubstructure.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, T processedObject) Returns true always.
boolean	RuleSMARTSubstructureCDK.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	AbstractRuleSmartSubstructure.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	AbstractRuleSmartSubstructure.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Uses of DecisionMethodException in toxtree.ui.tree

Methods in toxtree.ui.tree that throw DecisionMethodException

Modifier and Type	Method and Description
IDecisionMethod	TreeEditorPanel.edit(Component owner, IDecisionMethod method)

Uses of DecisionMethodException in toxtree.ui.tree.actions

Methods in toxtree.ui.tree.actions that throw DecisionMethodException

Modifier and Type	Method and Description
static DecisionMethodsList	NewRuleAction.forestFromTree(IDecisionMethod tree) Creates forest of trees, each tree consists of a single rule.
static IDecisionMethod	NewRuleAction.treeFromRule(IDecisionRule rule)

Uses of DecisionMethodException in verhaar

Constructors in verhaar that throw DecisionMethodException

Constructor and Description
VerhaarScheme()
VerhaarScheme(boolean reversed)

Uses of DecisionMethodException in verhaar.rules

Methods in verhaar.rules that throw DecisionMethodException

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IRingSet	Rule144.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IRingSet	Rule142.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
protected org.openscience.cdk.interfaces.IRingSet	Rule143.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule21.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	Rule143.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
boolean	RuleLogPRange.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule03.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule152.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule153.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule23.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleIonicGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule151.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule21.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule161.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule11.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule141.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule154.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule24.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule142.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule143.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	Rule152.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	Rule23.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	Rule171.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	RuleIonicGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	Rule21.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	Rule161.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
boolean	Rule24.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)

Uses of DecisionMethodException in verhaar.rules.helper

Methods in verhaar.rules.helper that throw DecisionMethodException

Modifier and Type	Method and Description
boolean	RuleOnlyAllowedSubstructuresCounter.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleElementsCounter.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
boolean	RuleAnySubstructureCounter.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)