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PREV NEXT | FRAMES NO FRAMES |
Packages that use DecisionMethodException | |
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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 |
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Methods in com.molecularnetworks.start that throw DecisionMethodException | |
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java.lang.StringBuffer |
BiodgeradationRules.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in com.molecularnetworks.start that throw DecisionMethodException | |
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BiodgeradationRules()
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Uses of DecisionMethodException in com.molecularnetworks.start.rules |
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Methods in com.molecularnetworks.start.rules that throw DecisionMethodException | |
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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 |
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Methods in cramer2 that throw DecisionMethodException | |
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java.lang.StringBuffer |
CramerRulesWithExtensions.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in cramer2 that throw DecisionMethodException | |
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CramerRulesWithExtensions()
|
Uses of DecisionMethodException in cramer2.rules |
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Methods in cramer2.rules that throw DecisionMethodException | |
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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 |
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Methods in eye that throw DecisionMethodException | |
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java.lang.StringBuffer |
EyeIrritationRules.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in eye that throw DecisionMethodException | |
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EyeIrritationRules()
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Uses of DecisionMethodException in eye.rules |
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Methods in eye.rules that throw DecisionMethodException | |
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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 |
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Methods in mic that throw DecisionMethodException | |
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java.lang.StringBuffer |
MICRules.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in mic that throw DecisionMethodException | |
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MICRules()
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Uses of DecisionMethodException in mic.rules |
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Methods in mic.rules that throw DecisionMethodException | |
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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 |
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Methods in michaelacceptors that throw DecisionMethodException | |
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java.lang.StringBuffer |
MichaelAcceptorRules.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in michaelacceptors that throw DecisionMethodException | |
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MichaelAcceptorRules()
|
Uses of DecisionMethodException in mutant |
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Methods in mutant that throw DecisionMethodException | |
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java.lang.StringBuffer |
BB_CarcMutRules.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in mutant that throw DecisionMethodException | |
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BB_CarcMutRules()
|
Uses of DecisionMethodException in mutant.rules |
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Methods in mutant.rules that throw DecisionMethodException | |
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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 |
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Methods in sicret that throw DecisionMethodException | |
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java.lang.StringBuffer |
SicretRules.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in sicret that throw DecisionMethodException | |
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SicretRules()
|
Uses of DecisionMethodException in sicret.rules |
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Methods in sicret.rules that throw DecisionMethodException | |
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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 |
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Methods in toxTree.core that throw DecisionMethodException | |
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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 |
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Methods in toxtree.data that throw DecisionMethodException | |
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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 |
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Methods in toxTree.data that throw DecisionMethodException | |
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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 |
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Subclasses of DecisionMethodException in toxTree.exceptions | |
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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 |
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Methods in toxtree.plugins.dnabinding that throw DecisionMethodException | |
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java.lang.StringBuffer |
DNABindingPlugin.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in toxtree.plugins.dnabinding that throw DecisionMethodException | |
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DNABindingPlugin()
|
Uses of DecisionMethodException in toxtree.plugins.func |
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Methods in toxtree.plugins.func that throw DecisionMethodException | |
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java.lang.StringBuffer |
FuncRules.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in toxtree.plugins.func that throw DecisionMethodException | |
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FuncRules()
|
Uses of DecisionMethodException in toxtree.plugins.kroes.rules |
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Methods in toxtree.plugins.kroes.rules that throw DecisionMethodException | |
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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 |
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Constructors in toxtree.plugins.moa that throw DecisionMethodException | |
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MOARules()
|
Uses of DecisionMethodException in toxtree.plugins.moa.rules |
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Methods in toxtree.plugins.moa.rules that throw DecisionMethodException | |
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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 |
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Methods in toxtree.plugins.proteinbinding that throw DecisionMethodException | |
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java.lang.StringBuffer |
ProteinBindingPlugin.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in toxtree.plugins.proteinbinding that throw DecisionMethodException | |
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ProteinBindingPlugin()
|
Uses of DecisionMethodException in toxtree.plugins.search.rules |
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Methods in toxtree.plugins.search.rules that throw DecisionMethodException | |
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boolean |
Find.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
|
Uses of DecisionMethodException in toxtree.plugins.skinsensitisation |
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Methods in toxtree.plugins.skinsensitisation that throw DecisionMethodException | |
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java.lang.StringBuffer |
SkinSensitisationPlugin.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in toxtree.plugins.skinsensitisation that throw DecisionMethodException | |
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SkinSensitisationPlugin()
|
Uses of DecisionMethodException in toxtree.plugins.smartcyp |
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Methods in toxtree.plugins.smartcyp that throw DecisionMethodException | |
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java.lang.StringBuffer |
SMARTCYPPlugin.explainRules(IDecisionResult result,
boolean verbose)
|
Constructors in toxtree.plugins.smartcyp that throw DecisionMethodException | |
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SMARTCYPPlugin()
|
Uses of DecisionMethodException in toxtree.plugins.smartcyp.rules |
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Methods in toxtree.plugins.smartcyp.rules that throw DecisionMethodException | |
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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 |
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Constructors in toxtree.plugins.verhaar2 that throw DecisionMethodException | |
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VerhaarScheme2()
|
|
VerhaarScheme2(boolean reversed)
|
Uses of DecisionMethodException in toxTree.qsar |
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Methods in toxTree.qsar that throw DecisionMethodException | |
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boolean |
LinearDiscriminantRule.verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
|
Uses of DecisionMethodException in toxTree.tree |
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Methods in toxTree.tree that throw DecisionMethodException | |
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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 | |
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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 |
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Methods in toxTree.tree.cramer that throw DecisionMethodException | |
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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 | |
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CramerRules()
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Uses of DecisionMethodException in toxTree.tree.demo |
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Constructors in toxTree.tree.demo that throw DecisionMethodException | |
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SMARTSTree()
|
|
SubstructureTree()
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Uses of DecisionMethodException in toxTree.tree.rules |
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Methods in toxTree.tree.rules that throw DecisionMethodException | |
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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)
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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 |
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Methods in toxTree.tree.rules.smarts that throw DecisionMethodException | |
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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 |
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Methods in toxtree.ui.tree that throw DecisionMethodException | |
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IDecisionMethod |
TreeEditorPanel.edit(java.awt.Component owner,
IDecisionMethod method)
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Uses of DecisionMethodException in toxtree.ui.tree.actions |
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Methods in toxtree.ui.tree.actions that throw DecisionMethodException | |
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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 |
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Constructors in verhaar that throw DecisionMethodException | |
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VerhaarScheme()
|
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VerhaarScheme(boolean reversed)
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Uses of DecisionMethodException in verhaar.rules |
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Methods in verhaar.rules that throw DecisionMethodException | |
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protected org.openscience.cdk.interfaces.IRingSet |
Rule144.hasRingsToProcess(org.openscience.cdk.interfaces.IAtomContainer mol)
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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 |
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Methods in verhaar.rules.helper that throw DecisionMethodException | |
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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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