toxTree.tree.rules.smarts
Class AbstractRuleSmartSubstructure<T>
java.lang.Object
java.util.Observable
toxTree.tree.AbstractRule
toxTree.tree.rules.smarts.AbstractRuleSmartSubstructure<T>
- All Implemented Interfaces:
- ambit2.smarts.query.ISmartsPatternFactory, java.io.Serializable, java.lang.Cloneable, IDecisionRule, IImplementationDetails, XMLSerializable, IRuleSMARTSubstructures
- Direct Known Subclasses:
- RuleSMARTSSubstructureAmbit, RuleSMARTSubstructureCDK
public abstract class AbstractRuleSmartSubstructure<T>
- extends AbstractRule
- implements IRuleSMARTSubstructures, ambit2.smarts.query.ISmartsPatternFactory
- See Also:
- Serialized Form
Fields inherited from class toxTree.tree.AbstractRule |
changes, editable, ERR_STRUCTURENOTPREPROCESSED, examples, explanation, id, logger, MSG_NO, MSG_YES, no, residueIDHidden, title |
Fields inherited from interface toxTree.core.XMLSerializable |
xmltag_CATEGORIES, xmltag_CATEGORY, xmltag_CATEGORYTHRESHOLD, xmltag_CLASS, xmltag_EXPLANATION, xmltag_ID, xmltag_METHOD, xmltag_METHODPARAMETER, xmltag_METHODS, xmltag_NAME, xmltag_RULE, xmltag_RULEEXAMPLE, xmltag_RULES, xmltag_TREEROOT |
Method Summary |
void |
addSubstructure(java.lang.String smarts)
|
void |
addSubstructure(java.lang.String title,
java.lang.String smarts)
|
void |
addSubstructure(java.lang.String title,
java.lang.String smarts,
boolean negate)
|
void |
clearSubstructures()
|
boolean |
containsAllSubstructures()
|
void |
deleteSubstructure(java.lang.String title)
|
boolean |
equals(java.lang.Object obj)
|
java.lang.String |
getImplementationDetails()
|
protected abstract T |
getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
|
ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> |
getSelector()
|
java.util.Hashtable<java.lang.String,ambit2.smarts.query.ISmartsPattern<T>> |
getSmartsPatterns()
|
java.lang.String |
getSubstructure(java.lang.String title)
|
void |
initSingleSMARTS(java.util.Hashtable<java.lang.String,ambit2.smarts.query.ISmartsPattern<T>> table,
java.lang.String id,
java.lang.String smartPattern)
|
protected boolean |
isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol,
T processedObject)
Returns true always. |
boolean |
isImplemented()
|
void |
removeSingleSMARTS(java.util.Hashtable table,
java.lang.String id)
|
void |
setContainsAllSubstructures(boolean allSmarts)
|
void |
setSmartsPatterns(java.util.Hashtable<java.lang.String,ambit2.smarts.query.ISmartsPattern<T>> smartsPatterns)
|
void |
setSubstructure(java.lang.String title,
java.lang.String smarts)
|
void |
setSubstructure(java.lang.String title,
java.lang.String smarts,
boolean negate)
|
boolean |
verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
This is the core of a IDecisionRule behaviour. |
boolean |
verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer selected)
|
Methods inherited from class toxTree.tree.AbstractRule |
addPropertyChangeListener, clearFlags, clone, createRule, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getTitle, hideResiduesID, isEditable, isResidueIDHidden, log, log, log, makeMolecule, removePropertyChangeListener, setEditable, setExampleMolecule, setExamples, setExplanation, setID, setNum, setTitle, toShallowXML, toString, toXML |
Methods inherited from class java.util.Observable |
addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged |
Methods inherited from class java.lang.Object |
finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface ambit2.smarts.query.ISmartsPatternFactory |
createSmartsPattern |
smartsPatterns
protected java.util.Hashtable<java.lang.String,ambit2.smarts.query.ISmartsPattern<T>> smartsPatterns
containsAllSubstructures
protected boolean containsAllSubstructures
final_and_patch
protected ambit2.smarts.query.ISmartsPattern final_and_patch
AbstractRuleSmartSubstructure
public AbstractRuleSmartSubstructure()
addSubstructure
public void addSubstructure(java.lang.String title,
java.lang.String smarts,
boolean negate)
throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
addSubstructure
public void addSubstructure(java.lang.String title,
java.lang.String smarts)
throws ambit2.smarts.query.SMARTSException
- Specified by:
addSubstructure
in interface IRuleSMARTSubstructures
- Throws:
ambit2.smarts.query.SMARTSException
addSubstructure
public void addSubstructure(java.lang.String smarts)
throws ambit2.smarts.query.SMARTSException
- Specified by:
addSubstructure
in interface IRuleSMARTSubstructures
- Throws:
ambit2.smarts.query.SMARTSException
setSubstructure
public void setSubstructure(java.lang.String title,
java.lang.String smarts,
boolean negate)
throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
setSubstructure
public void setSubstructure(java.lang.String title,
java.lang.String smarts)
throws ambit2.smarts.query.SMARTSException
- Specified by:
setSubstructure
in interface IRuleSMARTSubstructures
- Throws:
ambit2.smarts.query.SMARTSException
getSubstructure
public java.lang.String getSubstructure(java.lang.String title)
throws ambit2.smarts.query.SMARTSException
- Specified by:
getSubstructure
in interface IRuleSMARTSubstructures
- Returns:
- smarts, corresponding to title
- Throws:
ambit2.smarts.query.SMARTSException
clearSubstructures
public void clearSubstructures()
- Specified by:
clearSubstructures
in interface IRuleSMARTSubstructures
deleteSubstructure
public void deleteSubstructure(java.lang.String title)
- Specified by:
deleteSubstructure
in interface IRuleSMARTSubstructures
getObjectToVerify
protected abstract T getObjectToVerify(org.openscience.cdk.interfaces.IAtomContainer mol)
getSelector
public ambit2.base.interfaces.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.renderer.selection.IChemObjectSelection> getSelector()
- Specified by:
getSelector
in interface IDecisionRule
- Overrides:
getSelector
in class AbstractRule
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
org.openscience.cdk.interfaces.IAtomContainer selected)
throws DecisionMethodException
- Throws:
DecisionMethodException
verifyRule
public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
throws DecisionMethodException
- Description copied from interface:
IDecisionRule
- This is the core of a
IDecisionRule
behaviour. The method returns true
if the answer of the rule is YES for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer
and FALSE
if the answer of the rule is NO for the analyzed molecule org.openscience.cdk.interfaces.AtomContainer
??
- Specified by:
verifyRule
in interface IDecisionRule
- Parameters:
mol
- org.openscience.cdk.interfaces.AtomContainer
- Returns:
- rule result, boolean
- Throws:
DecisionMethodException
removeSingleSMARTS
public void removeSingleSMARTS(java.util.Hashtable table,
java.lang.String id)
throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
initSingleSMARTS
public void initSingleSMARTS(java.util.Hashtable<java.lang.String,ambit2.smarts.query.ISmartsPattern<T>> table,
java.lang.String id,
java.lang.String smartPattern)
throws ambit2.smarts.query.SMARTSException
- Throws:
ambit2.smarts.query.SMARTSException
isImplemented
public boolean isImplemented()
- Specified by:
isImplemented
in interface IDecisionRule
- Overrides:
isImplemented
in class AbstractRule
- Returns:
- false if the rule is not implemented and true if it is
containsAllSubstructures
public boolean containsAllSubstructures()
- Specified by:
containsAllSubstructures
in interface IRuleSMARTSubstructures
setContainsAllSubstructures
public void setContainsAllSubstructures(boolean allSmarts)
- Specified by:
setContainsAllSubstructures
in interface IRuleSMARTSubstructures
getSmartsPatterns
public java.util.Hashtable<java.lang.String,ambit2.smarts.query.ISmartsPattern<T>> getSmartsPatterns()
setSmartsPatterns
public void setSmartsPatterns(java.util.Hashtable<java.lang.String,ambit2.smarts.query.ISmartsPattern<T>> smartsPatterns)
getImplementationDetails
public java.lang.String getImplementationDetails()
- Specified by:
getImplementationDetails
in interface IImplementationDetails
isAPossibleHit
protected boolean isAPossibleHit(org.openscience.cdk.interfaces.IAtomContainer mol,
T processedObject)
throws DecisionMethodException
- Returns true always. Override to apply simple prescreening for the rule;
- Parameters:
mol
-
- Returns:
-
- Throws:
DecisionMethodException
equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in class AbstractRule
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