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IDecisionRule
interface.AbstractAction
descendant , performing an action on a preset IDecisionRule
IDecisionMethod
interface.AbstractAction
descendant, performing an action on a preset IDecisionMethod
IDecisionRule
otherwise returns false
IDecisionRule
AbstractAction
Used in toxTree.ui
Launches a dialog with a list of all available categories IDecisionCategory
and adds the selected one to the listIDecisionRule
AtomContainer
to the rule
AromaticQueryBond
is fixedorg.openscience.cdk.interfaces.Molecule
obtained by
getProperties()IBatchProcessing
DecisionResultsList
as IDecisionMethod
.IBatchProcessing
object by a config file.IBatchProcessing
Exception
to be used in IBatchProcessing
IDecisionCategory
AbstractTableModel
descendant used in CategoriesPanel
EyeIrritationRules
are not able to estimate eye irritation or corrosive potential.SicretRules
are not able to estimate skin irritation or corrosive potential.FunctionalGroups.markMaps(IAtomContainer, IAtomContainer, List)
method
JPanel
descendant, displaying 2D structure diagram of the molecule at the bottom
and a table with molecule properties read by org.openscience.cdk.interfaces.Molecule#getProperties()
IDecisionRule.verifyRule(IAtomContainer)
CramerRules
is the implementation of Cramer rules [Cramer et al,78].DefaultCategory
descendant, implementation of
Cramer class 1 (see cramer2.CramerRulesExtendedExtended
)DefaultCategory
descendant, implementation of
Cramer class 1 (see CramerRules
)DefaultCategory
descendant, implementation of
Cramer class 2 (see cramer2.CramerRulesExtendedExtended
)DefaultCategory
descendant, implementation of
Cramer class 2 (see CramerRules
)DefaultCategory
descendant, implementation of
Cramer class 3 (see cramer2.CramerRulesExtendedExtended
)DefaultCategory
descendant, implementation of
Cramer class 3 (see CramerRules
)UserDefinedTree
descendant, implementing
the decision tree described in "Cramer G.UserDefinedTree
descendant, implementing
the decision tree described in "Cramer G.TreeResult
, to be used by cramer2.CramerRulesExtendedExtended
.TreeResult
, to be used by CramerRules
.ChemObjectWriter
ToxTreeModule
MoleculesIterator
and TTLogger
IDecisionMethod
DecisionResultsList
.UserDefinedTree
.DecisionNode
.DecisionNode
, implementing IDecisionRuleList
.DecisionNodesList
TreeModel
IDecisionCategory
interfaceFunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer)
procedure to work,
as the bond to break is the one with one atom having the property set, while the other has the property unset
IDecisionRuleEditor
of a preset rule.EstimateAction
SicretRules
is the implementation of BfR rules for estimating skin irritation and corrosion potential.IDecisionCategory
categories for
EyeIrritationRules
decision tree.IDecisionRule
rules for SicretRules
decision tree.VerhaarScheme
.ToxTreeApp
extension mechanism.
IDecisionMethodEditor
.
IDecisionRuleEditor
.
IDecisionRule.getEditor()
Tools.getFileFromResource(String)
but hides the exception
IDecisionRule
AtomContainer
at a given rules
ArrayList
of AtomContainer
defined for the rule
AbstractTableModel
for Hashtable
.ToxTreeApp
main screen.IDecisionCategory
instancesIDecisionMethod
results in assigning a category to the query chemical.IDecisionMethod
instancesIDecisionMethod
.IDecisionMethod
.IDecisionRule
should provides an editor, which is a class,
implementing this interface.IDecisionRule
IDecisionRule
in a decision tree IDecisionMethod
.Introspection
TreeLayout
in a JComponent
.LinearQSARModel
and returns true if LinearQSARModel.predict(IAtomContainer)
is >= LinearDiscriminantRule.getThreshold()
and false otherwise.org.openscience.cdk.interfaces.SetOfAtomContainers
interface
as a List
ListTableModel
.rows
* cols
components of parent
in
a grid.
rows
* cols
components of parent
in
a grid.
SmilesEntryPanel
entered by structure diagram editor toxTree.ui.molecule.JChemPaintDialog
UserDefinedTree
and launches toxTree.ui.tree.EditTreeFrame
DataModule.getDataContainer()
IteratingChemObjectReader
QueryAtomContainers
.ToxTreeApp
Rule141
.Rule141
.Rule15
but not alpha-, beta- halogen substituted compounds.CramerRules
)CramerRules
)CramerRules
)CramerRules
)RuleAqueousSolubility.AqueousSolubility
).CramerRules
)CramerRules
)cramer2.CramerRulesExtendedExtended
)CramerRules
)CramerRules
)CramerRules
)CramerRules
)QueryAssociationBond
ro verify if the query compound
has an ionic bond.CramerRules
)
Note this is descendant of RuleAromatic
and therefore
follows the Hueckel rule, rather than verifying for the presence of
benzene, furan, thiophene, pyridine or pyrrole ringCramerRules
)
Verifies if the substance is a terpeneCramerRules
)CramerRules
)CramerRules
)CramerRules
)CramerRules
)RuleLogP.LogKow
).RuleLogP.LogKow
).CramerRules
)CramerRules
)RuleDescriptorRange.getMinValue()
,RuleDescriptorRange.getMaxValue()
]
TODO add descriptionCramerRules
)CramerRules
)cramer2.CramerRulesExtendedExtended
)CramerRules
)CramerRules
)CramerRules
)CramerRules
)CramerRules
)IDecisionRule
application,
which contains the rule applied, the boolean result and the category assigned (if any).CramerRules
)CramerRules
)CramerRules
)RuleCarbohydrate
IDecisionRule
IDecisionRule
classes
Example :
RulesList(new String[] {
"toxTree.tree.rules.RuleSubstructure",
"toxTree.tree.rules.RuleAromatic"});
Rules are created from corresponding class names
CramerRules
)CramerRules
)CramerRules
)RuleVerifyProperty.getProperty()
value.IDecisionMethod
to a file
Uses serialization mechanism.JTabbedPane
.
List
.IDecisionCategory
If the user selects an object, the tree is created and returned Introspection.getAvailableCategoryTypes(ClassLoader)
IDecisionRule
If the user selects an object, a DecisionNode
containing the rule is created and returned Introspection.getAvailableRuleTypes(ClassLoader)
IDecisionRule
If the user selects an object, the rule is created and returned Introspection.getAvailableRuleTypes(ClassLoader)
IDecisionMethod
If the user selects a name, the tree is created and returned Introspection.getAvailableTreeTypes(ClassLoader)
SelectListDialog.selectNewTree(Component, ClassLoader)
to present a list of classes that
implement IDecisionMethod
.IDecisionMethod
should provides an editor, which is a class,
implementing this interface.
IDecisionRule
classes
Example :
setRules(new String[] {
"toxTree.tree.rules.RuleSubstructure",
"toxTree.tree.rules.RuleAromatic"});
Rules are created from corresponding class names
debug(Throwable)
.
SicretRules
is the implementation of BfR rules for estimating skin irritation and corrosion potential.IDecisionCategory
categories for
SicretRules
decision tree.IDecisionRule
rules for SicretRules
decision tree.RuleSMARTSubstructure
.JPanel
to enter a SMILES.ToxTreeApp
FunctionalGroups.sulphateOfAmine(int)
with the ionic bonnd between [N+] and [O-]
marked with FunctionalGroups.DONTMARK
so it can be broken by FunctionalGroups.detachGroup(IAtomContainer, QueryAtomContainer)
method
OrderQueryBond
with additional condition to be acyclic or cyclic.ToxTreeApp
ToxForestApp
(structures browser).ToxForestApp
.ToxForestApp
.ToxForestApp
(decision trees table).ToxTreeApp
toxtree.plugins.verhaar2.VerhaarScheme
is the implementation of modified Verhaar structural scheme, according to recommendation fromIDecisionRule
rules for VerhaarScheme
decision tree.toxTree.core
package.IDecisionCategory
categories.CramerRules
is the implementation of Cramer rules [Cramer et al,78].IDecisionRule
rulesToxTreeApp
user interfaceAbstractAction
used in ToxTreeApp
main menu.toxTree.io.batch
IDecisionMethod
AbstractAction
for the decision tree user interface
toxTree.ui.tree
IDecisionCategory
in a decision tree IDecisionMethod
ToxTreeApp
ChemObjectBatchProcessing
descendant , where processing is performed by IDecisionMethod
IToxTreeEditor
.ToxTreeApp
application
the current method IDecisionMethod
the result IDecisionResult
the list of available methods IDecisionMethodsList
the data DecisionMethodData
the tree data DecisionMethodData
the batch processing object ToxTreeBatchProcessing
Also contains some UI frames :
a Frame to view a decision tree TreeFrame
a Frame to edit a decision tree toxTree.ui.tree.EditTreeFrame
a dialog with structure diagram editor JChemPaintDialog
and a org.openscience.cdk.applications.jchempaint.JChemPaintModel
List
of ToxTreePackageEntry
ToxTreePackageEntries
.IDecisionMethodEditor
for AbstractTree
descendants.IDecisionMethod
by TreeDrawing
.IDecisionMethod
.JTree
component.IDecisionResult
Object
.
IDecisionMethod
interface.VerhaarScheme
is the implementation of Verhaar structural scheme for estimating toxicity mode of action.IDecisionCategory
categories for
VerhaarScheme
decision tree.IDecisionRule
rules for VerhaarScheme
decision tree.IDecisionRule
behaviour.
IDecisionRule
behaviour.
IDecisionRule
behaviour.
IDecisionRule
behaviour.
IDecisionRule
behaviour.
IDecisionRule
behaviour.
IDecisionRule
behaviour.
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
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule
behaviour.
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
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
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
RuleVerifyProperty.getProperty()
to molecule property with name given by RuleVerifyProperty.getPropertyName()
.
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
MolFlags
hydrolysis products
(to be used further )
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionRule.verifyRule(IAtomContainer)
IDecisionMethod
XMLSerializable
.
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