Uses of Class
toxTree.exceptions.DecisionMethodException

Packages that use DecisionMethodException
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.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.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
 java.lang.StringBuffer BiodgeradationRules.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in com.molecularnetworks.start that throw DecisionMethodException
BiodgeradationRules()
           
 

Uses of DecisionMethodException in com.molecularnetworks.start.rules
 

Methods in com.molecularnetworks.start.rules that throw DecisionMethodException
 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.
 boolean RuleTwoHalogensOnUnbranchedNonCyclic.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 RuleOneHalogenOnUnbranched.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          Overrides the default IDecisionRule behaviour.
 boolean RuleMoreThanTwoHydroxyOnAromaticRing.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          Overrides the default IDecisionRule behaviour.
 

Uses of DecisionMethodException in cramer2
 

Methods in cramer2 that throw DecisionMethodException
 java.lang.StringBuffer CramerRulesWithExtensions.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in cramer2 that throw DecisionMethodException
CramerRulesWithExtensions()
           
 

Uses of DecisionMethodException in cramer2.rules
 

Methods in cramer2.rules that throw DecisionMethodException
 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
 java.lang.StringBuffer EyeIrritationRules.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in eye that throw DecisionMethodException
EyeIrritationRules()
           
 

Uses of DecisionMethodException in eye.rules
 

Methods in eye.rules that throw DecisionMethodException
protected  boolean Rule38.acceptSubstituent(org.openscience.cdk.interfaces.IMolecule m)
           
protected  int Rule13_AliphaticMonoalcohols.countChain(org.openscience.cdk.interfaces.IMolecule m)
           
protected  org.openscience.cdk.interfaces.IMoleculeSet Rule13_AliphaticMonoalcohols.extractChains(org.openscience.cdk.interfaces.IAtomContainer mol, java.util.List<java.util.List<java.lang.Integer>> matchedAtoms)
           
 org.openscience.cdk.interfaces.IMolecule RuleMolWeight_12_2.getExampleMolecule(boolean ruleResult)
           
 org.openscience.cdk.interfaces.IMolecule RuleAqueousSolubility_10_2.getExampleMolecule(boolean ruleResult)
           
 boolean Rule38.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule13_AliphaticMonoalcohols.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 

Uses of DecisionMethodException in mic
 

Methods in mic that throw DecisionMethodException
 java.lang.StringBuffer MICRules.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in mic that throw DecisionMethodException
MICRules()
           
 

Uses of DecisionMethodException in mic.rules
 

Methods in mic.rules that throw DecisionMethodException
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 SA28.isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer processedObject)
           
protected  boolean SA27.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
 boolean SA26.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean SA18.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          Find essential rings through SSSRFinder.findEssentialRings.
 boolean SA10.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 

Uses of DecisionMethodException in michaelacceptors
 

Methods in michaelacceptors that throw DecisionMethodException
 java.lang.StringBuffer MichaelAcceptorRules.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in michaelacceptors that throw DecisionMethodException
MichaelAcceptorRules()
           
 

Uses of DecisionMethodException in mutant
 

Methods in mutant that throw DecisionMethodException
 java.lang.StringBuffer BB_CarcMutRules.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in mutant that throw DecisionMethodException
BB_CarcMutRules()
           
 

Uses of DecisionMethodException in mutant.rules
 

Methods in mutant.rules that throw DecisionMethodException
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 SA28bis_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 SA25_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)
           
 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 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 RuleAromaticDiazo.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleAromaticAmineNoSulfonicGroup.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
 java.lang.StringBuffer SicretRules.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in sicret that throw DecisionMethodException
SicretRules()
           
 

Uses of DecisionMethodException in sicret.rules
 

Methods in sicret.rules that throw DecisionMethodException
 java.lang.String RuleLogP.inputProperty(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleTriAndTetraHalogenatedBenzenes.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleQuaternaryOrganicAmmoniumAndPhosphoniumSalts.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleOandPQuinones.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleLactonesFusedOrUnsaturated.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 RuleDi_Tri_Nitrobenzenes.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleCatecholsResorcinolsHydroquinones.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleCarbamoylHalide.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleC10_C20AliphaticAlcohols.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleAromaticAmines.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleAcrylicAndMethacrylicEsters.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleAcrylicAcids.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleAcidAnhydrides.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 

Uses of DecisionMethodException in toxTree.core
 

Methods in toxTree.core that throw DecisionMethodException
 void IDecisionMethod.addDecisionRule(IDecisionRule rule)
           
 boolean IDecisionMethod.classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
           
 IDecisionMethod IDecisionMethodEditor.edit(java.awt.Component owner, IDecisionMethod method)
           
 java.lang.StringBuffer IDecisionMethod.explainRules(IDecisionResult result, boolean verbose)
           
 org.openscience.cdk.interfaces.IMolecule 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(java.lang.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
 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
 boolean IMoleculeLookup.find(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 int IMoleculeLookup.find(java.lang.Object property, java.lang.Object value)
           
 

Uses of DecisionMethodException in toxTree.exceptions
 

Subclasses of DecisionMethodException in toxTree.exceptions
 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.dnabinding
 

Methods in toxtree.plugins.dnabinding that throw DecisionMethodException
 java.lang.StringBuffer DNABindingPlugin.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in toxtree.plugins.dnabinding that throw DecisionMethodException
DNABindingPlugin()
           
 

Uses of DecisionMethodException in toxtree.plugins.func
 

Methods in toxtree.plugins.func that throw DecisionMethodException
 java.lang.StringBuffer FuncRules.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in toxtree.plugins.func that throw DecisionMethodException
FuncRules()
           
 

Uses of DecisionMethodException in toxtree.plugins.kroes.rules
 

Methods in toxtree.plugins.kroes.rules that throw DecisionMethodException
 boolean RuleKroesFig1Q1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean KroesRule8.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 

Uses of DecisionMethodException in toxtree.plugins.moa
 

Constructors in toxtree.plugins.moa that throw DecisionMethodException
MOARules()
           
 

Uses of DecisionMethodException in toxtree.plugins.moa.rules
 

Methods in toxtree.plugins.moa.rules that throw DecisionMethodException
 boolean RuleAlertsNarcosis1_1_2_1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleAlertsNarcosis1_1_1_1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleAlertsNarcosis1_1_1.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 

Uses of DecisionMethodException in toxtree.plugins.proteinbinding
 

Methods in toxtree.plugins.proteinbinding that throw DecisionMethodException
 java.lang.StringBuffer ProteinBindingPlugin.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in toxtree.plugins.proteinbinding that throw DecisionMethodException
ProteinBindingPlugin()
           
 

Uses of DecisionMethodException in toxtree.plugins.search.rules
 

Methods in toxtree.plugins.search.rules that throw DecisionMethodException
 boolean Find.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 

Uses of DecisionMethodException in toxtree.plugins.skinsensitisation
 

Methods in toxtree.plugins.skinsensitisation that throw DecisionMethodException
 java.lang.StringBuffer SkinSensitisationPlugin.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in toxtree.plugins.skinsensitisation that throw DecisionMethodException
SkinSensitisationPlugin()
           
 

Uses of DecisionMethodException in toxtree.plugins.smartcyp
 

Methods in toxtree.plugins.smartcyp that throw DecisionMethodException
 java.lang.StringBuffer SMARTCYPPlugin.explainRules(IDecisionResult result, boolean verbose)
           
 

Constructors in toxtree.plugins.smartcyp that throw DecisionMethodException
SMARTCYPPlugin()
           
 

Uses of DecisionMethodException in toxtree.plugins.smartcyp.rules
 

Methods in toxtree.plugins.smartcyp.rules that throw DecisionMethodException
 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
VerhaarScheme2()
           
VerhaarScheme2(boolean reversed)
           
 

Uses of DecisionMethodException in toxTree.qsar
 

Methods in toxTree.qsar that throw DecisionMethodException
 boolean LinearDiscriminantRule.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 

Uses of DecisionMethodException in toxTree.tree
 

Methods in toxTree.tree that throw DecisionMethodException
 void BatchDecisionResultsList.addDecisionRule(IDecisionRule rule)
           
 void AbstractTree.addDecisionRule(IDecisionRule rule)
           
 boolean BatchDecisionResultsList.classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
           
 boolean AbstractTree.classify(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
           
 DecisionNodesList IDecisionNodesFactory.createNodesList(IDecisionCategories classes, java.lang.String[] customRules, int[][] customTransitions)
           
 DecisionNodesList DecisionNodesFactory.createNodesList(IDecisionCategories classes, java.lang.String[] customRules, int[][] customTransitions)
           
static IDecisionRule AbstractRule.createRule(java.lang.String className)
           
 java.lang.StringBuffer BatchDecisionResultsList.explainRules(IDecisionResult result, boolean verbose)
           
 java.lang.StringBuffer AbstractTree.explainRules(IDecisionResult result, boolean verbose)
           
 org.openscience.cdk.interfaces.IMolecule DecisionNode.getExampleMolecule(boolean ruleResult)
           
 org.openscience.cdk.interfaces.IMolecule AbstractRule.getExampleMolecule(boolean ruleResult)
           
static org.openscience.cdk.interfaces.IMolecule 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 BatchDecisionResultsList.setDecisionRule(IDecisionRule rule)
           
 void AbstractTree.setDecisionRule(IDecisionRule rule)
           
 void RulesList.setRules(java.lang.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(java.lang.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 BatchDecisionResultsList.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
           
 boolean AbstractTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result)
          IDecisionRule.verifyRule(IAtomContainer)
protected  boolean UserDefinedTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result, IDecisionRule topRule)
           
protected abstract  boolean AbstractTree.verifyRules(org.openscience.cdk.interfaces.IAtomContainer mol, IDecisionResult result, IDecisionRule rule)
          abstract method, to be implemented in the child class
 prefuse.data.Node Tree2PrefuseGraph.walkRules(IDecisionMethod tree)
           
protected  prefuse.data.Node Tree2PrefuseGraph.walkRules(IDecisionMethod tree, IDecisionRule rule, java.util.ArrayList<java.lang.Integer> visited)
           
protected  void AbstractTree.walkRules(IDecisionRule rule, java.util.ArrayList<java.lang.Integer> visited, IProcessRule processor)
           
 void BatchDecisionResultsList.walkRules(IDecisionRule rule, IProcessRule processor)
           
 void AbstractTree.walkRules(IDecisionRule rule, IProcessRule processor)
           
 

Constructors in toxTree.tree that throw DecisionMethodException
RulesList(java.lang.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, java.lang.String[] customRules, int[][] customTransitions, IDecisionNodesFactory nodesFactory)
           
 

Uses of DecisionMethodException in toxTree.tree.cramer
 

Methods in toxTree.tree.cramer that throw DecisionMethodException
 java.lang.StringBuffer CramerRules.explainRules(IDecisionResult result, boolean verbose)
           
protected  org.openscience.cdk.interfaces.IRingSet RuleSomeBenzeneDerivatives.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
           
protected  org.openscience.cdk.interfaces.IRingSet RuleMonocarbocyclic.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 RuleSomeBenzeneDerivatives.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
           
 boolean RuleRingComplexSubstituents30.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
           
 boolean RuleOnlyFuncGroupsQ30.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
           
 boolean RuleHeterocyclicComplexSubstituents.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
           
 boolean RuleToxicFunctionalGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleSufficientSulphonateGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer molecule)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleSomeBenzeneDerivatives.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleSimplyBranchedAliphaticHydrocarbon.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleRingComplexSubstituents30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleReadilyHydrolysedToCommonterpene.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleReadilyHydrolysedMononuclear.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleOnlyFuncGroupsQ30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleMonocycloalkanoneEtc.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleMonocarbocyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleLactonesFusedOrUnsaturated.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleLactoneOrCyclicDiester.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleKetoneAlcoholEtc.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleHeteroaromatic.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 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 RuleAliphaticWithSomeFuncGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleAcyclicAcetalEsterOfQ30.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule3MemberedHeterocycle.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean Rule3FuncGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean Rule32.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleToxicFunctionalGroups.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 RuleOnlyFuncGroupsQ30.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 RuleMonocarbocyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IAtomContainer selected)
           
 boolean RuleHeterocyclicComplexSubstituents.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 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)
           
 boolean Rule3FuncGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
           
 

Constructors in toxTree.tree.cramer that throw DecisionMethodException
CramerRules()
           
 

Uses of DecisionMethodException in toxTree.tree.demo
 

Constructors in toxTree.tree.demo that throw DecisionMethodException
SMARTSTree()
           
SubstructureTree()
           
 

Uses of DecisionMethodException in toxTree.tree.rules
 

Methods in toxTree.tree.rules that throw DecisionMethodException
 boolean LookupFile.find(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean InChILookupFile.find(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean ILookupFile.find(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 org.openscience.cdk.interfaces.IMolecule RuleVerifyProperty.getExampleMolecule(boolean ruleResult)
           
protected  org.openscience.cdk.interfaces.IRingSet RuleRings.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 java.lang.String RuleVerifyProperty.inputProperty(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 org.openscience.cdk.interfaces.IAtomContainer LookupFile.lookup(org.openscience.cdk.interfaces.IAtomContainer mol)
           
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 RuleRingAllowedSubstituents.substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place)
           
 boolean UserInputRule.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean StructureAlertCDK.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean StructureAlertAmbit.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean StructureAlert.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleVerifyProperty.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleVerifyAlertsCounter.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleStructuresList.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleRingSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleRingOtherThanAllowedSubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          return true if other than listed substructures are found in a ring substituent
 boolean RuleRingAllowedSubstituents.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 RuleOpenChain.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleOnlyAllowedSubstructures.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleManyAromaticRings.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 RuleInitAlertCounter.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          Assings value returned by RuleVerifyProperty.getProperty() to molecule property with name given by RuleVerifyProperty.getPropertyName().
 boolean RuleHeterocyclic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleElements.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleDescriptorRange.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleCommonTerpene.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleCarbohydrate.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleAromatic.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleAnySubstructure.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 boolean RuleAnySubstituents.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
          IDecisionRule.verifyRule(IAtomContainer)
 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 RuleSubstructures.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected)
           
 boolean RuleStructuresList.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 RuleRingOtherThanAllowedSubstituents.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 RuleOnlyAllowedSubstructures.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 RuleDescriptor.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 RuleCarbohydrate.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)
           
 

Uses of DecisionMethodException in toxTree.tree.rules.smarts
 

Methods in toxTree.tree.rules.smarts that throw DecisionMethodException
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
 IDecisionMethod TreeEditorPanel.edit(java.awt.Component owner, IDecisionMethod method)
           
 

Uses of DecisionMethodException in toxtree.ui.tree.actions
 

Methods in toxtree.ui.tree.actions that throw DecisionMethodException
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
VerhaarScheme()
           
VerhaarScheme(boolean reversed)
           
 

Uses of DecisionMethodException in verhaar.rules
 

Methods in verhaar.rules that throw DecisionMethodException
protected  org.openscience.cdk.interfaces.IRingSet Rule144.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
           
protected  org.openscience.cdk.interfaces.IRingSet Rule143.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
           
protected  org.openscience.cdk.interfaces.IRingSet Rule142.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 RuleIonicGroups.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule24.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule23.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 Rule154.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule153.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule152.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule151.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule143.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule142.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule141.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule11.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean Rule03.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
           
 boolean RuleIonicGroups.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)
           
 boolean Rule23.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 Rule171.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 Rule152.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
 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)
           
 



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